Query 030129
Match_columns 182
No_of_seqs 139 out of 830
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 08:58:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030129.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030129hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00423 tfb transcription ini 100.0 9.1E-47 2E-51 320.7 12.9 176 3-180 11-209 (310)
2 KOG1597 Transcription initiati 100.0 7.9E-44 1.7E-48 293.6 13.6 169 4-173 1-184 (308)
3 COG1405 SUA7 Transcription ini 100.0 3.9E-40 8.6E-45 275.9 10.4 169 3-180 1-184 (285)
4 KOG1598 Transcription initiati 99.8 1.3E-21 2.8E-26 172.9 7.3 137 4-176 1-149 (521)
5 PF08271 TF_Zn_Ribbon: TFIIB z 99.7 8.4E-18 1.8E-22 103.2 3.5 43 4-47 1-43 (43)
6 PF00382 TFIIB: Transcription 99.6 1E-14 2.2E-19 98.5 6.4 59 112-170 1-71 (71)
7 PRK00423 tfb transcription ini 99.0 3.3E-10 7.1E-15 96.7 5.9 72 108-179 219-302 (310)
8 COG1405 SUA7 Transcription ini 98.8 6.2E-09 1.3E-13 87.8 6.1 69 106-174 192-272 (285)
9 KOG1597 Transcription initiati 98.6 8.3E-08 1.8E-12 80.3 5.1 69 106-174 201-281 (308)
10 cd00043 CYCLIN Cyclin box fold 98.4 1E-06 2.2E-11 59.4 5.8 68 107-174 4-84 (88)
11 smart00385 CYCLIN domain prese 98.3 1.2E-06 2.6E-11 58.5 5.2 64 111-174 2-78 (83)
12 PF11781 RRN7: RNA polymerase 97.2 0.00034 7.3E-09 41.0 2.3 27 5-34 10-36 (36)
13 PF08792 A2L_zn_ribbon: A2L zi 97.0 0.00075 1.6E-08 38.8 3.0 31 1-33 1-31 (33)
14 PRK00415 rps27e 30S ribosomal 96.7 0.00084 1.8E-08 43.5 1.7 30 4-34 12-41 (59)
15 COG2051 RPS27A Ribosomal prote 96.7 0.0011 2.5E-08 43.7 2.3 31 4-35 20-50 (67)
16 PHA00626 hypothetical protein 96.7 0.0015 3.2E-08 41.8 2.6 31 4-35 1-35 (59)
17 PF01667 Ribosomal_S27e: Ribos 96.7 0.00081 1.8E-08 43.1 1.2 30 4-34 8-37 (55)
18 PF14803 Nudix_N_2: Nudix N-te 96.6 0.0026 5.7E-08 36.8 2.7 28 4-33 1-32 (34)
19 PF01857 RB_B: Retinoblastoma- 96.5 0.013 2.8E-07 44.4 6.9 53 104-156 10-71 (135)
20 COG5333 CCL1 Cdk activating ki 96.5 0.0037 7.9E-08 53.0 4.2 59 102-160 41-109 (297)
21 PLN00209 ribosomal protein S27 96.2 0.0029 6.2E-08 44.0 2.0 31 4-35 37-67 (86)
22 KOG1598 Transcription initiati 96.2 0.0013 2.9E-08 59.3 0.5 70 106-175 164-248 (521)
23 PTZ00083 40S ribosomal protein 96.2 0.0035 7.7E-08 43.4 2.1 31 4-35 36-66 (85)
24 PRK00420 hypothetical protein; 96.2 0.0043 9.3E-08 45.5 2.7 31 1-34 21-51 (112)
