Query 033869
Match_columns 110
No_of_seqs 148 out of 941
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 07:13:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033869.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033869hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2906 RNA polymerase III sub 100.0 1.5E-46 3.2E-51 236.9 5.4 104 1-110 1-105 (105)
2 KOG2691 RNA polymerase II subu 100.0 2.9E-41 6.3E-46 216.0 6.1 108 1-110 4-113 (113)
3 COG1594 RPB9 DNA-directed RNA 100.0 7.4E-39 1.6E-43 210.4 8.5 104 1-110 2-112 (113)
4 TIGR01384 TFS_arch transcripti 100.0 1E-38 2.2E-43 206.8 8.9 101 2-110 1-102 (104)
5 KOG2907 RNA polymerase I trans 100.0 3.5E-33 7.7E-38 180.3 3.1 104 1-110 7-114 (116)
6 smart00440 ZnF_C2C2 C2C2 Zinc 99.9 9.2E-27 2E-31 127.1 4.9 40 69-110 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 99.9 2E-25 4.3E-30 121.2 4.5 39 69-109 1-39 (39)
8 PHA02998 RNA polymerase subuni 99.8 1.8E-21 3.9E-26 135.1 4.9 44 64-109 138-182 (195)
9 TIGR01385 TFSII transcription 99.7 7.3E-18 1.6E-22 126.7 4.6 41 67-109 257-297 (299)
10 PF02150 RNA_POL_M_15KD: RNA p 99.5 4.8E-15 1E-19 78.5 1.4 34 1-37 1-34 (35)
11 smart00661 RPOL9 RNA polymeras 99.1 9.5E-11 2.1E-15 66.6 4.8 41 2-46 1-41 (52)
12 KOG1105 Transcription elongati 99.0 4.6E-10 1E-14 84.1 3.8 40 68-109 255-294 (296)
13 PF14803 Nudix_N_2: Nudix N-te 98.5 1E-07 2.3E-12 49.9 2.0 33 2-34 1-33 (34)
14 PRK00432 30S ribosomal protein 98.2 1.3E-06 2.8E-11 49.6 2.5 27 2-34 21-48 (50)
15 PF04606 Ogr_Delta: Ogr/Delta- 97.6 9.9E-05 2.1E-09 41.1 3.3 38 70-109 1-38 (47)
16 COG1998 RPS31 Ribosomal protei 97.4 0.00018 3.8E-09 40.5 2.4 28 2-35 20-49 (51)
17 PRK09678 DNA-binding transcrip 97.3 0.00024 5.2E-09 43.2 2.9 38 69-109 2-40 (72)
18 PHA00626 hypothetical protein 96.9 0.001 2.2E-08 38.4 2.4 36 2-37 1-37 (59)
19 PF13248 zf-ribbon_3: zinc-rib 96.7 0.00075 1.6E-08 33.0 1.0 24 1-32 2-25 (26)
20 PF09297 zf-NADH-PPase: NADH p 96.6 0.0016 3.5E-08 33.3 2.0 28 2-33 4-31 (32)
21 PF01396 zf-C4_Topoisom: Topoi 96.6 0.0032 7E-08 33.7 3.0 34 2-37 2-38 (39)
22 PF10571 UPF0547: Uncharacteri 96.6 0.0011 2.4E-08 32.6 1.0 24 3-34 2-25 (26)
23 PF13240 zinc_ribbon_2: zinc-r 96.4 0.0015 3.1E-08 31.2 0.9 22 3-32 1-22 (23)
24 PF01396 zf-C4_Topoisom: Topoi 96.4 0.0042 9.1E-08 33.2 2.8 32 68-107 1-33 (39)
25 PF07754 DUF1610: Domain of un 96.2 0.0049 1.1E-07 29.7 2.2 24 4-31 1-24 (24)
26 PRK03564 formate dehydrogenase 96.2 0.022 4.8E-07 43.5 6.8 72 2-109 188-263 (309)
27 cd00350 rubredoxin_like Rubred 96.2 0.0042 9.1E-08 32.0 2.0 15 68-82 17-31 (33)
28 PF08274 PhnA_Zn_Ribbon: PhnA 95.9 0.002 4.4E-08 32.7 -0.0 27 70-109 4-30 (30)
29 PF04216 FdhE: Protein involve 95.9 0.0093 2E-07 44.7 3.4 72 2-109 173-249 (290)
30 PRK00398 rpoP DNA-directed RNA 95.9 0.012 2.6E-07 32.3 3.0 31 3-37 5-35 (46)
31 PHA00626 hypothetical protein 95.8 0.0095 2E-07 34.4 2.4 33 70-109 2-34 (59)
32 TIGR01562 FdhE formate dehydro 95.8 0.046 1E-06 41.7 6.9 72 3-108 186-262 (305)
33 PF09855 DUF2082: Nucleic-acid 95.8 0.019 4.1E-07 34.1 3.7 11 70-80 2-12 (64)
34 COG1773 Rubredoxin [Energy pro 95.7 0.014 3.1E-07 33.6 3.1 49 23-84 3-52 (55)
35 cd00730 rubredoxin Rubredoxin; 95.7 0.0079 1.7E-07 34.0 1.7 47 23-82 1-48 (50)
36 PF12760 Zn_Tnp_IS1595: Transp 95.5 0.013 2.8E-07 32.2 2.3 28 69-107 19-46 (46)
37 PF00301 Rubredoxin: Rubredoxi 95.5 0.017 3.7E-07 32.2 2.7 46 23-81 1-47 (47)
38 cd00729 rubredoxin_SM Rubredox 95.5 0.016 3.4E-07 30.1 2.4 12 23-34 2-13 (34)
39 COG2888 Predicted Zn-ribbon RN 95.4 0.0091 2E-07 34.9 1.4 26 3-32 11-36 (61)
40 PF12773 DZR: Double zinc ribb 95.4 0.008 1.7E-07 33.4 1.1 27 2-33 13-39 (50)
41 PF14353 CpXC: CpXC protein 95.2 0.018 3.8E-07 38.1 2.5 45 24-78 2-48 (128)
42 COG3478 Predicted nucleic-acid 95.1 0.018 4E-07 34.1 2.1 34 70-107 6-49 (68)
43 PF08274 PhnA_Zn_Ribbon: PhnA 95.0 0.015 3.3E-07 29.4 1.3 26 3-33 4-29 (30)
44 PRK14973 DNA topoisomerase I; 94.8 0.057 1.2E-06 46.7 5.2 33 67-107 634-666 (936)
45 PF09855 DUF2082: Nucleic-acid 94.7 0.018 3.8E-07 34.2 1.3 15 67-81 35-49 (64)
46 TIGR00244 transcriptional regu 94.6 0.044 9.5E-07 37.6 3.3 36 70-109 2-39 (147)
47 KOG3084 NADH pyrophosphatase I 94.6 0.048 1E-06 41.8 3.8 40 2-41 151-191 (345)
48 PF08271 TF_Zn_Ribbon: TFIIB z 94.6 0.023 4.9E-07 30.8 1.5 30 3-35 2-31 (43)
49 PRK06319 DNA topoisomerase I/S 94.5 0.11 2.3E-06 44.7 6.0 32 3-36 594-629 (860)
50 TIGR02098 MJ0042_CXXC MJ0042 f 94.4 0.035 7.6E-07 29.0 2.0 33 3-35 4-37 (38)
51 PRK14890 putative Zn-ribbon RN 94.3 0.031 6.6E-07 32.6 1.7 26 3-32 9-34 (59)
52 PF13719 zinc_ribbon_5: zinc-r 94.2 0.043 9.4E-07 28.9 2.1 32 3-34 4-36 (37)
53 COG1198 PriA Primosomal protei 94.2 0.014 3E-07 49.2 0.1 25 67-91 474-498 (730)
54 PF13453 zf-TFIIB: Transcripti 94.1 0.033 7.2E-07 29.8 1.5 29 4-34 2-30 (41)
55 COG2816 NPY1 NTP pyrophosphohy 94.1 0.066 1.4E-06 40.3 3.5 38 2-43 112-150 (279)
56 PF13453 zf-TFIIB: Transcripti 94.1 0.085 1.8E-06 28.2 3.1 30 70-109 1-30 (41)
57 smart00661 RPOL9 RNA polymeras 94.1 0.059 1.3E-06 29.9 2.5 12 96-109 20-31 (52)
58 PRK00464 nrdR transcriptional 94.0 0.077 1.7E-06 36.7 3.6 36 70-109 2-39 (154)
59 TIGR00595 priA primosomal prot 94.0 0.075 1.6E-06 42.9 4.0 27 4-34 225-251 (505)
60 smart00440 ZnF_C2C2 C2C2 Zinc 93.8 0.088 1.9E-06 28.2 2.8 30 4-33 3-38 (40)
61 PRK00241 nudC NADH pyrophospha 93.8 0.1 2.2E-06 38.7 4.1 32 1-36 99-130 (256)
62 PRK07220 DNA topoisomerase I; 93.6 0.25 5.5E-06 41.8 6.6 32 67-106 634-665 (740)
63 PRK09678 DNA-binding transcrip 93.6 0.12 2.7E-06 31.3 3.5 37 1-37 1-43 (72)
64 PF10058 DUF2296: Predicted in 93.6 0.062 1.3E-06 30.8 2.1 33 65-106 19-52 (54)
65 PF04606 Ogr_Delta: Ogr/Delta- 93.6 0.081 1.8E-06 29.2 2.5 34 4-37 2-41 (47)
66 TIGR00686 phnA alkylphosphonat 93.6 0.058 1.3E-06 35.1 2.1 30 2-36 3-32 (109)
67 PF09151 DUF1936: Domain of un 93.6 0.23 5.1E-06 25.3 3.9 32 69-107 2-35 (36)
68 PRK07219 DNA topoisomerase I; 93.5 0.28 6.2E-06 41.9 6.8 33 67-107 732-765 (822)
69 PF05876 Terminase_GpA: Phage 93.5 0.068 1.5E-06 43.7 2.9 42 67-110 199-241 (557)
70 TIGR01206 lysW lysine biosynth 93.4 0.12 2.6E-06 29.6 3.1 31 3-35 4-34 (54)
71 COG1645 Uncharacterized Zn-fin 93.4 0.079 1.7E-06 35.7 2.7 27 3-35 30-56 (131)
72 COG1779 C4-type Zn-finger prot 93.4 0.12 2.5E-06 37.2 3.6 42 66-110 12-55 (201)
73 PRK10220 hypothetical protein; 93.4 0.073 1.6E-06 34.7 2.3 31 2-37 4-34 (111)
74 COG4332 Uncharacterized protei 93.3 0.085 1.8E-06 37.5 2.8 44 64-109 13-60 (203)
75 PF12760 Zn_Tnp_IS1595: Transp 93.3 0.082 1.8E-06 29.0 2.2 27 3-32 20-46 (46)
76 PRK07219 DNA topoisomerase I; 93.1 0.36 7.8E-06 41.3 6.8 31 4-36 605-639 (822)
77 COG2023 RPR2 RNase P subunit R 93.0 0.079 1.7E-06 34.4 2.1 34 2-35 57-94 (105)
78 PF07282 OrfB_Zn_ribbon: Putat 92.9 0.092 2E-06 30.9 2.1 31 3-37 30-60 (69)
79 TIGR00340 zpr1_rel ZPR1-relate 92.8 0.21 4.5E-06 34.8 4.1 38 71-110 1-40 (163)
80 PF08271 TF_Zn_Ribbon: TFIIB z 92.8 0.077 1.7E-06 28.6 1.6 28 70-108 2-29 (43)
81 PRK14559 putative protein seri 92.7 0.092 2E-06 43.8 2.6 24 1-32 1-24 (645)
82 PF14353 CpXC: CpXC protein 92.6 0.2 4.4E-06 33.0 3.7 39 69-109 2-49 (128)
83 PRK14892 putative transcriptio 92.5 0.1 2.3E-06 33.5 2.2 31 3-35 23-54 (99)
84 PF10122 Mu-like_Com: Mu-like 92.4 0.072 1.6E-06 30.2 1.2 33 3-37 6-38 (51)
85 smart00647 IBR In Between Ring 92.4 0.19 4.1E-06 28.6 3.0 30 1-32 18-49 (64)
86 PRK14714 DNA polymerase II lar 92.1 0.14 3E-06 45.6 3.0 12 68-79 709-720 (1337)
87 PF01485 IBR: IBR domain; Int 91.8 0.11 2.4E-06 29.6 1.5 30 1-32 18-49 (64)
88 PRK05580 primosome assembly pr 91.7 0.25 5.4E-06 41.4 4.0 10 69-78 422-431 (679)
89 PF11781 RRN7: RNA polymerase 91.6 0.14 3E-06 26.9 1.6 25 4-33 11-35 (36)
90 PRK04023 DNA polymerase II lar 91.6 0.13 2.7E-06 44.9 2.2 21 2-32 627-647 (1121)
91 COG1327 Predicted transcriptio 91.5 0.13 2.8E-06 35.5 1.8 36 70-109 2-39 (156)
92 PF13717 zinc_ribbon_4: zinc-r 91.5 0.17 3.6E-06 26.5 1.8 30 4-33 5-35 (36)
93 PF12773 DZR: Double zinc ribb 91.4 0.13 2.7E-06 28.4 1.4 21 2-30 30-50 (50)
94 TIGR03655 anti_R_Lar restricti 91.2 0.47 1E-05 26.7 3.7 34 69-107 2-35 (53)
95 PF03119 DNA_ligase_ZBD: NAD-d 91.1 0.13 2.7E-06 25.5 1.1 21 3-27 1-21 (28)
96 PRK12286 rpmF 50S ribosomal pr 91.1 0.17 3.7E-06 29.3 1.8 24 2-34 28-51 (57)
97 COG1096 Predicted RNA-binding 91.1 0.22 4.7E-06 35.5 2.7 28 3-36 151-178 (188)
98 PRK14873 primosome assembly pr 90.9 0.31 6.6E-06 40.9 3.8 14 69-82 423-436 (665)
99 COG1592 Rubrerythrin [Energy p 90.9 0.14 2.9E-06 35.9 1.5 29 23-81 134-162 (166)
100 COG1997 RPL43A Ribosomal prote 90.8 0.24 5.2E-06 31.1 2.4 29 3-35 37-65 (89)
101 PF09526 DUF2387: Probable met 90.6 0.21 4.6E-06 30.1 2.0 35 3-37 10-44 (71)
102 COG0551 TopA Zn-finger domain 90.5 1.2 2.7E-05 29.7 5.9 37 66-108 58-95 (140)
103 PF05129 Elf1: Transcription e 90.5 0.16 3.4E-06 31.4 1.4 31 4-34 25-57 (81)
104 PRK00420 hypothetical protein; 90.5 0.3 6.5E-06 32.1 2.7 30 3-37 25-54 (112)
105 KOG2907 RNA polymerase I trans 90.2 0.31 6.8E-06 32.0 2.6 32 3-34 76-113 (116)
106 TIGR02443 conserved hypothetic 90.1 0.24 5.2E-06 28.9 1.8 35 3-37 11-45 (59)
107 PRK03824 hypA hydrogenase nick 89.9 0.57 1.2E-05 31.5 3.8 16 21-36 68-83 (135)
108 PF07295 DUF1451: Protein of u 89.9 0.32 6.9E-06 33.3 2.6 16 20-35 109-124 (146)
109 smart00709 Zpr1 Duplicated dom 89.8 0.57 1.2E-05 32.5 3.9 38 70-110 2-41 (160)
110 PF13408 Zn_ribbon_recom: Reco 89.6 0.25 5.4E-06 27.7 1.7 31 1-32 5-35 (58)
111 TIGR01053 LSD1 zinc finger dom 89.5 0.46 9.9E-06 24.1 2.4 26 3-32 3-28 (31)
112 PF06827 zf-FPG_IleRS: Zinc fi 89.4 0.16 3.5E-06 25.2 0.6 27 3-31 3-29 (30)
113 TIGR00515 accD acetyl-CoA carb 89.3 0.074 1.6E-06 40.2 -0.9 30 3-35 28-57 (285)
114 COG4640 Predicted membrane pro 89.3 0.2 4.4E-06 39.6 1.4 26 1-34 1-26 (465)
115 PRK05452 anaerobic nitric oxid 89.2 0.37 8.1E-06 38.7 2.9 52 20-84 422-474 (479)
116 CHL00174 accD acetyl-CoA carbo 89.1 0.072 1.6E-06 40.5 -1.1 31 3-36 40-70 (296)
117 smart00834 CxxC_CXXC_SSSS Puta 89.1 0.21 4.5E-06 26.2 1.0 28 3-31 7-34 (41)
118 COG2051 RPS27A Ribosomal prote 89.0 0.3 6.4E-06 29.1 1.7 30 67-107 18-47 (67)
119 PF03811 Zn_Tnp_IS1: InsA N-te 88.9 0.51 1.1E-05 24.7 2.4 33 65-101 2-34 (36)
120 COG0777 AccD Acetyl-CoA carbox 88.8 0.13 2.7E-06 38.9 0.0 31 3-36 30-60 (294)
121 PF10058 DUF2296: Predicted in 88.5 0.43 9.4E-06 27.2 2.1 27 4-32 25-53 (54)
122 TIGR01031 rpmF_bact ribosomal 88.5 0.3 6.5E-06 28.0 1.5 23 2-33 27-49 (55)
123 PF11792 Baculo_LEF5_C: Baculo 88.3 0.019 4.1E-07 31.4 -3.4 30 74-106 13-42 (43)
124 PRK06319 DNA topoisomerase I/S 88.3 1.1 2.3E-05 38.8 5.2 33 67-106 692-727 (860)
125 PF12172 DUF35_N: Rubredoxin-l 88.3 0.15 3.3E-06 26.5 0.1 21 3-31 13-33 (37)
126 PF04032 Rpr2: RNAse P Rpr2/Rp 88.3 0.2 4.3E-06 30.5 0.6 29 2-30 47-84 (85)
127 PF08772 NOB1_Zn_bind: Nin one 88.2 0.19 4.1E-06 30.6 0.5 9 2-10 25-33 (73)
128 PF06677 Auto_anti-p27: Sjogre 87.9 0.48 1E-05 25.6 1.9 23 3-30 19-41 (41)
129 KOG3507 DNA-directed RNA polym 87.9 0.32 6.9E-06 28.4 1.3 25 3-32 22-46 (62)
130 PF07282 OrfB_Zn_ribbon: Putat 87.8 0.53 1.2E-05 27.5 2.3 30 67-108 27-56 (69)
131 PRK05654 acetyl-CoA carboxylas 87.5 0.13 2.8E-06 39.0 -0.7 31 3-36 29-59 (292)
132 PF09862 DUF2089: Protein of u 87.4 0.59 1.3E-05 30.7 2.5 23 4-34 1-23 (113)
133 smart00659 RPOLCX RNA polymera 87.3 0.57 1.2E-05 25.6 2.0 25 4-33 5-29 (44)
134 PRK11032 hypothetical protein; 87.1 0.59 1.3E-05 32.5 2.5 16 20-35 121-136 (160)
135 COG0675 Transposase and inacti 87.1 0.44 9.6E-06 35.2 2.0 26 3-37 311-336 (364)
136 PF08792 A2L_zn_ribbon: A2L zi 86.8 0.87 1.9E-05 23.4 2.5 27 3-34 5-32 (33)
137 PF14205 Cys_rich_KTR: Cystein 86.2 0.69 1.5E-05 26.5 2.0 34 3-36 6-41 (55)
138 COG1326 Uncharacterized archae 85.9 0.26 5.6E-06 35.3 0.2 37 67-109 5-41 (201)
139 PHA02942 putative transposase; 85.8 0.7 1.5E-05 36.2 2.6 31 2-37 326-356 (383)
140 PF01780 Ribosomal_L37ae: Ribo 85.6 0.43 9.3E-06 30.2 1.1 29 2-34 36-64 (90)
141 COG2888 Predicted Zn-ribbon RN 85.2 0.85 1.8E-05 26.7 2.1 10 24-33 10-19 (61)
142 TIGR00310 ZPR1_znf ZPR1 zinc f 85.0 1.7 3.7E-05 31.0 4.1 39 70-110 2-42 (192)
143 TIGR01384 TFS_arch transcripti 84.9 1.1 2.3E-05 28.4 2.7 13 21-33 88-100 (104)
144 PF03604 DNA_RNApol_7kD: DNA d 84.9 0.28 6E-06 25.1 -0.0 25 4-33 3-27 (32)
145 PF09082 DUF1922: Domain of un 84.7 0.66 1.4E-05 27.8 1.5 28 4-37 6-33 (68)
146 PRK14890 putative Zn-ribbon RN 84.7 1.2 2.7E-05 25.9 2.6 8 24-31 8-15 (59)
147 PF06943 zf-LSD1: LSD1 zinc fi 84.5 1.1 2.3E-05 21.7 1.9 25 4-32 1-25 (25)
148 PF09986 DUF2225: Uncharacteri 84.5 0.88 1.9E-05 32.8 2.5 15 23-37 5-19 (214)
149 PRK11827 hypothetical protein; 84.4 1.3 2.8E-05 25.9 2.6 31 3-37 10-40 (60)
150 TIGR00311 aIF-2beta translatio 83.8 0.71 1.5E-05 31.1 1.6 33 3-36 99-131 (133)
151 COG3809 Uncharacterized protei 83.7 1 2.3E-05 27.8 2.1 35 1-37 1-35 (88)
152 PF09538 FYDLN_acid: Protein o 83.6 0.79 1.7E-05 29.8 1.7 31 2-37 10-40 (108)
153 PF04810 zf-Sec23_Sec24: Sec23 83.3 0.8 1.7E-05 24.3 1.4 35 2-36 3-37 (40)
154 PRK04136 rpl40e 50S ribosomal 82.9 0.78 1.7E-05 25.6 1.3 23 2-32 15-37 (48)
155 PRK03988 translation initiatio 82.8 0.85 1.8E-05 30.9 1.7 33 3-36 104-136 (138)
156 PRK09521 exosome complex RNA-b 82.4 1.4 3.1E-05 31.0 2.7 28 3-35 151-178 (189)
157 COG2176 PolC DNA polymerase II 82.3 1.6 3.5E-05 39.1 3.5 17 21-37 912-928 (1444)
158 PF06839 zf-GRF: GRF zinc fing 82.1 3.9 8.4E-05 22.1 3.9 30 70-102 2-31 (45)
159 PRK05582 DNA topoisomerase I; 82.1 2.7 5.8E-05 35.2 4.6 32 68-106 611-643 (650)
160 PF03367 zf-ZPR1: ZPR1 zinc-fi 81.8 1.2 2.6E-05 30.9 2.2 39 69-110 2-42 (161)
161 PF01783 Ribosomal_L32p: Ribos 81.7 0.49 1.1E-05 27.1 0.1 21 3-32 28-48 (56)
162 PRK00423 tfb transcription ini 81.6 1 2.2E-05 34.2 1.9 30 2-34 12-41 (310)
163 PF01599 Ribosomal_S27: Riboso 81.5 0.93 2E-05 25.2 1.2 27 2-32 19-47 (47)
164 PF09723 Zn-ribbon_8: Zinc rib 81.2 0.75 1.6E-05 24.7 0.8 10 22-31 25-34 (42)
165 PRK00415 rps27e 30S ribosomal 81.2 1 2.2E-05 26.3 1.4 30 67-107 10-39 (59)
166 COG1571 Predicted DNA-binding 81.2 0.87 1.9E-05 36.3 1.4 30 3-37 352-381 (421)
167 COG1545 Predicted nucleic-acid 81.1 0.79 1.7E-05 31.0 1.0 22 3-32 31-52 (140)
168 PF06044 DRP: Dam-replacing fa 81.1 1 2.2E-05 33.5 1.6 35 2-37 32-67 (254)
169 PF04216 FdhE: Protein involve 80.8 1.8 3.9E-05 32.4 3.0 36 68-109 172-208 (290)
170 PHA02998 RNA polymerase subuni 80.6 1.5 3.2E-05 31.2 2.2 34 3-36 145-184 (195)
171 PRK03954 ribonuclease P protei 80.1 1.4 3.1E-05 29.3 2.0 33 2-34 65-104 (121)
172 PRK12380 hydrogenase nickel in 80.0 0.76 1.7E-05 30.0 0.7 23 3-31 72-94 (113)
173 COG2835 Uncharacterized conser 79.8 2.4 5.2E-05 24.8 2.6 32 2-37 9-40 (60)
174 TIGR00155 pqiA_fam integral me 79.6 1.8 3.9E-05 34.2 2.7 28 4-33 16-43 (403)
175 PF01667 Ribosomal_S27e: Ribos 79.6 0.45 9.6E-06 27.4 -0.5 30 67-107 6-35 (55)
176 PF14446 Prok-RING_1: Prokaryo 79.5 1.5 3.3E-05 25.1 1.7 27 3-35 7-33 (54)
177 TIGR00100 hypA hydrogenase nic 79.5 0.84 1.8E-05 29.8 0.7 23 3-31 72-94 (115)
178 smart00531 TFIIE Transcription 79.4 0.63 1.4E-05 31.6 0.1 30 67-107 98-132 (147)
179 PF14311 DUF4379: Domain of un 79.4 2 4.4E-05 24.1 2.3 8 69-76 29-36 (55)
180 PRK00464 nrdR transcriptional 79.0 1.8 3.9E-05 29.9 2.3 33 3-35 2-40 (154)
181 TIGR00280 L37a ribosomal prote 78.9 1.7 3.6E-05 27.5 1.9 30 2-35 36-65 (91)
182 PF07191 zinc-ribbons_6: zinc- 78.5 2.1 4.6E-05 25.8 2.2 24 3-32 3-26 (70)
183 COG5415 Predicted integral mem 78.4 0.99 2.1E-05 32.9 0.9 36 64-107 188-223 (251)
184 PRK14559 putative protein seri 78.0 1.3 2.8E-05 37.1 1.6 11 2-12 16-26 (645)
185 COG1996 RPC10 DNA-directed RNA 78.0 2.2 4.7E-05 24.0 2.0 30 4-37 9-38 (49)
186 PRK12336 translation initiatio 77.9 1.4 3.1E-05 31.5 1.6 34 3-37 100-133 (201)
187 COG0333 RpmF Ribosomal protein 77.9 1.8 3.9E-05 25.0 1.7 25 1-34 27-51 (57)
188 PTZ00255 60S ribosomal protein 77.6 2.2 4.8E-05 26.9 2.2 30 2-35 37-66 (90)
189 PF14354 Lar_restr_allev: Rest 77.5 5.4 0.00012 22.6 3.7 34 69-106 4-37 (61)
190 PF01927 Mut7-C: Mut7-C RNAse 76.5 2.4 5.2E-05 28.7 2.3 32 2-33 92-134 (147)
191 PRK15103 paraquat-inducible me 75.4 2.7 5.9E-05 33.4 2.7 27 4-32 13-39 (419)
192 PF13005 zf-IS66: zinc-finger 75.1 2.7 5.9E-05 22.6 1.9 13 2-14 3-15 (47)
193 smart00778 Prim_Zn_Ribbon Zinc 75.0 3.9 8.4E-05 21.5 2.4 28 4-31 6-33 (37)
194 PRK00564 hypA hydrogenase nick 75.0 1.2 2.7E-05 29.1 0.6 25 3-32 73-97 (117)
195 COG2824 PhnA Uncharacterized Z 74.2 2.9 6.2E-05 27.3 2.1 29 1-34 3-31 (112)
196 PRK00750 lysK lysyl-tRNA synth 74.1 2.6 5.7E-05 34.2 2.3 34 2-36 176-212 (510)
197 PRK03976 rpl37ae 50S ribosomal 73.8 2.7 5.9E-05 26.5 1.8 30 2-35 37-66 (90)
198 PF12677 DUF3797: Domain of un 73.7 1.9 4E-05 24.2 1.0 12 68-79 13-24 (49)
199 COG4888 Uncharacterized Zn rib 72.9 3.5 7.6E-05 26.6 2.2 33 4-36 25-59 (104)
200 COG1326 Uncharacterized archae 72.4 2.7 5.8E-05 30.2 1.8 33 3-35 8-42 (201)
201 PF05502 Dynactin_p62: Dynacti 72.4 11 0.00024 30.5 5.5 35 1-36 5-39 (483)
202 PF06044 DRP: Dam-replacing fa 72.0 2.3 5E-05 31.6 1.4 33 68-108 31-63 (254)
203 PRK03681 hypA hydrogenase nick 71.9 1.8 3.9E-05 28.3 0.8 24 3-31 72-95 (114)
204 PRK09710 lar restriction allev 71.7 8.7 0.00019 22.7 3.6 32 68-108 6-37 (64)
205 PLN00209 ribosomal protein S27 71.6 2.5 5.4E-05 26.5 1.3 30 67-107 35-64 (86)
206 PF01873 eIF-5_eIF-2B: Domain 70.7 7.2 0.00016 25.9 3.5 30 69-107 94-123 (125)
207 TIGR02300 FYDLN_acid conserved 70.4 3.1 6.8E-05 27.9 1.6 31 2-37 10-40 (129)
208 PTZ00083 40S ribosomal protein 70.4 2.8 6.1E-05 26.2 1.3 30 67-107 34-63 (85)
209 TIGR00311 aIF-2beta translatio 70.1 7.3 0.00016 26.2 3.4 30 69-107 98-127 (133)
210 PF08273 Prim_Zn_Ribbon: Zinc- 69.6 4 8.7E-05 21.8 1.7 28 4-31 6-34 (40)
211 PF01921 tRNA-synt_1f: tRNA sy 69.4 1.2 2.6E-05 34.9 -0.6 36 2-37 175-213 (360)
212 COG1656 Uncharacterized conser 68.8 2.6 5.6E-05 29.5 1.0 31 3-34 99-141 (165)
213 PHA02942 putative transposase; 68.7 4.3 9.3E-05 31.8 2.4 29 67-108 324-352 (383)
214 KOG0006 E3 ubiquitin-protein l 68.1 12 0.00026 29.2 4.5 24 5-32 321-345 (446)
215 PRK01110 rpmF 50S ribosomal pr 68.0 3.1 6.6E-05 24.2 1.1 22 2-33 28-49 (60)
216 TIGR02605 CxxC_CxxC_SSSS putat 67.3 2.8 6.1E-05 23.0 0.8 25 3-31 7-34 (52)
217 COG1405 SUA7 Transcription ini 67.0 5.1 0.00011 30.4 2.4 31 2-35 2-32 (285)
218 PRK03988 translation initiatio 66.0 10 0.00022 25.7 3.5 30 69-107 103-132 (138)
219 TIGR00467 lysS_arch lysyl-tRNA 65.8 5.5 0.00012 32.6 2.5 34 2-36 169-203 (515)
220 PF04828 GFA: Glutathione-depe 65.3 1.6 3.5E-05 26.2 -0.5 13 2-14 49-61 (92)
221 COG3791 Uncharacterized conser 64.5 3 6.5E-05 27.8 0.7 13 2-14 70-82 (133)
222 COG0675 Transposase and inacti 64.3 5.7 0.00012 29.2 2.2 26 66-108 307-332 (364)
223 COG4416 Com Mu-like prophage p 64.3 1.8 4E-05 24.8 -0.3 32 3-36 6-37 (60)
224 KOG1842 FYVE finger-containing 63.7 1.6 3.5E-05 35.1 -0.8 25 2-32 181-205 (505)
225 PF01921 tRNA-synt_1f: tRNA sy 63.3 6.9 0.00015 30.7 2.5 35 67-108 173-209 (360)
226 PRK06266 transcription initiat 62.9 1.6 3.4E-05 30.8 -1.0 30 67-107 116-145 (178)
227 PRK12495 hypothetical protein; 62.7 6.6 0.00014 28.8 2.2 27 2-34 43-69 (226)
228 TIGR03037 anthran_nbaC 3-hydro 62.6 7.2 0.00016 27.1 2.3 15 19-33 110-124 (159)
229 PF03966 Trm112p: Trm112p-like 62.0 6.4 0.00014 23.0 1.7 17 21-37 51-67 (68)
230 PF08882 Acetone_carb_G: Aceto 61.7 3.3 7.1E-05 27.2 0.4 12 3-14 76-87 (112)
231 PF05191 ADK_lid: Adenylate ki 61.2 1.3 2.9E-05 23.1 -1.2 8 25-32 3-10 (36)
232 TIGR01562 FdhE formate dehydro 61.1 6.4 0.00014 30.1 2.0 38 68-109 184-221 (305)
233 COG1499 NMD3 NMD protein affec 61.1 7.2 0.00016 30.5 2.3 23 68-90 129-153 (355)
234 TIGR02820 formald_GSH S-(hydro 60.6 4.2 9.2E-05 28.8 0.9 13 2-14 90-102 (182)
235 cd00674 LysRS_core_class_I cat 60.1 7.4 0.00016 30.3 2.2 34 67-107 168-201 (353)
236 TIGR01405 polC_Gram_pos DNA po 59.9 6.5 0.00014 35.4 2.1 17 21-37 681-697 (1213)
237 PF02132 RecR: RecR protein; 59.9 2.4 5.3E-05 22.5 -0.3 10 2-11 18-27 (41)
238 PF11672 DUF3268: Protein of u 59.5 9.9 0.00022 24.5 2.4 33 69-105 3-38 (102)
239 PRK05417 glutathione-dependent 59.1 4.5 9.8E-05 28.9 0.8 14 2-15 94-107 (191)
240 PRK00448 polC DNA polymerase I 59.0 6.9 0.00015 35.9 2.1 17 21-37 906-922 (1437)
241 PF00628 PHD: PHD-finger; Int 58.4 16 0.00034 19.7 2.8 26 3-35 1-26 (51)
242 PRK13264 3-hydroxyanthranilate 58.1 8.8 0.00019 27.2 2.1 15 19-33 116-130 (177)
243 PF08063 PADR1: PADR1 (NUC008) 58.1 3.6 7.8E-05 23.5 0.2 19 3-27 16-35 (55)
244 TIGR00467 lysS_arch lysyl-tRNA 58.0 11 0.00025 30.8 3.0 33 67-107 167-199 (515)
245 smart00531 TFIIE Transcription 57.3 3.9 8.4E-05 27.7 0.2 21 87-109 90-110 (147)
246 smart00653 eIF2B_5 domain pres 57.0 20 0.00042 23.3 3.5 30 69-107 81-110 (110)
247 PF01155 HypA: Hydrogenase exp 56.2 1.4 3E-05 28.6 -2.0 23 3-31 72-94 (113)
248 PRK14973 DNA topoisomerase I; 55.6 6.8 0.00015 34.4 1.5 33 3-37 637-671 (936)
249 PRK12336 translation initiatio 55.5 18 0.0004 25.8 3.5 30 69-107 99-128 (201)
250 COG3877 Uncharacterized protei 55.5 9.7 0.00021 24.9 1.8 23 3-33 8-30 (122)
251 COG3364 Zn-ribbon containing p 55.4 7 0.00015 25.4 1.2 20 70-89 22-41 (112)
252 PF00130 C1_1: Phorbol esters/ 54.8 11 0.00024 20.5 1.8 28 2-34 12-39 (53)
253 PF10005 DUF2248: Uncharacteri 54.3 6.5 0.00014 30.6 1.0 25 4-36 2-26 (343)
254 PRK00222 methionine sulfoxide 54.2 13 0.00029 25.3 2.5 18 64-81 88-106 (142)
255 COG4647 AcxC Acetone carboxyla 53.9 5.4 0.00012 27.1 0.5 12 3-14 122-133 (165)
256 cd02673 Peptidase_C19Q A subfa 53.7 13 0.00029 27.2 2.6 16 22-37 80-95 (245)
257 COG3677 Transposase and inacti 53.3 11 0.00024 25.1 2.0 39 64-109 26-64 (129)
258 PRK05978 hypothetical protein; 53.3 6.9 0.00015 26.9 0.9 31 67-108 32-62 (148)
259 TIGR00373 conserved hypothetic 53.1 7.4 0.00016 26.8 1.1 13 94-108 107-119 (158)
260 cd04476 RPA1_DBD_C RPA1_DBD_C: 53.0 10 0.00022 25.8 1.8 26 3-33 36-61 (166)
261 TIGR00357 methionine-R-sulfoxi 52.9 13 0.00028 25.2 2.2 18 64-81 85-103 (134)
262 KOG3362 Predicted BBOX Zn-fing 52.5 4.1 8.9E-05 28.0 -0.3 21 2-33 119-139 (156)
263 KOG1812 Predicted E3 ubiquitin 52.1 8.5 0.00018 30.3 1.4 25 3-32 308-332 (384)
264 COG1552 RPL40A Ribosomal prote 51.8 2.6 5.7E-05 23.6 -1.1 23 4-34 17-39 (50)
265 COG2995 PqiA Uncharacterized p 51.7 10 0.00022 30.2 1.7 31 3-35 20-50 (418)
266 TIGR01051 topA_bact DNA topois 51.1 12 0.00027 31.0 2.3 31 69-107 575-606 (610)
267 PRK13130 H/ACA RNA-protein com 50.9 8.3 0.00018 22.2 0.9 22 1-32 5-26 (56)
268 PF04438 zf-HIT: HIT zinc fing 50.8 8 0.00017 19.2 0.7 18 3-31 4-21 (30)
269 PF13824 zf-Mss51: Zinc-finger 50.7 11 0.00024 21.6 1.3 25 3-34 1-25 (55)
270 cd00029 C1 Protein kinase C co 50.1 13 0.00029 19.6 1.6 28 2-34 12-39 (50)
271 PRK05508 methionine sulfoxide 49.7 21 0.00046 23.6 2.8 18 64-81 75-93 (119)
272 COG0375 HybF Zn finger protein 49.0 11 0.00023 24.9 1.3 22 4-31 73-94 (115)
273 KOG3799 Rab3 effector RIM1 and 48.9 8.6 0.00019 26.3 0.8 31 1-35 89-119 (169)
274 PF11331 DUF3133: Protein of u 48.8 15 0.00032 20.3 1.6 31 3-33 8-41 (46)
275 COG1545 Predicted nucleic-acid 48.7 16 0.00036 24.6 2.2 30 68-97 43-73 (140)
276 PF04194 PDCD2_C: Programmed c 48.6 20 0.00042 24.7 2.6 35 69-104 98-145 (164)
277 PF14690 zf-ISL3: zinc-finger 48.4 7 0.00015 20.8 0.3 12 69-80 3-14 (47)
278 TIGR03831 YgiT_finger YgiT-typ 48.0 21 0.00046 18.5 2.2 8 69-76 33-40 (46)
279 COG1571 Predicted DNA-binding 47.8 11 0.00023 30.3 1.3 29 68-109 350-378 (421)
280 TIGR03830 CxxCG_CxxCG_HTH puta 47.1 23 0.0005 22.6 2.7 6 70-75 33-38 (127)
281 PRK00762 hypA hydrogenase nick 47.0 9.3 0.0002 25.2 0.8 28 3-31 72-100 (124)
282 KOG1311 DHHC-type Zn-finger pr 47.0 8.3 0.00018 28.8 0.6 29 1-37 113-141 (299)
283 KOG2767 Translation initiation 46.9 8.4 0.00018 30.3 0.6 31 69-107 97-127 (400)
284 PF13909 zf-H2C2_5: C2H2-type 45.9 13 0.00029 16.8 1.0 11 24-34 1-11 (24)
285 PRK06266 transcription initiat 45.8 11 0.00024 26.5 1.0 19 89-109 110-128 (178)
286 smart00109 C1 Protein kinase C 45.8 14 0.0003 19.3 1.2 26 2-33 12-37 (49)
287 PF15135 UPF0515: Uncharacteri 44.9 12 0.00025 28.1 1.1 61 22-85 111-172 (278)
288 KOG2462 C2H2-type Zn-finger pr 44.8 14 0.00029 28.0 1.4 18 85-108 236-253 (279)
289 PRK08351 DNA-directed RNA poly 44.8 16 0.00034 21.4 1.4 25 3-37 5-29 (61)
290 PF14952 zf-tcix: Putative tre 44.8 10 0.00022 20.7 0.6 27 69-109 12-38 (44)
291 PF02591 DUF164: Putative zinc 44.8 7.4 0.00016 21.9 0.0 29 3-31 24-54 (56)
292 PRK12366 replication factor A; 44.1 13 0.00028 31.1 1.4 24 3-32 534-557 (637)
293 PF08646 Rep_fac-A_C: Replicat 43.5 18 0.00039 24.1 1.8 25 4-33 21-47 (146)
294 COG1885 Uncharacterized protei 43.4 22 0.00048 23.2 2.1 16 68-83 49-65 (115)
295 COG2093 DNA-directed RNA polym 43.0 18 0.00039 21.4 1.4 27 3-37 6-32 (64)
296 smart00532 LIGANc Ligase N fam 42.6 18 0.00039 29.1 1.9 26 2-31 400-427 (441)
297 PF07649 C1_3: C1-like domain; 42.1 20 0.00044 17.3 1.4 12 22-33 14-25 (30)
298 PRK03564 formate dehydrogenase 42.0 24 0.00052 27.1 2.4 36 68-109 187-223 (309)
299 PRK08402 replication factor A; 41.7 18 0.00038 28.3 1.7 26 3-32 214-239 (355)
300 PRK04023 DNA polymerase II lar 41.3 19 0.00042 32.1 2.0 14 24-37 664-677 (1121)
301 PRK07218 replication factor A; 41.1 14 0.0003 29.6 1.0 25 3-37 299-323 (423)
302 PRK07561 DNA topoisomerase I s 41.0 32 0.00068 29.9 3.2 23 3-27 589-611 (859)
303 TIGR01057 topA_arch DNA topois 40.9 21 0.00046 29.7 2.2 26 68-101 589-614 (618)
304 PF01641 SelR: SelR domain; I 40.7 12 0.00027 24.9 0.6 18 64-81 82-100 (124)
305 cd00974 DSRD Desulforedoxin (D 40.6 18 0.00039 18.1 1.1 11 95-107 3-13 (34)
306 smart00547 ZnF_RBZ Zinc finger 40.4 16 0.00034 16.9 0.8 11 4-14 5-15 (26)
307 PF09845 DUF2072: Zn-ribbon co 40.2 20 0.00043 24.2 1.6 20 70-89 21-40 (131)
308 TIGR00319 desulf_FeS4 desulfof 40.1 19 0.00041 18.0 1.1 11 95-107 6-16 (34)
309 COG3880 Modulator of heat shoc 39.1 22 0.00047 25.1 1.7 33 70-106 2-34 (176)
310 cd02674 Peptidase_C19R A subfa 38.9 77 0.0017 22.0 4.6 17 21-37 49-65 (230)
311 PF05180 zf-DNL: DNL zinc fing 38.9 12 0.00026 22.3 0.3 33 69-106 5-37 (66)
312 PRK14810 formamidopyrimidine-D 38.8 40 0.00087 25.1 3.2 30 66-105 242-271 (272)
313 PRK07220 DNA topoisomerase I; 38.4 28 0.00061 29.7 2.5 31 3-34 637-668 (740)
314 PRK00750 lysK lysyl-tRNA synth 38.3 39 0.00084 27.6 3.2 36 67-108 174-209 (510)
315 smart00401 ZnF_GATA zinc finge 37.7 21 0.00046 19.8 1.2 34 68-109 3-36 (52)
316 PRK08579 anaerobic ribonucleos 37.3 17 0.00037 30.6 1.0 22 2-31 569-590 (625)
317 PF06750 DiS_P_DiS: Bacterial 36.9 16 0.00035 22.9 0.7 31 3-33 35-68 (92)
318 PF00096 zf-C2H2: Zinc finger, 36.8 22 0.00048 15.6 1.0 11 97-109 1-11 (23)
319 PRK01103 formamidopyrimidine/5 36.8 55 0.0012 24.3 3.7 30 67-106 244-273 (274)
320 PF06573 Churchill: Churchill 36.7 33 0.00072 22.4 2.1 10 68-77 58-67 (112)
321 PF10825 DUF2752: Protein of u 36.0 2.4 5.1E-05 23.9 -2.9 19 67-85 8-26 (52)
322 PRK14811 formamidopyrimidine-D 35.7 51 0.0011 24.5 3.3 30 67-106 234-263 (269)
323 PF14369 zf-RING_3: zinc-finge 35.6 30 0.00064 17.7 1.5 27 2-31 3-29 (35)
324 PHA02325 hypothetical protein 35.4 43 0.00093 19.9 2.3 23 68-90 3-28 (72)
325 COG1601 GCD7 Translation initi 35.0 8.3 0.00018 26.6 -0.9 33 3-36 107-139 (151)
326 PF07975 C1_4: TFIIH C1-like d 34.9 16 0.00036 20.5 0.4 30 4-33 2-31 (51)
327 PF07503 zf-HYPF: HypF finger; 34.5 5.7 0.00012 20.6 -1.4 28 4-31 2-29 (35)
328 PF13894 zf-C2H2_4: C2H2-type 34.4 26 0.00057 15.0 1.1 11 97-109 1-11 (24)
329 COG0229 Conserved domain frequ 34.2 38 0.00082 23.1 2.2 18 64-81 87-105 (140)
330 PF09463 Opy2: Opy2 protein; 34.1 42 0.00092 17.4 1.9 17 70-86 10-26 (35)
331 PF14169 YdjO: Cold-inducible 33.6 36 0.00078 19.8 1.7 26 80-105 2-27 (59)
332 KOG2767 Translation initiation 33.5 13 0.00029 29.2 -0.1 32 3-37 98-132 (400)
333 PRK06260 threonine synthase; V 33.2 25 0.00054 27.5 1.4 23 3-31 5-27 (397)
334 KOG4537 Zn-ribbon-containing p 33.2 11 0.00023 26.4 -0.6 26 3-33 42-67 (178)
335 PF06397 Desulfoferrod_N: Desu 33.1 26 0.00055 18.3 1.0 12 94-107 4-15 (36)
336 TIGR00375 conserved hypothetic 32.9 15 0.00032 28.9 0.1 27 2-32 241-267 (374)
337 PRK04351 hypothetical protein; 32.6 33 0.00072 23.4 1.7 13 21-33 110-122 (149)
338 PRK13945 formamidopyrimidine-D 32.5 64 0.0014 24.1 3.4 29 67-105 253-281 (282)
339 PF01020 Ribosomal_L40e: Ribos 32.3 10 0.00022 21.5 -0.7 24 3-34 19-44 (52)
340 PRK08329 threonine synthase; V 32.3 36 0.00079 26.1 2.1 24 1-32 1-24 (347)