25 TIGR00569 ccl1 cyclin ccl1. Un 96.1 0.018 3.9E-07 49.3 6.8 55 102-156 52-116 (305)
26 PRK00398 rpoP DNA-directed RNA 96.1 0.005 1.1E-07 37.8 2.3 31 1-33 1-31 (46)
27 COG1645 Uncharacterized Zn-fin 96.0 0.0043 9.4E-08 46.6 1.9 29 1-33 26-55 (131)
28 PF13248 zf-ribbon_3: zinc-rib 95.9 0.0046 9.9E-08 33.5 1.2 22 4-31 3-24 (26)
29 PF02150 RNA_POL_M_15KD: RNA p 95.8 0.01 2.2E-07 34.5 2.7 31 3-34 1-31 (35)
30 PRK00432 30S ribosomal protein 95.8 0.0078 1.7E-07 37.8 2.3 28 3-33 20-47 (50)
31 PF13240 zinc_ribbon_2: zinc-r 95.7 0.0047 1E-07 32.5 0.9 22 5-32 1-22 (23)
32 smart00778 Prim_Zn_Ribbon Zinc 95.6 0.013 2.8E-07 34.6 2.6 29 3-31 3-33 (37)
33 TIGR01206 lysW lysine biosynth 95.5 0.011 2.4E-07 37.7 2.3 30 4-34 3-33 (54)
34 PRK11827 hypothetical protein; 95.3 0.017 3.6E-07 37.7 2.5 28 4-33 9-36 (60)
35 TIGR02098 MJ0042_CXXC MJ0042 f 95.0 0.016 3.4E-07 33.9 1.7 29 4-34 3-36 (38)
36 PF08274 PhnA_Zn_Ribbon: PhnA 95.0 0.032 6.9E-07 31.3 2.8 27 4-33 3-29 (30)
37 PF00134 Cyclin_N: Cyclin, N-t 94.9 0.11 2.4E-06 37.6 6.5 52 104-155 30-88 (127)
38 COG1997 RPL43A Ribosomal prote 94.9 0.027 6E-07 39.3 2.8 29 4-34 36-64 (89)
39 COG1998 RPS31 Ribosomal protei 94.8 0.019 4.1E-07 35.8 1.8 27 4-32 20-46 (51)
40 KOG0794 CDK8 kinase-activating 94.8 0.067 1.5E-06 44.0 5.3 49 107-155 43-98 (264)
41 KOG0834 CDK9 kinase-activating 94.7 0.091 2E-06 45.3 6.2 51 106-156 40-97 (323)
42 PF09297 zf-NADH-PPase: NADH p 94.6 0.062 1.3E-06 30.3 3.4 29 3-33 3-31 (32)
43 smart00661 RPOL9 RNA polymeras 94.5 0.038 8.3E-07 34.3 2.7 28 5-34 2-31 (52)
44 PRK00464 nrdR transcriptional 94.5 0.031 6.8E-07 43.2 2.7 30 4-33 1-38 (154)
45 PF10571 UPF0547: Uncharacteri 94.5 0.019 4.1E-07 31.1 1.0 24 5-34 2-25 (26)
46 PF09538 FYDLN_acid: Protein o 94.4 0.024 5.2E-07 41.3 1.8 31 3-36 9-39 (108)
47 PF06677 Auto_anti-p27: Sjogre 94.4 0.041 8.9E-07 33.1 2.5 27 1-30 15-41 (41)
48 PF03966 Trm112p: Trm112p-like 94.4 0.058 1.3E-06 35.8 3.5 17 17-33 47-63 (68)
49 PF14354 Lar_restr_allev: Rest 93.9 0.076 1.6E-06 34.1 3.2 28 3-31 3-37 (61)
50 COG2835 Uncharacterized conser 93.8 0.056 1.2E-06 35.1 2.3 30 2-33 7-36 (60)
51 PF08273 Prim_Zn_Ribbon: Zinc- 93.7 0.065 1.4E-06 32.1 2.3 29 4-32 4-35 (40)
52 TIGR00244 transcriptional regu 93.6 0.072 1.6E-06 40.8 3.1 30 4-33 1-38 (147)
53 PRK10220 hypothetical protein; 92.9 0.09 2E-06 38.2 2.5 30 1-33 1-30 (111)