341 COG1655 Uncharacterized protei 32.1 23 0.00049 26.4 0.9 15 23-37 19-33 (267)
342 PRK10445 endonuclease VIII; Pr 31.9 77 0.0017 23.5 3.7 29 67-105 234-262 (263)
343 PF06200 tify: tify domain; I 31.7 35 0.00075 17.8 1.3 7 91-97 6-12 (36)
344 PF13913 zf-C2HC_2: zinc-finge 31.4 25 0.00053 16.5 0.7 8 69-76 3-10 (25)
345 PF01529 zf-DHHC: DHHC palmito 31.0 27 0.00058 23.5 1.1 26 2-35 49-74 (174)
346 COG1384 LysS Lysyl-tRNA synthe 30.8 78 0.0017 26.2 3.8 33 67-107 170-203 (521)
347 cd02249 ZZ Zinc finger, ZZ typ 30.8 59 0.0013 17.3 2.3 21 3-31 2-22 (46)
348 PRK08173 DNA topoisomerase III 30.8 36 0.00078 29.7 2.0 25 3-33 626-650 (862)
349 COG1675 TFA1 Transcription ini 30.7 21 0.00045 25.2 0.5 12 3-14 134-145 (176)
350 PF01363 FYVE: FYVE zinc finge 30.6 54 0.0012 18.7 2.3 26 3-34 11-36 (69)
351 KOG2703 C4-type Zn-finger prot 30.5 42 0.00091 27.0 2.2 10 70-79 70-79 (460)
352 KOG3092 Casein kinase II, beta 30.2 22 0.00047 25.8 0.5 12 3-14 136-147 (216)
353 TIGR00354 polC DNA polymerase, 30.2 26 0.00057 31.1 1.1 22 68-107 625-646 (1095)
354 TIGR00577 fpg formamidopyrimid 29.8 82 0.0018 23.4 3.6 28 67-104 244-271 (272)
355 PF00320 GATA: GATA zinc finge 29.4 8.4 0.00018 19.8 -1.3 31 71-109 1-31 (36)
356 COG5349 Uncharacterized protei 29.3 23 0.00049 23.7 0.5 12 68-79 21-32 (126)
357 PRK08271 anaerobic ribonucleos 28.6 30 0.00065 29.1 1.1 22 2-31 567-588 (623)
358 PRK06393 rpoE DNA-directed RNA 28.5 29 0.00062 20.5 0.7 21 3-33 7-27 (64)
359 KOG4323 Polycomb-like PHD Zn-f 28.4 23 0.0005 28.8 0.4 33 1-33 185-225 (464)
360 PF14255 Cys_rich_CPXG: Cystei 28.0 46 0.001 18.7 1.5 29 3-31 2-32 (52)
361 PF11023 DUF2614: Protein of u 27.9 26 0.00057 23.0 0.6 12 67-78 68-79 (114)
362 PF03107 C1_2: C1 domain; Int 27.9 75 0.0016 15.3 2.2 23 4-33 3-25 (30)
363 PF02148 zf-UBP: Zn-finger in 27.7 40 0.00087 19.2 1.3 16 21-36 9-24 (63)
364 smart00064 FYVE Protein presen 27.6 41 0.00089 19.2 1.3 25 2-32 11-35 (68)
365 PRK06599 DNA topoisomerase I; 27.5 60 0.0013 27.4 2.7 7 25-31 639-645 (675)
366 PF05495 zf-CHY: CHY zinc fing 27.5 33 0.00072 20.3 0.9 14 23-36 41-54 (71)
367 COG3024 Uncharacterized protei 27.4 36 0.00077 20.2 1.0 14 66-79 5-18 (65)
368 TIGR03829 YokU_near_AblA uncha 27.4 89 0.0019 19.6 2.9 8 69-76 36-43 (89)
369 smart00249 PHD PHD zinc finger 27.3 57 0.0012 16.3 1.8 25 3-34 1-25 (47)
370 KOG3214 Uncharacterized Zn rib 27.2 34 0.00073 22.1 1.0 30 4-33 26-57 (109)
371 PF06906 DUF1272: Protein of u 26.9 35 0.00075 19.7 0.9 10 68-77 41-50 (57)
372 PRK11088 rrmA 23S rRNA methylt 26.6 60 0.0013 23.7 2.4 28 2-36 3-30 (272)
373 PRK14018 trifunctional thiored 26.5 67 0.0014 26.5 2.8 18 64-81 463-481 (521)
374 KOG0402 60S ribosomal protein 26.4 34 0.00074 21.4 0.9 29 3-35 38-66 (92)
375 COG1579 Zn-ribbon protein, pos 26.3 20 0.00042 26.6 -0.3 8 23-30 221-228 (239)
376 TIGR03826 YvyF flagellar opero 26.2 20 0.00044 24.3 -0.2 26 1-33 3-28 (137)
377 KOG0696 Serine/threonine prote 26.0 13 0.00027 30.5 -1.4 25 2-31 122-146 (683)
378 PF14787 zf-CCHC_5: GAG-polypr 26.0 34 0.00073 17.9 0.7 10 70-79 4-13 (36)
379 PF06353 DUF1062: Protein of u 25.8 38 0.00083 23.0 1.1 16 21-36 11-26 (142)
380 PF15499 Peptidase_C98: Ubiqui 25.8 59 0.0013 24.6 2.2 12 23-34 134-145 (275)
381 COG2260 Predicted Zn-ribbon RN 25.5 35 0.00076 19.8 0.7 12 68-79 17-28 (59)
382 PHA02611 51 baseplate hub asse 25.1 54 0.0012 24.5 1.8 17 68-84 82-98 (249)
383 COG0272 Lig NAD-dependent DNA 25.0 50 0.0011 28.1 1.8 27 2-32 405-434 (667)
384 COG5273 Uncharacterized protei 24.8 29 0.00064 26.5 0.5 26 2-35 110-135 (309)
385 smart00154 ZnF_AN1 AN1-like Zi 24.4 71 0.0015 16.6 1.8 11 23-33 12-22 (39)
386 KOG2463 Predicted RNA-binding 24.2 91 0.002 24.5 2.9 17 68-84 257-273 (376)
387 COG1379 PHP family phosphoeste 24.2 20 0.00044 28.1 -0.6 26 4-32 249-274 (403)
388 COG3529 Predicted nucleic-acid 24.1 23 0.0005 20.8 -0.2 35 3-37 12-46 (66)
389 PF13465 zf-H2C2_2: Zinc-finge 23.5 51 0.0011 15.3 1.0 11 97-109 15-25 (26)
390 PHA02540 61 DNA primase; Provi 23.4 1.1E+02 0.0023 23.8 3.3 33 67-106 26-63 (337)
391 cd00065 FYVE FYVE domain; Zinc 23.1 60 0.0013 17.6 1.4 25 2-32 3-27 (57)
392 smart00782 PhnA_Zn_Ribbon PhnA 22.8 1.1E+02 0.0025 16.7 2.5 40 65-106 4-44 (47)
393 cd01675 RNR_III Class III ribo 22.6 58 0.0013 26.9 1.8 14 69-82 533-546 (555)
394 smart00746 TRASH metallochaper 22.6 66 0.0014 14.5 1.4 9 4-12 1-9 (39)
395 COG4469 CoiA Competence protei 22.6 38 0.00082 26.4 0.6 13 2-14 26-38 (342)
396 PF08209 Sgf11: Sgf11 (transcr 22.5 83 0.0018 16.0 1.7 14 22-35 3-16 (33)
397 PF13878 zf-C2H2_3: zinc-finge 22.3 44 0.00095 17.6 0.7 8 68-75 13-20 (41)
398 cd02337 ZZ_CBP Zinc finger, ZZ 22.2 86 0.0019 16.5 1.8 9 22-30 12-20 (41)
399 COG3357 Predicted transcriptio 22.2 36 0.00079 21.6 0.4 12 24-35 59-70 (97)
400 PRK07111 anaerobic ribonucleos 22.0 47 0.001 28.5 1.2 21 2-31 681-701 (735)
401 COG1107 Archaea-specific RecJ- 21.7 2.8E+02 0.006 23.8 5.4 31 1-37 2-32 (715)
402 PF12387 Peptidase_C74: Pestiv 21.6 47 0.001 23.6 0.9 11 68-78 175-185 (200)
403 PRK14714 DNA polymerase II lar 21.6 55 0.0012 30.0 1.5 22 3-33 681-702 (1337)
404 PF10601 zf-LITAF-like: LITAF- 21.5 54 0.0012 19.2 1.1 17 65-81 55-71 (73)
405 PLN00162 transport protein sec 21.5 54 0.0012 28.2 1.4 35 3-37 55-89 (761)
406 PF02701 zf-Dof: Dof domain, z 21.5 79 0.0017 18.6 1.7 35 68-109 5-41 (63)
407 PF15616 TerY-C: TerY-C metal 21.5 77 0.0017 21.3 1.9 13 23-35 105-117 (131)
408 PF13597 NRDD: Anaerobic ribon 21.4 52 0.0011 27.1 1.3 16 68-83 504-519 (546)
409 PF02012 BNR: BNR/Asp-box repe 21.4 32 0.00069 13.6 0.0 8 87-94 2-9 (12)
410 KOG4080 Mitochondrial ribosoma 21.3 42 0.0009 23.7 0.6 10 69-78 94-103 (176)
411 PRK07591 threonine synthase; V 21.2 55 0.0012 25.9 1.3 22 3-31 20-41 (421)
412 PF06170 DUF983: Protein of un 21.1 51 0.0011 20.4 0.9 13 67-79 7-19 (86)
413 smart00290 ZnF_UBP Ubiquitin C 20.9 1E+02 0.0022 16.3 2.0 13 23-35 11-23 (50)
414 PRK07225 DNA-directed RNA poly 20.7 49 0.0011 27.8 1.0 27 2-32 545-571 (605)
415 PRK09263 anaerobic ribonucleos 20.6 96 0.0021 26.6 2.7 28 2-33 642-669 (711)
416 PF14835 zf-RING_6: zf-RING of 20.5 57 0.0012 19.3 1.0 12 3-14 9-20 (65)
417 PF10080 DUF2318: Predicted me 20.4 79 0.0017 20.3 1.7 30 3-37 37-66 (102)
418 TIGR02827 RNR_anaer_Bdell anae 20.4 73 0.0016 26.7 1.9 14 69-82 547-560 (586)
419 PRK06599 DNA topoisomerase I; 20.2 82 0.0018 26.6 2.2 31 69-107 638-669 (675)
No 1
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=100.00 E-value=1.5e-46 Score=236.93 Aligned_cols=104 Identities=49% Similarity=0.940 Sum_probs=97.8
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCce
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKA 79 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a 79 (110)
|.|||.|||||.++ ++....+|.|++|+|..++.. .|.++..+..|++++|++++.+|+ .+.+++.||+|||++|
T Consensus 1 m~FCP~Cgn~Live--~g~~~~rf~C~tCpY~~~I~~--ei~~r~~~~~Kevd~vlgg~~a~~nv~~t~~~Cp~Cgh~ra 76 (105)
T KOG2906|consen 1 MLFCPTCGNMLIVE--SGESCNRFSCRTCPYVFPISR--EISSRKYPKLKEVDDVLGGDEAWENVDQTEATCPTCGHERA 76 (105)
T ss_pred CcccCCCCCEEEEe--cCCeEeeEEcCCCCceeeEee--eeeccccCchhhhhhhcCCcccccchhhccCcCCCCCCCce
Confidence 89999999999999 555578999999999999987 788888889999999999988898 8899999999999999
Q ss_pred EEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869 80 VYHELQTRSADEPMSIFYMCANKNCKHRWNE 110 (110)
Q Consensus 80 ~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre 110 (110)
+|+|+|+||||||||+||.|++ |+|+|||
T Consensus 77 yF~qlQtRSADEPmT~FYkC~~--C~~~Wre 105 (105)
T KOG2906|consen 77 YFMQLQTRSADEPMTTFYKCCK--CKHRWRE 105 (105)
T ss_pred EEEEeeeccCCCcHhHhhhhhc--ccccccC
Confidence 9999999999999999999999 9999997
No 2
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=100.00 E-value=2.9e-41 Score=216.02 Aligned_cols=108 Identities=34% Similarity=0.682 Sum_probs=94.0
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCC-CcccCCCCCCCc
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQ-TEVTCPACKHGK 78 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~-~~~~CpkCg~~~ 78 (110)
++||++|||||||+||+.++.+.|+||+|.|++.++++...+.....+.++.+.++.+...+| +|+ .++.||+|||++
T Consensus 4 ~rfC~eCNNmLYPkEDked~~L~laCrnCd~ve~A~s~~vY~~~~~~e~dE~t~ii~Dl~~DPTLPrts~~~C~~C~~~e 83 (113)
T KOG2691|consen 4 IRFCRECNNMLYPKEDKEDRILLLACRNCDYVEEADSSRVYVNELSHEHDELTQIIMDLASDPTLPRTSDKHCPKCGHRE 83 (113)
T ss_pred cchhhhhhccccccccccccEEEEEecCCcceEecCCcceEcCCcccchhhHHHHHHhhccCCCcCccccccCCccCCcc
Confidence 589999999999999999999999999999999999943333334445567666665556678 998 589999999999
Q ss_pred eEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869 79 AVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110 (110)
Q Consensus 79 a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre 110 (110)
|+|||.|+|.||++|++||+|++ |+|+|+|
T Consensus 84 avffQ~~~~r~d~~m~l~yvC~~--C~h~wte 113 (113)
T KOG2691|consen 84 AVFFQAQTRRADEAMRLFYVCCS--CGHRWTE 113 (113)
T ss_pred eEEEecccccccceEEEEEEecc--ccccccC
Confidence 99999999999999999999999 9999986
No 3
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=100.00 E-value=7.4e-39 Score=210.38 Aligned_cols=104 Identities=35% Similarity=0.726 Sum_probs=78.1
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCceEEEEeccc----C-ccccccccc-cccccC-CCCCcccCCC
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPL----S-KKEIQPIFT-QDAMME-GPQTEVTCPA 73 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~----~-~~~~~~~~~-~~~~~~-~~~~~~~Cpk 73 (110)
|+|||+|||||+|+ ++..+..++|++|||..++... .+++... . .+.+..+.. .....+ +++..+.||+
T Consensus 2 m~FCp~Cgsll~p~--~~~~~~~l~C~kCgye~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cpk 77 (113)
T COG1594 2 MRFCPKCGSLLYPK--KDDEGGKLVCRKCGYEEEASNK--KVYRYSVKEAVEKKKEVVLVVEDETQGAKTLPTAKEKCPK 77 (113)
T ss_pred ccccCCccCeeEEe--EcCCCcEEECCCCCcchhcccc--ceeEEEEeeccCCcceeeeeecccccCccccccccccCCC
Confidence 89999999999999 4333559999999999999872 2222221 1 111111111 111223 5566889999
Q ss_pred CCCCceEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869 74 CKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110 (110)
Q Consensus 74 Cg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre 110 (110)
||+++|+|||+|+||||||||+||+|++ |||+||+
T Consensus 78 Cg~~ea~y~~~QtRsaDEp~T~Fy~C~~--Cg~~wre 112 (113)
T COG1594 78 CGNKEAYYWQLQTRSADEPETRFYKCTR--CGYRWRE 112 (113)
T ss_pred CCCceeEEEeeehhccCCCceEEEEecc--cCCEeec
Confidence 9999999999999999999999999999 9999996
No 4
>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=100.00 E-value=1e-38 Score=206.81 Aligned_cols=101 Identities=36% Similarity=0.755 Sum_probs=80.1
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceE
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAV 80 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~ 80 (110)
.|||+||+||++. . ..+.|+.|+|.+.......++++..++.+..++++..++..+ +|++++.||+|||++|+
T Consensus 1 ~fC~~Cg~~l~~~--~----~~~~C~~C~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~~~a~ 74 (104)
T TIGR01384 1 KFCPKCGSLMTPK--N----GVYVCPSCGYEKEKKPEDDYKVTEKVKHKIKETIIIREEDSETLPTTRVECPKCGHKEAY 74 (104)
T ss_pred CCCcccCcccccC--C----CeEECcCCCCccccccccccEEEEEeccccccceeeccccccCCCcccCCCCCCCCCeeE
Confidence 5999999999887 2 389999999998875222455555554443333322333336 89999999999999999
Q ss_pred EEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869 81 YHELQTRSADEPMSIFYMCANKNCKHRWNE 110 (110)
Q Consensus 81 ~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre 110 (110)
|||+|+||||||||+||+|++ |+|+||+
T Consensus 75 f~~~Q~RsadE~~T~fy~C~~--C~~~w~~ 102 (104)
T TIGR01384 75 YWLLQTRRADEPETRFYKCTK--CGYVWRE 102 (104)
T ss_pred EEEeccCCCCCCcEEEEEeCC--CCCeeEe
Confidence 999999999999999999999 9999996
No 5
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=99.97 E-value=3.5e-33 Score=180.26 Aligned_cols=104 Identities=28% Similarity=0.578 Sum_probs=76.2
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCce-EEE-EecccCccccccccc-cccccC-CCCCcccCCCCCC
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRV-KIK-RKQPLSKKEIQPIFT-QDAMME-GPQTEVTCPACKH 76 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~-~~~-~~~~~~~~~~~~~~~-~~~~~~-~~~~~~~CpkCg~ 76 (110)
+.||+.||+||+.+ . ......|..|+..++.+... ..+ .+..+.......... ...... +|+++++||||||
T Consensus 7 ~~FC~~CG~ll~~~--~--~~~~~~C~~Ck~~~~v~~~~~~~v~~~~~~~~~~~A~~~~ve~~~~~~ga~I~~kCpkCgh 82 (116)
T KOG2907|consen 7 LDFCSDCGSLLEEP--S--AQSTVLCIRCKIEYPVSQFSGLVVETKSLFDEFTSALAEKVENESSADGAVIKHKCPKCGH 82 (116)
T ss_pred cchhhhhhhhcccc--c--ccCceEeccccccCCHHHhCCeeEEEEEeecccchhhhhhhcccccccccchhccCcccCC
Confidence 46999999999998 3 35577899999988876521 222 222222211111111 111223 8999999999999
Q ss_pred CceEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869 77 GKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110 (110)
Q Consensus 77 ~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre 110 (110)
++|.|.++|+||||||+|+||+|++ |+|++++
T Consensus 83 e~m~Y~T~QlRSADEGQTVFYTC~k--C~~k~~e 114 (116)
T KOG2907|consen 83 EEMSYHTLQLRSADEGQTVFYTCPK--CKYKFTE 114 (116)
T ss_pred chhhhhhhhcccccCCceEEEEcCc--cceeeec
Confidence 9999999999999999999999999 9999875
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=99.93 E-value=9.2e-27 Score=127.11 Aligned_cols=40 Identities=55% Similarity=1.262 Sum_probs=38.5
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre 110 (110)
.+||+|||++|+|||+|+||||||||+||+|++ |+|+|++
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~--C~~~w~~ 40 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTK--CGHRWRE 40 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCC--CCCEeCC
Confidence 379999999999999999999999999999999 9999986
No 7
>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=99.92 E-value=2e-25 Score=121.22 Aligned_cols=39 Identities=59% Similarity=1.382 Sum_probs=35.0
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
.+||+|||++|+|+|+|+||||||||+||+|.+ |+|+||
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~--C~~~wr 39 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCN--CGHRWR 39 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESS--STEEEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCC--CCCeeC
Confidence 479999999999999999999999999999999 999997
No 8
>PHA02998 RNA polymerase subunit; Provisional
Probab=99.84 E-value=1.8e-21 Score=135.08 Aligned_cols=44 Identities=32% Similarity=0.613 Sum_probs=42.6
Q ss_pred CCC-CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 64 GPQ-TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 64 ~~~-~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
+|+ +++.||+|||++|+|||+|+||||||||+||.|.+ |||+|+
T Consensus 138 lpkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~--CG~~wk 182 (195)
T PHA02998 138 LDEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRD--CKKHFK 182 (195)
T ss_pred cCcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCC--CCCccC
Confidence 777 89999999999999999999999999999999999 999997
No 9
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=99.71 E-value=7.3e-18 Score=126.68 Aligned_cols=41 Identities=51% Similarity=1.005 Sum_probs=39.3
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
....||+||+++++|||+|+||||||||+||+|++ |||+|+
T Consensus 257 ~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~--Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEE--CGNRWK 297 (299)
T ss_pred ccccCCCCCCccceEEEecccCCCCCCeEEEEcCC--CCCeee
Confidence 35799999999999999999999999999999999 999997
No 10
>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=99.51 E-value=4.8e-15 Score=78.49 Aligned_cols=34 Identities=32% Similarity=0.764 Sum_probs=25.7
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
|+|||+|||||+|++++... . +|++|||++++++
T Consensus 1 m~FCp~C~nlL~p~~~~~~~--~-~C~~C~Y~~~~~~ 34 (35)
T PF02150_consen 1 MRFCPECGNLLYPKEDKEKR--V-ACRTCGYEEPISQ 34 (35)
T ss_dssp --BETTTTSBEEEEEETTTT--E-EESSSS-EEE-SS
T ss_pred CeeCCCCCccceEcCCCccC--c-CCCCCCCccCCCC
Confidence 89999999999999666543 4 9999999999875
No 11
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=99.14 E-value=9.5e-11 Score=66.59 Aligned_cols=41 Identities=37% Similarity=0.721 Sum_probs=32.1
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCceEEEEecc
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQP 46 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~ 46 (110)
.|||+||+||+++++. ...+++|+.|||...+.. .++++..
T Consensus 1 ~FCp~Cg~~l~~~~~~--~~~~~vC~~Cg~~~~~~~--~~~~~~~ 41 (52)
T smart00661 1 KFCPKCGNMLIPKEGK--EKRRFVCRKCGYEEPIEQ--KYVYKEK 41 (52)
T ss_pred CCCCCCCCccccccCC--CCCEEECCcCCCeEECCC--cEEEEEE
Confidence 5999999999999433 235999999999999887 5555433
No 12
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=98.97 E-value=4.6e-10 Score=84.15 Aligned_cols=40 Identities=48% Similarity=0.998 Sum_probs=38.5
Q ss_pred cccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 68 EVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 68 ~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
..+|.+|+.....|+|+|+||||||||.|-.|.. ||++|+
T Consensus 255 ~fkcgkckk~~cty~q~Qtrs~DePmtTfv~C~e--cgnrWk 294 (296)
T KOG1105|consen 255 LFKCGKCKKKNCTYTQLQTRSADEPMTTFVTCNE--CGNRWK 294 (296)
T ss_pred ceeeccccccceeEEeeccCCCCCCcceeeeecc--cCCccc
Confidence 4799999999999999999999999999999999 999996
No 13
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=98.46 E-value=1e-07 Score=49.89 Aligned_cols=33 Identities=39% Similarity=1.007 Sum_probs=21.4
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
+|||.||..|..+++.++...+++|+.||++..
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGFIHY 33 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTEEE-
T ss_pred CccccccChhhhhcCCCCCccceECCCCCCEEe
Confidence 599999999999988888899999999998753
No 14
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=98.18 E-value=1.3e-06 Score=49.57 Aligned_cols=27 Identities=33% Similarity=0.942 Sum_probs=23.2
Q ss_pred CCCcCCCC-CcccccCCCCCCceEEcCCCCCeee
Q 033869 2 EFCPTCGT-MLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 2 ~FCp~C~n-lL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
+|||.||+ +|.+. . .++.|..|||++.
T Consensus 21 ~fCP~Cg~~~m~~~--~----~r~~C~~Cgyt~~ 48 (50)
T PRK00432 21 KFCPRCGSGFMAEH--L----DRWHCGKCGYTEF 48 (50)
T ss_pred CcCcCCCcchhecc--C----CcEECCCcCCEEe
Confidence 59999999 88887 2 4899999999864
No 15
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=97.58 E-value=9.9e-05 Score=41.14 Aligned_cols=38 Identities=21% Similarity=0.553 Sum_probs=27.2
Q ss_pred cCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 70 TCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
.||.||+.-..--..++ .++--.++|.|.|+.|||+|.
T Consensus 1 ~CP~Cg~~a~ir~S~~~--s~~~~~~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQL--SPLTRELYCQCTNPECGHTFV 38 (47)
T ss_pred CcCCCCCeeEEEEchhh--CcceEEEEEEECCCcCCCEEE
Confidence 59999986544433332 334455899999999999985
No 16
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=97.35 E-value=0.00018 Score=40.48 Aligned_cols=28 Identities=32% Similarity=0.895 Sum_probs=22.1
Q ss_pred CCCcCCC--CCcccccCCCCCCceEEcCCCCCeeee
Q 033869 2 EFCPTCG--TMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 2 ~FCp~C~--nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
+|||.|| .+|--- ..+++|-.|||++-.
T Consensus 20 ~~CPrCG~gvfmA~H------~dR~~CGkCgyTe~~ 49 (51)
T COG1998 20 RFCPRCGPGVFMADH------KDRWACGKCGYTEFK 49 (51)
T ss_pred ccCCCCCCcchhhhc------CceeEeccccceEee
Confidence 5999999 555444 459999999998754
No 17
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=97.31 E-value=0.00024 Score=43.18 Aligned_cols=38 Identities=24% Similarity=0.594 Sum_probs=27.7
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCce-EEEEecCCCCCcccc
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMS-IFYMCANKNCKHRWN 109 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T-~fY~C~~~~C~~~wr 109 (110)
..||.||+.-. ..-+|..+++.. ++|.|.|..|||+|.
T Consensus 2 m~CP~Cg~~a~---irtSr~~s~~~~~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 2 FHCPLCQHAAH---ARTSRYITDTTKERYHQCQNVNCSATFI 40 (72)
T ss_pred ccCCCCCCccE---EEEChhcChhhheeeeecCCCCCCCEEE
Confidence 37999999763 233455555543 899999888999985
No 18
>PHA00626 hypothetical protein
Probab=96.85 E-value=0.001 Score=38.42 Aligned_cols=36 Identities=22% Similarity=0.480 Sum_probs=24.9
Q ss_pred CCCcCCCCCcccccCCCC-CCceEEcCCCCCeeeeCC
Q 033869 2 EFCPTCGTMLQYELPHMD-RPSRFSCPACPYVCNMES 37 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~-~~~~~~C~~C~y~~~~~~ 37 (110)
+.||+||+--..+..... ....|.|+.|||....+.
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCeechhh
Confidence 479999995444412222 267999999999876553
No 19
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=96.70 E-value=0.00075 Score=33.00 Aligned_cols=24 Identities=33% Similarity=0.843 Sum_probs=18.4
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
+++||.||..+... .-.|+.||..
T Consensus 2 ~~~Cp~Cg~~~~~~--------~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEIDPD--------AKFCPNCGAK 25 (26)
T ss_pred cCCCcccCCcCCcc--------cccChhhCCC
Confidence 46999999965444 5689999963
No 20
>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=96.63 E-value=0.0016 Score=33.25 Aligned_cols=28 Identities=25% Similarity=0.497 Sum_probs=18.0
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
+||+.||.-+.+. .. .-...|+.|+...
T Consensus 4 rfC~~CG~~t~~~--~~--g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 4 RFCGRCGAPTKPA--PG--GWARRCPSCGHEH 31 (32)
T ss_dssp SB-TTT--BEEE---SS--SS-EEESSSS-EE
T ss_pred cccCcCCccccCC--CC--cCEeECCCCcCEe
Confidence 6999999999998 33 4689999999764
No 21
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=96.57 E-value=0.0032 Score=33.67 Aligned_cols=34 Identities=26% Similarity=0.626 Sum_probs=27.8
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCC---CCCeeeeCC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPA---CPYVCNMES 37 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~---C~y~~~~~~ 37 (110)
..||.||..|..+ ....+..+.|.+ |.|+..+..
T Consensus 2 ~~CP~Cg~~lv~r--~~k~g~F~~Cs~yP~C~~~~~~~~ 38 (39)
T PF01396_consen 2 EKCPKCGGPLVLR--RGKKGKFLGCSNYPECKYTEPLPK 38 (39)
T ss_pred cCCCCCCceeEEE--ECCCCCEEECCCCCCcCCeEeCCC
Confidence 4699999999999 555568999997 999887653
No 22
>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=96.56 E-value=0.0011 Score=32.55 Aligned_cols=24 Identities=33% Similarity=0.820 Sum_probs=19.9
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
=||+|+..+... .-.|+.|||...
T Consensus 2 ~CP~C~~~V~~~--------~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPES--------AKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhh--------cCcCCCCCCCCc
Confidence 499999998666 678999999764
No 23
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=96.40 E-value=0.0015 Score=31.16 Aligned_cols=22 Identities=32% Similarity=0.970 Sum_probs=17.2
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
|||.||+-+... .-.|+.||..
T Consensus 1 ~Cp~CG~~~~~~--------~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDD--------AKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCc--------CcchhhhCCc
Confidence 899999988654 4459999863
No 24
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=96.39 E-value=0.0042 Score=33.24 Aligned_cols=32 Identities=34% Similarity=0.720 Sum_probs=22.7
Q ss_pred cccCCCCCCCceEEEEeccCCCCCCceEEEEecC-CCCCcc
Q 033869 68 EVTCPACKHGKAVYHELQTRSADEPMSIFYMCAN-KNCKHR 107 (110)
Q Consensus 68 ~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~-~~C~~~ 107 (110)
++.||+|| ..++. |.+--| .||-|.+ |.|.++
T Consensus 1 ~~~CP~Cg-~~lv~-----r~~k~g--~F~~Cs~yP~C~~~ 33 (39)
T PF01396_consen 1 VEKCPKCG-GPLVL-----RRGKKG--KFLGCSNYPECKYT 33 (39)
T ss_pred CcCCCCCC-ceeEE-----EECCCC--CEEECCCCCCcCCe
Confidence 36899999 44433 444445 9999998 689875
No 25
>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=96.24 E-value=0.0049 Score=29.66 Aligned_cols=24 Identities=29% Similarity=1.003 Sum_probs=19.6
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
|..||-.|.++ .+...|.|++||+
T Consensus 1 C~sC~~~i~~r----~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPR----EQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCc----ccCceEeCCCCCC
Confidence 67899999988 2356999999995
No 26
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=96.21 E-value=0.022 Score=43.46 Aligned_cols=72 Identities=22% Similarity=0.558 Sum_probs=41.2
Q ss_pred CCCcCCCCCcccc---cCCCCCCceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccCCCCCcccCCCCCCC-
Q 033869 2 EFCPTCGTMLQYE---LPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHG- 77 (110)
Q Consensus 2 ~FCp~C~nlL~~~---~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~- 77 (110)
.+||-||+.=... ....++.-++.|..|+..+... ...||.||+.
T Consensus 188 ~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~-------------------------------R~~C~~Cg~~~ 236 (309)
T PRK03564 188 QFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVV-------------------------------RVKCSNCEQSG 236 (309)
T ss_pred CCCCCCCCcchhheeeccCCCCceEEEcCCCCCccccc-------------------------------CccCCCCCCCC
Confidence 4788888762111 0012334577888888655432 3468888864
Q ss_pred ceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 78 KAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 78 ~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
+..||.+- .+++-...++|.. |+.-++
T Consensus 237 ~l~y~~~~---~~~~~~r~e~C~~--C~~YlK 263 (309)
T PRK03564 237 KLHYWSLD---SEQAAVKAESCGD--CGTYLK 263 (309)
T ss_pred ceeeeeec---CCCcceEeeeccc--ccccce
Confidence 55565552 1224457788887 876543
No 27
>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=96.18 E-value=0.0042 Score=31.96 Aligned_cols=15 Identities=27% Similarity=0.685 Sum_probs=11.9
Q ss_pred cccCCCCCCCceEEE
Q 033869 68 EVTCPACKHGKAVYH 82 (110)
Q Consensus 68 ~~~CpkCg~~~a~~~ 82 (110)
+..||.||..+..|.
T Consensus 17 ~~~CP~Cg~~~~~F~ 31 (33)
T cd00350 17 PWVCPVCGAPKDKFE 31 (33)
T ss_pred CCcCcCCCCcHHHcE
Confidence 458999999877664
No 28
>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=95.90 E-value=0.002 Score=32.65 Aligned_cols=27 Identities=33% Similarity=0.966 Sum_probs=14.3
Q ss_pred cCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 70 TCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
+||+||....+ .| ...|+|.. |+|.|.
T Consensus 4 ~Cp~C~se~~y--------~D---~~~~vCp~--C~~ew~ 30 (30)
T PF08274_consen 4 KCPLCGSEYTY--------ED---GELLVCPE--CGHEWN 30 (30)
T ss_dssp --TTT-----E--------E----SSSEEETT--TTEEE-
T ss_pred CCCCCCCccee--------cc---CCEEeCCc--ccccCC
Confidence 79999998877 22 22489999 999994
No 29
>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=95.88 E-value=0.0093 Score=44.74 Aligned_cols=72 Identities=21% Similarity=0.489 Sum_probs=30.5
Q ss_pred CCCcCCCCC-----cccccCCCCCCceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccCCCCCcccCCCCCC
Q 033869 2 EFCPTCGTM-----LQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKH 76 (110)
Q Consensus 2 ~FCp~C~nl-----L~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~ 76 (110)
.+||-||+. |...++ .+.-++.|..|+..+... ...||.||+
T Consensus 173 g~CPvCGs~P~~s~l~~~~~--~G~R~L~Cs~C~t~W~~~-------------------------------R~~Cp~Cg~ 219 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGER--EGKRYLHCSLCGTEWRFV-------------------------------RIKCPYCGN 219 (290)
T ss_dssp SS-TTT---EEEEEEE--------EEEEEETTT--EEE---------------------------------TTS-TTT--
T ss_pred CcCCCCCCcCceEEEecCCC--CccEEEEcCCCCCeeeec-------------------------------CCCCcCCCC
Confidence 368888875 222211 123577888888765532 336999998
Q ss_pred CceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 77 GKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 77 ~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
.+..=+.. ....+++.-..++|-+ |+.-++
T Consensus 220 ~~~~~l~~-~~~e~~~~~rve~C~~--C~~YlK 249 (290)
T PF04216_consen 220 TDHEKLEY-FTVEGEPAYRVEVCES--CGSYLK 249 (290)
T ss_dssp -SS-EEE---------SEEEEEETT--TTEEEE
T ss_pred CCCcceee-EecCCCCcEEEEECCc--ccchHH
Confidence 65432222 2245667888899999 987654
No 30
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=95.87 E-value=0.012 Score=32.34 Aligned_cols=31 Identities=23% Similarity=0.673 Sum_probs=23.2
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
=|+.||..+... ... ..+.|+.||.......
T Consensus 5 ~C~~CG~~~~~~--~~~--~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 5 KCARCGREVELD--EYG--TGVRCPYCGYRILFKE 35 (46)
T ss_pred ECCCCCCEEEEC--CCC--CceECCCCCCeEEEcc
Confidence 399999998887 322 2799999998665544
No 31
>PHA00626 hypothetical protein
Probab=95.80 E-value=0.0095 Score=34.41 Aligned_cols=33 Identities=30% Similarity=0.631 Sum_probs=22.3
Q ss_pred cCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 70 TCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
.||+||+.+.+ -....| .+..-|+|.. |||.++
T Consensus 2 ~CP~CGS~~Iv-rcg~cr----~~snrYkCkd--CGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIA-KEKTMR----GWSDDYVCCD--CGYNDS 34 (59)
T ss_pred CCCCCCCceee-eeceec----ccCcceEcCC--CCCeec
Confidence 69999997764 211112 2345599998 999875
No 32
>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=95.80 E-value=0.046 Score=41.67 Aligned_cols=72 Identities=21% Similarity=0.482 Sum_probs=41.7
Q ss_pred CCcCCCCCccc---cc-CCCCCCceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccCCCCCcccCCCCCCC-
Q 033869 3 FCPTCGTMLQY---EL-PHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHG- 77 (110)
Q Consensus 3 FCp~C~nlL~~---~~-~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~- 77 (110)
+||-||+.=.. .. ...++.-++.|..|+..+... ...||.||+.
T Consensus 186 ~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~-------------------------------R~~C~~Cg~~~ 234 (305)
T TIGR01562 186 LCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYV-------------------------------RVKCSHCEESK 234 (305)
T ss_pred cCCCCCChhhhhhhcccCCCCCceEEEcCCCCCccccc-------------------------------CccCCCCCCCC
Confidence 78888876322 10 012334578888888665432 3468888865
Q ss_pred ceEEEEeccCCCCCCceEEEEecCCCCCccc
Q 033869 78 KAVYHELQTRSADEPMSIFYMCANKNCKHRW 108 (110)
Q Consensus 78 ~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~w 108 (110)
+..||.+-. ..+++-....+|.. |+.-+
T Consensus 235 ~l~y~~~e~-~~~~~~~r~e~C~~--C~~Yl 262 (305)
T TIGR01562 235 HLAYLSLEH-DAEKAVLKAETCDS--CQGYL 262 (305)
T ss_pred ceeeEeecC-CCCCcceEEeeccc--cccch
Confidence 344665532 11234567788887 87644
No 33
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=95.76 E-value=0.019 Score=34.09 Aligned_cols=11 Identities=27% Similarity=0.809 Sum_probs=6.8
Q ss_pred cCCCCCCCceE
Q 033869 70 TCPACKHGKAV 80 (110)
Q Consensus 70 ~CpkCg~~~a~ 80 (110)
.|||||+.+..
T Consensus 2 ~C~KCg~~~~e 12 (64)
T PF09855_consen 2 KCPKCGNEEYE 12 (64)
T ss_pred CCCCCCCccee
Confidence 57777775543
No 34
>COG1773 Rubredoxin [Energy production and conversion]
Probab=95.74 E-value=0.014 Score=33.55 Aligned_cols=49 Identities=29% Similarity=0.572 Sum_probs=30.1
Q ss_pred eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEEEe
Q 033869 23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYHEL 84 (110)
Q Consensus 23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~~~ 84 (110)
.|.|+.|||+++.... .....|-.+. .+. +| .+..||.||-.+..|..+
T Consensus 3 ~~~C~~CG~vYd~e~G-----------dp~~gi~pgT-~fedlP-d~w~CP~Cg~~K~~F~~~ 52 (55)
T COG1773 3 RWRCSVCGYVYDPEKG-----------DPRCGIAPGT-PFEDLP-DDWVCPECGVGKKDFEMI 52 (55)
T ss_pred ceEecCCceEeccccC-----------CccCCCCCCC-chhhCC-CccCCCCCCCCHhHeeec
Confidence 6899999998876541 1111222111 122 22 478999999888877654
No 35
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=95.66 E-value=0.0079 Score=34.00 Aligned_cols=47 Identities=23% Similarity=0.572 Sum_probs=27.3
Q ss_pred eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEE
Q 033869 23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYH 82 (110)
Q Consensus 23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~ 82 (110)
.|.|+.|||+++.... .....|..+. .+. ||. +..||.||..+..|-
T Consensus 1 ~y~C~~CgyiYd~~~G-----------d~~~~i~pGt-~f~~Lp~-~w~CP~C~a~K~~F~ 48 (50)
T cd00730 1 KYECRICGYIYDPAEG-----------DPDEGIPPGT-PFEDLPD-DWVCPVCGAGKDDFE 48 (50)
T ss_pred CcCCCCCCeEECCCCC-----------CcccCcCCCC-CHhHCCC-CCCCCCCCCcHHHcE
Confidence 3789999998875431 0001122111 122 443 789999998876653
No 36
>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=95.53 E-value=0.013 Score=32.24 Aligned_cols=28 Identities=25% Similarity=0.599 Sum_probs=20.8
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
..||+||+.+++.... ...|.|.+ |+++
T Consensus 19 ~~CP~Cg~~~~~~~~~---------~~~~~C~~--C~~q 46 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKT---------RGRYRCKA--CRKQ 46 (46)
T ss_pred CCCCCCCCeeeEEeCC---------CCeEECCC--CCCc
Confidence 5699999995555432 45699999 9874
No 37
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=95.48 E-value=0.017 Score=32.18 Aligned_cols=46 Identities=28% Similarity=0.622 Sum_probs=23.8
Q ss_pred eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEE
Q 033869 23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVY 81 (110)
Q Consensus 23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~ 81 (110)
.|.|+.|||+.+.... +....|..+. .+. || .+..||.||..+..|
T Consensus 1 ky~C~~CgyvYd~~~G-----------d~~~~i~pGt-~F~~Lp-~~w~CP~C~a~K~~F 47 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKG-----------DPENGIPPGT-PFEDLP-DDWVCPVCGAPKSDF 47 (47)
T ss_dssp EEEETTTSBEEETTTB-----------BGGGTB-TT---GGGS--TT-B-TTTSSBGGGE
T ss_pred CcCCCCCCEEEcCCcC-----------CcccCcCCCC-CHHHCC-CCCcCcCCCCccccC
Confidence 4899999998875441 1111222211 122 43 368999999876433
No 38
>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=95.47 E-value=0.016 Score=30.06 Aligned_cols=12 Identities=33% Similarity=1.115 Sum_probs=10.1
Q ss_pred eEEcCCCCCeee
Q 033869 23 RFSCPACPYVCN 34 (110)
Q Consensus 23 ~~~C~~C~y~~~ 34 (110)
.|.|+.|||+..
T Consensus 2 ~~~C~~CG~i~~ 13 (34)
T cd00729 2 VWVCPVCGYIHE 13 (34)
T ss_pred eEECCCCCCEeE
Confidence 689999999754
No 39
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=95.41 E-value=0.0091 Score=34.87 Aligned_cols=26 Identities=31% Similarity=0.885 Sum_probs=15.1
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
-|.-||-.|.|. .+...|.|++||.+
T Consensus 11 ~CtSCg~~i~p~----e~~v~F~CPnCGe~ 36 (61)
T COG2888 11 VCTSCGREIAPG----ETAVKFPCPNCGEV 36 (61)
T ss_pred eeccCCCEeccC----CceeEeeCCCCCce
Confidence 356666666665 22346677777743
No 40
>PF12773 DZR: Double zinc ribbon
Probab=95.38 E-value=0.008 Score=33.36 Aligned_cols=27 Identities=41% Similarity=0.833 Sum_probs=18.7
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
.||+.||..|... ....+.|+.||+..
T Consensus 13 ~fC~~CG~~l~~~-----~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 13 KFCPHCGTPLPPP-----DQSKKICPNCGAEN 39 (50)
T ss_pred cCChhhcCChhhc-----cCCCCCCcCCcCCC
Confidence 6888888888822 13467888888753
No 41
>PF14353 CpXC: CpXC protein
Probab=95.17 E-value=0.018 Score=38.10 Aligned_cols=45 Identities=22% Similarity=0.440 Sum_probs=25.2
Q ss_pred EEcCCCCCeeeeCCceEEEEeccc--CccccccccccccccCCCCCcccCCCCCCCc
Q 033869 24 FSCPACPYVCNMESRVKIKRKQPL--SKKEIQPIFTQDAMMEGPQTEVTCPACKHGK 78 (110)
Q Consensus 24 ~~C~~C~y~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~~ 78 (110)
+.|+.|+....++-. ..+.. ...-.+.++.++ --...||+||+.-
T Consensus 2 itCP~C~~~~~~~v~----~~I~~~~~p~l~e~il~g~------l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVW----TSINADEDPELKEKILDGS------LFSFTCPSCGHKF 48 (128)
T ss_pred cCCCCCCCeeEEEEE----eEEcCcCCHHHHHHHHcCC------cCEEECCCCCCce
Confidence 579999998776542 11221 121122344322 2367999999854
No 42
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=95.09 E-value=0.018 Score=34.11 Aligned_cols=34 Identities=26% Similarity=0.696 Sum_probs=20.9
Q ss_pred cCCCCCCCceEEEEeccCCCCCCceEEE----------EecCCCCCcc
Q 033869 70 TCPACKHGKAVYHELQTRSADEPMSIFY----------MCANKNCKHR 107 (110)
Q Consensus 70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY----------~C~~~~C~~~ 107 (110)
+|||||+++ |.+.+++...++..-|| .|.+ |||+
T Consensus 6 kCpKCgn~~--~~ekei~~tg~~lskifdvq~n~f~~itCk~--CgYt 49 (68)
T COG3478 6 KCPKCGNTN--YEEKEIAATGGGLSKIFDVQNNKFIVITCKN--CGYT 49 (68)
T ss_pred cCCCcCCcc--hhhceeeccCCCcceeEEecccEEEEEEecc--CCch
Confidence 488888765 35555556656655443 4667 7764
No 43
>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=94.97 E-value=0.015 Score=29.42 Aligned_cols=26 Identities=35% Similarity=0.821 Sum_probs=15.1
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
=||.|++-.... | +..|+|+.|+++.
T Consensus 4 ~Cp~C~se~~y~-D----~~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTYE-D----GELLVCPECGHEW 29 (30)
T ss_dssp --TTT-----EE------SSSEEETTTTEEE
T ss_pred CCCCCCCcceec-c----CCEEeCCcccccC
Confidence 499999887775 2 4599999999875
No 44
>PRK14973 DNA topoisomerase I; Provisional
Probab=94.80 E-value=0.057 Score=46.74 Aligned_cols=33 Identities=24% Similarity=0.415 Sum_probs=21.8
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
++..||+||.+. .+.+|...-|+ |.-|.. |+|.
T Consensus 634 ~~~~Cp~CG~p~----~~~~r~Gr~g~--fl~CP~--C~~~ 666 (936)
T PRK14973 634 TDEVCPIHHLNH----VRLIRKGARPW--DIGCPL--CSHI 666 (936)
T ss_pred CCCCCCCCCCCc----eEEeecCCCcc--cccCcc--ccch
Confidence 356899999862 22235555566 778966 9884
No 45
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=94.70 E-value=0.018 Score=34.22 Aligned_cols=15 Identities=27% Similarity=0.476 Sum_probs=12.0
Q ss_pred CcccCCCCCCCceEE
Q 033869 67 TEVTCPACKHGKAVY 81 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~ 81 (110)
+-+.|++||+.|.+-
T Consensus 35 ~~v~C~~CGYTE~Y~ 49 (64)
T PF09855_consen 35 TTVSCTNCGYTEFYK 49 (64)
T ss_pred EEEECCCCCCEEEEe
Confidence 456899999998755
No 46
>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=94.62 E-value=0.044 Score=37.58 Aligned_cols=36 Identities=31% Similarity=0.704 Sum_probs=28.5
Q ss_pred cCCCCCCCceEEEEeccCCCCCCceEE--EEecCCCCCcccc
Q 033869 70 TCPACKHGKAVYHELQTRSADEPMSIF--YMCANKNCKHRWN 109 (110)
Q Consensus 70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~f--Y~C~~~~C~~~wr 109 (110)
+||.|||.+-.- +-+|++++|.++= -.|.+ |+++|.
T Consensus 2 ~CP~C~~~dtkV--iDSR~~~dg~~IRRRReC~~--C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRV--LDSRLVEDGQSIRRRRECLE--CHERFT 39 (147)
T ss_pred CCCCCCCCCCEe--eeccccCCCCeeeecccCCc--cCCccc
Confidence 699999976644 4579999997764 68998 999885
No 47
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=94.61 E-value=0.048 Score=41.82 Aligned_cols=40 Identities=28% Similarity=0.585 Sum_probs=27.2
Q ss_pred CCCcCCCCCcccccCCCCCCce-EEcCCCCCeeeeCCceEE
Q 033869 2 EFCPTCGTMLQYELPHMDRPSR-FSCPACPYVCNMESRVKI 41 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~-~~C~~C~y~~~~~~~~~~ 41 (110)
+|||.||+-+.|++........ -.|+.|++.++..++.+|
T Consensus 151 kFCp~CG~~tkp~e~g~k~~Cs~~~C~~~n~~yPr~dPvVI 191 (345)
T KOG3084|consen 151 KFCPGCGSPTKPEEAGTKLQCSDETCPSCNVIYPRTDPVVI 191 (345)
T ss_pred ccCcccCCCcccccCCccceeecccCCcCCeeccCCCCeEE
Confidence 6999999999999544322222 346666778887776443
No 48
>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=94.59 E-value=0.023 Score=30.78 Aligned_cols=30 Identities=27% Similarity=0.668 Sum_probs=20.1
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
.||.||+-. +..|. ....++|+.||.+..-
T Consensus 2 ~Cp~Cg~~~-~~~D~--~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDP--ERGELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSE-EEEET--TTTEEEETTT-BBEE-
T ss_pred CCcCCcCCc-eEEcC--CCCeEECCCCCCEeec
Confidence 699999865 33233 3568899999987553
No 49
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=94.49 E-value=0.11 Score=44.73 Aligned_cols=32 Identities=25% Similarity=0.530 Sum_probs=22.9
Q ss_pred CCcCCCC-CcccccCCCCCCceEEcCC---CCCeeeeC
Q 033869 3 FCPTCGT-MLQYELPHMDRPSRFSCPA---CPYVCNME 36 (110)
Q Consensus 3 FCp~C~n-lL~~~~~~~~~~~~~~C~~---C~y~~~~~ 36 (110)
=||.||. .|..+ .+..+..+.|.+ |.|..++.
T Consensus 594 ~CP~Cg~~~L~~k--~gr~G~Fl~Cs~yP~C~~t~~~~ 629 (860)
T PRK06319 594 DCPKCHKGKLVKI--WAKNRYFYGCSEYPECDYKTSEE 629 (860)
T ss_pred ccCCCCCcceeEE--ecCCCceeeccCCccccccCCcc
Confidence 4999964 77766 445567999976 88876554
No 50
>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=94.45 E-value=0.035 Score=29.04 Aligned_cols=33 Identities=21% Similarity=0.489 Sum_probs=23.5
Q ss_pred CCcCCCCCcccccCCC-CCCceEEcCCCCCeeee
Q 033869 3 FCPTCGTMLQYELPHM-DRPSRFSCPACPYVCNM 35 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~-~~~~~~~C~~C~y~~~~ 35 (110)
=||.|+....+..+.. ..+..+.|++|+....+
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEEe
Confidence 3999999887774332 23348999999987653
No 51
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=94.34 E-value=0.031 Score=32.62 Aligned_cols=26 Identities=31% Similarity=0.857 Sum_probs=18.1
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
.|.-||-.|.+. ++...|.|++||..
T Consensus 9 ~CtSCg~~i~~~----~~~~~F~CPnCG~~ 34 (59)
T PRK14890 9 KCTSCGIEIAPR----EKAVKFLCPNCGEV 34 (59)
T ss_pred cccCCCCcccCC----CccCEeeCCCCCCe
Confidence 577788777776 22457888888864
No 52
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.24 E-value=0.043 Score=28.85 Aligned_cols=32 Identities=25% Similarity=0.606 Sum_probs=24.2
Q ss_pred CCcCCCCCcccccCCC-CCCceEEcCCCCCeee
Q 033869 3 FCPTCGTMLQYELPHM-DRPSRFSCPACPYVCN 34 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~-~~~~~~~C~~C~y~~~ 34 (110)
=||.|+..+.++.++- ..+..+.|+.|+..+.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 3999999988874431 3456899999998764
No 53
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=94.15 E-value=0.014 Score=49.18 Aligned_cols=25 Identities=20% Similarity=0.331 Sum_probs=16.2
Q ss_pred CcccCCCCCCCceEEEEeccCCCCC
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADE 91 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE 91 (110)
+-..||+||....+++-.-|....|
T Consensus 474 ~p~~Cp~Cgs~~L~~~G~Gteriee 498 (730)
T COG1198 474 IPQSCPECGSEHLRAVGPGTERIEE 498 (730)
T ss_pred CCCCCCCCCCCeeEEecccHHHHHH
Confidence 3457999988877776655444333
No 54
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=94.12 E-value=0.033 Score=29.82 Aligned_cols=29 Identities=31% Similarity=0.655 Sum_probs=23.0
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
||.|++.|... .........|+.|+-...
T Consensus 2 CP~C~~~l~~~--~~~~~~id~C~~C~G~W~ 30 (41)
T PF13453_consen 2 CPRCGTELEPV--RLGDVEIDVCPSCGGIWF 30 (41)
T ss_pred cCCCCcccceE--EECCEEEEECCCCCeEEc
Confidence 99999988877 434467889999997654
No 55
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=94.09 E-value=0.066 Score=40.32 Aligned_cols=38 Identities=24% Similarity=0.334 Sum_probs=29.5
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeee-eCCceEEEE
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN-MESRVKIKR 43 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~-~~~~~~~~~ 43 (110)
+||+.||.-+++. .......|+.||+... ..++.+|+-
T Consensus 112 RFCg~CG~~~~~~----~~g~~~~C~~cg~~~fPR~dP~vIv~ 150 (279)
T COG2816 112 RFCGRCGTKTYPR----EGGWARVCPKCGHEHFPRIDPCVIVA 150 (279)
T ss_pred cCCCCCCCcCccc----cCceeeeCCCCCCccCCCCCCeEEEE
Confidence 7999999999999 3356899999998754 455655543
No 56
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=94.07 E-value=0.085 Score=28.19 Aligned_cols=30 Identities=23% Similarity=0.534 Sum_probs=20.9
Q ss_pred cCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 70 TCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
.||+|+. .+.=..+ +-...+.|.+ |+-.|=
T Consensus 1 ~CP~C~~-~l~~~~~-------~~~~id~C~~--C~G~W~ 30 (41)
T PF13453_consen 1 KCPRCGT-ELEPVRL-------GDVEIDVCPS--CGGIWF 30 (41)
T ss_pred CcCCCCc-ccceEEE-------CCEEEEECCC--CCeEEc
Confidence 5999998 4432222 3367799999 999884
No 57
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=94.06 E-value=0.059 Score=29.89 Aligned_cols=12 Identities=17% Similarity=0.517 Sum_probs=9.1
Q ss_pred EEEecCCCCCcccc
Q 033869 96 FYMCANKNCKHRWN 109 (110)
Q Consensus 96 fY~C~~~~C~~~wr 109 (110)
.|+|.. |||.++
T Consensus 20 ~~vC~~--Cg~~~~ 31 (52)
T smart00661 20 RFVCRK--CGYEEP 31 (52)
T ss_pred EEECCc--CCCeEE
Confidence 778887 888764
No 58
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=94.04 E-value=0.077 Score=36.67 Aligned_cols=36 Identities=25% Similarity=0.636 Sum_probs=24.5
Q ss_pred cCCCCCCCceEEEEeccCCCCCC--ceEEEEecCCCCCcccc
Q 033869 70 TCPACKHGKAVYHELQTRSADEP--MSIFYMCANKNCKHRWN 109 (110)
Q Consensus 70 ~CpkCg~~~a~~~~~Q~RsaDE~--~T~fY~C~~~~C~~~wr 109 (110)
+||-||+....- .-.|...+| -+.||.|.+ ||.+|.
T Consensus 2 ~cp~c~~~~~~~--~~s~~~~~~~~~~~~~~c~~--c~~~f~ 39 (154)
T PRK00464 2 RCPFCGHPDTRV--IDSRPAEDGNAIRRRRECLA--CGKRFT 39 (154)
T ss_pred cCCCCCCCCCEe--EeccccCCCCceeeeeeccc--cCCcce
Confidence 799999976211 123334465 567899999 999874
No 59
>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=94.02 E-value=0.075 Score=42.95 Aligned_cols=27 Identities=30% Similarity=0.816 Sum_probs=12.8
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
||.|+.-|... +. ...+.|..|||...
T Consensus 225 C~~C~~~l~~h--~~--~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 225 CPNCDVSLTYH--KK--EGKLRCHYCGYQEP 251 (505)
T ss_pred CCCCCCceEEe--cC--CCeEEcCCCcCcCC
Confidence 45555444444 21 23555555555444
No 60
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=93.83 E-value=0.088 Score=28.19 Aligned_cols=30 Identities=23% Similarity=0.496 Sum_probs=19.6
Q ss_pred CcCCCCCc------ccccCCCCCCceEEcCCCCCee
Q 033869 4 CPTCGTML------QYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 4 Cp~C~nlL------~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
||.||+-- ..+...+...+.|.|.+|++..
T Consensus 3 Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w 38 (40)
T smart00440 3 CPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW 38 (40)
T ss_pred CCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence 89999752 1221122346789999999865
No 61
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=93.79 E-value=0.1 Score=38.65 Aligned_cols=32 Identities=22% Similarity=0.480 Sum_probs=25.2
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
.+|||.||+-|... .+ .....|..|+......
T Consensus 99 ~~fC~~CG~~~~~~--~~--~~~~~C~~c~~~~yp~ 130 (256)
T PRK00241 99 HRFCGYCGHPMHPS--KT--EWAMLCPHCRERYYPR 130 (256)
T ss_pred CccccccCCCCeec--CC--ceeEECCCCCCEECCC
Confidence 47999999999876 32 4578999999877643
No 62
>PRK07220 DNA topoisomerase I; Validated
Probab=93.63 E-value=0.25 Score=41.79 Aligned_cols=32 Identities=19% Similarity=0.357 Sum_probs=19.0
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKH 106 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~ 106 (110)
++..||+||...... .+....+ -||.|.+ |.+
T Consensus 634 ~~~~Cp~Cg~~~~k~----~~~g~~~--~~~~Cp~--C~~ 665 (740)
T PRK07220 634 TDKVCEAHGLNHIRI----INGGKRP--WDLGCPQ--CNF 665 (740)
T ss_pred CCCCCCCCCCceEEE----EecCCcc--ceeeCCC--CCC
Confidence 356899999754311 1222122 2889977 986
No 63
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=93.63 E-value=0.12 Score=31.29 Aligned_cols=37 Identities=16% Similarity=0.354 Sum_probs=27.5
Q ss_pred CCCCcCCCCCcccccCC----CCCCceEEcC--CCCCeeeeCC
Q 033869 1 MEFCPTCGTMLQYELPH----MDRPSRFSCP--ACPYVCNMES 37 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~----~~~~~~~~C~--~C~y~~~~~~ 37 (110)
|+.||.||+-..+...+ ....+++.|. .||+..-...
T Consensus 1 mm~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 1 MFHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFITYE 43 (72)
T ss_pred CccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEEEE
Confidence 89999999988665222 1347899999 7999876544
No 64
>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=93.62 E-value=0.062 Score=30.78 Aligned_cols=33 Identities=24% Similarity=0.491 Sum_probs=24.1
Q ss_pred CCCcccCCCCC-CCceEEEEeccCCCCCCceEEEEecCCCCCc
Q 033869 65 PQTEVTCPACK-HGKAVYHELQTRSADEPMSIFYMCANKNCKH 106 (110)
Q Consensus 65 ~~~~~~CpkCg-~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~ 106 (110)
.+.-..|++|. |++++. ..|...+-|+|.. |++
T Consensus 19 ~r~aLIC~~C~~hNGla~-------~~~~~~i~y~C~~--Cg~ 52 (54)
T PF10058_consen 19 NRYALICSKCFSHNGLAP-------KEEFEEIQYRCPY--CGA 52 (54)
T ss_pred CceeEECcccchhhcccc-------cccCCceEEEcCC--CCC
Confidence 34567899999 455543 4566777899999 986
No 65
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=93.60 E-value=0.081 Score=29.22 Aligned_cols=34 Identities=21% Similarity=0.523 Sum_probs=25.4
Q ss_pred CcCCCCCcccccCC----CCCCceEEcCC--CCCeeeeCC
Q 033869 4 CPTCGTMLQYELPH----MDRPSRFSCPA--CPYVCNMES 37 (110)
Q Consensus 4 Cp~C~nlL~~~~~~----~~~~~~~~C~~--C~y~~~~~~ 37 (110)
||.||+.+..+... ....+++.|.+ ||+...+..
T Consensus 2 CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~~~ 41 (47)
T PF04606_consen 2 CPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVANL 41 (47)
T ss_pred cCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEEEE
Confidence 99999988876222 23478899999 999876543
No 66
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=93.56 E-value=0.058 Score=35.12 Aligned_cols=30 Identities=30% Similarity=0.816 Sum_probs=24.1
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
.=||.|++-...+ . +..|.|+.|+|++...
T Consensus 3 p~CP~C~seytY~--d---g~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 3 PPCPKCNSEYTYH--D---GTQLICPSCLYEWNEN 32 (109)
T ss_pred CcCCcCCCcceEe--c---CCeeECcccccccccc
Confidence 4599999988887 2 3479999999998654
No 67
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=93.56 E-value=0.23 Score=25.29 Aligned_cols=32 Identities=28% Similarity=0.718 Sum_probs=18.1
Q ss_pred ccCCCCCCC--ceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 69 VTCPACKHG--KAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 69 ~~CpkCg~~--~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
..|||||-. +.+|-+ .|....|.|.||.|.+.
T Consensus 2 hlcpkcgvgvl~pvy~~-------kgeikvfrcsnpacdye 35 (36)
T PF09151_consen 2 HLCPKCGVGVLEPVYNQ-------KGEIKVFRCSNPACDYE 35 (36)
T ss_dssp -B-TTTSSSBEEEEE-T-------TS-EEEEEES-TT---E
T ss_pred ccCCccCceEEEEeecC-------CCcEEEEEcCCCccccC
Confidence 469999986 445532 37788899999999763
No 68
>PRK07219 DNA topoisomerase I; Validated
Probab=93.54 E-value=0.28 Score=41.92 Aligned_cols=33 Identities=21% Similarity=0.385 Sum_probs=19.0
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEec-CCCCCcc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCA-NKNCKHR 107 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~-~~~C~~~ 107 (110)
+...||+||..-. ....+. | .|+.|. .+.|++.
T Consensus 732 ~~~~CpkCg~~l~---~~k~~~---g--~~~~Cs~~p~C~~~ 765 (822)
T PRK07219 732 TDEKCPECGLPLL---RVKGGF---G--DELGCCNNPKCNYT 765 (822)
T ss_pred ccCCCCCCCCeEE---EEecCC---C--ceeeeCCCCCCCcc
Confidence 5679999997522 222222 2 378883 2448764
No 69
>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=93.46 E-value=0.068 Score=43.71 Aligned_cols=42 Identities=24% Similarity=0.560 Sum_probs=29.7
Q ss_pred CcccCCCCCCC-ceEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869 67 TEVTCPACKHG-KAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110 (110)
Q Consensus 67 ~~~~CpkCg~~-~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre 110 (110)
-.+.||.||+. ...|-.++--....+.+..|+|.. ||+.|.+
T Consensus 199 ~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~--Cg~~i~e 241 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPH--CGCEIEE 241 (557)
T ss_pred EEccCCCCCCCccccccceeecCCCCccceEEECCC--CcCCCCH
Confidence 36799999985 444444544111168999999998 9998864
No 70
>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=93.44 E-value=0.12 Score=29.64 Aligned_cols=31 Identities=23% Similarity=0.555 Sum_probs=24.6
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
=||.||.-+.++ ....+..+.|+.||....+
T Consensus 4 ~CP~CG~~iev~--~~~~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 4 ECPDCGAEIELE--NPELGELVICDECGAELEV 34 (54)
T ss_pred CCCCCCCEEecC--CCccCCEEeCCCCCCEEEE
Confidence 599999999887 3333678999999987664
No 71
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=93.43 E-value=0.079 Score=35.68 Aligned_cols=27 Identities=37% Similarity=0.824 Sum_probs=22.2
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
-||.||.-|.-+ ....+|+.|||....
T Consensus 30 hCp~Cg~PLF~K------dG~v~CPvC~~~~~~ 56 (131)
T COG1645 30 HCPKCGTPLFRK------DGEVFCPVCGYREVV 56 (131)
T ss_pred hCcccCCcceee------CCeEECCCCCceEEE
Confidence 499999999886 448999999986543
No 72
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=93.39 E-value=0.12 Score=37.17 Aligned_cols=42 Identities=19% Similarity=0.323 Sum_probs=33.7
Q ss_pred CCcccCCCCCCCceEEEEeccCCCCCC--ceEEEEecCCCCCccccC
Q 033869 66 QTEVTCPACKHGKAVYHELQTRSADEP--MSIFYMCANKNCKHRWNE 110 (110)
Q Consensus 66 ~~~~~CpkCg~~~a~~~~~Q~RsaDE~--~T~fY~C~~~~C~~~wre 110 (110)
.....||-||+ ..+..+.+..-.-.| +-..+.|-+ |||+.++
T Consensus 12 ~~~~~CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~--CgYR~~D 55 (201)
T COG1779 12 ETRIDCPVCGG-TLKAHMYLYDIPYFGEVLISTGVCER--CGYRSTD 55 (201)
T ss_pred eeeecCCcccc-eeeEEEeeecCCccceEEEEEEEccc--cCCcccc
Confidence 35789999999 777777777776666 566789999 9999864
No 73
>PRK10220 hypothetical protein; Provisional
Probab=93.37 E-value=0.073 Score=34.73 Aligned_cols=31 Identities=29% Similarity=0.749 Sum_probs=24.6
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
.=||.|++-..+. . +..|.|+.|+|++...+
T Consensus 4 P~CP~C~seytY~--d---~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 4 PHCPKCNSEYTYE--D---NGMYICPECAHEWNDAE 34 (111)
T ss_pred CcCCCCCCcceEc--C---CCeEECCcccCcCCccc
Confidence 4599999988877 1 34799999999987654
No 74
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=93.29 E-value=0.085 Score=37.46 Aligned_cols=44 Identities=25% Similarity=0.566 Sum_probs=31.9
Q ss_pred CCCCcccCCCCCCCceEEEEeccCCCCCCc----eEEEEecCCCCCcccc
Q 033869 64 GPQTEVTCPACKHGKAVYHELQTRSADEPM----SIFYMCANKNCKHRWN 109 (110)
Q Consensus 64 ~~~~~~~CpkCg~~~a~~~~~Q~RsaDE~~----T~fY~C~~~~C~~~wr 109 (110)
+|..-..|++||..+++--.--.|---.|- =++|.|++ |.++|-
T Consensus 13 ~pq~~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~--Cd~tWN 60 (203)
T COG4332 13 APQPAKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTH--CDYTWN 60 (203)
T ss_pred CChhhhhCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeec--cCCccc
Confidence 567778999999988865444444444442 36899999 999994
No 75
>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=93.25 E-value=0.082 Score=28.99 Aligned_cols=27 Identities=30% Similarity=0.834 Sum_probs=18.6
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
.||.||+. ... .......|.|..|++.
T Consensus 20 ~CP~Cg~~-~~~--~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 20 VCPHCGST-KHY--RLKTRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCe-eeE--EeCCCCeEECCCCCCc
Confidence 49999987 222 2223579999999863
No 76
>PRK07219 DNA topoisomerase I; Validated
Probab=93.15 E-value=0.36 Score=41.31 Aligned_cols=31 Identities=26% Similarity=0.611 Sum_probs=21.5
Q ss_pred CcCCCCCcccccCCCCCC-ceEEcCC---CCCeeeeC
Q 033869 4 CPTCGTMLQYELPHMDRP-SRFSCPA---CPYVCNME 36 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~-~~~~C~~---C~y~~~~~ 36 (110)
||.||.-|..+ +...+ ..+.|.+ |++..+..
T Consensus 605 CP~Cg~~l~~r--~~~~g~~F~gCs~yp~C~~t~~lp 639 (822)
T PRK07219 605 CPECGGDLIII--RTDKGSRFVGCSGYPDCRNTFPLP 639 (822)
T ss_pred CCCCCCcceee--eccCCceeeecCCCcCCCCeeecC
Confidence 99999866555 22223 4689987 99887654
No 77
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=92.97 E-value=0.079 Score=34.36 Aligned_cols=34 Identities=18% Similarity=0.276 Sum_probs=25.4
Q ss_pred CCCcCCCCCcccccCC----CCCCceEEcCCCCCeeee
Q 033869 2 EFCPTCGTMLQYELPH----MDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~----~~~~~~~~C~~C~y~~~~ 35 (110)
.||+.|+++|.|-..- ..+.+.+.|..||++.-.
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~ 94 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRY 94 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEe
Confidence 4899999999996221 133589999999987543
No 78
>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=92.85 E-value=0.092 Score=30.88 Aligned_cols=31 Identities=26% Similarity=0.730 Sum_probs=23.9
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
=||.||..+.-. . ..-.|.|+.||+..+++-
T Consensus 30 ~C~~CG~~~~~~--~--~~r~~~C~~Cg~~~~rD~ 60 (69)
T PF07282_consen 30 TCPRCGHRNKKR--R--SGRVFTCPNCGFEMDRDV 60 (69)
T ss_pred CccCcccccccc--c--ccceEEcCCCCCEECcHH
Confidence 499999988773 2 244899999999877653
No 79
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=92.79 E-value=0.21 Score=34.85 Aligned_cols=38 Identities=21% Similarity=0.385 Sum_probs=22.8
Q ss_pred CCCCCCCceEEEEeccCCCCCC--ceEEEEecCCCCCccccC
Q 033869 71 CPACKHGKAVYHELQTRSADEP--MSIFYMCANKNCKHRWNE 110 (110)
Q Consensus 71 CpkCg~~~a~~~~~Q~RsaDE~--~T~fY~C~~~~C~~~wre 110 (110)
||.||+..+.+.+..+.-.-=+ .-.-|.|.+ |||+..|
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~--CGyr~~e 40 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEK--CGYRSTD 40 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCC--CCCchhh
Confidence 7888877555544444433333 233478887 8887654
No 80
>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=92.78 E-value=0.077 Score=28.65 Aligned_cols=28 Identities=29% Similarity=0.710 Sum_probs=19.0
Q ss_pred cCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccc
Q 033869 70 TCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108 (110)
Q Consensus 70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~w 108 (110)
+||.||+...++ - ..+-.++|.+ ||...
T Consensus 2 ~Cp~Cg~~~~~~-D--------~~~g~~vC~~--CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKEIVF-D--------PERGELVCPN--CGLVL 29 (43)
T ss_dssp SBTTTSSSEEEE-E--------TTTTEEEETT--T-BBE
T ss_pred CCcCCcCCceEE-c--------CCCCeEECCC--CCCEe
Confidence 699999988322 2 3444579999 98754
No 81
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=92.71 E-value=0.092 Score=43.79 Aligned_cols=24 Identities=25% Similarity=0.506 Sum_probs=18.3
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
|.+||.||.-.... .-.|..||..
T Consensus 1 M~~Cp~Cg~~n~~~--------akFC~~CG~~ 24 (645)
T PRK14559 1 MLICPQCQFENPNN--------NRFCQKCGTS 24 (645)
T ss_pred CCcCCCCCCcCCCC--------CccccccCCC
Confidence 88999999876444 4578888874
No 82
>PF14353 CpXC: CpXC protein
Probab=92.58 E-value=0.2 Score=32.96 Aligned_cols=39 Identities=23% Similarity=0.612 Sum_probs=27.3
Q ss_pred ccCCCCCCC-ceEEEEeccCCCC--------CCceEEEEecCCCCCcccc
Q 033869 69 VTCPACKHG-KAVYHELQTRSAD--------EPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 69 ~~CpkCg~~-~a~~~~~Q~RsaD--------E~~T~fY~C~~~~C~~~wr 109 (110)
..||+||+. ++..|+.=.-+.| +|.--.|+|.+ ||+..+
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~--Cg~~~~ 49 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPS--CGHKFR 49 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCC--CCCcee
Confidence 579999985 6777776443333 34445799999 999764
No 83
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=92.55 E-value=0.1 Score=33.48 Aligned_cols=31 Identities=19% Similarity=0.613 Sum_probs=22.3
Q ss_pred CCcCCCC-CcccccCCCCCCceEEcCCCCCeeee
Q 033869 3 FCPTCGT-MLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 3 FCp~C~n-lL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
-||.||+ .|..+.++ +....+|++||+....
T Consensus 23 ~CP~Cge~~v~v~~~k--~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 23 ECPRCGKVSISVKIKK--NIAIITCGNCGLYTEF 54 (99)
T ss_pred ECCCCCCeEeeeecCC--CcceEECCCCCCccCE
Confidence 4999994 34445333 5789999999987553
No 84
>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=92.45 E-value=0.072 Score=30.15 Aligned_cols=33 Identities=18% Similarity=0.468 Sum_probs=25.5
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
=|+.||.+|--- .+-..+.+.|+.|+....+..
T Consensus 6 RC~~CnklLa~~--g~~~~leIKCpRC~tiN~~~a 38 (51)
T PF10122_consen 6 RCGHCNKLLAKA--GEVIELEIKCPRCKTINHVRA 38 (51)
T ss_pred eccchhHHHhhh--cCccEEEEECCCCCccceEec
Confidence 499999999875 334468999999998766544
No 85
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=92.37 E-value=0.19 Score=28.59 Aligned_cols=30 Identities=23% Similarity=0.834 Sum_probs=21.6
Q ss_pred CCCCc--CCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 1 MEFCP--TCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 1 M~FCp--~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
+.+|| .|+.++... .+.....+.|+.|++.
T Consensus 18 ~~~CP~~~C~~~~~~~--~~~~~~~v~C~~C~~~ 49 (64)
T smart00647 18 LKWCPAPDCSAAIIVT--EEEGCNRVTCPKCGFS 49 (64)
T ss_pred ccCCCCCCCcceEEec--CCCCCCeeECCCCCCe
Confidence 35799 999888776 2234568888888875
No 86
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=92.10 E-value=0.14 Score=45.57 Aligned_cols=12 Identities=33% Similarity=0.830 Sum_probs=8.2
Q ss_pred cccCCCCCCCce
Q 033869 68 EVTCPACKHGKA 79 (110)
Q Consensus 68 ~~~CpkCg~~~a 79 (110)
...||+||.+-.
T Consensus 709 a~~CP~CGtplv 720 (1337)
T PRK14714 709 RVECPRCDVELT 720 (1337)
T ss_pred cccCCCCCCccc
Confidence 347999987543
No 87
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=91.83 E-value=0.11 Score=29.60 Aligned_cols=30 Identities=20% Similarity=0.698 Sum_probs=15.1
Q ss_pred CCCCcC--CCCCcccccCCCCCCceEEcCCCCCe
Q 033869 1 MEFCPT--CGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 1 M~FCp~--C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
+++||. |+.++... .......+.|+.|++.
T Consensus 18 ~~~Cp~~~C~~~~~~~--~~~~~~~~~C~~C~~~ 49 (64)
T PF01485_consen 18 IRWCPNPDCEYIIEKD--DGCNSPIVTCPSCGTE 49 (64)
T ss_dssp CC--TTSST---ECS---SSTTS--CCTTSCCSE
T ss_pred ccCCCCCCCcccEEec--CCCCCCeeECCCCCCc
Confidence 358977 99998887 3332224888888875
No 88
>PRK05580 primosome assembly protein PriA; Validated
Probab=91.66 E-value=0.25 Score=41.37 Aligned_cols=10 Identities=30% Similarity=0.919 Sum_probs=5.7
Q ss_pred ccCCCCCCCc
Q 033869 69 VTCPACKHGK 78 (110)
Q Consensus 69 ~~CpkCg~~~ 78 (110)
..||+||...
T Consensus 422 ~~Cp~Cg~~~ 431 (679)
T PRK05580 422 KACPECGSTD 431 (679)
T ss_pred CCCCCCcCCe
Confidence 3566666654
No 89
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=91.65 E-value=0.14 Score=26.89 Aligned_cols=25 Identities=28% Similarity=0.777 Sum_probs=19.8
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
|+.|++.+... . ...+.|..||.+.