54 TIGR02300 FYDLN_acid conserved 92.9 0.067 1.4E-06 40.0 1.9 31 3-36 9-39 (129)
55 TIGR03655 anti_R_Lar restricti 92.5 0.08 1.7E-06 33.4 1.7 31 4-34 2-37 (53)
56 TIGR01384 TFS_arch transcripti 92.5 0.08 1.7E-06 37.8 1.8 28 4-35 1-28 (104)
57 PF09862 DUF2089: Protein of u 91.9 0.16 3.6E-06 37.2 2.8 25 6-36 1-25 (113)
58 PF01780 Ribosomal_L37ae: Ribo 91.8 0.13 2.9E-06 36.2 2.2 29 4-34 36-64 (90)
59 KOG1779 40s ribosomal protein 91.5 0.11 2.5E-06 35.5 1.5 29 4-33 35-63 (84)
60 COG1594 RPB9 DNA-directed RNA 91.3 0.15 3.3E-06 37.3 2.2 34 3-36 2-35 (113)
61 PF07282 OrfB_Zn_ribbon: Putat 91.3 0.18 3.9E-06 33.2 2.3 29 4-34 29-57 (69)
62 PF13719 zinc_ribbon_5: zinc-r 90.8 0.12 2.6E-06 30.2 1.0 28 4-33 3-35 (37)
63 PF12760 Zn_Tnp_IS1595: Transp 90.4 0.31 6.8E-06 29.7 2.7 27 4-31 19-45 (46)
64 PRK12495 hypothetical protein; 90.3 0.19 4.1E-06 40.9 2.1 31 1-35 40-70 (226)
65 PTZ00255 60S ribosomal protein 90.1 0.26 5.5E-06 34.8 2.3 29 4-34 37-65 (90)
66 PF05191 ADK_lid: Adenylate ki 90.1 0.054 1.2E-06 31.6 -0.9 29 5-33 3-31 (36)
67 smart00834 CxxC_CXXC_SSSS Puta 90.1 0.15 3.3E-06 29.8 1.1 30 4-33 6-36 (41)
68 COG2824 PhnA Uncharacterized Z 89.9 0.3 6.4E-06 35.4 2.6 33 1-36 1-33 (112)
69 COG4888 Uncharacterized Zn rib 89.8 0.21 4.5E-06 35.8 1.7 29 5-34 24-57 (104)
70 PRK14892 putative transcriptio 89.5 0.19 4E-06 36.1 1.3 30 4-34 22-53 (99)
71 COG1327 Predicted transcriptio 89.1 0.28 6.1E-06 37.7 2.1 30 4-33 1-38 (156)
72 KOG0835 Cyclin L [General func 89.0 0.86 1.9E-05 39.4 5.1 49 107-155 140-197 (367)
73 TIGR00280 L37a ribosomal prote 89.0 0.31 6.8E-06 34.4 2.1 29 4-34 36-64 (91)
74 TIGR00686 phnA alkylphosphonat 88.5 0.43 9.2E-06 34.7 2.6 28 4-34 3-30 (109)
75 COG2888 Predicted Zn-ribbon RN 88.4 0.31 6.7E-06 31.6 1.6 26 5-32 11-36 (61)
76 PF05129 Elf1: Transcription e 88.1 0.22 4.9E-06 34.3 0.9 32 5-36 24-59 (81)
77 PRK03976 rpl37ae 50S ribosomal 88.0 0.39 8.5E-06 33.8 2.0 29 4-34 37-65 (90)
78 smart00659 RPOLCX RNA polymera 88.0 0.43 9.3E-06 29.1 2.0 27 4-33 3-29 (44)
79 COG4640 Predicted membrane pro 87.8 0.28 6E-06 43.3 1.4 28 3-36 1-28 (465)
80 smart00440 ZnF_C2C2 C2C2 Zinc 87.3 0.62 1.3E-05 27.7 2.4 27 5-32 2-37 (40)
81 PRK09710 lar restriction allev 87.3 0.63 1.4E-05 30.7 2.5 28 4-32 7-36 (64)
82 PRK05978 hypothetical protein; 87.2 0.42 9.1E-06 36.7 2.0 32 4-36 34-65 (148)