T Consensus 11 C~~C~~~~~~~--~---dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 11 CPVCGSRWFYS--D---DGFYYCDRCGHQS 35 (36)
T ss_pred CCCCCCeEeEc--c---CCEEEhhhCceEc
Confidence 99999996666 2 3499999999763
No 90
>PRK04023 DNA polymerase II large subunit; Validated
Probab=91.62 E-value=0.13 Score=44.90 Aligned_cols=21 Identities=33% Similarity=0.752 Sum_probs=16.9
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
+|||.||..+ ..+.|+.||..
T Consensus 627 RfCpsCG~~t----------~~frCP~CG~~ 647 (1121)
T PRK04023 627 RKCPSCGKET----------FYRRCPFCGTH 647 (1121)
T ss_pred ccCCCCCCcC----------CcccCCCCCCC
Confidence 6999999874 25789999965
No 91
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=91.52 E-value=0.13 Score=35.49 Aligned_cols=36 Identities=31% Similarity=0.694 Sum_probs=25.0
Q ss_pred cCCCCCCCceEEEEeccCCCCCCceE--EEEecCCCCCcccc
Q 033869 70 TCPACKHGKAVYHELQTRSADEPMSI--FYMCANKNCKHRWN 109 (110)
Q Consensus 70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~--fY~C~~~~C~~~wr 109 (110)
.||.|+|++-.. +-.|.+++|.++ =-.|.+ |+++|.
T Consensus 2 ~CPfC~~~~tkV--iDSR~~edg~aIRRRReC~~--C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKV--IDSRPAEEGNAIRRRRECLE--CGERFT 39 (156)
T ss_pred CCCCCCCCCCee--eecccccccchhhhhhcccc--cccccc
Confidence 588888876544 446788887664 357877 887764
No 92
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=91.48 E-value=0.17 Score=26.48 Aligned_cols=30 Identities=20% Similarity=0.625 Sum_probs=20.2
Q ss_pred CcCCCCCcccccCCC-CCCceEEcCCCCCee
Q 033869 4 CPTCGTMLQYELPHM-DRPSRFSCPACPYVC 33 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~-~~~~~~~C~~C~y~~ 33 (110)
||.|+.-..+++++. ..+..+.|++|+.++
T Consensus 5 Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 5 CPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred CCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 888887766663322 345678888888754
No 93
>PF12773 DZR: Double zinc ribbon
Probab=91.37 E-value=0.13 Score=28.40 Aligned_cols=21 Identities=33% Similarity=0.874 Sum_probs=15.9
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACP 30 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~ 30 (110)
.+||.||..+.+. .-.|..||
T Consensus 30 ~~C~~Cg~~~~~~--------~~fC~~CG 50 (50)
T PF12773_consen 30 KICPNCGAENPPN--------AKFCPNCG 50 (50)
T ss_pred CCCcCCcCCCcCC--------cCccCccc
Confidence 5899999986665 55777776
No 94
>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=91.22 E-value=0.47 Score=26.68 Aligned_cols=34 Identities=18% Similarity=0.470 Sum_probs=21.9
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
+.||.||.....+. . +..|.+-.-+|.|.+ |+..
T Consensus 2 kPCPfCGg~~~~~~-~--~~~~~~~~~~~~C~~--Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLR-R--GFDPLDLSHYFECST--CGAS 35 (53)
T ss_pred CCCCCCCCcceeeE-e--ccCCCCCEEEEECCC--CCCC
Confidence 47999998554342 1 233455566668998 9874
No 95
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=91.15 E-value=0.13 Score=25.52 Aligned_cols=21 Identities=38% Similarity=0.842 Sum_probs=10.7
Q ss_pred CCcCCCCCcccccCCCCCCceEEcC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCP 27 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~ 27 (110)
+||.||+-|.-.++ .-.+.|.
T Consensus 1 ~CP~C~s~l~~~~~----ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEG----EVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CC----TTCEEE-
T ss_pred CcCCCCCEeEcCCC----CEeEECC
Confidence 69999999996522 2266665
No 96
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=91.10 E-value=0.17 Score=29.27 Aligned_cols=24 Identities=33% Similarity=0.741 Sum_probs=18.2
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
..||+||++..+ ..+|..|||-..
T Consensus 28 ~~C~~CG~~~~~---------H~vC~~CG~Y~g 51 (57)
T PRK12286 28 VECPNCGEPKLP---------HRVCPSCGYYKG 51 (57)
T ss_pred eECCCCCCccCC---------eEECCCCCcCCC
Confidence 469999988766 578999997543
No 97
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=91.07 E-value=0.22 Score=35.49 Aligned_cols=28 Identities=21% Similarity=0.514 Sum_probs=23.6
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
-|++|+..|..+ ...+.|++||+++..+
T Consensus 151 ~CsrC~~~L~~~------~~~l~Cp~Cg~tEkRK 178 (188)
T COG1096 151 RCSRCRAPLVKK------GNMLKCPNCGNTEKRK 178 (188)
T ss_pred EccCCCcceEEc------CcEEECCCCCCEEeee
Confidence 499999999986 4599999999987653
No 98
>PRK14873 primosome assembly protein PriA; Provisional
Probab=90.94 E-value=0.31 Score=40.88 Aligned_cols=14 Identities=21% Similarity=0.508 Sum_probs=7.4
Q ss_pred ccCCCCCCCceEEE
Q 033869 69 VTCPACKHGKAVYH 82 (110)
Q Consensus 69 ~~CpkCg~~~a~~~ 82 (110)
..||+||+....++
T Consensus 423 ~~Cp~Cgs~~l~~~ 436 (665)
T PRK14873 423 WRCPRCGSDRLRAV 436 (665)
T ss_pred ccCCCCcCCcceee
Confidence 35666666544433
No 99
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=90.87 E-value=0.14 Score=35.91 Aligned_cols=29 Identities=28% Similarity=0.746 Sum_probs=22.0
Q ss_pred eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccCCCCCcccCCCCCCCceEE
Q 033869 23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHGKAVY 81 (110)
Q Consensus 23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~~a~~ 81 (110)
.|+|+.|||...- . ....||-||+.+..|
T Consensus 134 ~~vC~vCGy~~~g-e-----------------------------~P~~CPiCga~k~~F 162 (166)
T COG1592 134 VWVCPVCGYTHEG-E-----------------------------APEVCPICGAPKEKF 162 (166)
T ss_pred EEEcCCCCCcccC-C-----------------------------CCCcCCCCCChHHHh
Confidence 8999999996442 1 134799999987766
No 100
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=90.78 E-value=0.24 Score=31.10 Aligned_cols=29 Identities=21% Similarity=0.579 Sum_probs=21.5
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
-||.|+.- ..+ +. ...+|.|+.||++.--
T Consensus 37 ~Cp~C~~~-~Vk--R~-a~GIW~C~kCg~~fAG 65 (89)
T COG1997 37 VCPFCGRT-TVK--RI-ATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCCCCCc-cee--ee-ccCeEEcCCCCCeecc
Confidence 59999998 444 22 2469999999998653
No 101
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=90.57 E-value=0.21 Score=30.14 Aligned_cols=35 Identities=20% Similarity=0.441 Sum_probs=24.9
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
-||.|+.|=.+.--.+++.....|-.|||.....+
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~ 44 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYTERQPD 44 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCeeccCC
Confidence 39999988333211334467999999999987766
No 102
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=90.53 E-value=1.2 Score=29.69 Aligned_cols=37 Identities=30% Similarity=0.609 Sum_probs=21.1
Q ss_pred CCcccCCCCCCCceEEEEeccCCCCCCceEEEEecC-CCCCccc
Q 033869 66 QTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCAN-KNCKHRW 108 (110)
Q Consensus 66 ~~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~-~~C~~~w 108 (110)
.+.+.||+||....+. |.+.-+ ..||.|.+ |.|.+.+
T Consensus 58 ~~~~~Cp~C~~~~~~~-----k~~~~~-~~f~~~~~~Pkc~~~~ 95 (140)
T COG0551 58 KTGVKCPKCGKGLLVL-----KKGRFG-KNFLGCSNYPKCRFTE 95 (140)
T ss_pred cCceeCCCCCCCceEE-----EeccCC-ceEEeecCCCcCceee
Confidence 3577899999744433 222222 67887754 2355544
No 103
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=90.53 E-value=0.16 Score=31.41 Aligned_cols=31 Identities=19% Similarity=0.523 Sum_probs=18.7
Q ss_pred CcCCCC--CcccccCCCCCCceEEcCCCCCeee
Q 033869 4 CPTCGT--MLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 4 Cp~C~n--lL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
||.||+ -+..+.++......+.|+.||....
T Consensus 25 CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 25 CPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQ 57 (81)
T ss_dssp -TTT--SS-EEEEEETTTTEEEEEESSS--EEE
T ss_pred CCcCCCCCeEEEEEEccCCEEEEEecCCCCeEE
Confidence 888883 3666666667778899999987654
No 104
>PRK00420 hypothetical protein; Validated
Probab=90.46 E-value=0.3 Score=32.08 Aligned_cols=30 Identities=30% Similarity=0.538 Sum_probs=22.8
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
-||.||.-|.-- + .....|++||....+.+
T Consensus 25 ~CP~Cg~pLf~l--k---~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 25 HCPVCGLPLFEL--K---DGEVVCPVHGKVYIVKS 54 (112)
T ss_pred CCCCCCCcceec--C---CCceECCCCCCeeeecc
Confidence 599999888763 1 34899999998766544
No 105
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=90.18 E-value=0.31 Score=31.99 Aligned_cols=32 Identities=31% Similarity=0.780 Sum_probs=22.4
Q ss_pred CCcCCCCC------cccccCCCCCCceEEcCCCCCeee
Q 033869 3 FCPTCGTM------LQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 3 FCp~C~nl------L~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
-||.||+- |..+...++....|.|.+|+|.+.
T Consensus 76 kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 76 KCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred cCcccCCchhhhhhhhcccccCCceEEEEcCccceeee
Confidence 49999963 445533345567899999999764
No 106
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=90.13 E-value=0.24 Score=28.88 Aligned_cols=35 Identities=17% Similarity=0.441 Sum_probs=24.8
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
-||.|+.|=.+.--.++......|-.|||.+..++
T Consensus 11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~~~ 45 (59)
T TIGR02443 11 VCPACSAQDTLAMWKENNIELVECVECGYQEQQKD 45 (59)
T ss_pred cCCCCcCccEEEEEEeCCceEEEeccCCCccccCC
Confidence 39999987333222344556899999999987665
No 107
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=89.92 E-value=0.57 Score=31.51 Aligned_cols=16 Identities=13% Similarity=0.449 Sum_probs=13.4
Q ss_pred CceEEcCCCCCeeeeC
Q 033869 21 PSRFSCPACPYVCNME 36 (110)
Q Consensus 21 ~~~~~C~~C~y~~~~~ 36 (110)
...+.|+.||+.....
T Consensus 68 p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 68 EAVLKCRNCGNEWSLK 83 (135)
T ss_pred ceEEECCCCCCEEecc
Confidence 4689999999988765
No 108
>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=89.89 E-value=0.32 Score=33.34 Aligned_cols=16 Identities=19% Similarity=0.584 Sum_probs=12.4
Q ss_pred CCceEEcCCCCCeeee
Q 033869 20 RPSRFSCPACPYVCNM 35 (110)
Q Consensus 20 ~~~~~~C~~C~y~~~~ 35 (110)
+...|+|.+||+....
T Consensus 109 g~G~l~C~~Cg~~~~~ 124 (146)
T PF07295_consen 109 GPGTLVCENCGHEVEL 124 (146)
T ss_pred cCceEecccCCCEEEe
Confidence 3568999999987544
No 109
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=89.81 E-value=0.57 Score=32.49 Aligned_cols=38 Identities=29% Similarity=0.467 Sum_probs=22.7
Q ss_pred cCCCCCCCceEEEEeccCCCCCCceE--EEEecCCCCCccccC
Q 033869 70 TCPACKHGKAVYHELQTRSADEPMSI--FYMCANKNCKHRWNE 110 (110)
Q Consensus 70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~--fY~C~~~~C~~~wre 110 (110)
.||.||++ ...-...+.-..-+-.+ -|.|.+ |||+..|
T Consensus 2 ~Cp~C~~~-~~~~~~~~~IP~F~evii~sf~C~~--CGyk~~e 41 (160)
T smart00709 2 DCPSCGGN-GTTRMLLTSIPYFREVIIMSFECEH--CGYRNNE 41 (160)
T ss_pred cCCCCCCC-CEEEEEEecCCCcceEEEEEEECCC--CCCccce
Confidence 48888865 34444445444444333 478887 8887654
No 110
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=89.63 E-value=0.25 Score=27.66 Aligned_cols=31 Identities=13% Similarity=0.337 Sum_probs=22.8
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
+.||+.||+-|.....+ ....+|.|++....
T Consensus 5 ~l~C~~CG~~m~~~~~~-~~~~yy~C~~~~~~ 35 (58)
T PF13408_consen 5 LLRCGHCGSKMTRRKRK-GKYRYYRCSNRRRK 35 (58)
T ss_pred cEEcccCCcEeEEEECC-CCceEEEcCCCcCC
Confidence 46899999999987333 44578999877643
No 111
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=89.52 E-value=0.46 Score=24.11 Aligned_cols=26 Identities=35% Similarity=0.740 Sum_probs=21.1
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
-|..|+++|..+ .+ ...+.|..|...
T Consensus 3 ~C~~C~t~L~yP--~g--A~~vrCs~C~~v 28 (31)
T TIGR01053 3 VCGGCRTLLMYP--RG--ASSVRCALCQTV 28 (31)
T ss_pred CcCCCCcEeecC--CC--CCeEECCCCCeE
Confidence 489999999888 44 458999999865
No 112
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=89.40 E-value=0.16 Score=25.21 Aligned_cols=27 Identities=26% Similarity=0.698 Sum_probs=17.3
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
=||.|++.+... ..+....+.|+.|..
T Consensus 3 ~C~rC~~~~~~~--~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 3 KCPRCWNYIEDI--GINGRSTYLCPRCQK 29 (30)
T ss_dssp B-TTT--BBEEE--EETTEEEEE-TTTCC
T ss_pred cCccCCCcceEe--EecCCCCeECcCCcC
Confidence 389999998776 445677899999963
No 113
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=89.34 E-value=0.074 Score=40.18 Aligned_cols=30 Identities=30% Similarity=0.605 Sum_probs=23.4
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
=||.|+.+|+.++- ..+.++|+.|||-...
T Consensus 28 ~c~~c~~~~~~~~l---~~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 28 KCPKCGQVLYTKEL---ERNLEVCPKCDHHMRM 57 (285)
T ss_pred ECCCCcchhhHHHH---HhhCCCCCCCCCcCcC
Confidence 49999999999832 2346899999997654
No 114
>COG4640 Predicted membrane protein [Function unknown]
Probab=89.27 E-value=0.2 Score=39.58 Aligned_cols=26 Identities=31% Similarity=0.806 Sum_probs=17.8
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
|+|||.||+-=.- ..+.|..||....
T Consensus 1 M~fC~kcG~qk~E--------d~~qC~qCG~~~t 26 (465)
T COG4640 1 MKFCPKCGSQKAE--------DDVQCTQCGHKFT 26 (465)
T ss_pred CCccccccccccc--------ccccccccCCcCC
Confidence 9999999953111 1333999998643
No 115
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=89.21 E-value=0.37 Score=38.71 Aligned_cols=52 Identities=25% Similarity=0.604 Sum_probs=32.1
Q ss_pred CCceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEEEe
Q 033869 20 RPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYHEL 84 (110)
Q Consensus 20 ~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~~~ 84 (110)
....|.|+.|||+++.... +....|..+ ..+. +|- ++.||.||..+..|-.+
T Consensus 422 ~~~~~~c~~c~~~yd~~~g-----------~~~~~~~~g-t~~~~lp~-~~~cp~c~~~k~~f~~~ 474 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKG-----------EPMQDVAPG-TPWSEVPD-NFLCPECSLGKDVFDEL 474 (479)
T ss_pred CCCeEEECCCCeEECCCCC-----------CcccCCCCC-CChhhCCC-CCcCcCCCCcHHHhEec
Confidence 3568999999998875431 001112211 1223 553 88999999998876544
No 116
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=89.11 E-value=0.072 Score=40.49 Aligned_cols=31 Identities=19% Similarity=0.399 Sum_probs=23.8
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
=||.|+.+|+.++-. .+.++|+.|+|-...+
T Consensus 40 kc~~C~~~~~~~~l~---~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 40 QCENCYGLNYKKFLK---SKMNICEQCGYHLKMS 70 (296)
T ss_pred ECCCccchhhHHHHH---HcCCCCCCCCCCcCCC
Confidence 499999999998322 4579999999965443
No 117
>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=89.08 E-value=0.21 Score=26.20 Aligned_cols=28 Identities=25% Similarity=0.541 Sum_probs=17.1
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
.|++||+.......... .....|+.||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 48888885544321211 45677888886
No 118
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=88.99 E-value=0.3 Score=29.15 Aligned_cols=30 Identities=27% Similarity=0.665 Sum_probs=22.6
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
.+++||.|||...+|--.|+ --.|.. ||..
T Consensus 18 l~VkCpdC~N~q~vFshast---------~V~C~~--CG~~ 47 (67)
T COG2051 18 LRVKCPDCGNEQVVFSHAST---------VVTCLI--CGTT 47 (67)
T ss_pred EEEECCCCCCEEEEeccCce---------EEEecc--cccE
Confidence 37899999999999955443 257877 8753
No 119
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=88.90 E-value=0.51 Score=24.72 Aligned_cols=33 Identities=21% Similarity=0.539 Sum_probs=22.1
Q ss_pred CCCcccCCCCCCCceEEEEeccCCCCCCceEEEEecC
Q 033869 65 PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCAN 101 (110)
Q Consensus 65 ~~~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~ 101 (110)
+++++.||.|+..+.++-.=+. ..|-. =|.|..
T Consensus 2 a~i~v~CP~C~s~~~v~k~G~~---~~G~q-ryrC~~ 34 (36)
T PF03811_consen 2 AKIDVHCPRCQSTEGVKKNGKS---PSGHQ-RYRCKD 34 (36)
T ss_pred CcEeeeCCCCCCCCcceeCCCC---CCCCE-eEecCc
Confidence 4578999999999977744332 22333 377776
No 120
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=88.83 E-value=0.13 Score=38.86 Aligned_cols=31 Identities=29% Similarity=0.623 Sum_probs=24.5
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
=||.|+.|||-++- ..+.++|++|+|-..+.
T Consensus 30 KCp~c~~~~y~~eL---~~n~~vcp~c~~h~ri~ 60 (294)
T COG0777 30 KCPSCGEMLYRKEL---ESNLKVCPKCGHHMRIS 60 (294)
T ss_pred ECCCccceeeHHHH---HhhhhcccccCcccccC
Confidence 49999999999832 35689999999965543
No 121
>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=88.54 E-value=0.43 Score=27.23 Aligned_cols=27 Identities=22% Similarity=0.519 Sum_probs=17.8
Q ss_pred CcCCC--CCcccccCCCCCCceEEcCCCCCe
Q 033869 4 CPTCG--TMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 4 Cp~C~--nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
|+.|. |=|.++ .+.....|.|+.||+.
T Consensus 25 C~~C~~hNGla~~--~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 25 CSKCFSHNGLAPK--EEFEEIQYRCPYCGAL 53 (54)
T ss_pred Ccccchhhccccc--ccCCceEEEcCCCCCc
Confidence 67776 446665 3444568888888863
No 122
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=88.53 E-value=0.3 Score=27.99 Aligned_cols=23 Identities=35% Similarity=0.883 Sum_probs=16.4
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
..||+||++..+ ..+|..|||-.
T Consensus 27 ~~C~~cG~~~~~---------H~vc~~cG~Y~ 49 (55)
T TIGR01031 27 VVCPNCGEFKLP---------HRVCPSCGYYK 49 (55)
T ss_pred eECCCCCCcccC---------eeECCccCeEC
Confidence 358888886554 57888888643
No 123
>PF11792 Baculo_LEF5_C: Baculoviridae late expression factor 5 C-terminal domain; InterPro: IPR021758 This C-terminal domain is likely to be a zinc-binding domain.
Probab=88.35 E-value=0.019 Score=31.38 Aligned_cols=30 Identities=40% Similarity=0.674 Sum_probs=23.3
Q ss_pred CCCCceEEEEeccCCCCCCceEEEEecCCCCCc
Q 033869 74 CKHGKAVYHELQTRSADEPMSIFYMCANKNCKH 106 (110)
Q Consensus 74 Cg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~ 106 (110)
|.|.= +.-..|+|+.||.-+.+=.|.+ |+.
T Consensus 13 C~H~f-~~~E~Q~RAGDE~VSfI~~C~~--C~~ 42 (43)
T PF11792_consen 13 CKHKF-VTIEKQLRAGDEAVSFIKYCQK--CGQ 42 (43)
T ss_pred ceeee-eehhhhhcccchHHHHHHHHHH--hCC
Confidence 65543 3556899999999888888888 875
No 124
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=88.34 E-value=1.1 Score=38.75 Aligned_cols=33 Identities=30% Similarity=0.715 Sum_probs=19.3
Q ss_pred CcccCCC--CCCCceEEEEeccCCCCCCceEEEEecC-CCCCc
Q 033869 67 TEVTCPA--CKHGKAVYHELQTRSADEPMSIFYMCAN-KNCKH 106 (110)
Q Consensus 67 ~~~~Cpk--Cg~~~a~~~~~Q~RsaDE~~T~fY~C~~-~~C~~ 106 (110)
+...||+ ||.. ... |..--| ..||.|.+ +.|.+
T Consensus 692 ~~~~CP~~~C~g~---l~~---r~gr~G-~~f~~Cs~yp~C~~ 727 (860)
T PRK06319 692 ETVPCPAIGCTGH---IVK---RRSRFN-KMFYSCSEYPACSV 727 (860)
T ss_pred cCCCCCCcCCCCc---EEE---EecCCC-CeeeccCCCCCCce
Confidence 4568997 5642 222 333334 45888975 66875
No 125
>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=88.30 E-value=0.15 Score=26.52 Aligned_cols=21 Identities=33% Similarity=0.719 Sum_probs=12.4
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
-|+.||.+..|+ ...|+.|+-
T Consensus 13 rC~~Cg~~~~pP--------r~~Cp~C~s 33 (37)
T PF12172_consen 13 RCRDCGRVQFPP--------RPVCPHCGS 33 (37)
T ss_dssp E-TTT--EEES----------SEETTTT-
T ss_pred EcCCCCCEecCC--------CcCCCCcCc
Confidence 588999998888 568888873
No 126
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=88.26 E-value=0.2 Score=30.50 Aligned_cols=29 Identities=21% Similarity=0.564 Sum_probs=14.3
Q ss_pred CCCcCCCCCcccccCC---------CCCCceEEcCCCC
Q 033869 2 EFCPTCGTMLQYELPH---------MDRPSRFSCPACP 30 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~---------~~~~~~~~C~~C~ 30 (110)
.||..||++|.|-... ....+.+.|..||
T Consensus 47 ~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~ 84 (85)
T PF04032_consen 47 TICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCG 84 (85)
T ss_dssp TB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTT
T ss_pred ccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccC
Confidence 4899999998886221 1335566777776
No 127
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=88.19 E-value=0.19 Score=30.56 Aligned_cols=9 Identities=56% Similarity=1.693 Sum_probs=4.5
Q ss_pred CCCcCCCCC
Q 033869 2 EFCPTCGTM 10 (110)
Q Consensus 2 ~FCp~C~nl 10 (110)
.|||.|||-
T Consensus 25 ~FCp~CGn~ 33 (73)
T PF08772_consen 25 QFCPKCGNA 33 (73)
T ss_dssp -S-SSS--S
T ss_pred eeCcccCCC
Confidence 599999986
No 128
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=87.92 E-value=0.48 Score=25.60 Aligned_cols=23 Identities=35% Similarity=0.892 Sum_probs=17.5
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACP 30 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~ 30 (110)
.||.||..|.-. ++ ....|..|+
T Consensus 19 ~Cp~C~~PL~~~--k~---g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGTPLMRD--KD---GKIYCVSCG 41 (41)
T ss_pred ccCCCCCeeEEe--cC---CCEECCCCC
Confidence 699999888874 32 367899885
No 129
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=87.90 E-value=0.32 Score=28.36 Aligned_cols=25 Identities=24% Similarity=0.664 Sum_probs=16.1
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
-|-+||.-+.++ + +..+.||-|||.
T Consensus 22 iCgdC~~en~lk--~---~D~irCReCG~R 46 (62)
T KOG3507|consen 22 ICGDCGQENTLK--R---GDVIRCRECGYR 46 (62)
T ss_pred Eecccccccccc--C---CCcEehhhcchH
Confidence 367777666665 2 346777777774
No 130
>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=87.76 E-value=0.53 Score=27.55 Aligned_cols=30 Identities=30% Similarity=0.692 Sum_probs=23.2
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~w 108 (110)
+-..||.||+.... ......|.|.+ ||+.+
T Consensus 27 TSq~C~~CG~~~~~----------~~~~r~~~C~~--Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK----------RRSGRVFTCPN--CGFEM 56 (69)
T ss_pred CccCccCccccccc----------ccccceEEcCC--CCCEE
Confidence 67789999986553 24556799999 99876
No 131
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=87.52 E-value=0.13 Score=39.04 Aligned_cols=31 Identities=26% Similarity=0.596 Sum_probs=23.8
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
=||.|+.+++.++-. .+.++|+.|||-....
T Consensus 29 ~c~~c~~~~~~~~l~---~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 29 KCPSCGQVLYRKELE---ANLNVCPKCGHHMRIS 59 (292)
T ss_pred ECCCccchhhHHHHH---hcCCCCCCCCCCeeCC
Confidence 499999999998322 3468999999976543
No 132
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=87.41 E-value=0.59 Score=30.72 Aligned_cols=23 Identities=39% Similarity=0.989 Sum_probs=20.4
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
||-||.-|.+. .+.|..|+....
T Consensus 1 CPvCg~~l~vt--------~l~C~~C~t~i~ 23 (113)
T PF09862_consen 1 CPVCGGELVVT--------RLKCPSCGTEIE 23 (113)
T ss_pred CCCCCCceEEE--------EEEcCCCCCEEE
Confidence 99999999998 899999998643
No 133
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=87.28 E-value=0.57 Score=25.60 Aligned_cols=25 Identities=24% Similarity=0.636 Sum_probs=19.3
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
|.+||.-..++ . ...+.|+.||+..
T Consensus 5 C~~Cg~~~~~~--~---~~~irC~~CG~rI 29 (44)
T smart00659 5 CGECGRENEIK--S---KDVVRCRECGYRI 29 (44)
T ss_pred CCCCCCEeecC--C---CCceECCCCCceE
Confidence 88999877665 2 3579999999853
No 134
>PRK11032 hypothetical protein; Provisional
Probab=87.09 E-value=0.59 Score=32.53 Aligned_cols=16 Identities=13% Similarity=0.314 Sum_probs=12.0
Q ss_pred CCceEEcCCCCCeeee
Q 033869 20 RPSRFSCPACPYVCNM 35 (110)
Q Consensus 20 ~~~~~~C~~C~y~~~~ 35 (110)
+...++|.+||+...+
T Consensus 121 g~G~LvC~~Cg~~~~~ 136 (160)
T PRK11032 121 GLGNLVCEKCHHHLAF 136 (160)
T ss_pred ecceEEecCCCCEEEe
Confidence 3568999999986543
No 135
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=87.08 E-value=0.44 Score=35.19 Aligned_cols=26 Identities=38% Similarity=1.016 Sum_probs=20.8
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
=||.||. |. .-.+.|+.||++.+++-
T Consensus 311 ~C~~cg~-~~--------~r~~~C~~cg~~~~rD~ 336 (364)
T COG0675 311 TCPCCGH-LS--------GRLFKCPRCGFVHDRDV 336 (364)
T ss_pred cccccCC-cc--------ceeEECCCCCCeehhhH
Confidence 4999999 22 23899999999988875
No 136
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=86.83 E-value=0.87 Score=23.36 Aligned_cols=27 Identities=19% Similarity=0.252 Sum_probs=20.0
Q ss_pred CCcCCCCCccc-ccCCCCCCceEEcCCCCCeee
Q 033869 3 FCPTCGTMLQY-ELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 3 FCp~C~nlL~~-~~~~~~~~~~~~C~~C~y~~~ 34 (110)
-|+.||.-+.. + + +.++.|..||.+++
T Consensus 5 ~C~~C~~~~i~~~---~--~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 5 KCSKCGGNGIVNK---E--DDYEVCIFCGSSFP 32 (33)
T ss_pred EcCCCCCCeEEEe---c--CCeEEcccCCcEee
Confidence 48889866655 4 1 45999999998764
No 137
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=86.20 E-value=0.69 Score=26.53 Aligned_cols=34 Identities=24% Similarity=0.614 Sum_probs=26.1
Q ss_pred CCcCCCCC--cccccCCCCCCceEEcCCCCCeeeeC
Q 033869 3 FCPTCGTM--LQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 3 FCp~C~nl--L~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
.||-|||- +.+++|..-...-+.|+.|..+.-++
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~ 41 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLID 41 (55)
T ss_pred ECCCCCCccceeeecCceeccccccCCCCCceEEEE
Confidence 69999964 67776666667789999999876544
No 138
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=85.93 E-value=0.26 Score=35.32 Aligned_cols=37 Identities=19% Similarity=0.497 Sum_probs=24.3
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
+...||.||..+. -+.+ ++. .|....+.|.+ ||+.|+
T Consensus 5 iy~~Cp~Cg~eev-~hEV-ik~--~g~~~lvrC~e--CG~V~~ 41 (201)
T COG1326 5 IYIECPSCGSEEV-SHEV-IKE--RGREPLVRCEE--CGTVHP 41 (201)
T ss_pred EEEECCCCCcchh-hHHH-HHh--cCCceEEEccC--CCcEee
Confidence 4578999994443 1111 121 34558899999 999995
No 139
>PHA02942 putative transposase; Provisional
Probab=85.82 E-value=0.7 Score=36.22 Aligned_cols=31 Identities=29% Similarity=0.712 Sum_probs=23.0
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
+-||.||...... . .-.|.|..||+..+.+-
T Consensus 326 q~Cs~CG~~~~~l---~--~r~f~C~~CG~~~drD~ 356 (383)
T PHA02942 326 VSCPKCGHKMVEI---A--HRYFHCPSCGYENDRDV 356 (383)
T ss_pred ccCCCCCCccCcC---C--CCEEECCCCCCEeCcHH
Confidence 4699999876421 1 23799999999987764
No 140
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=85.60 E-value=0.43 Score=30.16 Aligned_cols=29 Identities=21% Similarity=0.449 Sum_probs=22.0
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
.+||.||..-.-+ . ...+|.|+.|++..-
T Consensus 36 y~Cp~Cgk~~vkR--~--a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 36 YTCPFCGKTSVKR--V--ATGIWKCKKCGKKFA 64 (90)
T ss_dssp BEESSSSSSEEEE--E--ETTEEEETTTTEEEE
T ss_pred CcCCCCCCceeEE--e--eeEEeecCCCCCEEe
Confidence 3799999988555 2 245899999998754
No 141
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=85.16 E-value=0.85 Score=26.66 Aligned_cols=10 Identities=20% Similarity=0.434 Sum_probs=5.4
Q ss_pred EEcCCCCCee
Q 033869 24 FSCPACPYVC 33 (110)
Q Consensus 24 ~~C~~C~y~~ 33 (110)
-+|..||-..
T Consensus 10 ~~CtSCg~~i 19 (61)
T COG2888 10 PVCTSCGREI 19 (61)
T ss_pred ceeccCCCEe
Confidence 3566666544
No 142
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=85.01 E-value=1.7 Score=31.04 Aligned_cols=39 Identities=23% Similarity=0.527 Sum_probs=21.5
Q ss_pred cCCCCCCC-ceEEEEec-cCCCCCCceEEEEecCCCCCccccC
Q 033869 70 TCPACKHG-KAVYHELQ-TRSADEPMSIFYMCANKNCKHRWNE 110 (110)
Q Consensus 70 ~CpkCg~~-~a~~~~~Q-~RsaDE~~T~fY~C~~~~C~~~wre 110 (110)
.||.||.+ ........ +=--.|=+-.-|.|.+ |||+.+|
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~--CGyr~~e 42 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEH--CGYRSND 42 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCC--CCCccce
Confidence 58999864 33333333 1111222334588888 9888764
No 143
>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=84.89 E-value=1.1 Score=28.43 Aligned_cols=13 Identities=31% Similarity=0.851 Sum_probs=7.6
Q ss_pred CceEEcCCCCCee
Q 033869 21 PSRFSCPACPYVC 33 (110)
Q Consensus 21 ~~~~~C~~C~y~~ 33 (110)
.+.|.|.+|+|.+
T Consensus 88 T~fy~C~~C~~~w 100 (104)
T TIGR01384 88 TRFYKCTKCGYVW 100 (104)
T ss_pred EEEEEeCCCCCee
Confidence 4556666666654
No 144
>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=84.87 E-value=0.28 Score=25.10 Aligned_cols=25 Identities=24% Similarity=0.676 Sum_probs=17.0
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
|.+||.....+ .. ..+.|+.|||..
T Consensus 3 C~~Cg~~~~~~--~~---~~irC~~CG~RI 27 (32)
T PF03604_consen 3 CGECGAEVELK--PG---DPIRCPECGHRI 27 (32)
T ss_dssp ESSSSSSE-BS--TS---STSSBSSSS-SE
T ss_pred CCcCCCeeEcC--CC---CcEECCcCCCeE
Confidence 78999887766 22 357999999853
No 145
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=84.66 E-value=0.66 Score=27.81 Aligned_cols=28 Identities=21% Similarity=0.534 Sum_probs=18.9
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
| .||+.||.+++ .-.=.| .||+.-.++.
T Consensus 6 C-~Cgr~lya~e~----~kTkkC-~CG~~l~vk~ 33 (68)
T PF09082_consen 6 C-DCGRYLYAKEG----AKTKKC-VCGKTLKVKE 33 (68)
T ss_dssp E-TTS--EEEETT-----SEEEE-TTTEEEE--S
T ss_pred e-cCCCEEEecCC----cceeEe-cCCCeeeeee
Confidence 7 79999999933 337899 9999887766
No 146
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=84.65 E-value=1.2 Score=25.89 Aligned_cols=8 Identities=25% Similarity=0.758 Sum_probs=4.3
Q ss_pred EEcCCCCC
Q 033869 24 FSCPACPY 31 (110)
Q Consensus 24 ~~C~~C~y 31 (110)
.+|..||-
T Consensus 8 ~~CtSCg~ 15 (59)
T PRK14890 8 PKCTSCGI 15 (59)
T ss_pred ccccCCCC
Confidence 35556654
No 147
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=84.54 E-value=1.1 Score=21.70 Aligned_cols=25 Identities=32% Similarity=0.755 Sum_probs=19.1
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
|..|..+|..+ .+ .....|..|+++
T Consensus 1 C~~Cr~~L~yp--~G--A~sVrCa~C~~V 25 (25)
T PF06943_consen 1 CGGCRTLLMYP--RG--APSVRCACCHTV 25 (25)
T ss_pred CCCCCceEEcC--CC--CCCeECCccCcC
Confidence 67899888887 44 458999999863
No 148
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=84.53 E-value=0.88 Score=32.83 Aligned_cols=15 Identities=20% Similarity=0.689 Sum_probs=12.0
Q ss_pred eEEcCCCCCeeeeCC
Q 033869 23 RFSCPACPYVCNMES 37 (110)
Q Consensus 23 ~~~C~~C~y~~~~~~ 37 (110)
.+.|+.|+.+.....
T Consensus 5 ~~~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 5 KITCPVCGKEFKTKK 19 (214)
T ss_pred ceECCCCCCeeeeeE
Confidence 589999999877654
No 149
>PRK11827 hypothetical protein; Provisional
Probab=84.45 E-value=1.3 Score=25.93 Aligned_cols=31 Identities=19% Similarity=0.466 Sum_probs=24.9
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
-||.|+.-|... .+ ...+.|..|+-.+++.+
T Consensus 10 aCP~ckg~L~~~--~~--~~~Lic~~~~laYPI~d 40 (60)
T PRK11827 10 ACPVCNGKLWYN--QE--KQELICKLDNLAFPLRD 40 (60)
T ss_pred ECCCCCCcCeEc--CC--CCeEECCccCeeccccC
Confidence 499999988876 32 34789999999888876
No 150
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=83.77 E-value=0.71 Score=31.15 Aligned_cols=33 Identities=21% Similarity=0.415 Sum_probs=21.4
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
-||.|+|-=.--+ ++++...+.|..||...++.
T Consensus 99 lC~~C~sPdT~l~-k~~r~~~l~C~ACGa~~~v~ 131 (133)
T TIGR00311 99 ICRECNRPDTRII-KEGRVSLLKCEACGAKAPLR 131 (133)
T ss_pred ECCCCCCCCcEEE-EeCCeEEEecccCCCCCccC
Confidence 3999998522111 22344567999999987764
No 151
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.68 E-value=1 Score=27.81 Aligned_cols=35 Identities=29% Similarity=0.461 Sum_probs=27.4
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
|.-||.||--|.++ ...+.-+-.|+.|+-++....
T Consensus 1 ~llCP~C~v~l~~~--~rs~vEiD~CPrCrGVWLDrG 35 (88)
T COG3809 1 MLLCPICGVELVMS--VRSGVEIDYCPRCRGVWLDRG 35 (88)
T ss_pred CcccCcCCceeeee--eecCceeeeCCccccEeecch
Confidence 67899999999888 333456789999998876544
No 152
>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=83.61 E-value=0.79 Score=29.84 Aligned_cols=31 Identities=26% Similarity=0.610 Sum_probs=24.1
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
+.||.||.-.|=- + +.-++|+.||..+....
T Consensus 10 R~Cp~CG~kFYDL----n-k~PivCP~CG~~~~~~~ 40 (108)
T PF09538_consen 10 RTCPSCGAKFYDL----N-KDPIVCPKCGTEFPPEP 40 (108)
T ss_pred ccCCCCcchhccC----C-CCCccCCCCCCccCccc
Confidence 5799999887755 1 24688999999988763
No 153
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=83.27 E-value=0.8 Score=24.32 Aligned_cols=35 Identities=17% Similarity=0.260 Sum_probs=19.1
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
.-|..|+..|-|-..=+.....|.|.-|+...++.
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~lp 37 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGTKNPLP 37 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEETTT--EEE--
T ss_pred cccCCCCCEECCcceEcCCCCEEECcCCCCcCCCC
Confidence 35899999998863233445699999999876654
No 154
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=82.95 E-value=0.78 Score=25.60 Aligned_cols=23 Identities=22% Similarity=0.677 Sum_probs=19.3
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
..|-.|+-.+.+. .-.||.|||.
T Consensus 15 ~ICrkC~ARnp~~--------A~~CRKCg~~ 37 (48)
T PRK04136 15 KICMRCNARNPWR--------ATKCRKCGYK 37 (48)
T ss_pred cchhcccCCCCcc--------ccccccCCCC
Confidence 4789999999998 5579999984
No 155
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=82.79 E-value=0.85 Score=30.94 Aligned_cols=33 Identities=24% Similarity=0.444 Sum_probs=22.3
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
-||+|+|.=.-- -++++...+.|..||...++.
T Consensus 104 lC~~C~spdT~l-~k~~r~~~l~C~ACGa~~~V~ 136 (138)
T PRK03988 104 ICPECGSPDTKL-IKEGRIWVLKCEACGAETPVK 136 (138)
T ss_pred ECCCCCCCCcEE-EEcCCeEEEEcccCCCCCcCC
Confidence 499999852211 123456789999999887654
No 156
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=82.38 E-value=1.4 Score=31.00 Aligned_cols=28 Identities=25% Similarity=0.634 Sum_probs=23.2
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
+|+.||..|.|. . ...+.|+.|+..+..
T Consensus 151 ~~~~~g~~~~~~--~---~~~~~c~~~~~~e~r 178 (189)
T PRK09521 151 MCSRCRTPLVKK--G---ENELKCPNCGNIETR 178 (189)
T ss_pred EccccCCceEEC--C---CCEEECCCCCCEEee
Confidence 699999999887 2 258999999988774
No 157
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=82.33 E-value=1.6 Score=39.14 Aligned_cols=17 Identities=29% Similarity=0.940 Sum_probs=13.9
Q ss_pred CceEEcCCCCCeeeeCC
Q 033869 21 PSRFSCPACPYVCNMES 37 (110)
Q Consensus 21 ~~~~~C~~C~y~~~~~~ 37 (110)
...|.|+.|.|.+-.++
T Consensus 912 ~PHY~Cp~Cky~Ef~~d 928 (1444)
T COG2176 912 PPHYLCPECKYSEFIDD 928 (1444)
T ss_pred CccccCCCCceeeeecC
Confidence 34799999999987765
No 158
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 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 presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=82.11 E-value=3.9 Score=22.06 Aligned_cols=30 Identities=33% Similarity=0.727 Sum_probs=18.9
Q ss_pred cCCCCCCCceEEEEeccCCCCCCceEEEEecCC
Q 033869 70 TCPACKHGKAVYHELQTRSADEPMSIFYMCANK 102 (110)
Q Consensus 70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~ 102 (110)
.|+ || ..++-+++. +..+.+=-+||.|.+.
T Consensus 2 ~C~-Cg-~~~~~~~s~-k~~~N~GR~Fy~C~~~ 31 (45)
T PF06839_consen 2 KCP-CG-EPAVRRTSK-KTGPNPGRRFYKCPNY 31 (45)
T ss_pred CCC-CC-CEeEEEEEe-CCCCCCCCcceECCCC
Confidence 366 66 445544443 2466677799999863
No 159
>PRK05582 DNA topoisomerase I; Validated
Probab=82.11 E-value=2.7 Score=35.15 Aligned_cols=32 Identities=31% Similarity=0.723 Sum_probs=18.1
Q ss_pred cccCCCCCCCceEEEEeccCCCCCCceEEEEecC-CCCCc
Q 033869 68 EVTCPACKHGKAVYHELQTRSADEPMSIFYMCAN-KNCKH 106 (110)
Q Consensus 68 ~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~-~~C~~ 106 (110)
...||+|+.. +.. |....+ ..|+.|.+ +.|++
T Consensus 611 ~~~CP~C~~~-l~l-----~k~k~g-k~f~~Cs~~p~C~~ 643 (650)
T PRK05582 611 GVKCPKCGGQ-IVE-----RKSKKG-RKFYGCSRYPECDF 643 (650)
T ss_pred CCCCCCCCCc-eEE-----EcCCCC-ceeeccCCCCCCCc
Confidence 4679999864 221 222223 25888865 34764
No 160
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=81.80 E-value=1.2 Score=30.88 Aligned_cols=39 Identities=26% Similarity=0.481 Sum_probs=17.7
Q ss_pred ccCCCCCCCceEEEEeccCCCC--CCceEEEEecCCCCCccccC
Q 033869 69 VTCPACKHGKAVYHELQTRSAD--EPMSIFYMCANKNCKHRWNE 110 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaD--E~~T~fY~C~~~~C~~~wre 110 (110)
..||.||+....-. +.+.--. |=.-.-|.|.+ ||++.+|
T Consensus 2 s~Cp~C~~~~~~~~-~~~~IP~F~evii~sf~C~~--CGyk~~e 42 (161)
T PF03367_consen 2 SLCPNCGENGTTRI-LLTDIPYFKEVIIMSFECEH--CGYKNNE 42 (161)
T ss_dssp EE-TTTSSCCEEEE-EEEEETTTEEEEEEEEE-TT--T--EEEE
T ss_pred CcCCCCCCCcEEEE-EEEcCCCCceEEEEEeECCC--CCCEeee
Confidence 36888887643221 2222211 22334478888 8887653
No 161
>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=81.67 E-value=0.49 Score=27.09 Aligned_cols=21 Identities=38% Similarity=0.921 Sum_probs=14.1
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
.||.||.+-.+. .+|..|||.
T Consensus 28 ~c~~cg~~~~~H---------~vc~~cG~y 48 (56)
T PF01783_consen 28 KCPNCGEPKLPH---------RVCPSCGYY 48 (56)
T ss_dssp ESSSSSSEESTT---------SBCTTTBBS
T ss_pred eeccCCCEeccc---------EeeCCCCeE
Confidence 588888655443 568888764
No 162
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=81.62 E-value=1 Score=34.23 Aligned_cols=30 Identities=23% Similarity=0.597 Sum_probs=20.5
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
..||+||+- .+-+|. ....++|..||++-.
T Consensus 12 ~~Cp~Cg~~-~iv~d~--~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 12 LVCPECGSD-KLIYDY--ERGEIVCADCGLVIE 41 (310)
T ss_pred CcCcCCCCC-CeeEEC--CCCeEeecccCCccc
Confidence 479999973 222222 356999999999643
No 163
>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=81.50 E-value=0.93 Score=25.24 Aligned_cols=27 Identities=30% Similarity=0.784 Sum_probs=16.8
Q ss_pred CCCc--CCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 2 EFCP--TCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 2 ~FCp--~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
+.|| +||.-...- .+..++.|-.|+|+
T Consensus 19 k~CP~~~CG~GvFMA----~H~dR~~CGKCg~T 47 (47)
T PF01599_consen 19 KECPSPRCGAGVFMA----EHKDRHYCGKCGYT 47 (47)
T ss_dssp EE-TSTTTTSSSEEE----E-SSEEEETTTSS-
T ss_pred hcCCCcccCCceEee----ecCCCccCCCcccC
Confidence 3688 999843332 23459999999974
No 164
>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=81.23 E-value=0.75 Score=24.66 Aligned_cols=10 Identities=30% Similarity=0.906 Sum_probs=5.1
Q ss_pred ceEEcCCCCC
Q 033869 22 SRFSCPACPY 31 (110)
Q Consensus 22 ~~~~C~~C~y 31 (110)
....|+.||-
T Consensus 25 ~~~~CP~Cg~ 34 (42)
T PF09723_consen 25 DPVPCPECGS 34 (42)
T ss_pred CCCcCCCCCC
Confidence 3455555554
No 165
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=81.22 E-value=1 Score=26.29 Aligned_cols=30 Identities=27% Similarity=0.678 Sum_probs=22.9
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
.+++||.|++...+|--.|+ --.|.. ||..
T Consensus 10 ~~VkCp~C~n~q~vFsha~t---------~V~C~~--Cg~~ 39 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHAST---------VVRCLV--CGKT 39 (59)
T ss_pred EEEECCCCCCeEEEEecCCc---------EEECcc--cCCC
Confidence 47899999999999966542 257877 8764
No 166
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=81.17 E-value=0.87 Score=36.25 Aligned_cols=30 Identities=27% Similarity=0.661 Sum_probs=24.2
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
-||.||.-|... .+. -|.|+.||+...-+.
T Consensus 352 ~Cp~Cg~~m~S~----G~~-g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKSA----GRN-GFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhhc----CCC-CcccccccccCCccc
Confidence 599999999877 223 899999999876554
No 167
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=81.14 E-value=0.79 Score=31.02 Aligned_cols=22 Identities=32% Similarity=0.701 Sum_probs=19.8
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
=|++||++..|+ +-.|+.|+..
T Consensus 31 kC~~CG~v~~PP--------r~~Cp~C~~~ 52 (140)
T COG1545 31 KCKKCGRVYFPP--------RAYCPKCGSE 52 (140)
T ss_pred EcCCCCeEEcCC--------cccCCCCCCC
Confidence 399999999999 7789999987
No 168
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=81.12 E-value=1 Score=33.50 Aligned_cols=35 Identities=29% Similarity=0.663 Sum_probs=14.8
Q ss_pred CCCcCCCCC-cccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 2 EFCPTCGTM-LQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 2 ~FCp~C~nl-L~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
.+||.||+. |.--+ .....--|.|..|+-..+.++
T Consensus 32 ~yCP~Cg~~~L~~f~-NN~PVaDF~C~~C~eeyELKS 67 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFE-NNRPVADFYCPNCNEEYELKS 67 (254)
T ss_dssp ---TTT--SS-EE---------EEE-TTT--EEEEEE
T ss_pred CcCCCCCChhHhhcc-CCCccceeECCCCchHHhhhh
Confidence 489999998 54431 233466799999999887665
No 169
>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=80.84 E-value=1.8 Score=32.43 Aligned_cols=36 Identities=22% Similarity=0.485 Sum_probs=17.6
Q ss_pred cccCCCCCCC-ceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 68 EVTCPACKHG-KAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 68 ~~~CpkCg~~-~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
.-.||-||.. .+.......+ +|. +|..|.- |++.|+
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~---~G~-R~L~Cs~--C~t~W~ 208 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGER---EGK-RYLHCSL--CGTEWR 208 (290)
T ss_dssp -SS-TTT---EEEEEEE---------E-EEEEETT--T--EEE
T ss_pred CCcCCCCCCcCceEEEecCCC---Ccc-EEEEcCC--CCCeee
Confidence 4699999976 3333222211 476 9999998 999996
No 170
>PHA02998 RNA polymerase subunit; Provisional
Probab=80.56 E-value=1.5 Score=31.22 Aligned_cols=34 Identities=21% Similarity=0.421 Sum_probs=21.8
Q ss_pred CCcCCCCC------cccccCCCCCCceEEcCCCCCeeeeC
Q 033869 3 FCPTCGTM------LQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 3 FCp~C~nl------L~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
=||.||+- |..+...+.....|.|..||+.+...
T Consensus 145 ~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 145 PCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCCc
Confidence 38899874 44442222335678999999876544
No 171
>PRK03954 ribonuclease P protein component 4; Validated
Probab=80.11 E-value=1.4 Score=29.26 Aligned_cols=33 Identities=15% Similarity=0.447 Sum_probs=23.7
Q ss_pred CCCcCCCCCcccccCCC----C---CCceEEcCCCCCeee
Q 033869 2 EFCPTCGTMLQYELPHM----D---RPSRFSCPACPYVCN 34 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~----~---~~~~~~C~~C~y~~~ 34 (110)
.||..|+++|.|-.... . ..+.+.|-.||++.-
T Consensus 65 ~~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR 104 (121)
T PRK03954 65 RYCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMR 104 (121)
T ss_pred HHhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEe
Confidence 48999999999852211 1 137889999998754
No 172
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=80.03 E-value=0.76 Score=29.96 Aligned_cols=23 Identities=22% Similarity=0.706 Sum_probs=14.5
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
+|+.||..-.+. ...+.|+.||-
T Consensus 72 ~C~~Cg~~~~~~------~~~~~CP~Cgs 94 (113)
T PRK12380 72 WCWDCSQVVEIH------QHDAQCPHCHG 94 (113)
T ss_pred EcccCCCEEecC------CcCccCcCCCC
Confidence 577888555444 23556888883
No 173
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=79.76 E-value=2.4 Score=24.78 Aligned_cols=32 Identities=25% Similarity=0.667 Sum_probs=26.1
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
.-||.|..-|... ++ +..+.|+.|+-.+++.+
T Consensus 9 LaCP~~kg~L~~~--~~--~~~L~c~~~~~aYpI~d 40 (60)
T COG2835 9 LACPVCKGPLVYD--EE--KQELICPRCKLAYPIRD 40 (60)
T ss_pred eeccCcCCcceEe--cc--CCEEEecccCceeeccc
Confidence 3599999999888 33 33999999999888876
No 174
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=79.65 E-value=1.8 Score=34.21 Aligned_cols=28 Identities=18% Similarity=0.685 Sum_probs=20.7
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
||+|+-+...+ +-..+....|++||..-
T Consensus 16 C~~Cd~l~~~~--~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 16 CSQCDMLVALP--RIESGQKAACPRCGTTL 43 (403)
T ss_pred CCCCCCccccc--CCCCCCeeECCCCCCCC
Confidence 89999887665 33345578899999864
No 175
>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=79.56 E-value=0.45 Score=27.39 Aligned_cols=30 Identities=30% Similarity=0.713 Sum_probs=18.2
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
.+++||.|++...+|-..|+ + -.|.. |+..
T Consensus 6 m~VkCp~C~~~q~vFSha~t--------~-V~C~~--Cg~~ 35 (55)
T PF01667_consen 6 MDVKCPGCYNIQTVFSHAQT--------V-VKCVV--CGTV 35 (55)
T ss_dssp EEEE-TTT-SEEEEETT-SS----------EE-SS--STSE
T ss_pred EEEECCCCCCeeEEEecCCe--------E-EEccc--CCCE
Confidence 37899999999999955443 2 46777 7653
No 176
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=79.49 E-value=1.5 Score=25.09 Aligned_cols=27 Identities=26% Similarity=0.655 Sum_probs=21.5
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
-|+.||--|.+. ....+|+.||..+..
T Consensus 7 ~C~~Cg~~~~~~------dDiVvCp~CgapyHR 33 (54)
T PF14446_consen 7 KCPVCGKKFKDG------DDIVVCPECGAPYHR 33 (54)
T ss_pred cChhhCCcccCC------CCEEECCCCCCcccH
Confidence 389999888877 349999999976554
No 177
>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=79.46 E-value=0.84 Score=29.82 Aligned_cols=23 Identities=26% Similarity=0.654 Sum_probs=14.6
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
+|+.||..-.+. ...+.|+.||-
T Consensus 72 ~C~~Cg~~~~~~------~~~~~CP~Cgs 94 (115)
T TIGR00100 72 ECEDCSEEVSPE------IDLYRCPKCHG 94 (115)
T ss_pred EcccCCCEEecC------CcCccCcCCcC
Confidence 577787555554 22567888874
No 178
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=79.42 E-value=0.63 Score=31.57 Aligned_cols=30 Identities=23% Similarity=0.714 Sum_probs=19.6
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEE-----EEecCCCCCcc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIF-----YMCANKNCKHR 107 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~f-----Y~C~~~~C~~~ 107 (110)
.--.||+||. .| +++|.+... |.|.+ ||..
T Consensus 98 ~~Y~Cp~C~~---~y------~~~ea~~~~d~~~~f~Cp~--Cg~~ 132 (147)
T smart00531 98 AYYKCPNCQS---KY------TFLEANQLLDMDGTFTCPR--CGEE 132 (147)
T ss_pred cEEECcCCCC---Ee------eHHHHHHhcCCCCcEECCC--CCCE
Confidence 4568999983 22 233444444 99999 9875
No 179
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=79.38 E-value=2 Score=24.08 Aligned_cols=8 Identities=50% Similarity=1.356 Sum_probs=4.3
Q ss_pred ccCCCCCC
Q 033869 69 VTCPACKH 76 (110)
Q Consensus 69 ~~CpkCg~ 76 (110)
.+|++|||
T Consensus 29 W~C~~Cgh 36 (55)
T PF14311_consen 29 WKCPKCGH 36 (55)
T ss_pred EECCCCCC
Confidence 45555554
No 180
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=79.00 E-value=1.8 Score=29.88 Aligned_cols=33 Identities=24% Similarity=0.352 Sum_probs=19.1
Q ss_pred CCcCCCCCc----ccccCCCC--CCceEEcCCCCCeeee
Q 033869 3 FCPTCGTML----QYELPHMD--RPSRFSCPACPYVCNM 35 (110)
Q Consensus 3 FCp~C~nlL----~~~~~~~~--~~~~~~C~~C~y~~~~ 35 (110)
=||.||+-- ....-+++ ..-.+.|++||+....
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~ 40 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT 40 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE
Confidence 499999632 22111111 1224899999997654
No 181
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=78.95 E-value=1.7 Score=27.53 Aligned_cols=30 Identities=20% Similarity=0.460 Sum_probs=21.2
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
..||.||..=.-+ ....+|.|+.|+++.--
T Consensus 36 y~CpfCgk~~vkR----~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 36 YVCPFCGKKTVKR----GSTGIWTCRKCGAKFAG 65 (91)
T ss_pred ccCCCCCCCceEE----EeeEEEEcCCCCCEEeC
Confidence 4799998654333 22569999999997643
No 182
>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=78.49 E-value=2.1 Score=25.80 Aligned_cols=24 Identities=29% Similarity=0.847 Sum_probs=16.9
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
-||.|.+-|.+. ...|.|..|+..
T Consensus 3 ~CP~C~~~L~~~------~~~~~C~~C~~~ 26 (70)
T PF07191_consen 3 TCPKCQQELEWQ------GGHYHCEACQKD 26 (70)
T ss_dssp B-SSS-SBEEEE------TTEEEETTT--E
T ss_pred cCCCCCCccEEe------CCEEECcccccc
Confidence 499999999998 259999999864
No 183
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=78.43 E-value=0.99 Score=32.94 Aligned_cols=36 Identities=33% Similarity=1.000 Sum_probs=25.1
Q ss_pred CCCCcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 64 GPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 64 ~~~~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
.|.-...||+|.|+..-| |-|.-+.. =|+|.+ |+|.
T Consensus 188 ~~~~alIC~~C~hhngl~-----~~~ek~~~-efiC~~--Cn~~ 223 (251)
T COG5415 188 SPFKALICPQCHHHNGLY-----RLAEKPII-EFICPH--CNHK 223 (251)
T ss_pred Cchhhhcccccccccccc-----ccccccch-heeccc--chhh
Confidence 555677999999876554 34444444 588999 9874
No 184
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=78.00 E-value=1.3 Score=37.13 Aligned_cols=11 Identities=55% Similarity=1.271 Sum_probs=9.1
Q ss_pred CCCcCCCCCcc
Q 033869 2 EFCPTCGTMLQ 12 (110)
Q Consensus 2 ~FCp~C~nlL~ 12 (110)
+||+.||.-|.
T Consensus 16 kFC~~CG~~l~ 26 (645)
T PRK14559 16 RFCQKCGTSLT 26 (645)
T ss_pred ccccccCCCCC
Confidence 68999998875
No 185
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=77.97 E-value=2.2 Score=23.95 Aligned_cols=30 Identities=20% Similarity=0.628 Sum_probs=20.9
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
|-.||..+... .....+.|+.||+......
T Consensus 9 C~~Cg~~~~~~----~~~~~irCp~Cg~rIl~K~ 38 (49)
T COG1996 9 CARCGREVELD----QETRGIRCPYCGSRILVKE 38 (49)
T ss_pred hhhcCCeeehh----hccCceeCCCCCcEEEEec
Confidence 77888888432 2345889999999765544
No 186
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=77.91 E-value=1.4 Score=31.55 Aligned_cols=34 Identities=24% Similarity=0.390 Sum_probs=23.7
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
-|+.|+|.=.-- -++++...+.|..||...+++.
T Consensus 100 ~C~~C~~pdT~l-~k~~~~~~l~C~aCGa~~~v~~ 133 (201)
T PRK12336 100 ICSECGLPDTRL-VKEDRVLMLRCDACGAHRPVKK 133 (201)
T ss_pred ECCCCCCCCcEE-EEcCCeEEEEcccCCCCccccc
Confidence 499999852111 1234566789999999988775
No 187
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=77.89 E-value=1.8 Score=25.04 Aligned_cols=25 Identities=28% Similarity=0.705 Sum_probs=17.6
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
|..||.||.+..+- -+|..|||-..
T Consensus 27 ~~~c~~cG~~~l~H---------rvc~~cg~Y~g 51 (57)
T COG0333 27 LSVCPNCGEYKLPH---------RVCLKCGYYKG 51 (57)
T ss_pred ceeccCCCCcccCc---------eEcCCCCCccC
Confidence 45788888877664 46888887543
No 188
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=77.61 E-value=2.2 Score=26.93 Aligned_cols=30 Identities=23% Similarity=0.556 Sum_probs=20.7
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
.+||.||..=.-+ ....+|.|+.|+++.--
T Consensus 37 y~CpfCgk~~vkR----~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 37 YFCPFCGKHAVKR----QAVGIWRCKGCKKTVAG 66 (90)
T ss_pred ccCCCCCCCceee----eeeEEEEcCCCCCEEeC
Confidence 3799998643333 12469999999997643
No 189
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=77.49 E-value=5.4 Score=22.56 Aligned_cols=34 Identities=21% Similarity=0.554 Sum_probs=21.0
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCc
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKH 106 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~ 106 (110)
+.||-||.......+ ...-+.++..+-.|.+ ||.
T Consensus 4 kPCPFCG~~~~~~~~--~~~~~~~~~~~V~C~~--Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQ--DEGFDYGMYYYVECTD--CGA 37 (61)
T ss_pred cCCCCCCCcceEeec--ccCCCCCCEEEEEcCC--CCC
Confidence 479999776655543 3333344445555988 975
No 190
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=76.55 E-value=2.4 Score=28.67 Aligned_cols=32 Identities=22% Similarity=0.508 Sum_probs=21.2
Q ss_pred CCCcCCCCCcccccCCC-----------CCCceEEcCCCCCee
Q 033869 2 EFCPTCGTMLQYELPHM-----------DRPSRFSCPACPYVC 33 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~-----------~~~~~~~C~~C~y~~ 33 (110)
.-|+.||..|.+-...+ ...-.+.|+.||..+
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 35999999886642111 123479999999764
No 191
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=75.42 E-value=2.7 Score=33.41 Aligned_cols=27 Identities=22% Similarity=0.830 Sum_probs=17.1
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
||+|+.+...+ ....+....|++||..
T Consensus 13 C~~Cd~l~~~~--~l~~g~~a~CpRCg~~ 39 (419)
T PRK15103 13 CPQCDMLVALP--RLEHGQKAACPRCGTT 39 (419)
T ss_pred CCCCCceeecC--CCCCCCeeECCCCCCC
Confidence 77887776554 3233446778888775
No 192
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=75.10 E-value=2.7 Score=22.58 Aligned_cols=13 Identities=38% Similarity=0.828 Sum_probs=9.3
Q ss_pred CCCcCCCCCcccc
Q 033869 2 EFCPTCGTMLQYE 14 (110)
Q Consensus 2 ~FCp~C~nlL~~~ 14 (110)
..||.||.-|..-
T Consensus 3 ~~C~~Cg~~l~~i 15 (47)
T PF13005_consen 3 RACPDCGGELKEI 15 (47)
T ss_pred CcCCCCCceeeEC
Confidence 4688888877743
No 193
>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=74.99 E-value=3.9 Score=21.52 Aligned_cols=28 Identities=25% Similarity=0.738 Sum_probs=17.3
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
||.||.-=-.+-+.......+.|+.|+.
T Consensus 6 CP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 6 CPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred CCCCCCccccccccCCCCcCEEeCCCCC
Confidence 8888874322212223456899999974
No 194
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=74.98 E-value=1.2 Score=29.15 Aligned_cols=25 Identities=16% Similarity=0.378 Sum_probs=16.0
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
+|+.||+...+. . ...+.|+.||-.
T Consensus 73 ~C~~Cg~~~~~~--~---~~~~~CP~Cgs~ 97 (117)
T PRK00564 73 ECKDCSHVFKPN--A---LDYGVCEKCHSK 97 (117)
T ss_pred EhhhCCCccccC--C---ccCCcCcCCCCC
Confidence 688899665554 1 123459999853
No 195
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=74.17 E-value=2.9 Score=27.29 Aligned_cols=29 Identities=31% Similarity=0.816 Sum_probs=23.3
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
|.-||.|++-.... . ...|.|+.|.+++.
T Consensus 3 lp~cp~c~sEytYe--d---~~~~~cpec~~ew~ 31 (112)
T COG2824 3 LPPCPKCNSEYTYE--D---GGQLICPECAHEWN 31 (112)
T ss_pred CCCCCccCCceEEe--c---CceEeCchhccccc
Confidence 45699999988877 2 34999999999876
No 196
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=74.07 E-value=2.6 Score=34.24 Aligned_cols=34 Identities=21% Similarity=0.583 Sum_probs=24.8
Q ss_pred CCCcCCCCCccccc---CCCCCCceEEcCCCCCeeeeC
Q 033869 2 EFCPTCGTMLQYEL---PHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 2 ~FCp~C~nlL~~~~---~~~~~~~~~~C~~C~y~~~~~ 36 (110)
.+||+||.++.... |.+.....|.|. ||+...++
T Consensus 176 pic~~cg~~~~~~~~~~d~~~~~v~y~~~-cG~~~~~~ 212 (510)
T PRK00750 176 PICPKCGKVLTTPVISYDAEAGTVTYDCE-CGHEGEVP 212 (510)
T ss_pred eeCCCCCccceEEEEEEeCCCCEEEEEcC-CCCEEEEe
Confidence 57999999998664 333444678886 99987654
No 197
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=73.77 E-value=2.7 Score=26.55 Aligned_cols=30 Identities=20% Similarity=0.439 Sum_probs=20.9
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
..||.||..=.-+ ....+|.|+.|++..--
T Consensus 37 y~CpfCgk~~vkR----~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 37 HVCPVCGRPKVKR----VGTGIWECRKCGAKFAG 66 (90)
T ss_pred ccCCCCCCCceEE----EEEEEEEcCCCCCEEeC
Confidence 3799997554443 22459999999997643
No 198
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=73.71 E-value=1.9 Score=24.18 Aligned_cols=12 Identities=33% Similarity=0.863 Sum_probs=9.5
Q ss_pred cccCCCCCCCce
Q 033869 68 EVTCPACKHGKA 79 (110)
Q Consensus 68 ~~~CpkCg~~~a 79 (110)
-..||+||+++.
T Consensus 13 Y~~Cp~CGN~~v 24 (49)
T PF12677_consen 13 YCKCPKCGNDKV 24 (49)
T ss_pred hccCcccCCcEe
Confidence 468999999654
No 199
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=72.90 E-value=3.5 Score=26.61 Aligned_cols=33 Identities=21% Similarity=0.441 Sum_probs=22.9
Q ss_pred CcCCCCCcccc--cCCCCCCceEEcCCCCCeeeeC
Q 033869 4 CPTCGTMLQYE--LPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 4 Cp~C~nlL~~~--~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
||.||...... .++........|.+||-.....
T Consensus 25 Cp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~e 59 (104)
T COG4888 25 CPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECE 59 (104)
T ss_pred cCccCCeeeeEEEEEecCceeEEEcccCcceEEEe
Confidence 88998876551 2245567788999999766544
No 200
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=72.42 E-value=2.7 Score=30.22 Aligned_cols=33 Identities=24% Similarity=0.489 Sum_probs=20.6
Q ss_pred CCcCCCCCcccc-cC-CCCCCceEEcCCCCCeeee
Q 033869 3 FCPTCGTMLQYE-LP-HMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 3 FCp~C~nlL~~~-~~-~~~~~~~~~C~~C~y~~~~ 35 (110)
-||.||..=.+. .- .......+.|..||+.+++
T Consensus 8 ~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 8 ECPSCGSEEVSHEVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred ECCCCCcchhhHHHHHhcCCceEEEccCCCcEeec
Confidence 499999332211 00 1133578999999999843
No 201
>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=72.40 E-value=11 Score=30.53 Aligned_cols=35 Identities=17% Similarity=0.459 Sum_probs=23.7
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
+.||+.|..+--+.--.. ....+.|++|-...+..
T Consensus 5 L~fC~~C~~irc~~c~~~-Ei~~~yCp~CL~~~p~~ 39 (483)
T PF05502_consen 5 LYFCEHCHKIRCPRCVSE-EIDSYYCPNCLFEVPSS 39 (483)
T ss_pred ceecccccccCChhhccc-ccceeECccccccCChh
Confidence 469999998876652222 25688999998655443
No 202
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=71.99 E-value=2.3 Score=31.63 Aligned_cols=33 Identities=27% Similarity=0.682 Sum_probs=11.6
Q ss_pred cccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccc
Q 033869 68 EVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108 (110)
Q Consensus 68 ~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~w 108 (110)
+.-||.||+....=|..=..+|| |.|.+ |+..+
T Consensus 31 n~yCP~Cg~~~L~~f~NN~PVaD------F~C~~--C~eey 63 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKFENNRPVAD------FYCPN--CNEEY 63 (254)
T ss_dssp H---TTT--SS-EE--------E------EE-TT--T--EE
T ss_pred CCcCCCCCChhHhhccCCCccce------eECCC--CchHH
Confidence 56899999986555544444444 67988 98764
No 203
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=71.93 E-value=1.8 Score=28.25 Aligned_cols=24 Identities=25% Similarity=0.635 Sum_probs=13.8
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
+|+.||..-... ....+.|+.||-
T Consensus 72 ~C~~Cg~~~~~~-----~~~~~~CP~Cgs 95 (114)
T PRK03681 72 WCETCQQYVTLL-----TQRVRRCPQCHG 95 (114)
T ss_pred EcccCCCeeecC-----CccCCcCcCcCC
Confidence 577888544333 112366888884
No 204
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=71.71 E-value=8.7 Score=22.72 Aligned_cols=32 Identities=19% Similarity=0.377 Sum_probs=22.0
Q ss_pred cccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccc
Q 033869 68 EVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108 (110)
Q Consensus 68 ~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~w 108 (110)
-+.||-||.+.+..-.. +-.-+++|.. |+-.|
T Consensus 6 lKPCPFCG~~~~~v~~~-------~g~~~v~C~~--CgA~~ 37 (64)
T PRK09710 6 VKPCPFCGCPSVTVKAI-------SGYYRAKCNG--CESRT 37 (64)
T ss_pred ccCCCCCCCceeEEEec-------CceEEEEcCC--CCcCc
Confidence 36899999988766431 3355678877 97654
No 205
>PLN00209 ribosomal protein S27; Provisional
Probab=71.62 E-value=2.5 Score=26.46 Aligned_cols=30 Identities=27% Similarity=0.656 Sum_probs=23.1
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
.+++||.|++...+|-.+|+ --.|.. ||..
T Consensus 35 m~VkCp~C~n~q~VFShA~t---------~V~C~~--Cg~~ 64 (86)
T PLN00209 35 MDVKCQGCFNITTVFSHSQT---------VVVCGS--CQTV 64 (86)
T ss_pred EEEECCCCCCeeEEEecCce---------EEEccc--cCCE
Confidence 48999999999999966553 256777 8754
No 206
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=70.65 E-value=7.2 Score=25.94 Aligned_cols=30 Identities=27% Similarity=0.552 Sum_probs=24.7
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
+.||.|++.+..+... +-++|-.|.. ||.+
T Consensus 94 VlC~~C~spdT~l~k~-------~r~~~l~C~a--CGa~ 123 (125)
T PF01873_consen 94 VLCPECGSPDTELIKE-------GRLIFLKCKA--CGAS 123 (125)
T ss_dssp SSCTSTSSSSEEEEEE-------TTCCEEEETT--TSCE
T ss_pred EEcCCCCCCccEEEEc-------CCEEEEEecc--cCCc
Confidence 6999999999877543 5678999999 9975
No 207
>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=70.41 E-value=3.1 Score=27.92 Aligned_cols=31 Identities=16% Similarity=0.172 Sum_probs=24.0
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
+-||.||.-.|=- ++.-.+|+.||..++...
T Consensus 10 r~Cp~cg~kFYDL-----nk~p~vcP~cg~~~~~~~ 40 (129)
T TIGR02300 10 RICPNTGSKFYDL-----NRRPAVSPYTGEQFPPEE 40 (129)
T ss_pred ccCCCcCcccccc-----CCCCccCCCcCCccCcch
Confidence 4699999887765 235789999999887663
No 208
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=70.39 E-value=2.8 Score=26.16 Aligned_cols=30 Identities=30% Similarity=0.822 Sum_probs=23.2
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
.+++||.|++...+|-.+|+ --.|.. ||..
T Consensus 34 m~VkCp~C~n~q~VFShA~t---------~V~C~~--Cg~~ 63 (85)
T PTZ00083 34 MDVKCPGCSQITTVFSHAQT---------VVLCGG--CSSQ 63 (85)
T ss_pred EEEECCCCCCeeEEEecCce---------EEEccc--cCCE
Confidence 48999999999999976653 256777 8754
No 209
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=70.12 E-value=7.3 Score=26.22 Aligned_cols=30 Identities=20% Similarity=0.486 Sum_probs=23.4
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
+.||.||+.+..+.- ++-..|-.|.. ||.+
T Consensus 98 VlC~~C~sPdT~l~k-------~~r~~~l~C~A--CGa~ 127 (133)
T TIGR00311 98 VICRECNRPDTRIIK-------EGRVSLLKCEA--CGAK 127 (133)
T ss_pred EECCCCCCCCcEEEE-------eCCeEEEeccc--CCCC
Confidence 699999999977642 24566779999 9975
No 210
>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=69.63 E-value=4 Score=21.83 Aligned_cols=28 Identities=25% Similarity=0.697 Sum_probs=13.4
Q ss_pred CcCCCCCcccc-cCCCCCCceEEcCCCCC
Q 033869 4 CPTCGTMLQYE-LPHMDRPSRFSCPACPY 31 (110)
Q Consensus 4 Cp~C~nlL~~~-~~~~~~~~~~~C~~C~y 31 (110)
||.||.--..+ -+.......+.|+.|+.
T Consensus 6 CP~CGG~DrFri~~d~~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 6 CPICGGKDRFRIFDDKDGRGTWICRQCGG 34 (40)
T ss_dssp -TTTT-TTTEEEETT----S-EEETTTTB
T ss_pred CCCCcCccccccCcCcccCCCEECCCCCC
Confidence 88998653332 11123357999999954
No 211
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=69.39 E-value=1.2 Score=34.85 Aligned_cols=36 Identities=17% Similarity=0.453 Sum_probs=20.3
Q ss_pred CCCcCCCCCccccc---CCCCCCceEEcCCCCCeeeeCC
Q 033869 2 EFCPTCGTMLQYEL---PHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 2 ~FCp~C~nlL~~~~---~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
.+|++||.++..+. |.+.....|.|+.||++..++-
T Consensus 175 piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~i 213 (360)
T PF01921_consen 175 PICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVDI 213 (360)
T ss_dssp EEETTTEE--EEEEEEE--SSSEEEEE--TTS---EEET
T ss_pred eeccccCCcccceeeEeecCCCEEEEEecCCCCEEEEec
Confidence 47999999876542 2345678999999999876543
No 212
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=68.80 E-value=2.6 Score=29.50 Aligned_cols=31 Identities=23% Similarity=0.539 Sum_probs=20.6
Q ss_pred CCcCCCCCcccccCCC------------CCCceEEcCCCCCeee
Q 033869 3 FCPTCGTMLQYELPHM------------DRPSRFSCPACPYVCN 34 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~------------~~~~~~~C~~C~y~~~ 34 (110)
=||+||..|..-. ++ .....+.|..||..+=
T Consensus 99 RCp~CN~~L~~vs-~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW 141 (165)
T COG1656 99 RCPECNGELEKVS-REEVKEKVPEKVYRNYEEFYRCPKCGKIYW 141 (165)
T ss_pred cCcccCCEeccCc-HHHHhhccchhhhhcccceeECCCCccccc
Confidence 3999998876541 11 1234678999997654
No 213
>PHA02942 putative transposase; Provisional
Probab=68.71 E-value=4.3 Score=31.84 Aligned_cols=29 Identities=28% Similarity=0.731 Sum_probs=20.8
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~w 108 (110)
+-..||.|||... . .....|.|.+ ||+.+
T Consensus 324 TSq~Cs~CG~~~~---~--------l~~r~f~C~~--CG~~~ 352 (383)
T PHA02942 324 SSVSCPKCGHKMV---E--------IAHRYFHCPS--CGYEN 352 (383)
T ss_pred CCccCCCCCCccC---c--------CCCCEEECCC--CCCEe
Confidence 5678999999642 0 1123799999 99975
No 214
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=68.07 E-value=12 Score=29.23 Aligned_cols=24 Identities=29% Similarity=0.724 Sum_probs=15.5
Q ss_pred cCCCCCcccccCCCCCCceEEcCC-CCCe
Q 033869 5 PTCGTMLQYELPHMDRPSRFSCPA-CPYV 32 (110)
Q Consensus 5 p~C~nlL~~~~~~~~~~~~~~C~~-C~y~ 32 (110)
|-||.=|.++ .+. -...|.. |||.
T Consensus 321 pgCG~gll~E--PD~--rkvtC~~gCgf~ 345 (446)
T KOG0006|consen 321 PGCGAGLLPE--PDQ--RKVTCEGGCGFA 345 (446)
T ss_pred CCCCcccccC--CCC--CcccCCCCchhH
Confidence 4688878777 332 2566776 7764
No 215
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=68.04 E-value=3.1 Score=24.21 Aligned_cols=22 Identities=18% Similarity=0.073 Sum_probs=14.8
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
..||.||.+..|. -+|. |||-.
T Consensus 28 ~~c~~cg~~~~pH---------~vc~-cG~Y~ 49 (60)
T PRK01110 28 SVDKTTGEYHLPH---------HVSP-KGYYK 49 (60)
T ss_pred eEcCCCCceeccc---------eecC-CcccC
Confidence 3588888877765 3477 88643
No 216
>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=67.28 E-value=2.8 Score=23.04 Aligned_cols=25 Identities=32% Similarity=0.660 Sum_probs=15.5
Q ss_pred CCcCCCC---CcccccCCCCCCceEEcCCCCC
Q 033869 3 FCPTCGT---MLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 3 FCp~C~n---lL~~~~~~~~~~~~~~C~~C~y 31 (110)
.|++||. +|.+. .+ .....|+.||.
T Consensus 7 ~C~~Cg~~fe~~~~~--~~--~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKM--SD--DPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEec--CC--CCCCCCCCCCC
Confidence 5888888 34332 11 34567888886
No 217
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=66.97 E-value=5.1 Score=30.35 Aligned_cols=31 Identities=23% Similarity=0.465 Sum_probs=22.1
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
.=||+||+.-... +.....++|..||-+-..
T Consensus 2 ~~CpeCg~~~~~~---d~~~ge~VC~~CG~Vi~~ 32 (285)
T COG1405 2 MSCPECGSTNIIT---DYERGEIVCADCGLVLED 32 (285)
T ss_pred CCCCCCCCcccee---eccCCeEEeccCCEEecc
Confidence 5699999993333 222569999999986543
No 218
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=66.03 E-value=10 Score=25.66 Aligned_cols=30 Identities=23% Similarity=0.506 Sum_probs=24.5
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
+.||.||+.+..+-- ++-+.|-.|.. ||..
T Consensus 103 VlC~~C~spdT~l~k-------~~r~~~l~C~A--CGa~ 132 (138)
T PRK03988 103 VICPECGSPDTKLIK-------EGRIWVLKCEA--CGAE 132 (138)
T ss_pred EECCCCCCCCcEEEE-------cCCeEEEEccc--CCCC
Confidence 699999999977632 35689999999 9975
No 219
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=65.84 E-value=5.5 Score=32.56 Aligned_cols=34 Identities=21% Similarity=0.439 Sum_probs=24.0
Q ss_pred CCCcCCCCCcccccCCC-CCCceEEcCCCCCeeeeC
Q 033869 2 EFCPTCGTMLQYELPHM-DRPSRFSCPACPYVCNME 36 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~-~~~~~~~C~~C~y~~~~~ 36 (110)
.+||+||.++.+-.+-+ .....|.|. ||+...++
T Consensus 169 pic~~cGrv~~~~~~~~~~~~v~Y~c~-cG~~g~~~ 203 (515)
T TIGR00467 169 VFCENCGRDTTTVNNYDNEYSIEYSCE-CGNQESVD 203 (515)
T ss_pred eecCCcCccCceEEEecCCceEEEEcC-CCCEEEEe
Confidence 57999999998643222 115789995 99987654
No 220
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=65.25 E-value=1.6 Score=26.18 Aligned_cols=13 Identities=62% Similarity=1.183 Sum_probs=8.7
Q ss_pred CCCcCCCCCcccc
Q 033869 2 EFCPTCGTMLQYE 14 (110)
Q Consensus 2 ~FCp~C~nlL~~~ 14 (110)
.||+.||+-|...
T Consensus 49 ~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 49 YFCPTCGSPLFSE 61 (92)
T ss_dssp EEETTT--EEEEE
T ss_pred cccCCCCCeeecc
Confidence 3899999988864
No 221
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=64.52 E-value=3 Score=27.80 Aligned_cols=13 Identities=54% Similarity=1.303 Sum_probs=12.1
Q ss_pred CCCcCCCCCcccc
Q 033869 2 EFCPTCGTMLQYE 14 (110)
Q Consensus 2 ~FCp~C~nlL~~~ 14 (110)
.||+.||+-|+-+
T Consensus 70 ~FC~~CGs~l~~~ 82 (133)
T COG3791 70 GFCPTCGSPLFWR 82 (133)
T ss_pred eecccCCCceEEe
Confidence 5999999999998
No 222
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=64.35 E-value=5.7 Score=29.21 Aligned_cols=26 Identities=31% Similarity=0.736 Sum_probs=20.4
Q ss_pred CCcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccc
Q 033869 66 QTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108 (110)
Q Consensus 66 ~~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~w 108 (110)
.+-..||.||+ -...-|.|.+ ||+.+
T Consensus 307 ~tS~~C~~cg~---------------~~~r~~~C~~--cg~~~ 332 (364)
T COG0675 307 YTSKTCPCCGH---------------LSGRLFKCPR--CGFVH 332 (364)
T ss_pred CCcccccccCC---------------ccceeEECCC--CCCee
Confidence 46689999999 1246699999 99875
No 223
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=64.29 E-value=1.8 Score=24.81 Aligned_cols=32 Identities=22% Similarity=0.437 Sum_probs=23.5
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
-|..||.+|.-- +...-+...|+.|.-.....