83 PF02984 Cyclin_C: Cyclin, C-t 87.2 1.5 3.2E-05 30.9 4.8 66 108-173 3-81 (118)
84 PRK09678 DNA-binding transcrip 86.9 0.79 1.7E-05 31.0 3.0 31 3-34 1-40 (72)
85 PF12773 DZR: Double zinc ribb 86.8 0.36 7.8E-06 29.6 1.2 11 23-33 29-39 (50)
86 PF03119 DNA_ligase_ZBD: NAD-d 86.7 0.72 1.5E-05 25.3 2.2 22 5-28 1-22 (28)
87 PF01096 TFIIS_C: Transcriptio 86.7 0.78 1.7E-05 27.1 2.5 27 5-32 2-37 (39)
88 KOG0835 Cyclin L [General func 86.5 3.4 7.4E-05 35.8 7.2 55 101-155 19-80 (367)
89 PRK06266 transcription initiat 85.4 0.2 4.3E-06 39.6 -0.6 29 5-35 119-148 (178)
90 PRK08402 replication factor A; 85.4 0.63 1.4E-05 40.7 2.4 27 4-32 213-239 (355)
91 PF14255 Cys_rich_CPXG: Cystei 85.2 0.67 1.5E-05 29.3 1.9 29 5-33 2-34 (52)
92 PF11672 DUF3268: Protein of u 85.2 0.95 2.1E-05 32.6 2.9 31 3-34 2-42 (102)
93 PRK02935 hypothetical protein; 85.1 0.64 1.4E-05 33.6 1.9 38 4-48 71-108 (110)
94 PF03604 DNA_RNApol_7kD: DNA d 85.0 0.56 1.2E-05 26.6 1.3 24 5-31 2-25 (32)
95 PF15616 TerY-C: TerY-C metal 83.8 0.71 1.5E-05 34.8 1.8 9 4-12 78-86 (131)
96 PF05876 Terminase_GpA: Phage 83.8 0.5 1.1E-05 43.7 1.1 43 4-46 201-255 (557)
97 KOG2496 Cdk activating kinase 83.5 3.1 6.6E-05 35.7 5.6 45 120-164 73-129 (325)
98 TIGR02605 CxxC_CxxC_SSSS putat 82.9 0.62 1.3E-05 28.9 1.0 28 4-31 6-34 (52)
99 PF08646 Rep_fac-A_C: Replicat 82.8 1.4 3E-05 33.2 3.1 27 5-34 20-48 (146)
100 PF13717 zinc_ribbon_4: zinc-r 82.7 0.57 1.2E-05 27.2 0.7 29 4-33 3-35 (36)
101 COG3478 Predicted nucleic-acid 82.3 0.99 2.1E-05 29.8 1.8 13 5-18 6-18 (68)
102 COG5349 Uncharacterized protei 82.1 0.67 1.5E-05 34.4 1.0 36 5-42 23-59 (126)
103 PF06827 zf-FPG_IleRS: Zinc fi 82.1 0.83 1.8E-05 25.1 1.2 28 4-31 2-29 (30)
104 PF10122 Mu-like_Com: Mu-like 81.7 0.37 8.1E-06 30.3 -0.4 32 1-33 2-34 (51)
105 cd04476 RPA1_DBD_C RPA1_DBD_C: 81.7 1.1 2.4E-05 34.4 2.2 26 5-33 36-61 (166)
106 KOG4164 Cyclin ik3-1/CABLES [C 81.6 3.6 7.7E-05 36.6 5.4 48 108-155 385-439 (497)
107 COG1996 RPC10 DNA-directed RNA 81.4 0.56 1.2E-05 29.3 0.3 28 4-33 7-34 (49)
108 PRK13130 H/ACA RNA-protein com 81.3 0.75 1.6E-05 29.6 0.9 24 2-33 4-27 (56)
109 PF09855 DUF2082: Nucleic-acid 81.1 1.6 3.5E-05 28.7 2.5 9 24-32 37-45 (64)
110 cd00350 rubredoxin_like Rubred 81.0 1.3 2.7E-05 25.1 1.7 23 5-31 3-25 (33)
111 PHA02942 putative transposase; 81.0 1.2 2.6E-05 39.3 2.4 28 4-34 326-353 (383)