T Consensus 6 RC~~CnKlLa~a--~~~~yle~KCPrCK~vN~~~ 37 (60)
T COG4416 6 RCAKCNKLLAEA--EGQAYLEKKCPRCKEVNEFY 37 (60)
T ss_pred ehHHHhHHHHhc--ccceeeeecCCccceeeeee
Confidence 378899988766 44446788999998765543
No 224
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=63.71 E-value=1.6 Score=35.07 Aligned_cols=25 Identities=32% Similarity=0.871 Sum_probs=19.8
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
.|||.|+|-..+. + -+-.||.||-+
T Consensus 181 ~~CP~Ca~~F~l~--r----RrHHCRLCG~V 205 (505)
T KOG1842|consen 181 QFCPECANSFGLT--R----RRHHCRLCGRV 205 (505)
T ss_pred cccccccchhhhH--H----HhhhhhhcchH
Confidence 5999999988776 2 26789999875
No 225
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=63.31 E-value=6.9 Score=30.67 Aligned_cols=35 Identities=23% Similarity=0.445 Sum_probs=20.6
Q ss_pred CcccCCCCCC-CceEEEEeccCCCC-CCceEEEEecCCCCCccc
Q 033869 67 TEVTCPACKH-GKAVYHELQTRSAD-EPMSIFYMCANKNCKHRW 108 (110)
Q Consensus 67 ~~~~CpkCg~-~~a~~~~~Q~RsaD-E~~T~fY~C~~~~C~~~w 108 (110)
....|++||. ....-. +-| ++-|+.|+|.. |||+-
T Consensus 173 f~piC~~cGri~tt~v~-----~~d~~~~~v~Y~c~~--cG~~g 209 (360)
T PF01921_consen 173 FLPICEKCGRIDTTEVT-----EYDPEGGTVTYRCEE--CGHEG 209 (360)
T ss_dssp EEEEETTTEE--EEEEE-----EE--SSSEEEEE--T--TS---
T ss_pred eeeeccccCCcccceee-----EeecCCCEEEEEecC--CCCEE
Confidence 3668999998 444332 233 67899999977 99963
No 226
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=62.93 E-value=1.6 Score=30.78 Aligned_cols=30 Identities=27% Similarity=0.645 Sum_probs=22.8
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
.--.||+|| ..| +.+|+|..-|.|.. ||..
T Consensus 116 ~~Y~Cp~C~---~ry------tf~eA~~~~F~Cp~--Cg~~ 145 (178)
T PRK06266 116 MFFFCPNCH---IRF------TFDEAMEYGFRCPQ--CGEM 145 (178)
T ss_pred CEEECCCCC---cEE------eHHHHhhcCCcCCC--CCCC
Confidence 346899998 334 55677888999999 9864
No 227
>PRK12495 hypothetical protein; Provisional
Probab=62.74 E-value=6.6 Score=28.77 Aligned_cols=27 Identities=22% Similarity=0.588 Sum_probs=21.3
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
.+|+.||.-|.-. .....|..|+....
T Consensus 43 ~hC~~CG~PIpa~------pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 43 AHCDECGDPIFRH------DGQEFCPTCQQPVT 69 (226)
T ss_pred hhcccccCcccCC------CCeeECCCCCCccc
Confidence 4899999999833 34889999997644
No 228
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=62.62 E-value=7.2 Score=27.11 Aligned_cols=15 Identities=20% Similarity=0.379 Sum_probs=11.7
Q ss_pred CCCceEEcCCCCCee
Q 033869 19 DRPSRFSCPACPYVC 33 (110)
Q Consensus 19 ~~~~~~~C~~C~y~~ 33 (110)
..+++|.|.+|+..-
T Consensus 110 ~d~~~wyc~~c~~~~ 124 (159)
T TIGR03037 110 LDGFQWFCPQCGHKL 124 (159)
T ss_pred CcceEEECCCCCCeE
Confidence 458899999997643
No 229
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=62.04 E-value=6.4 Score=23.04 Aligned_cols=17 Identities=18% Similarity=0.546 Sum_probs=14.1
Q ss_pred CceEEcCCCCCeeeeCC
Q 033869 21 PSRFSCPACPYVCNMES 37 (110)
Q Consensus 21 ~~~~~C~~C~y~~~~~~ 37 (110)
...+.|+.||..+++.+
T Consensus 51 eg~L~Cp~c~r~YPI~d 67 (68)
T PF03966_consen 51 EGELICPECGREYPIRD 67 (68)
T ss_dssp TTEEEETTTTEEEEEET
T ss_pred CCEEEcCCCCCEEeCCC
Confidence 45899999999988754
No 230
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=61.73 E-value=3.3 Score=27.16 Aligned_cols=12 Identities=58% Similarity=1.411 Sum_probs=10.3
Q ss_pred CCcCCCCCcccc
Q 033869 3 FCPTCGTMLQYE 14 (110)
Q Consensus 3 FCp~C~nlL~~~ 14 (110)
+||.||.||..+
T Consensus 76 yCP~Cgt~levE 87 (112)
T PF08882_consen 76 YCPGCGTQLEVE 87 (112)
T ss_pred ECCCCcceeEEc
Confidence 789999998877
No 231
>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=61.16 E-value=1.3 Score=23.10 Aligned_cols=8 Identities=38% Similarity=1.169 Sum_probs=3.6
Q ss_pred EcCCCCCe
Q 033869 25 SCPACPYV 32 (110)
Q Consensus 25 ~C~~C~y~ 32 (110)
.|+.||.+
T Consensus 3 ~C~~Cg~~ 10 (36)
T PF05191_consen 3 ICPKCGRI 10 (36)
T ss_dssp EETTTTEE
T ss_pred CcCCCCCc
Confidence 44444433
No 232
>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=61.11 E-value=6.4 Score=30.12 Aligned_cols=38 Identities=18% Similarity=0.553 Sum_probs=25.6
Q ss_pred cccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 68 EVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 68 ~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
...||-||..-. .-.++....++| -+|..|.- |++.|+
T Consensus 184 ~~~CPvCGs~P~-~s~~~~~~~~~G-~RyL~Csl--C~teW~ 221 (305)
T TIGR01562 184 RTLCPACGSPPV-ASMVRQGGKETG-LRYLSCSL--CATEWH 221 (305)
T ss_pred CCcCCCCCChhh-hhhhcccCCCCC-ceEEEcCC--CCCccc
Confidence 348999997542 111222233566 68899998 999996
No 233
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=61.10 E-value=7.2 Score=30.48 Aligned_cols=23 Identities=30% Similarity=0.553 Sum_probs=18.7
Q ss_pred cccCCCCCCCceEEEEe--ccCCCC
Q 033869 68 EVTCPACKHGKAVYHEL--QTRSAD 90 (110)
Q Consensus 68 ~~~CpkCg~~~a~~~~~--Q~RsaD 90 (110)
...||.|+.....||.+ |.|+.-
T Consensus 129 ~~~Cp~C~r~~~~y~eAivQvR~~~ 153 (355)
T COG1499 129 RTLCPRCSRFTGGYYEAIVQVRAKG 153 (355)
T ss_pred EeEChhhhccccceeEEEEEEEecc
Confidence 56999999988888865 988764
No 234
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=60.56 E-value=4.2 Score=28.85 Aligned_cols=13 Identities=31% Similarity=0.633 Sum_probs=11.4
Q ss_pred CCCcCCCCCcccc
Q 033869 2 EFCPTCGTMLQYE 14 (110)
Q Consensus 2 ~FCp~C~nlL~~~ 14 (110)
.||+.||+-|+..
T Consensus 90 ~FC~~CGS~L~~~ 102 (182)
T TIGR02820 90 HACKGCGTHMYGR 102 (182)
T ss_pred ecCCCCCCccccc
Confidence 4999999999876
No 235
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=60.11 E-value=7.4 Score=30.30 Aligned_cols=34 Identities=18% Similarity=0.464 Sum_probs=21.3
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
..-.||+||--. ..+ +.-..+.-|+.|.|. |||.
T Consensus 168 ~~p~c~~cg~~~---~~v-~~~d~~~~~v~y~c~---cG~~ 201 (353)
T cd00674 168 FMPYCEKCGKDT---TTV-EAYDAKAGTVTYKCE---CGHE 201 (353)
T ss_pred eeeecCCcCcce---eEE-EEEeCCCCeEEEEcC---CCCE
Confidence 356899999322 111 112234569999994 9985
No 236
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=59.88 E-value=6.5 Score=35.43 Aligned_cols=17 Identities=29% Similarity=0.880 Sum_probs=13.4
Q ss_pred CceEEcCCCCCeeeeCC
Q 033869 21 PSRFSCPACPYVCNMES 37 (110)
Q Consensus 21 ~~~~~C~~C~y~~~~~~ 37 (110)
...|.|++|.|.+-.++
T Consensus 681 ~phy~c~~c~~~ef~~~ 697 (1213)
T TIGR01405 681 PPHYLCPNCKYSEFITD 697 (1213)
T ss_pred cccccCccccccccccc
Confidence 34799999999877655
No 237
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=59.87 E-value=2.4 Score=22.53 Aligned_cols=10 Identities=40% Similarity=1.291 Sum_probs=4.7
Q ss_pred CCCcCCCCCc
Q 033869 2 EFCPTCGTML 11 (110)
Q Consensus 2 ~FCp~C~nlL 11 (110)
+||+.|||+=
T Consensus 18 ~~C~~C~nls 27 (41)
T PF02132_consen 18 KFCSICGNLS 27 (41)
T ss_dssp EE-SSS--EE
T ss_pred CccCCCCCcC
Confidence 5778887763
No 238
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=59.45 E-value=9.9 Score=24.50 Aligned_cols=33 Identities=24% Similarity=0.603 Sum_probs=18.7
Q ss_pred ccCCCCCCCceEEEEe-c--cCCCCCCceEEEEecCCCCC
Q 033869 69 VTCPACKHGKAVYHEL-Q--TRSADEPMSIFYMCANKNCK 105 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~-Q--~RsaDE~~T~fY~C~~~~C~ 105 (110)
..||-||.. +.+-.. . -++.|++. .+|+|.. |+
T Consensus 3 ~~CpYCg~~-~~l~~~~~iYg~~~~~~~-~~y~C~~--C~ 38 (102)
T PF11672_consen 3 IICPYCGGP-AELVDGSEIYGHRYDDGP-YLYVCTP--CD 38 (102)
T ss_pred cccCCCCCe-eEEcccchhcCccCCCCc-eeEECCC--CC
Confidence 579999972 111110 0 14555554 4599999 95
No 239
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=59.08 E-value=4.5 Score=28.90 Aligned_cols=14 Identities=21% Similarity=0.619 Sum_probs=12.1
Q ss_pred CCCcCCCCCccccc
Q 033869 2 EFCPTCGTMLQYEL 15 (110)
Q Consensus 2 ~FCp~C~nlL~~~~ 15 (110)
.||+.||+-|+...
T Consensus 94 ~FC~~CGS~L~~~~ 107 (191)
T PRK05417 94 HACKECGVHMYGRI 107 (191)
T ss_pred eeCCCCCCcccccc
Confidence 49999999998873
No 240
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=59.00 E-value=6.9 Score=35.89 Aligned_cols=17 Identities=29% Similarity=0.884 Sum_probs=13.5
Q ss_pred CceEEcCCCCCeeeeCC
Q 033869 21 PSRFSCPACPYVCNMES 37 (110)
Q Consensus 21 ~~~~~C~~C~y~~~~~~ 37 (110)
...|.|++|.|.+-.++
T Consensus 906 ~phy~C~~C~~~ef~~~ 922 (1437)
T PRK00448 906 PPHYVCPNCKYSEFFTD 922 (1437)
T ss_pred CccccCccccccccccc
Confidence 34799999999877655
No 241
>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=58.37 E-value=16 Score=19.65 Aligned_cols=26 Identities=27% Similarity=0.816 Sum_probs=18.4
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
||+-|+. .. .....+.|..|+.....
T Consensus 1 ~C~vC~~---~~----~~~~~i~C~~C~~~~H~ 26 (51)
T PF00628_consen 1 YCPVCGQ---SD----DDGDMIQCDSCNRWYHQ 26 (51)
T ss_dssp EBTTTTS---SC----TTSSEEEBSTTSCEEET
T ss_pred eCcCCCC---cC----CCCCeEEcCCCChhhCc
Confidence 6888888 22 23579999999965543
No 242
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=58.15 E-value=8.8 Score=27.18 Aligned_cols=15 Identities=13% Similarity=0.268 Sum_probs=11.7
Q ss_pred CCCceEEcCCCCCee
Q 033869 19 DRPSRFSCPACPYVC 33 (110)
Q Consensus 19 ~~~~~~~C~~C~y~~ 33 (110)
...++|.|.+|+..-
T Consensus 116 ~d~~~wyc~~c~~~~ 130 (177)
T PRK13264 116 LDGFQWYCDECNHKV 130 (177)
T ss_pred ccceEEECCCCCCeE
Confidence 457899999998643
No 243
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=58.07 E-value=3.6 Score=23.46 Aligned_cols=19 Identities=32% Similarity=0.880 Sum_probs=11.8
Q ss_pred CCcCCCC-CcccccCCCCCCceEEcC
Q 033869 3 FCPTCGT-MLQYELPHMDRPSRFSCP 27 (110)
Q Consensus 3 FCp~C~n-lL~~~~~~~~~~~~~~C~ 27 (110)
=||+|++ .|+.. ...|.|.
T Consensus 16 ~Cp~C~~~~l~~~------~~~Y~C~ 35 (55)
T PF08063_consen 16 PCPKCKGGQLYFD------GSGYKCT 35 (55)
T ss_dssp --SSSSE-EEEEE------TTEEEEE
T ss_pred CCCCCCCCeEEec------CCccEeC
Confidence 4899998 56665 2278875
No 244
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=57.99 E-value=11 Score=30.79 Aligned_cols=33 Identities=24% Similarity=0.520 Sum_probs=21.6
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
..-.||+||.-.... . ...++. |+-|.|. |||.
T Consensus 167 ~~pic~~cGrv~~~~--~-~~~~~~--~v~Y~c~---cG~~ 199 (515)
T TIGR00467 167 ISVFCENCGRDTTTV--N-NYDNEY--SIEYSCE---CGNQ 199 (515)
T ss_pred eeeecCCcCccCceE--E-EecCCc--eEEEEcC---CCCE
Confidence 466899999863311 1 233333 8999995 9985
No 245
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=57.28 E-value=3.9 Score=27.68 Aligned_cols=21 Identities=29% Similarity=0.858 Sum_probs=16.5
Q ss_pred CCCCCCceEEEEecCCCCCcccc
Q 033869 87 RSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 87 RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
|-..|....||.|.+ |+.+|.
T Consensus 90 ~l~~e~~~~~Y~Cp~--C~~~y~ 110 (147)
T smart00531 90 KLEDETNNAYYKCPN--CQSKYT 110 (147)
T ss_pred HHhcccCCcEEECcC--CCCEee
Confidence 444566778999999 999885
No 246
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=57.05 E-value=20 Score=23.33 Aligned_cols=30 Identities=27% Similarity=0.585 Sum_probs=23.5
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
+.|+.||+.+..+-.. +-+.|-.|.. ||.+
T Consensus 81 VlC~~C~spdT~l~k~-------~r~~~l~C~a--CGa~ 110 (110)
T smart00653 81 VLCPECGSPDTELIKE-------NRLFFLKCEA--CGAR 110 (110)
T ss_pred EECCCCCCCCcEEEEe-------CCeEEEEccc--cCCC
Confidence 6999999998766432 4578889998 9864
No 247
>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=56.15 E-value=1.4 Score=28.64 Aligned_cols=23 Identities=35% Similarity=0.849 Sum_probs=10.2
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
+|..||.-..+. ...+.|+.||-
T Consensus 72 ~C~~Cg~~~~~~------~~~~~CP~Cgs 94 (113)
T PF01155_consen 72 RCRDCGHEFEPD------EFDFSCPRCGS 94 (113)
T ss_dssp EETTTS-EEECH------HCCHH-SSSSS
T ss_pred ECCCCCCEEecC------CCCCCCcCCcC
Confidence 355555555544 11244565554
No 248
>PRK14973 DNA topoisomerase I; Provisional
Probab=55.56 E-value=6.8 Score=34.36 Aligned_cols=33 Identities=21% Similarity=0.460 Sum_probs=24.1
Q ss_pred CCcCCCC--CcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGT--MLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~n--lL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
-||+||. ++..+ .+..+..+.|+.|.|.+....
T Consensus 637 ~Cp~CG~p~~~~~r--~Gr~g~fl~CP~C~~~~~~~~ 671 (936)
T PRK14973 637 VCPIHHLNHVRLIR--KGARPWDIGCPLCSHIESNTE 671 (936)
T ss_pred CCCCCCCCceEEee--cCCCcccccCccccchhhccc
Confidence 4999997 56656 555566788999999776543
No 249
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=55.54 E-value=18 Score=25.82 Aligned_cols=30 Identities=20% Similarity=0.489 Sum_probs=24.2
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
+.|+.||+.+..+.- ++-+.|-.|.. ||..
T Consensus 99 V~C~~C~~pdT~l~k-------~~~~~~l~C~a--CGa~ 128 (201)
T PRK12336 99 VICSECGLPDTRLVK-------EDRVLMLRCDA--CGAH 128 (201)
T ss_pred EECCCCCCCCcEEEE-------cCCeEEEEccc--CCCC
Confidence 799999999977742 25688899999 9875
No 250
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.49 E-value=9.7 Score=24.92 Aligned_cols=23 Identities=30% Similarity=0.818 Sum_probs=19.1
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
=||.||.-|..- .+.|++|+.+.
T Consensus 8 ~cPvcg~~~iVT--------eL~c~~~etTV 30 (122)
T COG3877 8 RCPVCGRKLIVT--------ELKCSNCETTV 30 (122)
T ss_pred CCCcccccceeE--------EEecCCCCceE
Confidence 489999888777 89999999753
No 251
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=55.38 E-value=7 Score=25.36 Aligned_cols=20 Identities=35% Similarity=0.693 Sum_probs=15.5
Q ss_pred cCCCCCCCceEEEEeccCCC
Q 033869 70 TCPACKHGKAVYHELQTRSA 89 (110)
Q Consensus 70 ~CpkCg~~~a~~~~~Q~Rsa 89 (110)
=||+||.+.-.|.-.-.|.|
T Consensus 22 GCp~CG~nkF~yv~~e~rpa 41 (112)
T COG3364 22 GCPKCGCNKFLYVPEEKRPA 41 (112)
T ss_pred cCccccchheEecccccccc
Confidence 49999999988876655554
No 252
>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=54.78 E-value=11 Score=20.47 Aligned_cols=28 Identities=25% Similarity=0.782 Sum_probs=19.0
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
.+|..|+.+|... ...-|.|..|++...
T Consensus 12 ~~C~~C~~~i~g~-----~~~g~~C~~C~~~~H 39 (53)
T PF00130_consen 12 TYCDVCGKFIWGL-----GKQGYRCSWCGLVCH 39 (53)
T ss_dssp EB-TTSSSBECSS-----SSCEEEETTTT-EEE
T ss_pred CCCcccCcccCCC-----CCCeEEECCCCChHh
Confidence 4799999999322 235899999998654
No 253
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=54.35 E-value=6.5 Score=30.61 Aligned_cols=25 Identities=28% Similarity=0.836 Sum_probs=20.4
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
|+.||+.|+.+ .-.|-+||..-...
T Consensus 2 C~~Cg~~v~Fe--------Nt~C~~Cg~~LGf~ 26 (343)
T PF10005_consen 2 CPNCGQPVFFE--------NTRCLSCGSALGFD 26 (343)
T ss_pred CCCCCCcceeC--------CCccccCCccccCC
Confidence 99999999999 45799999865443
No 254
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=54.21 E-value=13 Score=25.33 Aligned_cols=18 Identities=33% Similarity=0.575 Sum_probs=14.6
Q ss_pred CCCCcccCCCCCC-CceEE
Q 033869 64 GPQTEVTCPACKH-GKAVY 81 (110)
Q Consensus 64 ~~~~~~~CpkCg~-~~a~~ 81 (110)
..|+++.|.+||. -..+|
T Consensus 88 m~RtEv~C~~Cg~HLGHVF 106 (142)
T PRK00222 88 MVRTEVRCANCDSHLGHVF 106 (142)
T ss_pred ceEEEEEeCCCCCccCccc
Confidence 5678999999995 47777
No 255
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=53.86 E-value=5.4 Score=27.06 Aligned_cols=12 Identities=42% Similarity=1.182 Sum_probs=10.8
Q ss_pred CCcCCCCCcccc
Q 033869 3 FCPTCGTMLQYE 14 (110)
Q Consensus 3 FCp~C~nlL~~~ 14 (110)
|||+||-|+..+
T Consensus 122 icpecg~l~eve 133 (165)
T COG4647 122 ICPECGILHEVE 133 (165)
T ss_pred hCccccceeeec
Confidence 899999999887
No 256
>cd02673 Peptidase_C19Q A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=53.71 E-value=13 Score=27.16 Aligned_cols=16 Identities=25% Similarity=0.702 Sum_probs=12.5
Q ss_pred ceEEcCCCCCeeeeCC
Q 033869 22 SRFSCPACPYVCNMES 37 (110)
Q Consensus 22 ~~~~C~~C~y~~~~~~ 37 (110)
..+.|..|+++....+
T Consensus 80 s~i~C~~C~~~s~~~e 95 (245)
T cd02673 80 SSYVCIGCSFEENVSD 95 (245)
T ss_pred eEEEecCCCCeeeecc
Confidence 4689999998876554
No 257
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=53.29 E-value=11 Score=25.09 Aligned_cols=39 Identities=28% Similarity=0.536 Sum_probs=26.6
Q ss_pred CCCCcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 64 GPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 64 ~~~~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
.......||.|+..- +.-.-..+.. -.=|.|.. |+..|.
T Consensus 26 ~~~~~~~cP~C~s~~-~~k~g~~~~~----~qRyrC~~--C~~tf~ 64 (129)
T COG3677 26 MQITKVNCPRCKSSN-VVKIGGIRRG----HQRYKCKS--CGSTFT 64 (129)
T ss_pred hhcccCcCCCCCccc-eeeECCcccc----ccccccCC--cCccee
Confidence 445678999999877 4444443332 33499999 998875
No 258
>PRK05978 hypothetical protein; Provisional
Probab=53.27 E-value=6.9 Score=26.90 Aligned_cols=31 Identities=29% Similarity=0.574 Sum_probs=20.4
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~w 108 (110)
..-+||+||..+++=- -.++-=.|.. ||..+
T Consensus 32 l~grCP~CG~G~LF~g---------~Lkv~~~C~~--CG~~~ 62 (148)
T PRK05978 32 FRGRCPACGEGKLFRA---------FLKPVDHCAA--CGEDF 62 (148)
T ss_pred HcCcCCCCCCCccccc---------ccccCCCccc--cCCcc
Confidence 3679999999887421 2334456777 77654
No 259
>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=53.05 E-value=7.4 Score=26.75 Aligned_cols=13 Identities=31% Similarity=0.927 Sum_probs=6.1
Q ss_pred eEEEEecCCCCCccc
Q 033869 94 SIFYMCANKNCKHRW 108 (110)
Q Consensus 94 T~fY~C~~~~C~~~w 108 (110)
..||.|.+ |+.+|
T Consensus 107 ~~~Y~Cp~--c~~r~ 119 (158)
T TIGR00373 107 NMFFICPN--MCVRF 119 (158)
T ss_pred CCeEECCC--CCcEe
Confidence 34455544 44444
No 260
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=53.00 E-value=10 Score=25.81 Aligned_cols=26 Identities=23% Similarity=0.621 Sum_probs=20.4
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
-||.|+.-|... . ...|.|..|+...
T Consensus 36 aC~~C~kkv~~~--~---~~~~~C~~C~~~~ 61 (166)
T cd04476 36 ACPGCNKKVVEE--G---NGTYRCEKCNKSV 61 (166)
T ss_pred cccccCcccEeC--C---CCcEECCCCCCcC
Confidence 599999988765 2 1589999999764
No 261
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=52.87 E-value=13 Score=25.18 Aligned_cols=18 Identities=39% Similarity=0.652 Sum_probs=14.7
Q ss_pred CCCCcccCCCCC-CCceEE
Q 033869 64 GPQTEVTCPACK-HGKAVY 81 (110)
Q Consensus 64 ~~~~~~~CpkCg-~~~a~~ 81 (110)
..++++.|.+|| |-..+|
T Consensus 85 m~RtEv~C~~Cg~HLGHVF 103 (134)
T TIGR00357 85 MIRTEVRCRNCDAHLGHVF 103 (134)
T ss_pred cEEEEEEecCCCCccCccc
Confidence 567999999999 457777
No 262
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=52.51 E-value=4.1 Score=27.99 Aligned_cols=21 Identities=33% Similarity=0.936 Sum_probs=14.0
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
.||.-|| +++ .|.|-+||...
T Consensus 119 ~fCaVCG---~~S--------~ysC~~CG~ky 139 (156)
T KOG3362|consen 119 KFCAVCG---YDS--------KYSCVNCGTKY 139 (156)
T ss_pred hhhhhcC---CCc--------hhHHHhcCCce
Confidence 4777787 344 67788887643
No 263
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.15 E-value=8.5 Score=30.28 Aligned_cols=25 Identities=24% Similarity=0.717 Sum_probs=20.2
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
=||.|+.++... .+-+.+.|| ||+.
T Consensus 308 ~CpkC~~~ie~~----~GCnhm~Cr-C~~~ 332 (384)
T KOG1812|consen 308 QCPKCKFMIELS----EGCNHMTCR-CGHQ 332 (384)
T ss_pred cCcccceeeeec----CCcceEEee-cccc
Confidence 499999998665 337899999 9974
No 264
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=51.82 E-value=2.6 Score=23.61 Aligned_cols=23 Identities=22% Similarity=0.430 Sum_probs=16.7
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
|-.||-...+. .-.||.|+|...
T Consensus 17 C~rC~Arnp~~--------A~kCRkC~~k~L 39 (50)
T COG1552 17 CRRCYARNPPR--------ATKCRKCGYKNL 39 (50)
T ss_pred HHHhcCCCCcc--------hhHHhhccCCCc
Confidence 66777777666 557999998643
No 265
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=51.68 E-value=10 Score=30.21 Aligned_cols=31 Identities=23% Similarity=0.666 Sum_probs=23.4
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
-||+|+-+...+ .-+....-.|+.||.+-..
T Consensus 20 ~C~eCd~~~~~P--~l~~~q~A~CPRC~~~l~~ 50 (418)
T COG2995 20 LCPECDMLVSLP--RLDSGQSAYCPRCGHTLTR 50 (418)
T ss_pred cCCCCCceeccc--cCCCCCcccCCCCCCcccc
Confidence 599999887777 5455668899999986443
No 266
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=51.13 E-value=12 Score=31.03 Aligned_cols=31 Identities=26% Similarity=0.577 Sum_probs=19.7
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCceEEEEecC-CCCCcc
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCAN-KNCKHR 107 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~-~~C~~~ 107 (110)
..||+||+. + ..|+...| .||.|.+ +.|++.
T Consensus 575 ~~CP~Cg~~-~-----~~~~~~~g--kf~gCs~y~~C~~~ 606 (610)
T TIGR01051 575 QDCPLCGRP-M-----VVKLGKYG--PFLACSNFPECKYT 606 (610)
T ss_pred CCCCCCCCe-e-----EEEecCCC--ceeeCCCCCCCCCC
Confidence 579999974 2 22333334 4899987 667654
No 267
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=50.91 E-value=8.3 Score=22.16 Aligned_cols=22 Identities=32% Similarity=0.798 Sum_probs=13.7
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
|+.|+.||..=. + -.|+.||-.
T Consensus 5 mr~C~~CgvYTL-k---------~~CP~CG~~ 26 (56)
T PRK13130 5 IRKCPKCGVYTL-K---------EICPVCGGK 26 (56)
T ss_pred ceECCCCCCEEc-c---------ccCcCCCCC
Confidence 567888875422 2 357888854
No 268
>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=50.76 E-value=8 Score=19.23 Aligned_cols=18 Identities=33% Similarity=1.169 Sum_probs=10.5
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
+|.-||+ .. .|.|+.|+.
T Consensus 4 ~C~vC~~---~~--------kY~Cp~C~~ 21 (30)
T PF04438_consen 4 LCSVCGN---PA--------KYRCPRCGA 21 (30)
T ss_dssp EETSSSS---EE--------SEE-TTT--
T ss_pred CCccCcC---CC--------EEECCCcCC
Confidence 5677776 33 688888875
No 269
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=50.73 E-value=11 Score=21.64 Aligned_cols=25 Identities=32% Similarity=0.833 Sum_probs=18.4
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
+||-|+.-+.. ...|.|+.||....
T Consensus 1 ~Cpv~~~~~~~-------~v~~~Cp~cGipth 25 (55)
T PF13824_consen 1 LCPVCKKDLPA-------HVNFECPDCGIPTH 25 (55)
T ss_pred CCCCCcccccc-------ccCCcCCCCCCcCc
Confidence 68888877622 35899999997644
No 270
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=50.07 E-value=13 Score=19.59 Aligned_cols=28 Identities=21% Similarity=0.554 Sum_probs=20.5
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
.||.-|+..|... ...-+.|+.|++...
T Consensus 12 ~~C~~C~~~i~~~-----~~~~~~C~~C~~~~H 39 (50)
T cd00029 12 TFCDVCRKSIWGL-----FKQGLRCSWCKVKCH 39 (50)
T ss_pred CChhhcchhhhcc-----ccceeEcCCCCCchh
Confidence 4899999988753 134788999998643
No 271
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=49.68 E-value=21 Score=23.65 Aligned_cols=18 Identities=33% Similarity=0.724 Sum_probs=14.8
Q ss_pred CCCCcccCCCCCC-CceEE
Q 033869 64 GPQTEVTCPACKH-GKAVY 81 (110)
Q Consensus 64 ~~~~~~~CpkCg~-~~a~~ 81 (110)
..|+++.|.+||. -..+|
T Consensus 75 ~~RtEv~C~~C~~HLGHVF 93 (119)
T PRK05508 75 GRRTEIVCANCGGHLGHVF 93 (119)
T ss_pred CcEEEEEeCCCCCccCccc
Confidence 5689999999994 57777
No 272
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=49.03 E-value=11 Score=24.93 Aligned_cols=22 Identities=32% Similarity=0.925 Sum_probs=13.3
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
|..|+.-..+. .+.+.|+.||-
T Consensus 73 C~~C~~~~~~e------~~~~~CP~C~s 94 (115)
T COG0375 73 CLDCGQEVELE------ELDYRCPKCGS 94 (115)
T ss_pred eccCCCeecch------hheeECCCCCC
Confidence 66676555554 33555888874
No 273
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=48.87 E-value=8.6 Score=26.29 Aligned_cols=31 Identities=19% Similarity=0.577 Sum_probs=24.5
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
.+||..||.-..++ .+..+|+|..|.....+
T Consensus 89 ~r~CARCGGrv~lr----sNKv~wvcnlc~k~q~i 119 (169)
T KOG3799|consen 89 TRFCARCGGRVSLR----SNKVMWVCNLCRKQQEI 119 (169)
T ss_pred hhHHHhcCCeeeec----cCceEEeccCCcHHHHH
Confidence 36999999998888 33569999999976554
No 274
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=48.77 E-value=15 Score=20.28 Aligned_cols=31 Identities=26% Similarity=0.582 Sum_probs=22.3
Q ss_pred CCcCCCCCcccccCCC---CCCceEEcCCCCCee
Q 033869 3 FCPTCGTMLQYELPHM---DRPSRFSCPACPYVC 33 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~---~~~~~~~C~~C~y~~ 33 (110)
.|..|.++|..+.+.. .+...+.|-.|..+.
T Consensus 8 ~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl 41 (46)
T PF11331_consen 8 VCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVL 41 (46)
T ss_pred ECccHHHHHcCCCccCCCccceeEEeCCCCceeE
Confidence 5899999999884443 224578899888643
No 275
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=48.67 E-value=16 Score=24.56 Aligned_cols=30 Identities=23% Similarity=0.524 Sum_probs=19.9
Q ss_pred cccCCCCCCC-ceEEEEeccCCCCCCceEEE
Q 033869 68 EVTCPACKHG-KAVYHELQTRSADEPMSIFY 97 (110)
Q Consensus 68 ~~~CpkCg~~-~a~~~~~Q~RsaDE~~T~fY 97 (110)
...||+||.. ++.+..+-.+-.=+..|+.|
T Consensus 43 r~~Cp~C~~~~~~E~vels~~G~V~t~Tv~~ 73 (140)
T COG1545 43 RAYCPKCGSETELEWVELSGEGKVETYTVVY 73 (140)
T ss_pred cccCCCCCCCCceEEEEeCCCeEEEEEEEEe
Confidence 4469999987 66777765555444555555
No 276
>PF04194 PDCD2_C: Programmed cell death protein 2, C-terminal putative domain ; InterPro: IPR007320 PDCD2 is localized predominantly in the cytosol of cells situated at the opposite pole of the germinal centre from the centroblasts as well as in cells in the mantle zone. It has been shown to interact with BCL6, an evolutionarily conserved Kruppel-type zinc finger protein that functions as a strong transcriptional repressor and is required for germinal centre development. The rat homologue, Rp8, is associated with programmed cell death in thymocytes.; GO: 0005737 cytoplasm
Probab=48.64 E-value=20 Score=24.71 Aligned_cols=35 Identities=20% Similarity=0.491 Sum_probs=24.0
Q ss_pred ccCCCCCCCceEEEEe------ccCCC-------CCCceEEEEecCCCC
Q 033869 69 VTCPACKHGKAVYHEL------QTRSA-------DEPMSIFYMCANKNC 104 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~------Q~Rsa-------DE~~T~fY~C~~~~C 104 (110)
-.|+.||..+..=||+ .++.. |=|.-+.|+|.+ .|
T Consensus 98 p~C~~Cg~~R~FEfQlmP~li~~L~~~~~~~~~~dwgtv~VyTCs~-sC 145 (164)
T PF04194_consen 98 PKCENCGSPRVFEFQLMPQLIYYLEVDDEGSDSMDWGTVLVYTCSA-SC 145 (164)
T ss_pred CCCccCCCccEEEEEechHHHHHhhccccCCCCceeeEEEEEEehH-Hc
Confidence 3799999988865555 22222 445678999984 57
No 277
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=48.36 E-value=7 Score=20.78 Aligned_cols=12 Identities=25% Similarity=0.642 Sum_probs=9.1
Q ss_pred ccCCCCCCCceE
Q 033869 69 VTCPACKHGKAV 80 (110)
Q Consensus 69 ~~CpkCg~~~a~ 80 (110)
..||.||....+
T Consensus 3 ~~Cp~Cg~~~~~ 14 (47)
T PF14690_consen 3 PRCPHCGSPSVH 14 (47)
T ss_pred ccCCCcCCCceE
Confidence 479999987644
No 278
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=47.96 E-value=21 Score=18.49 Aligned_cols=8 Identities=38% Similarity=1.310 Sum_probs=4.8
Q ss_pred ccCCCCCC
Q 033869 69 VTCPACKH 76 (110)
Q Consensus 69 ~~CpkCg~ 76 (110)
..|+.||.
T Consensus 33 ~~C~~CGE 40 (46)
T TIGR03831 33 LVCPQCGE 40 (46)
T ss_pred cccccCCC
Confidence 35666664
No 279
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=47.80 E-value=11 Score=30.27 Aligned_cols=29 Identities=28% Similarity=0.592 Sum_probs=22.2
Q ss_pred cccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 68 EVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 68 ~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
+-.||.||.. +.|| |.. -|.|.+ ||++.+
T Consensus 350 ~p~Cp~Cg~~--------m~S~--G~~-g~rC~k--Cg~~~~ 378 (421)
T COG1571 350 NPVCPRCGGR--------MKSA--GRN-GFRCKK--CGTRAR 378 (421)
T ss_pred CCCCCccCCc--------hhhc--CCC-Cccccc--ccccCC
Confidence 4589999974 4566 444 899999 999875
No 280
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=47.06 E-value=23 Score=22.60 Aligned_cols=6 Identities=67% Similarity=1.663 Sum_probs=2.7
Q ss_pred cCCCCC
Q 033869 70 TCPACK 75 (110)
Q Consensus 70 ~CpkCg 75 (110)
.||.||
T Consensus 33 ~C~~CG 38 (127)
T TIGR03830 33 YCPACG 38 (127)
T ss_pred ECCCCC
Confidence 444444
No 281
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=47.05 E-value=9.3 Score=25.21 Aligned_cols=28 Identities=21% Similarity=0.521 Sum_probs=15.0
Q ss_pred CCcCCCCCcccccCCC-CCCceEEcCCCCC
Q 033869 3 FCPTCGTMLQYELPHM-DRPSRFSCPACPY 31 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~-~~~~~~~C~~C~y 31 (110)
+| .||..-.+..... .....+.|+.||-
T Consensus 72 ~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs 100 (124)
T PRK00762 72 EC-ECGYEGVVDEDEIDHYAAVIECPVCGN 100 (124)
T ss_pred Ee-eCcCcccccccchhccccCCcCcCCCC
Confidence 68 8986644431111 1112367999983
No 282
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=47.01 E-value=8.3 Score=28.80 Aligned_cols=29 Identities=17% Similarity=0.374 Sum_probs=21.9
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
+.||..|+..-+|+ ...|+.|+.-...-+
T Consensus 113 ~~~C~~C~~~rPpR--------s~HCsvC~~CV~rfD 141 (299)
T KOG1311|consen 113 WKYCDTCQLYRPPR--------SSHCSVCNNCVLRFD 141 (299)
T ss_pred eEEcCcCcccCCCC--------cccchhhcccccccC
Confidence 46899999887776 678999998655433
No 283
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=46.88 E-value=8.4 Score=30.26 Aligned_cols=31 Identities=26% Similarity=0.595 Sum_probs=25.9
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
+.||.|++++..++-.. -+|+-+.|.. ||++
T Consensus 97 VlC~~C~NPETel~itk------~q~i~~~CkA--CG~r 127 (400)
T KOG2767|consen 97 VLCPSCENPETELIITK------KQTISLKCKA--CGFR 127 (400)
T ss_pred eeCcCCCCCceeEEecc------cchhhhHHHH--cCCc
Confidence 68999999998886642 4889999999 9986
No 284
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=45.88 E-value=13 Score=16.76 Aligned_cols=11 Identities=36% Similarity=1.289 Sum_probs=6.9
Q ss_pred EEcCCCCCeee
Q 033869 24 FSCPACPYVCN 34 (110)
Q Consensus 24 ~~C~~C~y~~~ 34 (110)
|.|+.|+|...
T Consensus 1 y~C~~C~y~t~ 11 (24)
T PF13909_consen 1 YKCPHCSYSTS 11 (24)
T ss_dssp EE-SSSS-EES
T ss_pred CCCCCCCCcCC
Confidence 67999998754
No 285
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=45.85 E-value=11 Score=26.48 Aligned_cols=19 Identities=32% Similarity=0.964 Sum_probs=15.2
Q ss_pred CCCCceEEEEecCCCCCcccc
Q 033869 89 ADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 89 aDE~~T~fY~C~~~~C~~~wr 109 (110)
..|.-..||.|.+ |+.+|.
T Consensus 110 ~~e~~~~~Y~Cp~--C~~ryt 128 (178)
T PRK06266 110 EEEENNMFFFCPN--CHIRFT 128 (178)
T ss_pred hhccCCCEEECCC--CCcEEe
Confidence 3455678999999 999885
No 286
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=45.75 E-value=14 Score=19.31 Aligned_cols=26 Identities=19% Similarity=0.505 Sum_probs=19.6
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
.||.-|+..|... . ..+.|+.|++..
T Consensus 12 ~~C~~C~~~i~~~--~----~~~~C~~C~~~~ 37 (49)
T smart00109 12 TKCCVCRKSIWGS--F----QGLRCSWCKVKC 37 (49)
T ss_pred CCccccccccCcC--C----CCcCCCCCCchH
Confidence 5899999988764 1 257899998754
No 287
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=44.94 E-value=12 Score=28.15 Aligned_cols=61 Identities=21% Similarity=0.420 Sum_probs=31.9
Q ss_pred ceEEcCCCCCeeeeCCc-eEEEEecccCccccccccccccccCCCCCcccCCCCCCCceEEEEec
Q 033869 22 SRFSCPACPYVCNMESR-VKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHGKAVYHELQ 85 (110)
Q Consensus 22 ~~~~C~~C~y~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~~a~~~~~Q 85 (110)
-+|+|..|.+.+-..-+ .+-|++-.--++..+.|.. +.. .......||+|+|.=--|-|+-
T Consensus 111 rqFaC~~Cd~~WwRrvp~rKeVSRCr~C~~rYDPVP~-dkm--wG~aef~C~~C~h~F~G~~qm~ 172 (278)
T PF15135_consen 111 RQFACSSCDHMWWRRVPQRKEVSRCRKCRKRYDPVPC-DKM--WGIAEFHCPKCRHNFRGFAQMG 172 (278)
T ss_pred eeeeccccchHHHhccCcccccccccccccccCCCcc-ccc--cceeeeecccccccchhhhhcC
Confidence 47999999987543221 0122222222233333332 111 3445778999998755554443
No 288
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=44.85 E-value=14 Score=28.04 Aligned_cols=18 Identities=28% Similarity=0.482 Sum_probs=11.1
Q ss_pred ccCCCCCCceEEEEecCCCCCccc
Q 033869 85 QTRSADEPMSIFYMCANKNCKHRW 108 (110)
Q Consensus 85 Q~RsaDE~~T~fY~C~~~~C~~~w 108 (110)
||-|.++ -|.|.. |+..|
T Consensus 236 QTHS~~K----~~qC~~--C~KsF 253 (279)
T KOG2462|consen 236 QTHSDVK----KHQCPR--CGKSF 253 (279)
T ss_pred HhhcCCc----cccCcc--hhhHH
Confidence 5666555 367776 76655
No 289
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=44.84 E-value=16 Score=21.42 Aligned_cols=25 Identities=20% Similarity=0.503 Sum_probs=17.9
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
=|.+|+.++... .|++||.....++
T Consensus 5 AC~~C~~i~~~~----------~CP~Cgs~~~T~~ 29 (61)
T PRK08351 5 ACRHCHYITTED----------RCPVCGSRDLSDE 29 (61)
T ss_pred hhhhCCcccCCC----------cCCCCcCCccccc
Confidence 588999888322 4999998765444
No 290
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=44.83 E-value=10 Score=20.72 Aligned_cols=27 Identities=37% Similarity=0.826 Sum_probs=17.1
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
.+||+||---. +|+ ..|.|..|++.++
T Consensus 12 rkCp~CGt~NG------~R~--------~~CKN~~C~~~~~ 38 (44)
T PF14952_consen 12 RKCPKCGTYNG------TRG--------LSCKNKSCPQVFN 38 (44)
T ss_pred ccCCcCcCccC------ccc--------ccccCCccchhhh
Confidence 58999995321 232 4677777776654
No 291
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=44.77 E-value=7.4 Score=21.85 Aligned_cols=29 Identities=21% Similarity=0.385 Sum_probs=17.0
Q ss_pred CCcCCCCCcccccCCC--CCCceEEcCCCCC
Q 033869 3 FCPTCGTMLQYELPHM--DRPSRFSCPACPY 31 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~--~~~~~~~C~~C~y 31 (110)
-|.-|+-.|.+..-.. .......|++||.
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCCCc
Confidence 3666776666652221 2245788888874
No 292
>PRK12366 replication factor A; Reviewed
Probab=44.09 E-value=13 Score=31.13 Aligned_cols=24 Identities=25% Similarity=0.724 Sum_probs=19.0
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
=||.|+.-|... ...|.|+.|+..
T Consensus 534 aCp~CnkKv~~~------~g~~~C~~c~~~ 557 (637)
T PRK12366 534 LCPNCRKRVEEV------DGEYICEFCGEV 557 (637)
T ss_pred cccccCeEeEcC------CCcEECCCCCCC
Confidence 499999987532 358999999987
No 293
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=43.55 E-value=18 Score=24.06 Aligned_cols=25 Identities=20% Similarity=0.692 Sum_probs=16.9
Q ss_pred Cc--CCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 4 CP--TCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 4 Cp--~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
|| .|+.-+... . ...|.|..|+...
T Consensus 21 C~~~~C~kKv~~~--~---~~~y~C~~C~~~~ 47 (146)
T PF08646_consen 21 CPNEKCNKKVTEN--G---DGSYRCEKCNKTV 47 (146)
T ss_dssp -TSTTTS-B-EEE--T---TTEEEETTTTEEE
T ss_pred CCCccCCCEeecC--C---CcEEECCCCCCcC
Confidence 89 999977766 2 2479999999764
No 294
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=43.40 E-value=22 Score=23.15 Aligned_cols=16 Identities=19% Similarity=0.692 Sum_probs=11.9
Q ss_pred cccCCCCCCC-ceEEEE
Q 033869 68 EVTCPACKHG-KAVYHE 83 (110)
Q Consensus 68 ~~~CpkCg~~-~a~~~~ 83 (110)
...||+||.+ +++|.-
T Consensus 49 ~t~CP~Cg~~~e~~fvv 65 (115)
T COG1885 49 STSCPKCGEPFESAFVV 65 (115)
T ss_pred cccCCCCCCccceeEEE
Confidence 3589999965 777754
No 295
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=42.99 E-value=18 Score=21.36 Aligned_cols=27 Identities=22% Similarity=0.481 Sum_probs=19.4
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
-|-.|..++... .-.|+.||-.....+
T Consensus 6 AC~~Ck~l~~~d--------~e~CP~Cgs~~~te~ 32 (64)
T COG2093 6 ACKNCKRLTPED--------TEICPVCGSTDLTEE 32 (64)
T ss_pred HHhhccccCCCC--------CccCCCCCCcccchh
Confidence 477788777665 446999998766555
No 296
>smart00532 LIGANc Ligase N family.
Probab=42.65 E-value=18 Score=29.06 Aligned_cols=26 Identities=38% Similarity=0.906 Sum_probs=18.1
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCC--CCC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPA--CPY 31 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~--C~y 31 (110)
.+||.||+.|...+ + ...+.|.+ |.-
T Consensus 400 ~~CP~C~s~l~~~~--~--~~~~~C~n~~C~a 427 (441)
T smart00532 400 THCPSCGSELVREE--G--EVDIRCPNPLCPA 427 (441)
T ss_pred CCCCCCCCEeEecC--C--ceEEEeCCCCCHH
Confidence 58999999997652 2 34778874 653
No 297
>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=42.14 E-value=20 Score=17.35 Aligned_cols=12 Identities=17% Similarity=0.606 Sum_probs=5.6
Q ss_pred ceEEcCCCCCee
Q 033869 22 SRFSCPACPYVC 33 (110)
Q Consensus 22 ~~~~C~~C~y~~ 33 (110)
..|.|..|+|.-
T Consensus 14 ~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 14 WFYRCSECDFDL 25 (30)
T ss_dssp -EEE-TTT----
T ss_pred ceEECccCCCcc
Confidence 589999998853
No 298
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=42.05 E-value=24 Score=27.12 Aligned_cols=36 Identities=19% Similarity=0.618 Sum_probs=25.1
Q ss_pred cccCCCCCCCc-eEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 68 EVTCPACKHGK-AVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 68 ~~~CpkCg~~~-a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
...||-||..- +.. +.. ..++|. +|..|.- |++.|+
T Consensus 187 ~~~CPvCGs~P~~s~--v~~-~~~~G~-RyL~Csl--C~teW~ 223 (309)
T PRK03564 187 RQFCPVCGSMPVSSV--VQI-GTTQGL-RYLHCNL--CESEWH 223 (309)
T ss_pred CCCCCCCCCcchhhe--eec-cCCCCc-eEEEcCC--CCCccc
Confidence 57899999754 332 222 234555 8999999 999996
No 299
>PRK08402 replication factor A; Reviewed
Probab=41.75 E-value=18 Score=28.31 Aligned_cols=26 Identities=27% Similarity=0.721 Sum_probs=19.2
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
=||.|+.-+... . ....|.|+.||-.
T Consensus 214 aCp~CnKkv~~~--~--~~~~~~Ce~~~~v 239 (355)
T PRK08402 214 ACPECRRKVDYD--P--ATDTWICPEHGEV 239 (355)
T ss_pred cCCCCCeEEEEe--c--CCCCEeCCCCCCc
Confidence 499999988754 1 2348999999854
No 300
>PRK04023 DNA polymerase II large subunit; Validated
Probab=41.29 E-value=19 Score=32.06 Aligned_cols=14 Identities=21% Similarity=0.168 Sum_probs=8.4
Q ss_pred EEcCCCCCeeeeCC
Q 033869 24 FSCPACPYVCNMES 37 (110)
Q Consensus 24 ~~C~~C~y~~~~~~ 37 (110)
+.|++||..-....
T Consensus 664 y~CPKCG~El~~~s 677 (1121)
T PRK04023 664 DECEKCGREPTPYS 677 (1121)
T ss_pred CcCCCCCCCCCccc
Confidence 45777777655443
No 301
>PRK07218 replication factor A; Provisional
Probab=41.14 E-value=14 Score=29.61 Aligned_cols=25 Identities=28% Similarity=0.628 Sum_probs=19.1
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
=||+|+..|. .+.|+.||..++...
T Consensus 299 rCP~C~r~v~----------~~~C~~hG~ve~~~d 323 (423)
T PRK07218 299 RCPECGRVIQ----------KGQCRSHGAVEGEDD 323 (423)
T ss_pred cCcCcccccc----------CCcCCCCCCcCCeee
Confidence 4999999882 268999998766544
No 302
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=41.01 E-value=32 Score=29.95 Aligned_cols=23 Identities=26% Similarity=0.551 Sum_probs=16.0
Q ss_pred CCcCCCCCcccccCCCCCCceEEcC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCP 27 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~ 27 (110)
=||.||.-|..+ .+..+..+.|.
T Consensus 589 ~CP~Cg~~l~~r--~gr~G~Fl~Cs 611 (859)
T PRK07561 589 DCPTCGRGMGIR--TGKTGVFLGCS 611 (859)
T ss_pred cCcccCCcceEE--ecCCCCeeecc
Confidence 489998777766 44445678886
No 303
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=40.91 E-value=21 Score=29.68 Aligned_cols=26 Identities=31% Similarity=0.576 Sum_probs=15.4
Q ss_pred cccCCCCCCCceEEEEeccCCCCCCceEEEEecC
Q 033869 68 EVTCPACKHGKAVYHELQTRSADEPMSIFYMCAN 101 (110)
Q Consensus 68 ~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~ 101 (110)
...||+||++ +. .|...-+ .||-|.+
T Consensus 589 ~~~CPkCg~~-l~-----~~~~k~g--~f~gCs~ 614 (618)
T TIGR01057 589 VGKCPKCGGK-LV-----SKYAKKG--RFVGCSN 614 (618)
T ss_pred cCCCCcCCCe-ee-----eeecCCc--cEEECCC
Confidence 3579999974 11 1212212 5999976
No 304
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=40.74 E-value=12 Score=24.92 Aligned_cols=18 Identities=33% Similarity=0.595 Sum_probs=14.6
Q ss_pred CCCCcccCCCCCCC-ceEE
Q 033869 64 GPQTEVTCPACKHG-KAVY 81 (110)
Q Consensus 64 ~~~~~~~CpkCg~~-~a~~ 81 (110)
..++++.|.+||.+ ..+|
T Consensus 82 ~~R~Ev~C~~Cg~HLGHVF 100 (124)
T PF01641_consen 82 MVRTEVRCARCGSHLGHVF 100 (124)
T ss_dssp SEEEEEEETTTCCEEEEEE
T ss_pred ceEEEEEecCCCCccccEe
Confidence 56789999999955 6666
No 305
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=40.61 E-value=18 Score=18.14 Aligned_cols=11 Identities=27% Similarity=0.658 Sum_probs=9.0
Q ss_pred EEEEecCCCCCcc
Q 033869 95 IFYMCANKNCKHR 107 (110)
Q Consensus 95 ~fY~C~~~~C~~~ 107 (110)
-||.|.. ||+.
T Consensus 3 ~~ykC~~--CGni 13 (34)
T cd00974 3 EVYKCEI--CGNI 13 (34)
T ss_pred cEEEcCC--CCcE
Confidence 4899998 9874
No 306
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=40.45 E-value=16 Score=16.94 Aligned_cols=11 Identities=27% Similarity=0.700 Sum_probs=4.8
Q ss_pred CcCCCCCcccc
Q 033869 4 CPTCGTMLQYE 14 (110)
Q Consensus 4 Cp~C~nlL~~~ 14 (110)
|+.|+.+=.+.
T Consensus 5 C~~C~~~N~~~ 15 (26)
T smart00547 5 CPACTFLNFAS 15 (26)
T ss_pred CCCCCCcChhh
Confidence 44454443333
No 307
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=40.21 E-value=20 Score=24.17 Aligned_cols=20 Identities=25% Similarity=0.532 Sum_probs=14.6
Q ss_pred cCCCCCCCceEEEEeccCCC
Q 033869 70 TCPACKHGKAVYHELQTRSA 89 (110)
Q Consensus 70 ~CpkCg~~~a~~~~~Q~Rsa 89 (110)
=||.||.+.-.|.....+..
T Consensus 21 GCP~CGg~kF~yv~~~~~~~ 40 (131)
T PF09845_consen 21 GCPECGGNKFQYVPEEKDAE 40 (131)
T ss_pred cCcccCCcceEEcCCCcccc
Confidence 49999999988866544433
No 308
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=40.11 E-value=19 Score=18.04 Aligned_cols=11 Identities=27% Similarity=0.700 Sum_probs=9.1
Q ss_pred EEEEecCCCCCcc
Q 033869 95 IFYMCANKNCKHR 107 (110)
Q Consensus 95 ~fY~C~~~~C~~~ 107 (110)
.||.|.. ||+.
T Consensus 6 ~~ykC~~--Cgni 16 (34)
T TIGR00319 6 QVYKCEV--CGNI 16 (34)
T ss_pred cEEEcCC--CCcE
Confidence 4999999 9874
No 309
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=39.07 E-value=22 Score=25.11 Aligned_cols=33 Identities=21% Similarity=0.593 Sum_probs=26.1
Q ss_pred cCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCc
Q 033869 70 TCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKH 106 (110)
Q Consensus 70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~ 106 (110)
.|.+|+.+.|.+.-.|+-+++ -+.+|+|.+ |-.
T Consensus 2 iCq~CqqnpAti~~tkI~~~~--k~e~~vCe~--Ca~ 34 (176)
T COG3880 2 ICQNCQQNPATIHFTKIINGE--KIELYVCET--CAK 34 (176)
T ss_pred cchhhcCCcceEEEEEeecCC--eeEeehhhc--CCC
Confidence 699999999998887775553 455999998 854
No 310
>cd02674 Peptidase_C19R A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=38.91 E-value=77 Score=21.97 Aligned_cols=17 Identities=24% Similarity=0.466 Sum_probs=12.7
Q ss_pred CceEEcCCCCCeeeeCC
Q 033869 21 PSRFSCPACPYVCNMES 37 (110)
Q Consensus 21 ~~~~~C~~C~y~~~~~~ 37 (110)
.....|..|++.....+
T Consensus 49 ~~~~~C~~C~~~~~~~e 65 (230)
T cd02674 49 KSRLTCLTCGKTSTTFE 65 (230)
T ss_pred eCcEEcCCCcCCcceec
Confidence 45789999998766544
No 311
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=38.89 E-value=12 Score=22.27 Aligned_cols=33 Identities=27% Similarity=0.488 Sum_probs=20.8
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCc
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKH 106 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~ 106 (110)
..|..|++..+.-+..| |-+-=+++-.|.+ |..
T Consensus 5 FTC~~C~~Rs~~~~sk~---aY~~GvViv~C~g--C~~ 37 (66)
T PF05180_consen 5 FTCNKCGTRSAKMFSKQ---AYHKGVVIVQCPG--CKN 37 (66)
T ss_dssp EEETTTTEEEEEEEEHH---HHHTSEEEEE-TT--S--
T ss_pred EEcCCCCCccceeeCHH---HHhCCeEEEECCC--Ccc
Confidence 46888888777666654 4444458888877 864
No 312
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=38.82 E-value=40 Score=25.09 Aligned_cols=30 Identities=27% Similarity=0.443 Sum_probs=17.9
Q ss_pred CCcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCC
Q 033869 66 QTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCK 105 (110)
Q Consensus 66 ~~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~ 105 (110)
+....||+||..=..-.+ .-|+ -|.|.+ |.
T Consensus 242 R~g~pCprCG~~I~~~~~-~gR~-------t~~CP~--CQ 271 (272)
T PRK14810 242 RTGEPCLNCKTPIRRVVV-AGRS-------SHYCPH--CQ 271 (272)
T ss_pred CCCCcCCCCCCeeEEEEE-CCCc-------cEECcC--Cc
Confidence 346799999964322222 2233 377888 85
No 313
>PRK07220 DNA topoisomerase I; Validated
Probab=38.42 E-value=28 Score=29.72 Aligned_cols=31 Identities=23% Similarity=0.562 Sum_probs=17.8
Q ss_pred CCcCCCC-CcccccCCCCCCceEEcCCCCCeee
Q 033869 3 FCPTCGT-MLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 3 FCp~C~n-lL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
-||+||. ++... ..+.....+.|+.|.|...
T Consensus 637 ~Cp~Cg~~~~k~~-~~g~~~~~~~Cp~C~~~~~ 668 (740)
T PRK07220 637 VCEAHGLNHIRII-NGGKRPWDLGCPQCNFIEW 668 (740)
T ss_pred CCCCCCCceEEEE-ecCCccceeeCCCCCCccc
Confidence 4999986 33322 1111122679999998543
No 314
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=38.31 E-value=39 Score=27.58 Aligned_cols=36 Identities=22% Similarity=0.361 Sum_probs=22.5
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~w 108 (110)
..-.||+||.-.-+-.. .--.+.-||.|.|. |||..
T Consensus 174 ~~pic~~cg~~~~~~~~---~~d~~~~~v~y~~~---cG~~~ 209 (510)
T PRK00750 174 FLPICPKCGKVLTTPVI---SYDAEAGTVTYDCE---CGHEG 209 (510)
T ss_pred eeeeCCCCCccceEEEE---EEeCCCCEEEEEcC---CCCEE
Confidence 36689999985432221 11223458999985 99864
No 315
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=37.73 E-value=21 Score=19.83 Aligned_cols=34 Identities=15% Similarity=0.387 Sum_probs=21.8
Q ss_pred cccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 68 EVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 68 ~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
...|..|+-.+.-.| |....|. -..|-. |+-.|+
T Consensus 3 ~~~C~~C~~~~T~~W----R~g~~g~--~~LCna--Cgl~~~ 36 (52)
T smart00401 3 GRSCSNCGTTETPLW----RRGPSGN--KTLCNA--CGLYYK 36 (52)
T ss_pred CCCcCCCCCCCCCcc----ccCCCCC--CcEeec--ccHHHH
Confidence 457999997766444 6766666 234555 776664
No 316
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=37.30 E-value=17 Score=30.55 Aligned_cols=22 Identities=27% Similarity=0.673 Sum_probs=16.5
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
.+|++||..+ . +..+.|+.||.
T Consensus 569 ~~C~~CG~~~--~------g~~~~CP~CGs 590 (625)
T PRK08579 569 TVCNKCGRST--T------GLYTRCPRCGS 590 (625)
T ss_pred ccCCCCCCcc--C------CCCCcCcCCCC
Confidence 4799999844 2 23689999996
No 317
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=36.86 E-value=16 Score=22.85 Aligned_cols=31 Identities=26% Similarity=0.327 Sum_probs=18.7
Q ss_pred CCcCCCCCcccccCCC---CCCceEEcCCCCCee
Q 033869 3 FCPTCGTMLQYELPHM---DRPSRFSCPACPYVC 33 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~---~~~~~~~C~~C~y~~ 33 (110)
+|+.|+..|...+.=. ---+.-.|+.|+...
T Consensus 35 ~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I 68 (92)
T PF06750_consen 35 HCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPI 68 (92)
T ss_pred cCcCCCCcCcccccchHHHHHHhCCCCcccCCCC
Confidence 7888888888761110 002345788888643
No 318
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=36.85 E-value=22 Score=15.61 Aligned_cols=11 Identities=27% Similarity=0.929 Sum_probs=7.0
Q ss_pred EEecCCCCCcccc
Q 033869 97 YMCANKNCKHRWN 109 (110)
Q Consensus 97 Y~C~~~~C~~~wr 109 (110)
|+|.. |+..++
T Consensus 1 y~C~~--C~~~f~ 11 (23)
T PF00096_consen 1 YKCPI--CGKSFS 11 (23)
T ss_dssp EEETT--TTEEES
T ss_pred CCCCC--CCCccC
Confidence 66766 776554
No 319
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=36.76 E-value=55 Score=24.29 Aligned_cols=30 Identities=20% Similarity=0.525 Sum_probs=18.7
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKH 106 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~ 106 (110)
....||+||..=.. ..+--|++ |-|.. |..
T Consensus 244 ~g~pC~~Cg~~I~~-~~~~gR~t-------~~CP~--CQ~ 273 (274)
T PRK01103 244 EGEPCRRCGTPIEK-IKQGGRST-------FFCPR--CQK 273 (274)
T ss_pred CCCCCCCCCCeeEE-EEECCCCc-------EECcC--CCC
Confidence 45789999976433 33323433 77888 864
No 320
>PF06573 Churchill: Churchill protein; InterPro: IPR009508 This family consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signalling during neural development. The slow induction by FGF of a transcription factor (Churchill) in the neural plate in turn induces expression of Sip1 (Smad interacting protein-1), which inhibits mesodermal genes and sensitizes cells to later neural inducing factors [].; GO: 0008270 zinc ion binding, 0007275 multicellular organismal development, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2JOX_A.
Probab=36.68 E-value=33 Score=22.38 Aligned_cols=10 Identities=30% Similarity=0.870 Sum_probs=6.5
Q ss_pred cccCCCCCCC
Q 033869 68 EVTCPACKHG 77 (110)
Q Consensus 68 ~~~CpkCg~~ 77 (110)
+..|++|+|-
T Consensus 58 ~HvC~nC~Hv 67 (112)
T PF06573_consen 58 DHVCKNCHHV 67 (112)
T ss_dssp EEEETTT--E
T ss_pred eeccCccceE
Confidence 7889999983
No 321
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=36.02 E-value=2.4 Score=23.85 Aligned_cols=19 Identities=32% Similarity=0.677 Sum_probs=14.1
Q ss_pred CcccCCCCCCCceEEEEec
Q 033869 67 TEVTCPACKHGKAVYHELQ 85 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q 85 (110)
+...||-||-.+|....+|
T Consensus 8 tG~~CPgCG~tRa~~~ll~ 26 (52)
T PF10825_consen 8 TGIPCPGCGMTRAFIALLH 26 (52)
T ss_pred hCCCCCCCcHHHHHHHHHC
Confidence 5678999998887655443
No 322
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=35.72 E-value=51 Score=24.53 Aligned_cols=30 Identities=20% Similarity=0.486 Sum_probs=19.1
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCc
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKH 106 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~ 106 (110)
....||+||..=..... .-|++ |.|.. |..
T Consensus 234 ~g~pC~~Cg~~I~~~~~-~gR~t-------y~Cp~--CQ~ 263 (269)
T PRK14811 234 EGQPCPRCGTPIEKIVV-GGRGT-------HFCPQ--CQP 263 (269)
T ss_pred CcCCCCcCCCeeEEEEE-CCCCc-------EECCC--CcC
Confidence 35789999976443322 22443 77988 865
No 323
>PF14369 zf-RING_3: zinc-finger
Probab=35.55 E-value=30 Score=17.73 Aligned_cols=27 Identities=22% Similarity=0.608 Sum_probs=17.1
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
-||=.|+....+..+.. ....|+.|+-
T Consensus 3 ywCh~C~~~V~~~~~~~---~~~~CP~C~~ 29 (35)
T PF14369_consen 3 YWCHQCNRFVRIAPSPD---SDVACPRCHG 29 (35)
T ss_pred EeCccCCCEeEeCcCCC---CCcCCcCCCC
Confidence 37888888877752222 1236999974
No 324
>PHA02325 hypothetical protein
Probab=35.38 E-value=43 Score=19.91 Aligned_cols=23 Identities=17% Similarity=0.434 Sum_probs=14.0
Q ss_pred cccCCCCCC---CceEEEEeccCCCC
Q 033869 68 EVTCPACKH---GKAVYHELQTRSAD 90 (110)
Q Consensus 68 ~~~CpkCg~---~~a~~~~~Q~RsaD 90 (110)
.+.||+||. +.-.||.---|-++
T Consensus 3 ~k~CPkC~A~WldgqhYWsgTgk~g~ 28 (72)
T PHA02325 3 TKICPKCGARWLDGQHYWSGTGKKGN 28 (72)
T ss_pred ccccCccCCEeEcceeeeccCCCcCC
Confidence 468999996 35556654334333
No 325
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=34.97 E-value=8.3 Score=26.59 Aligned_cols=33 Identities=21% Similarity=0.441 Sum_probs=23.9
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
-|+.||++=..-.-. .+.+.++|..||-..++.
T Consensus 107 ~C~~c~s~dt~l~~~-~R~~~l~c~acGa~~pv~ 139 (151)
T COG1601 107 KCKECGSPDTELIKE-ERLLFLKCEACGAIRPVK 139 (151)
T ss_pred EeccCCCCchhhhhh-hhhHhhHHHHhCCcccch
Confidence 388999886654222 567788999999877765
No 326
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=34.85 E-value=16 Score=20.52 Aligned_cols=30 Identities=23% Similarity=0.516 Sum_probs=11.0
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
|--|..-|....++.....+|.|+.|+...
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~F 31 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHF 31 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCcc
Confidence 334444444432233335789999998643
No 327
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=34.47 E-value=5.7 Score=20.58 Aligned_cols=28 Identities=18% Similarity=0.208 Sum_probs=12.2
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
|++|-.-+.-+.++--+-....|..||=
T Consensus 2 C~~C~~Ey~~p~~RR~~~~~isC~~CGP 29 (35)
T PF07503_consen 2 CDDCLKEYFDPSNRRFHYQFISCTNCGP 29 (35)
T ss_dssp -HHHHHHHCSTTSTTTT-TT--BTTCC-
T ss_pred CHHHHHHHcCCCCCcccCcCccCCCCCC
Confidence 5555544433323333345678888883
No 328
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=34.44 E-value=26 Score=14.99 Aligned_cols=11 Identities=18% Similarity=0.842 Sum_probs=5.2
Q ss_pred EEecCCCCCcccc
Q 033869 97 YMCANKNCKHRWN 109 (110)
Q Consensus 97 Y~C~~~~C~~~wr 109 (110)
|.|.. |+..++
T Consensus 1 ~~C~~--C~~~~~ 11 (24)
T PF13894_consen 1 FQCPI--CGKSFR 11 (24)
T ss_dssp EE-SS--TS-EES
T ss_pred CCCcC--CCCcCC
Confidence 56666 666554
No 329
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=34.19 E-value=38 Score=23.09 Aligned_cols=18 Identities=33% Similarity=0.575 Sum_probs=14.5
Q ss_pred CCCCcccCCCCCC-CceEE
Q 033869 64 GPQTEVTCPACKH-GKAVY 81 (110)
Q Consensus 64 ~~~~~~~CpkCg~-~~a~~ 81 (110)
..|+++.|.+|+. -..||
T Consensus 87 M~RtEVrc~~c~sHLGHVF 105 (140)
T COG0229 87 MVRTEVRCANCDSHLGHVF 105 (140)
T ss_pred cEEEEEEecCCCCcccccc
Confidence 5578999999994 47777
No 330
>PF09463 Opy2: Opy2 protein; InterPro: IPR018571 Opy2p acts as a membrane anchor in the HOG signalling pathway []. This entry represents a conserved N-terminal domain.
Probab=34.15 E-value=42 Score=17.39 Aligned_cols=17 Identities=35% Similarity=0.788 Sum_probs=13.4
Q ss_pred cCCCCCCCceEEEEecc
Q 033869 70 TCPACKHGKAVYHELQT 86 (110)
Q Consensus 70 ~CpkCg~~~a~~~~~Q~ 86 (110)
.||.|+.++.-.++.|+
T Consensus 10 ~CP~C~~ge~C~~t~~t 26 (35)
T PF09463_consen 10 SCPSCPSGEECVLTSQT 26 (35)
T ss_pred CCCCCCCCCEEEecCCC
Confidence 79999998877766553
No 331
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=33.55 E-value=36 Score=19.78 Aligned_cols=26 Identities=12% Similarity=0.448 Sum_probs=16.7
Q ss_pred EEEEeccCCCCCCceEEEEecCCCCC
Q 033869 80 VYHELQTRSADEPMSIFYMCANKNCK 105 (110)
Q Consensus 80 ~~~~~Q~RsaDE~~T~fY~C~~~~C~ 105 (110)
+|.-.+.-...+-.|..+.|++-+|.
T Consensus 2 y~~kk~~e~~p~e~t~VW~Ct~e~C~ 27 (59)
T PF14169_consen 2 YFRKKNQEEIPEEETKVWECTSEDCN 27 (59)
T ss_pred CccccCCCCCCceeeeeEEeCCCCCC
Confidence 34344444555557888999887784
No 332
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=33.46 E-value=13 Score=29.20 Aligned_cols=32 Identities=25% Similarity=0.719 Sum_probs=24.5
Q ss_pred CCcCCCCC---cccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTM---LQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nl---L~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
-||.|+|- |.+. + .+.+.+.|..|||...++.
T Consensus 98 lC~~C~NPETel~it--k-~q~i~~~CkACG~r~~~d~ 132 (400)
T KOG2767|consen 98 LCPSCENPETELIIT--K-KQTISLKCKACGFRSDMDL 132 (400)
T ss_pred eCcCCCCCceeEEec--c-cchhhhHHHHcCCcccccc
Confidence 49999985 4443 3 5578899999999887765
No 333
>PRK06260 threonine synthase; Validated
Probab=33.24 E-value=25 Score=27.46 Aligned_cols=23 Identities=26% Similarity=0.712 Sum_probs=17.7
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
.|+.||..+.+. ...+.|+.||-
T Consensus 5 ~C~~cg~~~~~~------~~~~~Cp~cg~ 27 (397)
T PRK06260 5 KCIECGKEYDPD------EIIYTCPECGG 27 (397)
T ss_pred EECCCCCCCCCC------CccccCCCCCC
Confidence 599999887655 34688999984
No 334
>KOG4537 consensus Zn-ribbon-containing protein implicated in mitosis [Cell cycle control, cell division, chromosome partitioning; Defense mechanisms]
Probab=33.22 E-value=11 Score=26.37 Aligned_cols=26 Identities=23% Similarity=0.641 Sum_probs=19.9
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
.||.|+.+|.-. + .+-..|-.|....
T Consensus 42 ~Cp~C~~Ilm~d--r---~~~~~CVsC~~~~ 67 (178)
T KOG4537|consen 42 ICPKCEKILMRD--R---DNPMFCVSCINDL 67 (178)
T ss_pred hcchHHHHHHhh--c---cCceEEEeeeccc
Confidence 699999997765 3 4578888887654
No 335
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=33.11 E-value=26 Score=18.30 Aligned_cols=12 Identities=33% Similarity=0.916 Sum_probs=7.1
Q ss_pred eEEEEecCCCCCcc
Q 033869 94 SIFYMCANKNCKHR 107 (110)
Q Consensus 94 T~fY~C~~~~C~~~ 107 (110)
.-||.|.. ||+.
T Consensus 4 ~~~YkC~~--CGni 15 (36)
T PF06397_consen 4 GEFYKCEH--CGNI 15 (36)
T ss_dssp TEEEE-TT--T--E
T ss_pred ccEEEccC--CCCE
Confidence 46899998 9874
No 336
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=32.88 E-value=15 Score=28.93 Aligned_cols=27 Identities=26% Similarity=0.508 Sum_probs=20.8
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
-+|..|+..|.+.+.. ...+.|+ ||..
T Consensus 241 ~~c~~C~~~~~~~~~~---~~~~~Cp-CG~~ 267 (374)
T TIGR00375 241 TACEACGEPAVSEDAE---TACANCP-CGGR 267 (374)
T ss_pred hhhcccCCcCCchhhh---hcCCCCC-CCCc
Confidence 4799999999987322 3468999 9986
No 337
>PRK04351 hypothetical protein; Provisional
Probab=32.59 E-value=33 Score=23.43 Aligned_cols=13 Identities=15% Similarity=0.485 Sum_probs=8.5
Q ss_pred CceEEcCCCCCee
Q 033869 21 PSRFSCPACPYVC 33 (110)
Q Consensus 21 ~~~~~C~~C~y~~ 33 (110)
.-.|.|..||...
T Consensus 110 ~y~Y~C~~Cg~~~ 122 (149)
T PRK04351 110 NYLYECQSCGQQY 122 (149)
T ss_pred eEEEECCCCCCEe
Confidence 3567787787643
No 338
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=32.49 E-value=64 Score=24.12 Aligned_cols=29 Identities=28% Similarity=0.468 Sum_probs=17.8
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCC
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCK 105 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~ 105 (110)
....||+||..=..-.. --|+ -|.|.+ |.
T Consensus 253 ~g~pC~~Cg~~I~~~~~-~gR~-------t~~CP~--CQ 281 (282)
T PRK13945 253 TGKPCRKCGTPIERIKL-AGRS-------THWCPN--CQ 281 (282)
T ss_pred CcCCCCcCCCeeEEEEE-CCCc-------cEECCC--Cc
Confidence 36799999975433222 2233 377887 85
No 339
>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 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 contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=32.27 E-value=10 Score=21.52 Aligned_cols=24 Identities=25% Similarity=0.503 Sum_probs=12.5
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCC--CCCeee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPA--CPYVCN 34 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~--C~y~~~ 34 (110)
-|-.|+.-|.|+ ...||. ||+...
T Consensus 19 ICrkCyarl~~~--------A~nCRKkkCGhsn~ 44 (52)
T PF01020_consen 19 ICRKCYARLPPR--------ATNCRKKKCGHSNN 44 (52)
T ss_dssp EETTT--EE-TT--------SSS-TSSSCTS-S-
T ss_pred ecccccCcCCCC--------ccceecccCCCCcc
Confidence 467788888877 445887 887644
No 340
>PRK08329 threonine synthase; Validated
Probab=32.26 E-value=36 Score=26.06 Aligned_cols=24 Identities=25% Similarity=0.629 Sum_probs=17.4
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
|..|+.||....+. . .+.| .|+-.
T Consensus 1 ~l~C~~Cg~~~~~~------~-~~~C-~c~~~ 24 (347)
T PRK08329 1 MLRCTKCGRTYEEK------F-KLRC-DCGGT 24 (347)
T ss_pred CcCcCCCCCCcCCC------C-ceec-CCCCc
Confidence 78899999887532 2 3889 69743
No 341
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.07 E-value=23 Score=26.41 Aligned_cols=15 Identities=27% Similarity=0.658 Sum_probs=12.5
Q ss_pred eEEcCCCCCeeeeCC
Q 033869 23 RFSCPACPYVCNMES 37 (110)
Q Consensus 23 ~~~C~~C~y~~~~~~ 37 (110)
.+.|+.|+.+.....
T Consensus 19 ~ieCPvC~tkFkkee 33 (267)
T COG1655 19 TIECPVCNTKFKKEE 33 (267)
T ss_pred eeccCcccchhhhhh
Confidence 789999999877665
No 342
>PRK10445 endonuclease VIII; Provisional
Probab=31.88 E-value=77 Score=23.45 Aligned_cols=29 Identities=28% Similarity=0.667 Sum_probs=17.4
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCC
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCK 105 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~ 105 (110)
....||+||..=. ...+--|+ -|.|.+ |.
T Consensus 234 ~g~~Cp~Cg~~I~-~~~~~gR~-------t~~CP~--CQ 262 (263)
T PRK10445 234 DGEACERCGGIIE-KTTLSSRP-------FYWCPG--CQ 262 (263)
T ss_pred CCCCCCCCCCEeE-EEEECCCC-------cEECCC--Cc
Confidence 4679999996532 22222233 277887 85
No 343
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=31.67 E-value=35 Score=17.77 Aligned_cols=7 Identities=43% Similarity=1.089 Sum_probs=5.8
Q ss_pred CCceEEE
Q 033869 91 EPMSIFY 97 (110)
Q Consensus 91 E~~T~fY 97 (110)
..+|+||
T Consensus 6 ~qLTIfY 12 (36)
T PF06200_consen 6 AQLTIFY 12 (36)
T ss_pred CcEEEEE
Confidence 4699999
No 344
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=31.42 E-value=25 Score=16.51 Aligned_cols=8 Identities=50% Similarity=1.364 Sum_probs=6.0
Q ss_pred ccCCCCCC
Q 033869 69 VTCPACKH 76 (110)
Q Consensus 69 ~~CpkCg~ 76 (110)
+.||.||.
T Consensus 3 ~~C~~CgR 10 (25)
T PF13913_consen 3 VPCPICGR 10 (25)
T ss_pred CcCCCCCC
Confidence 46888885
No 345
>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=30.97 E-value=27 Score=23.46 Aligned_cols=26 Identities=19% Similarity=0.543 Sum_probs=17.9
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
++|+.|+....++ ...|+.|+.-...
T Consensus 49 ~~C~~C~~~kp~R--------s~HC~~C~~CV~~ 74 (174)
T PF01529_consen 49 KYCSTCKIIKPPR--------SHHCRVCNRCVLR 74 (174)
T ss_pred EECcccCCcCCCc--------ceecccccccccc
Confidence 4788888776666 6678888765443
No 346
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=30.83 E-value=78 Score=26.19 Aligned_cols=33 Identities=21% Similarity=0.383 Sum_probs=22.2
Q ss_pred CcccCCCCCC-CceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 67 TEVTCPACKH-GKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 67 ~~~~CpkCg~-~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
..-.||+||. ....-. +-|..-|+-|.|. |||.
T Consensus 170 ~~piC~kcGri~~t~v~-----~~d~~~~v~Y~Ce---~Gh~ 203 (521)
T COG1384 170 FMPICEKCGRILTTPVI-----EWDGEGTVEYRCE---CGHE 203 (521)
T ss_pred ccccccccCCcceeEEE-----EecCCceEEEEec---CCcc
Confidence 4568999998 433222 2233479999998 8873
No 347
>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=30.77 E-value=59 Score=17.29 Aligned_cols=21 Identities=24% Similarity=0.558 Sum_probs=14.9
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
.|..|+..+.. .+|.|..|..
T Consensus 2 ~C~~C~~~i~g--------~r~~C~~C~d 22 (46)
T cd02249 2 SCDGCLKPIVG--------VRYHCLVCED 22 (46)
T ss_pred CCcCCCCCCcC--------CEEECCCCCC
Confidence 57888883322 4999999983
No 348
>PRK08173 DNA topoisomerase III; Validated
Probab=30.77 E-value=36 Score=29.71 Aligned_cols=25 Identities=36% Similarity=1.014 Sum_probs=17.8
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
-||.||.-|. . ....|.|.+|++..
T Consensus 626 ~CP~Cg~~~~-~-----~~~~~~Cs~C~f~~ 650 (862)
T PRK08173 626 PCPNCGGVVK-E-----NYRRFACTKCDFSI 650 (862)
T ss_pred cCCccccccc-c-----cCceeEcCCCCccc
Confidence 4999998652 1 12369999999764
No 349
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=30.68 E-value=21 Score=25.24 Aligned_cols=12 Identities=42% Similarity=0.897 Sum_probs=10.0
Q ss_pred CCcCCCCCcccc
Q 033869 3 FCPTCGTMLQYE 14 (110)
Q Consensus 3 FCp~C~nlL~~~ 14 (110)
=||.||++|...
T Consensus 134 ~Cp~Cg~~L~~~ 145 (176)
T COG1675 134 TCPKCGEDLEEY 145 (176)
T ss_pred CCCCCCchhhhc
Confidence 399999998876
No 350
>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=30.60 E-value=54 Score=18.68 Aligned_cols=26 Identities=27% Similarity=0.562 Sum_probs=12.4
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCN 34 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~ 34 (110)
.|..|+.-..+- .-...|+.||...=
T Consensus 11 ~C~~C~~~F~~~------~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 11 NCMICGKKFSLF------RRRHHCRNCGRVVC 36 (69)
T ss_dssp B-TTT--B-BSS------S-EEE-TTT--EEE
T ss_pred cCcCcCCcCCCc------eeeEccCCCCCEEC
Confidence 578888776554 23789999997643
No 351
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=30.46 E-value=42 Score=26.97 Aligned_cols=10 Identities=40% Similarity=1.132 Sum_probs=5.0
Q ss_pred cCCCCCCCce
Q 033869 70 TCPACKHGKA 79 (110)
Q Consensus 70 ~CpkCg~~~a 79 (110)
.||+|||.-.