112 PRK00241 nudC NADH pyrophospha 80.9 1.3 2.7E-05 37.0 2.4 29 3-33 99-127 (256)
113 KOG2906 RNA polymerase III sub 80.7 1.4 3.1E-05 31.5 2.2 31 3-34 1-32 (105)
114 PRK12286 rpmF 50S ribosomal pr 80.5 0.9 2E-05 29.2 1.1 26 4-36 28-53 (57)
115 COG3877 Uncharacterized protei 80.4 1.5 3.3E-05 31.8 2.3 27 4-36 7-33 (122)
116 PRK12366 replication factor A; 80.2 1.1 2.3E-05 42.2 2.0 25 4-32 533-557 (637)
117 COG1326 Uncharacterized archae 80.1 0.68 1.5E-05 37.1 0.5 31 4-35 7-42 (201)
118 COG1656 Uncharacterized conser 79.8 0.88 1.9E-05 35.5 1.0 11 23-33 130-140 (165)
119 PF10058 DUF2296: Predicted in 78.7 1 2.2E-05 28.6 0.9 29 4-32 23-53 (54)
120 KOG1088 Uncharacterized conser 78.4 0.97 2.1E-05 33.3 0.8 18 17-34 92-109 (124)
121 TIGR00515 accD acetyl-CoA carb 78.4 0.41 8.9E-06 40.6 -1.3 30 4-34 27-56 (285)
122 PF00301 Rubredoxin: Rubredoxi 78.3 1.2 2.6E-05 27.5 1.1 16 24-39 2-17 (47)
123 TIGR02443 conserved hypothetic 78.0 2.4 5.3E-05 27.4 2.5 29 4-32 10-40 (59)
124 CHL00174 accD acetyl-CoA carbo 78.0 0.42 9E-06 40.8 -1.4 30 4-34 39-68 (296)
125 PF11023 DUF2614: Protein of u 77.7 0.73 1.6E-05 33.7 0.0 39 4-49 70-108 (114)
126 PRK14559 putative protein seri 77.4 1.4 3E-05 41.6 1.7 7 5-11 3-9 (645)
127 PF14122 YokU: YokU-like prote 76.6 2 4.3E-05 29.9 1.9 24 20-43 32-55 (87)
128 TIGR01031 rpmF_bact ribosomal 76.2 2 4.3E-05 27.4 1.7 24 4-34 27-50 (55)
129 cd00730 rubredoxin Rubredoxin; 76.2 2.1 4.7E-05 26.7 1.9 14 24-37 2-15 (50)
130 KOG2593 Transcription initiati 75.8 1.4 3E-05 39.3 1.3 32 3-34 128-164 (436)
131 TIGR03826 YvyF flagellar opero 75.7 0.5 1.1E-05 35.9 -1.3 30 1-35 1-30 (137)
132 PRK05654 acetyl-CoA carboxylas 75.6 0.55 1.2E-05 40.0 -1.3 30 4-34 28-57 (292)
133 KOG0402 60S ribosomal protein 75.6 0.99 2.1E-05 31.3 0.2 29 4-34 37-65 (92)
134 PF04161 Arv1: Arv1-like famil 75.4 1.4 3.1E-05 35.4 1.1 34 4-37 1-38 (208)
135 PF07754 DUF1610: Domain of un 75.2 2.3 5E-05 22.5 1.5 23 6-31 1-24 (24)
136 smart00401 ZnF_GATA zinc finge 74.6 2.8 6.1E-05 26.2 2.1 32 3-34 3-36 (52)
137 PF14353 CpXC: CpXC protein 74.6 3 6.4E-05 30.7 2.6 12 23-34 38-49 (128)
138 COG1773 Rubredoxin [Energy pro 74.3 2.5 5.4E-05 27.0 1.8 11 24-34 4-14 (55)
139 PF01599 Ribosomal_S27: Riboso 74.1 3.9 8.4E-05 25.3 2.6 26 4-31 19-46 (47)
140 PRK12380 hydrogenase nickel in 74.1 2 4.4E-05 31.3 1.6 6 25-30 88-93 (113)