T Consensus 70 ~CpHCG~kN~ 79 (460)
T KOG2703|consen 70 ECPHCGHKNN 79 (460)
T ss_pred ecCccCCccc
Confidence 4555555443
No 352
>KOG3092 consensus Casein kinase II, beta subunit [Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Transcription]
Probab=30.22 E-value=22 Score=25.80 Aligned_cols=12 Identities=25% Similarity=0.949 Sum_probs=5.6
Q ss_pred CCcCCCCCcccc
Q 033869 3 FCPTCGTMLQYE 14 (110)
Q Consensus 3 FCp~C~nlL~~~ 14 (110)
+||.|.++..|+
T Consensus 136 YCP~C~dvY~P~ 147 (216)
T KOG3092|consen 136 YCPSCEDVYIPK 147 (216)
T ss_pred eCCCcccccccc
Confidence 444444444444
No 353
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=30.16 E-value=26 Score=31.12 Aligned_cols=22 Identities=27% Similarity=0.711 Sum_probs=17.3
Q ss_pred cccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869 68 EVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR 107 (110)
Q Consensus 68 ~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~ 107 (110)
..+||+||+ .|.+..|.+ ||-.
T Consensus 625 ~RKCPkCG~----------------yTlk~rCP~--CG~~ 646 (1095)
T TIGR00354 625 IRKCPQCGK----------------ESFWLKCPV--CGEL 646 (1095)
T ss_pred EEECCCCCc----------------ccccccCCC--CCCc
Confidence 458999987 677888988 8754
No 354
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.76 E-value=82 Score=23.41 Aligned_cols=28 Identities=18% Similarity=0.477 Sum_probs=17.1
Q ss_pred CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCC
Q 033869 67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNC 104 (110)
Q Consensus 67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C 104 (110)
....||+||..=.. ..+--|++ |-|.+ |
T Consensus 244 ~g~pC~~Cg~~I~~-~~~~gR~t-------~~CP~--C 271 (272)
T TIGR00577 244 KGEPCRRCGTPIEK-IKVGGRGT-------HFCPQ--C 271 (272)
T ss_pred CCCCCCCCCCeeEE-EEECCCCC-------EECCC--C
Confidence 35799999976433 33333433 66877 7
No 355
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=29.40 E-value=8.4 Score=19.79 Aligned_cols=31 Identities=19% Similarity=0.487 Sum_probs=15.0
Q ss_pred CCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 71 CPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 71 CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
|-.|+-.+. .+-|++..|..+ .|-. |+-.|+
T Consensus 1 C~~C~tt~t----~~WR~~~~g~~~--LCn~--Cg~~~k 31 (36)
T PF00320_consen 1 CSNCGTTET----PQWRRGPNGNRT--LCNA--CGLYYK 31 (36)
T ss_dssp -TTT--ST-----SSEEEETTSEE---EEHH--HHHHHH
T ss_pred CcCCcCCCC----chhhcCCCCCCH--HHHH--HHHHHH
Confidence 556766553 333555544443 7777 776664
No 356
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.30 E-value=23 Score=23.69 Aligned_cols=12 Identities=33% Similarity=0.952 Sum_probs=10.0
Q ss_pred cccCCCCCCCce
Q 033869 68 EVTCPACKHGKA 79 (110)
Q Consensus 68 ~~~CpkCg~~~a 79 (110)
.-.||+||..+.
T Consensus 21 ~grCP~CGeGrL 32 (126)
T COG5349 21 RGRCPRCGEGRL 32 (126)
T ss_pred cCCCCCCCCchh
Confidence 569999998765
No 357
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=28.59 E-value=30 Score=29.13 Aligned_cols=22 Identities=23% Similarity=0.658 Sum_probs=16.3
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
..|++||.+. . +..+.|+.||.
T Consensus 567 ~iC~~CG~~~--~------g~~~~CP~CGs 588 (623)
T PRK08271 567 TICNDCHHID--K------RTGKRCPICGS 588 (623)
T ss_pred ccCCCCCCcC--C------CCCcCCcCCCC
Confidence 3699999762 1 24689999996
No 358
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=28.45 E-value=29 Score=20.53 Aligned_cols=21 Identities=19% Similarity=0.461 Sum_probs=14.4
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
-|.+|+.+.... .|+.||...
T Consensus 7 AC~~C~~i~~~~----------~Cp~Cgs~~ 27 (64)
T PRK06393 7 ACKKCKRLTPEK----------TCPVHGDEK 27 (64)
T ss_pred hHhhCCcccCCC----------cCCCCCCCc
Confidence 477888777211 789998763
No 359
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=28.38 E-value=23 Score=28.75 Aligned_cols=33 Identities=18% Similarity=0.196 Sum_probs=23.2
Q ss_pred CCCCcCCCCCccc-----c---cCCCCCCceEEcCCCCCee
Q 033869 1 MEFCPTCGTMLQY-----E---LPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 1 M~FCp~C~nlL~~-----~---~~~~~~~~~~~C~~C~y~~ 33 (110)
|.||..|+++..- . +-.++....|.|..|.+.-
T Consensus 185 mlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~ 225 (464)
T KOG4323|consen 185 MLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGP 225 (464)
T ss_pred eeeecccccHHHHHhccCCCCHhhccCccceEeehhhccch
Confidence 7899999998431 1 1113567789999999853
No 360
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=27.99 E-value=46 Score=18.70 Aligned_cols=29 Identities=21% Similarity=0.453 Sum_probs=16.4
Q ss_pred CCcCCCCCcccccCCCCC--CceEEcCCCCC
Q 033869 3 FCPTCGTMLQYELPHMDR--PSRFSCPACPY 31 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~--~~~~~C~~C~y 31 (110)
-||.||-.+....|...+ .-.--|..|-.
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~ 32 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCR 32 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCC
Confidence 478888766665555433 22334666654
No 361
>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=27.89 E-value=26 Score=23.03 Aligned_cols=12 Identities=33% Similarity=0.941 Sum_probs=9.7
Q ss_pred CcccCCCCCCCc
Q 033869 67 TEVTCPACKHGK 78 (110)
Q Consensus 67 ~~~~CpkCg~~~ 78 (110)
+..+||.||+..
T Consensus 68 v~V~CP~C~K~T 79 (114)
T PF11023_consen 68 VQVECPNCGKQT 79 (114)
T ss_pred eeeECCCCCChH
Confidence 478999999854
No 362
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=27.89 E-value=75 Score=15.35 Aligned_cols=23 Identities=17% Similarity=0.551 Sum_probs=14.5
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
|.-|+..+... . .|.|..|++.-
T Consensus 3 C~~C~~~~~~~------~-~Y~C~~c~f~l 25 (30)
T PF03107_consen 3 CDVCRRKIDGF------Y-FYHCSECCFTL 25 (30)
T ss_pred CCCCCCCcCCC------E-eEEeCCCCCeE
Confidence 55565554443 2 89999888653
No 363
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=27.75 E-value=40 Score=19.21 Aligned_cols=16 Identities=25% Similarity=0.513 Sum_probs=11.4
Q ss_pred CceEEcCCCCCeeeeC
Q 033869 21 PSRFSCPACPYVCNME 36 (110)
Q Consensus 21 ~~~~~C~~C~y~~~~~ 36 (110)
...|.|-.||+.-=..
T Consensus 9 ~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 9 SNLWLCLTCGYVGCGR 24 (63)
T ss_dssp SSEEEETTTS-EEETT
T ss_pred CceEEeCCCCcccccC
Confidence 3489999999976543
No 364
>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 PRK06599 DNA topoisomerase I; Validated
Probab=27.54 E-value=60 Score=27.42 Aligned_cols=7 Identities=43% Similarity=1.175 Sum_probs=3.9
Q ss_pred EcCCCCC
Q 033869 25 SCPACPY 31 (110)
Q Consensus 25 ~C~~C~y 31 (110)
.|+.|+.
T Consensus 639 ~Cp~C~~ 645 (675)
T PRK06599 639 KCPKCGG 645 (675)
T ss_pred CCCCCCC
Confidence 4666654
No 366
>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=27.50 E-value=33 Score=20.28 Aligned_cols=14 Identities=21% Similarity=0.506 Sum_probs=6.0
Q ss_pred eEEcCCCCCeeeeC
Q 033869 23 RFSCPACPYVCNME 36 (110)
Q Consensus 23 ~~~C~~C~y~~~~~ 36 (110)
.+.|..|+.+..++
T Consensus 41 ~v~Cg~C~~~~~~~ 54 (71)
T PF05495_consen 41 RVICGKCRTEQPID 54 (71)
T ss_dssp EEEETTT--EEES-
T ss_pred CeECCCCCCccChh
Confidence 55555555555443
No 367
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.42 E-value=36 Score=20.17 Aligned_cols=14 Identities=29% Similarity=0.757 Sum_probs=10.7
Q ss_pred CCcccCCCCCCCce
Q 033869 66 QTEVTCPACKHGKA 79 (110)
Q Consensus 66 ~~~~~CpkCg~~~a 79 (110)
++.+.||-||..-.
T Consensus 5 ~~~v~CP~Cgkpv~ 18 (65)
T COG3024 5 RITVPCPTCGKPVV 18 (65)
T ss_pred cccccCCCCCCccc
Confidence 35789999998644
No 368
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=27.39 E-value=89 Score=19.63 Aligned_cols=8 Identities=25% Similarity=1.032 Sum_probs=5.3
Q ss_pred ccCCCCCC
Q 033869 69 VTCPACKH 76 (110)
Q Consensus 69 ~~CpkCg~ 76 (110)
..|+.||-
T Consensus 36 ~~C~~CGe 43 (89)
T TIGR03829 36 ISCSHCGM 43 (89)
T ss_pred ccccCCCc
Confidence 36777764
No 369
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=27.24 E-value=34 Score=22.14 Aligned_cols=30 Identities=20% Similarity=0.422 Sum_probs=13.9
Q ss_pred CcCCCCC--cccccCCCCCCceEEcCCCCCee
Q 033869 4 CPTCGTM--LQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 4 Cp~C~nl--L~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
||.|+-. +.-..|+........|+-|+-.+
T Consensus 26 ClfcnHek~v~~~~Dk~~~iG~~sC~iC~esF 57 (109)
T KOG3214|consen 26 CLFCNHEKSVSCTLDKKHNIGKASCRICEESF 57 (109)
T ss_pred cCccccccceeeeehhhcCcceeeeeehhhhh
Confidence 5555532 22223333445556666666443
No 371
>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=26.90 E-value=35 Score=19.68 Aligned_cols=10 Identities=30% Similarity=0.820 Sum_probs=7.9
Q ss_pred cccCCCCCCC
Q 033869 68 EVTCPACKHG 77 (110)
Q Consensus 68 ~~~CpkCg~~ 77 (110)
...||+||.+
T Consensus 41 ~~~CPNCgGe 50 (57)
T PF06906_consen 41 NGVCPNCGGE 50 (57)
T ss_pred cCcCcCCCCc
Confidence 4579999975
No 372
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=26.63 E-value=60 Score=23.71 Aligned_cols=28 Identities=25% Similarity=0.532 Sum_probs=20.6
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME 36 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~ 36 (110)
.=||.|+.-|... ...+.|.+ ++..+..
T Consensus 3 ~~CP~C~~~l~~~------~~~~~C~~-~h~fd~a 30 (272)
T PRK11088 3 YQCPLCHQPLTLE------ENSWICPQ-NHQFDCA 30 (272)
T ss_pred ccCCCCCcchhcC------CCEEEcCC-CCCCccc
Confidence 4699999999654 23699999 6666544
No 373
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=26.54 E-value=67 Score=26.50 Aligned_cols=18 Identities=33% Similarity=0.320 Sum_probs=15.1
Q ss_pred CCCCcccCCCCC-CCceEE
Q 033869 64 GPQTEVTCPACK-HGKAVY 81 (110)
Q Consensus 64 ~~~~~~~CpkCg-~~~a~~ 81 (110)
..|+++.|.+|| |-..+|
T Consensus 463 ~~R~Ev~c~~c~~HLGHvf 481 (521)
T PRK14018 463 MRRTEVRSRAADSHLGHVF 481 (521)
T ss_pred ceEEEEEECCCCCcCCccc
Confidence 567899999999 557777
No 374
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=26.39 E-value=34 Score=21.38 Aligned_cols=29 Identities=21% Similarity=0.449 Sum_probs=20.6
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
+|+.||..-.-+ ....+|.|..|..+..-
T Consensus 38 ~CsfCGK~~vKR----~AvGiW~C~~C~kv~ag 66 (92)
T KOG0402|consen 38 TCSFCGKKTVKR----KAVGIWKCGSCKKVVAG 66 (92)
T ss_pred hhhhcchhhhhh----hceeEEecCCccceecc
Confidence 688888766555 22568999999876543
No 375
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=26.32 E-value=20 Score=26.61 Aligned_cols=8 Identities=38% Similarity=0.903 Sum_probs=3.2
Q ss_pred eEEcCCCC
Q 033869 23 RFSCPACP 30 (110)
Q Consensus 23 ~~~C~~C~ 30 (110)
...|+.||
T Consensus 221 iv~CP~Cg 228 (239)
T COG1579 221 IVFCPYCG 228 (239)
T ss_pred CccCCccc
Confidence 33344443
No 376
>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=26.18 E-value=20 Score=24.25 Aligned_cols=26 Identities=31% Similarity=0.750 Sum_probs=18.5
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
+.-||.||.+.... ..-.|+.|....
T Consensus 3 l~nC~~CgklF~~~-------~~~iCp~C~~~~ 28 (137)
T TIGR03826 3 LANCPKCGRLFVKT-------GRDVCPSCYEEE 28 (137)
T ss_pred Cccccccchhhhhc-------CCccCHHHhHHH
Confidence 45799999976553 234699999753
No 377
>KOG0696 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=26.04 E-value=13 Score=30.49 Aligned_cols=25 Identities=28% Similarity=0.798 Sum_probs=18.6
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
-||..||+|||--.- .-+.|.+|.-
T Consensus 122 TFCDhCGsLLyGl~H-----QGmKC~~C~m 146 (683)
T KOG0696|consen 122 TFCDHCGSLLYGLIH-----QGMKCDTCDM 146 (683)
T ss_pred chhhhHHHHHHHHHh-----cccccccccc
Confidence 499999999997511 2467888875
No 378
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=25.97 E-value=34 Score=17.90 Aligned_cols=10 Identities=40% Similarity=1.022 Sum_probs=6.6
Q ss_pred cCCCCCCCce
Q 033869 70 TCPACKHGKA 79 (110)
Q Consensus 70 ~CpkCg~~~a 79 (110)
.||+||....
T Consensus 4 ~CprC~kg~H 13 (36)
T PF14787_consen 4 LCPRCGKGFH 13 (36)
T ss_dssp C-TTTSSSCS
T ss_pred cCcccCCCcc
Confidence 6999997543
No 379
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=25.85 E-value=38 Score=23.03 Aligned_cols=16 Identities=31% Similarity=0.658 Sum_probs=13.7
Q ss_pred CceEEcCCCCCeeeeC
Q 033869 21 PSRFSCPACPYVCNME 36 (110)
Q Consensus 21 ~~~~~C~~C~y~~~~~ 36 (110)
=|+|.|..|+++...+
T Consensus 11 WLIYrC~~C~~TwN~t 26 (142)
T PF06353_consen 11 WLIYRCEKCDYTWNMT 26 (142)
T ss_pred EEEEEcccCcCccccc
Confidence 3789999999998875
No 380
>PF15499 Peptidase_C98: Ubiquitin-specific peptidase-like, SUMO isopeptidase
Probab=25.84 E-value=59 Score=24.58 Aligned_cols=12 Identities=25% Similarity=0.708 Sum_probs=10.0
Q ss_pred eEEcCCCCCeee
Q 033869 23 RFSCPACPYVCN 34 (110)
Q Consensus 23 ~~~C~~C~y~~~ 34 (110)
.|.|..|||...
T Consensus 134 eFeC~~Cg~~~~ 145 (275)
T PF15499_consen 134 EFECSQCGHKYQ 145 (275)
T ss_pred EEEccccCChhh
Confidence 589999999754
No 381
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=25.48 E-value=35 Score=19.82 Aligned_cols=12 Identities=25% Similarity=0.761 Sum_probs=8.9
Q ss_pred cccCCCCCCCce
Q 033869 68 EVTCPACKHGKA 79 (110)
Q Consensus 68 ~~~CpkCg~~~a 79 (110)
.++||.||....
T Consensus 17 ke~Cp~CG~~t~ 28 (59)
T COG2260 17 KEKCPVCGGDTK 28 (59)
T ss_pred cccCCCCCCccc
Confidence 468999997543
No 382
>PHA02611 51 baseplate hub assembly protein; Provisional
Probab=25.15 E-value=54 Score=24.51 Aligned_cols=17 Identities=47% Similarity=0.935 Sum_probs=13.2
Q ss_pred cccCCCCCCCceEEEEe
Q 033869 68 EVTCPACKHGKAVYHEL 84 (110)
Q Consensus 68 ~~~CpkCg~~~a~~~~~ 84 (110)
.+.||+||+..-+++.+
T Consensus 82 ~~tCp~Cg~e~~v~~~l 98 (249)
T PHA02611 82 TFTCPKCKKEKTVLFNL 98 (249)
T ss_pred EEECCCCCCceeEEEEe
Confidence 46999999996666555
No 383
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=25.01 E-value=50 Score=28.11 Aligned_cols=27 Identities=33% Similarity=0.746 Sum_probs=20.4
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCC---CCCe
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPA---CPYV 32 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~---C~y~ 32 (110)
.+||.||+-|...++ ...+.|.+ |+-.
T Consensus 405 ~~CP~C~s~l~r~~~----e~~~rC~n~~~C~aq 434 (667)
T COG0272 405 THCPVCGSELVREEG----EVVIRCTNGLNCPAQ 434 (667)
T ss_pred CCCCCCCCeeEeccC----ceeEecCCCCCChHH
Confidence 489999999988522 34889987 8753
No 384
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=24.85 E-value=29 Score=26.45 Aligned_cols=26 Identities=23% Similarity=0.557 Sum_probs=19.5
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM 35 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~ 35 (110)
.||.+|...-+++ .-.|+.|+.-...
T Consensus 110 ~~C~~C~~~KP~R--------S~HC~~Cn~CV~k 135 (309)
T COG5273 110 NFCSTCNIYKPPR--------SHHCSICNRCVLK 135 (309)
T ss_pred eeccccccccCCC--------Cccchhhcchhhc
Confidence 5899998887777 5678888875443
No 385
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=24.41 E-value=71 Score=16.63 Aligned_cols=11 Identities=27% Similarity=0.770 Sum_probs=8.5
Q ss_pred eEEcCCCCCee
Q 033869 23 RFSCPACPYVC 33 (110)
Q Consensus 23 ~~~C~~C~y~~ 33 (110)
-+.|+.|+...
T Consensus 12 ~f~C~~C~~~F 22 (39)
T smart00154 12 GFKCRHCGNLF 22 (39)
T ss_pred CeECCccCCcc
Confidence 58899998653
No 386
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=24.21 E-value=91 Score=24.50 Aligned_cols=17 Identities=24% Similarity=0.567 Sum_probs=11.7
Q ss_pred cccCCCCCCCceEEEEe
Q 033869 68 EVTCPACKHGKAVYHEL 84 (110)
Q Consensus 68 ~~~CpkCg~~~a~~~~~ 84 (110)
...||+|||....=-.+
T Consensus 257 k~FCp~CG~~TL~K~aV 273 (376)
T KOG2463|consen 257 KDFCPSCGHKTLTKCAV 273 (376)
T ss_pred hhcccccCCCeeeEEEE
Confidence 56899999985443333
No 387
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=24.18 E-value=20 Score=28.09 Aligned_cols=26 Identities=31% Similarity=0.686 Sum_probs=19.5
Q ss_pred CcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 4 CPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
|..|.....++ +...+.+.|++||-.
T Consensus 249 C~rC~t~y~le---~A~~~~wrCpkCGg~ 274 (403)
T COG1379 249 CSRCYTRYSLE---EAKSLRWRCPKCGGK 274 (403)
T ss_pred HHHhhhccCcc---hhhhhcccCcccccc
Confidence 77888777776 233678999999973
No 388
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=24.07 E-value=23 Score=20.79 Aligned_cols=35 Identities=14% Similarity=0.325 Sum_probs=21.8
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
-||.|+..=.+.-=.+++.....|-.|||.....+
T Consensus 12 ~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~~~~ 46 (66)
T COG3529 12 VCPACQAQDTLAMWRENNVEIVECVKCGHHMREAD 46 (66)
T ss_pred CCcccchhhHHHHHHhcCCceEehhhcchHhhhcc
Confidence 38888865322111334566899999999765443
No 389
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=23.54 E-value=51 Score=15.32 Aligned_cols=11 Identities=27% Similarity=0.972 Sum_probs=7.0
Q ss_pred EEecCCCCCcccc
Q 033869 97 YMCANKNCKHRWN 109 (110)
Q Consensus 97 Y~C~~~~C~~~wr 109 (110)
|.|.. |+.++.
T Consensus 15 ~~C~~--C~k~F~ 25 (26)
T PF13465_consen 15 YKCPY--CGKSFS 25 (26)
T ss_dssp EEESS--SSEEES
T ss_pred CCCCC--CcCeeC
Confidence 67766 766653
No 390
>PHA02540 61 DNA primase; Provisional
Probab=23.43 E-value=1.1e+02 Score=23.85 Aligned_cols=33 Identities=24% Similarity=0.525 Sum_probs=25.0
Q ss_pred CcccCCCCCC-----CceEEEEeccCCCCCCceEEEEecCCCCCc
Q 033869 67 TEVTCPACKH-----GKAVYHELQTRSADEPMSIFYMCANKNCKH 106 (110)
Q Consensus 67 ~~~~CpkCg~-----~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~ 106 (110)
-...||-||. +++.||-.+.+. -.||.|=+ ||.
T Consensus 26 ~~~~CPf~~ds~~~~~kpsF~V~p~k~-----~~~yhCFg--CGa 63 (337)
T PHA02540 26 YNFRCPICGDSQKDKNKARGWIYEKKD-----GGVFKCHN--CGY 63 (337)
T ss_pred EEecCCCCCCccccCcCCcEEEeccCC-----ceEEEecC--CCC
Confidence 4679999997 357888765432 67999988 985
No 391
>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=23.07 E-value=60 Score=17.63 Aligned_cols=25 Identities=24% Similarity=0.639 Sum_probs=17.4
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
..|+.|+.-+..- .-...|+.||..
T Consensus 3 ~~C~~C~~~F~~~------~rk~~Cr~Cg~~ 27 (57)
T cd00065 3 SSCMGCGKPFTLT------RRRHHCRNCGRI 27 (57)
T ss_pred CcCcccCccccCC------ccccccCcCcCC
Confidence 4688888766654 125788888875
No 392
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=22.76 E-value=1.1e+02 Score=16.69 Aligned_cols=40 Identities=18% Similarity=0.386 Sum_probs=22.9
Q ss_pred CCCcccCCCCCCCc-eEEEEeccCCCCCCceEEEEecCCCCCc
Q 033869 65 PQTEVTCPACKHGK-AVYHELQTRSADEPMSIFYMCANKNCKH 106 (110)
Q Consensus 65 ~~~~~~CpkCg~~~-a~~~~~Q~RsaDE~~T~fY~C~~~~C~~ 106 (110)
.|.+-+|+=||.++ ...|.+.--+.+..-.-.+.|.. |..
T Consensus 4 ~Rs~~kCELC~a~~~L~vy~Vpp~~~~~~d~~iliC~t--C~~ 44 (47)
T smart00782 4 ARCESKCELCGSDSPLVVYAVPPSSDVTADNSVMLCDT--CHS 44 (47)
T ss_pred HHcCCcccCcCCCCCceEEecCCCCCCCccceeeechH--HHH
Confidence 35677899999754 35556632222222223588877 753
No 393
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=22.65 E-value=58 Score=26.86 Aligned_cols=14 Identities=21% Similarity=0.565 Sum_probs=8.8
Q ss_pred ccCCCCCCCceEEE
Q 033869 69 VTCPACKHGKAVYH 82 (110)
Q Consensus 69 ~~CpkCg~~~a~~~ 82 (110)
..||+||++....+
T Consensus 533 ~~CP~CGs~~~~~~ 546 (555)
T cd01675 533 FKCPKCGSEDVEVI 546 (555)
T ss_pred CCCcCCCCcCceEE
Confidence 47888876654443
No 394
>smart00746 TRASH metallochaperone-like domain.
Probab=22.62 E-value=66 Score=14.55 Aligned_cols=9 Identities=33% Similarity=0.962 Sum_probs=5.4
Q ss_pred CcCCCCCcc
Q 033869 4 CPTCGTMLQ 12 (110)
Q Consensus 4 Cp~C~nlL~ 12 (110)
|+.||..+.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 556666655
No 395
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=22.56 E-value=38 Score=26.43 Aligned_cols=13 Identities=46% Similarity=1.145 Sum_probs=11.9
Q ss_pred CCCcCCCCCcccc
Q 033869 2 EFCPTCGTMLQYE 14 (110)
Q Consensus 2 ~FCp~C~nlL~~~ 14 (110)
.|||-||+-|.++
T Consensus 26 ffCPaC~~~l~lK 38 (342)
T COG4469 26 FFCPACGSQLILK 38 (342)
T ss_pred cccCCCCCeeeee
Confidence 3999999999998
No 396
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=22.48 E-value=83 Score=15.97 Aligned_cols=14 Identities=21% Similarity=0.548 Sum_probs=9.3
Q ss_pred ceEEcCCCCCeeee
Q 033869 22 SRFSCPACPYVCNM 35 (110)
Q Consensus 22 ~~~~C~~C~y~~~~ 35 (110)
..+.|++|+....+
T Consensus 3 ~~~~C~nC~R~v~a 16 (33)
T PF08209_consen 3 PYVECPNCGRPVAA 16 (33)
T ss_dssp -EEE-TTTSSEEEG
T ss_pred CeEECCCCcCCcch
Confidence 47899999986544
No 397
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=22.27 E-value=44 Score=17.63 Aligned_cols=8 Identities=50% Similarity=1.356 Sum_probs=6.5
Q ss_pred cccCCCCC
Q 033869 68 EVTCPACK 75 (110)
Q Consensus 68 ~~~CpkCg 75 (110)
...|+.||
T Consensus 13 ~~~C~~Cg 20 (41)
T PF13878_consen 13 ATTCPTCG 20 (41)
T ss_pred CcCCCCCC
Confidence 46899996
No 398
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=22.22 E-value=86 Score=16.52 Aligned_cols=9 Identities=33% Similarity=1.195 Sum_probs=7.5
Q ss_pred ceEEcCCCC
Q 033869 22 SRFSCPACP 30 (110)
Q Consensus 22 ~~~~C~~C~ 30 (110)
.+|.|..|+
T Consensus 12 ~r~~C~~C~ 20 (41)
T cd02337 12 TRWHCTVCE 20 (41)
T ss_pred CceECCCCc
Confidence 489999997
No 399
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=22.21 E-value=36 Score=21.61 Aligned_cols=12 Identities=17% Similarity=0.489 Sum_probs=9.4
Q ss_pred EEcCCCCCeeee
Q 033869 24 FSCPACPYVCNM 35 (110)
Q Consensus 24 ~~C~~C~y~~~~ 35 (110)
-.|+.|||+...
T Consensus 59 a~CkkCGfef~~ 70 (97)
T COG3357 59 ARCKKCGFEFRD 70 (97)
T ss_pred hhhcccCccccc
Confidence 369999997654
No 400
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.03 E-value=47 Score=28.50 Aligned_cols=21 Identities=33% Similarity=0.887 Sum_probs=14.6
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
..|++||.+ . ...+.|+.||.
T Consensus 681 ~~C~~CG~~---~------~~~~~CP~CG~ 701 (735)
T PRK07111 681 DRCPVCGYL---G------VIEDKCPKCGS 701 (735)
T ss_pred eecCCCCCC---C------CcCccCcCCCC
Confidence 369999932 2 12489999996
No 401
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=21.75 E-value=2.8e+02 Score=23.76 Aligned_cols=31 Identities=23% Similarity=0.507 Sum_probs=21.5
Q ss_pred CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
|.-||.|+.-=+.. ...-.|+.|+..-..++
T Consensus 2 ~~~C~~C~g~G~i~------v~~e~c~vc~gtG~~~~ 32 (715)
T COG1107 2 IKKCPECGGKGKIV------VGEEECPVCHGTGFSDD 32 (715)
T ss_pred CccccccCCCceEe------eeeeecccccccccccc
Confidence 45799999844443 33567999998766644
No 402
>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=21.59 E-value=47 Score=23.62 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=8.1
Q ss_pred cccCCCCCCCc
Q 033869 68 EVTCPACKHGK 78 (110)
Q Consensus 68 ~~~CpkCg~~~ 78 (110)
...|||||...
T Consensus 175 g~~CPKCGr~G 185 (200)
T PF12387_consen 175 GGNCPKCGRHG 185 (200)
T ss_pred CCCCCcccCCC
Confidence 34699999654
No 403
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=21.58 E-value=55 Score=30.03 Aligned_cols=22 Identities=36% Similarity=0.896 Sum_probs=12.6
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
|||+||.-+.+ .+.|+.||...
T Consensus 681 fCP~CGs~te~---------vy~CPsCGaev 702 (1337)
T PRK14714 681 RCPDCGTHTEP---------VYVCPDCGAEV 702 (1337)
T ss_pred cCcccCCcCCC---------ceeCccCCCcc
Confidence 67777766533 34566666543
No 404
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=21.51 E-value=54 Score=19.16 Aligned_cols=17 Identities=24% Similarity=0.454 Sum_probs=12.8
Q ss_pred CCCcccCCCCCCCceEE
Q 033869 65 PQTEVTCPACKHGKAVY 81 (110)
Q Consensus 65 ~~~~~~CpkCg~~~a~~ 81 (110)
..+...||+||+.-++|
T Consensus 55 kd~~H~Cp~C~~~lg~~ 71 (73)
T PF10601_consen 55 KDVYHYCPNCGAFLGTY 71 (73)
T ss_pred cCceEECCCCCCEeEEE
Confidence 34678999999876655
No 405
>PLN00162 transport protein sec23; Provisional
Probab=21.50 E-value=54 Score=28.19 Aligned_cols=35 Identities=20% Similarity=0.312 Sum_probs=25.8
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
-|..|+..|.|-..=+.+...|.|+-|+...+...
T Consensus 55 RC~~CraylNPf~~~d~~~~~W~C~~C~~~N~~P~ 89 (761)
T PLN00162 55 RCRTCRAVLNPYCRVDFQAKIWICPFCFQRNHFPP 89 (761)
T ss_pred ccCCCcCEECCceEEecCCCEEEccCCCCCCCCch
Confidence 58999999988633334456999999998766543
No 406
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=21.48 E-value=79 Score=18.59 Aligned_cols=35 Identities=23% Similarity=0.762 Sum_probs=20.3
Q ss_pred cccCCCCCCCce--EEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869 68 EVTCPACKHGKA--VYHELQTRSADEPMSIFYMCANKNCKHRWN 109 (110)
Q Consensus 68 ~~~CpkCg~~~a--~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr 109 (110)
...||+|+.... -||.-- +. .|-+ |.|.. |.-.|+
T Consensus 5 ~~~CPRC~S~nTKFcYyNNy--~~--~QPR-~~Ck~--C~rywT 41 (63)
T PF02701_consen 5 PLPCPRCDSTNTKFCYYNNY--NL--SQPR-YFCKS--CRRYWT 41 (63)
T ss_pred CCCCCCcCCCCCEEEeecCC--CC--CCcc-hhhHH--HHHHHH
Confidence 468999997543 344321 11 1222 66877 877775
No 407
>PF15616 TerY-C: TerY-C metal binding domain
Probab=21.46 E-value=77 Score=21.32 Aligned_cols=13 Identities=23% Similarity=0.631 Sum_probs=9.5
Q ss_pred eEEcCCCCCeeee
Q 033869 23 RFSCPACPYVCNM 35 (110)
Q Consensus 23 ~~~C~~C~y~~~~ 35 (110)
...|+-|+..-..
T Consensus 105 ~~~CPwCg~~g~~ 117 (131)
T PF15616_consen 105 EVTCPWCGNEGSF 117 (131)
T ss_pred CEECCCCCCeeee
Confidence 7888888876544
No 408
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=21.43 E-value=52 Score=27.09 Aligned_cols=16 Identities=19% Similarity=0.407 Sum_probs=7.3
Q ss_pred cccCCCCCCCceEEEE
Q 033869 68 EVTCPACKHGKAVYHE 83 (110)
Q Consensus 68 ~~~CpkCg~~~a~~~~ 83 (110)
...||+||++.+..+.
T Consensus 504 ~~~CP~CGs~~~~~~~ 519 (546)
T PF13597_consen 504 GDKCPKCGSENIEVYS 519 (546)
T ss_dssp EEE-CCC----EEEEB
T ss_pred CCCCCCCCCcccceEE
Confidence 4479999988765554
No 409
>PF02012 BNR: BNR/Asp-box repeat; InterPro: IPR002860 Members of this entry contain multiple BNR (bacterial neuraminidase repeat) repeats or Asp-boxes. The repeats are short, however the repeats are never found closer than 40 residues together suggesting that the repeat is structurally longer. These repeats are found in a variety of non-homologous proteins, including bacterial ribonucleases, sulphite oxidases, reelin, netrins, sialidases, neuraminidases, some lipoprotein receptors, and a variety of glycosyl hydrolases [].; PDB: 2JKB_A 2VW0_A 2VW2_A 2VW1_A 2CN2_D 2CN3_B 2VK7_B 2VK5_A 2VK6_A 2BF6_A ....
Probab=21.41 E-value=32 Score=13.60 Aligned_cols=8 Identities=25% Similarity=0.144 Sum_probs=4.7
Q ss_pred CCCCCCce
Q 033869 87 RSADEPMS 94 (110)
Q Consensus 87 RsaDE~~T 94 (110)
+|.|.|.|
T Consensus 2 ~S~D~G~T 9 (12)
T PF02012_consen 2 YSTDGGKT 9 (12)
T ss_dssp EESSTTSS
T ss_pred EeCCCccc
Confidence 45666655
No 410
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=21.26 E-value=42 Score=23.66 Aligned_cols=10 Identities=70% Similarity=1.228 Sum_probs=8.1
Q ss_pred ccCCCCCCCc
Q 033869 69 VTCPACKHGK 78 (110)
Q Consensus 69 ~~CpkCg~~~ 78 (110)
..||.|||-.
T Consensus 94 ~~CP~CGh~k 103 (176)
T KOG4080|consen 94 NTCPACGHIK 103 (176)
T ss_pred ccCcccCccc
Confidence 5899999843
No 411
>PRK07591 threonine synthase; Validated
Probab=21.17 E-value=55 Score=25.88 Aligned_cols=22 Identities=27% Similarity=0.641 Sum_probs=15.4
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPY 31 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y 31 (110)
.|..||....+. .. +.|+.||-
T Consensus 20 ~C~~Cg~~~~~~------~~-~~C~~cg~ 41 (421)
T PRK07591 20 KCRECGAEYPLG------PI-HVCEECFG 41 (421)
T ss_pred EeCCCCCcCCCC------CC-ccCCCCCC
Confidence 588888876543 23 88888873
No 412
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=21.07 E-value=51 Score=20.40 Aligned_cols=13 Identities=23% Similarity=0.613 Sum_probs=9.7
Q ss_pred CcccCCCCCCCce
Q 033869 67 TEVTCPACKHGKA 79 (110)
Q Consensus 67 ~~~~CpkCg~~~a 79 (110)
...+|+.||.+=.
T Consensus 7 ~~~~C~~CG~d~~ 19 (86)
T PF06170_consen 7 VAPRCPHCGLDYS 19 (86)
T ss_pred CCCcccccCCccc
Confidence 4568999998643
No 413
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=20.86 E-value=1e+02 Score=16.27 Aligned_cols=13 Identities=23% Similarity=0.345 Sum_probs=10.4
Q ss_pred eEEcCCCCCeeee
Q 033869 23 RFSCPACPYVCNM 35 (110)
Q Consensus 23 ~~~C~~C~y~~~~ 35 (110)
.|.|-.|++..-.
T Consensus 11 l~~CL~C~~~~c~ 23 (50)
T smart00290 11 LWLCLTCGQVGCG 23 (50)
T ss_pred eEEecCCCCcccC
Confidence 8899999986543
No 414
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=20.71 E-value=49 Score=27.79 Aligned_cols=27 Identities=30% Similarity=0.779 Sum_probs=18.8
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYV 32 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~ 32 (110)
..|..||.++... . ....+.|+.|+..
T Consensus 545 ~vC~~CG~~~~~~--~--~~~~~~C~~C~~~ 571 (605)
T PRK07225 545 YVCAKCGMIAIYD--K--KRNRKYCPICGEE 571 (605)
T ss_pred EeecCcCcceehh--c--ccCceeecccCCC
Confidence 4689999988654 2 1236789999764
No 415
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.56 E-value=96 Score=26.55 Aligned_cols=28 Identities=29% Similarity=0.604 Sum_probs=16.4
Q ss_pred CCCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869 2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVC 33 (110)
Q Consensus 2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~ 33 (110)
..|++||.. -...-. ...+.|+.||...
T Consensus 642 ~~C~~CG~~--Ge~~~~--~~~~~CP~CG~~~ 669 (711)
T PRK09263 642 DECYECGFT--GEFECT--EKGFTCPKCGNHD 669 (711)
T ss_pred cccCCCCCC--ccccCC--CCCCcCcCCCCCC
Confidence 479999962 110001 1238999999754
No 416
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=20.48 E-value=57 Score=19.31 Aligned_cols=12 Identities=25% Similarity=0.534 Sum_probs=5.2
Q ss_pred CCcCCCCCcccc
Q 033869 3 FCPTCGTMLQYE 14 (110)
Q Consensus 3 FCp~C~nlL~~~ 14 (110)
-|+.|+++|..+
T Consensus 9 rCs~C~~~l~~p 20 (65)
T PF14835_consen 9 RCSICFDILKEP 20 (65)
T ss_dssp S-SSS-S--SS-
T ss_pred CCcHHHHHhcCC
Confidence 478888887766
No 417
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=20.44 E-value=79 Score=20.25 Aligned_cols=30 Identities=23% Similarity=0.604 Sum_probs=22.6
Q ss_pred CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869 3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES 37 (110)
Q Consensus 3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~ 37 (110)
.|.-|+..=|.. + +..++|.+|+......+
T Consensus 37 aCeiC~~~GY~q--~---g~~lvC~~C~~~~~~~~ 66 (102)
T PF10080_consen 37 ACEICGPKGYYQ--E---GDQLVCKNCGVRFNLPT 66 (102)
T ss_pred eccccCCCceEE--E---CCEEEEecCCCEEehhh
Confidence 588887776665 2 35899999999877654
No 418
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=20.40 E-value=73 Score=26.70 Aligned_cols=14 Identities=29% Similarity=0.743 Sum_probs=8.9
Q ss_pred ccCCCCCCCceEEE
Q 033869 69 VTCPACKHGKAVYH 82 (110)
Q Consensus 69 ~~CpkCg~~~a~~~ 82 (110)
..||+||+..+..+
T Consensus 547 ~~CP~CGs~~~ev~ 560 (586)
T TIGR02827 547 HRCPVCGSANIDYG 560 (586)
T ss_pred CcCcCCCCccceEE
Confidence 57888886554433
No 419
>PRK06599 DNA topoisomerase I; Validated
Probab=20.23 E-value=82 Score=26.61 Aligned_cols=31 Identities=26% Similarity=0.581 Sum_probs=17.6
Q ss_pred ccCCCCCCCceEEEEeccCCCCCCceEEEEecC-CCCCcc
Q 033869 69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCAN-KNCKHR 107 (110)
Q Consensus 69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~-~~C~~~ 107 (110)
..||+||.. ... |..--+ .|+.|.+ +.|++.
T Consensus 638 ~~Cp~C~~~---~~~---kkgk~g--~f~~Cs~yp~ck~~ 669 (675)
T PRK06599 638 EKCPKCGGP---LVL---KKGRYG--KFLACSGYPECKHI 669 (675)
T ss_pred CCCCCCCCe---eEE---EeCCCC--ceeeCCCCCCCCce
Confidence 379999974 222 332223 4888853 347643
Done!