141 PF09723 Zn-ribbon_8: Zinc rib 74.0 1.4 3.1E-05 26.3 0.6 28 4-31 6-34 (42)
142 PF14446 Prok-RING_1: Prokaryo 73.9 2.2 4.8E-05 27.2 1.5 26 4-33 6-31 (54)
143 PF01783 Ribosomal_L32p: Ribos 73.6 2 4.3E-05 27.4 1.3 24 4-34 27-50 (56)
144 PF13453 zf-TFIIB: Transcripti 72.2 3.2 7E-05 24.5 1.9 26 5-33 1-29 (41)
145 PF10668 Phage_terminase: Phag 72.0 1.1 2.4E-05 29.2 -0.2 20 156-175 25-44 (60)
146 TIGR03830 CxxCG_CxxCG_HTH puta 71.9 3.5 7.6E-05 29.9 2.4 11 24-34 32-42 (127)
147 PRK12336 translation initiatio 71.5 2.7 5.9E-05 33.8 1.9 29 4-32 99-128 (201)
148 TIGR00100 hypA hydrogenase nic 71.5 2.6 5.6E-05 30.8 1.6 19 14-32 61-79 (115)
149 PRK14890 putative Zn-ribbon RN 71.3 3.8 8.2E-05 26.6 2.1 28 2-32 6-34 (59)
150 PF09526 DUF2387: Probable met 71.2 4.2 9.2E-05 27.3 2.5 30 4-33 9-40 (71)
151 PF06397 Desulfoferrod_N: Desu 71.1 2.6 5.7E-05 24.5 1.3 22 4-26 7-28 (36)
152 PRK08351 DNA-directed RNA poly 71.1 2.5 5.4E-05 27.6 1.3 23 1-31 1-23 (61)
153 TIGR00155 pqiA_fam integral me 70.3 3.1 6.8E-05 37.0 2.2 29 5-34 15-44 (403)
154 PF04216 FdhE: Protein involve 69.9 3 6.5E-05 35.2 1.9 29 4-32 173-206 (290)
155 PF04502 DUF572: Family of unk 69.2 2.4 5.1E-05 36.6 1.1 28 4-32 78-105 (324)
156 PF13790 DUF4182: Domain of un 68.9 3 6.5E-05 24.6 1.2 13 22-34 2-14 (38)
157 PRK03824 hypA hydrogenase nick 68.6 3.2 7E-05 31.2 1.7 21 14-34 61-81 (135)
158 PRK14559 putative protein seri 68.2 3.1 6.7E-05 39.3 1.8 24 5-34 29-52 (645)
159 PRK06260 threonine synthase; V 68.2 2.5 5.4E-05 37.2 1.1 30 1-34 1-30 (397)
160 PF03811 Zn_Tnp_IS1: InsA N-te 67.9 5.8 0.00013 23.0 2.3 25 4-29 6-35 (36)
161 PF14952 zf-tcix: Putative tre 67.4 2.8 6.1E-05 25.5 0.9 25 4-34 12-38 (44)
162 COG0777 AccD Acetyl-CoA carbox 67.2 1.5 3.2E-05 37.1 -0.5 30 4-34 29-58 (294)
163 PF06044 DRP: Dam-replacing fa 67.0 3.9 8.5E-05 34.0 1.9 30 4-34 32-64 (254)
164 PF13824 zf-Mss51: Zinc-finger 67.0 4 8.6E-05 26.1 1.6 24 5-33 1-24 (55)
165 PF01155 HypA: Hydrogenase exp 66.5 1.5 3.4E-05 31.9 -0.5 24 5-32 72-95 (113)
166 PRK07218 replication factor A; 66.5 2.6 5.6E-05 37.8 0.9 21 4-32 298-318 (423)
167 PRK03564 formate dehydrogenase 66.3 5.5 0.00012 34.2 2.8 10 24-33 253-262 (309)
168 PF03833 PolC_DP2: DNA polymer 66.0 2 4.3E-05 41.6 0.0 11 24-34 681-691 (900)
169 TIGR01384 TFS_arch transcripti 65.8 6.9 0.00015 27.6 2.9 29 3-32 62-99 (104)
170 KOG2907 RNA polymerase I trans 65.8 2.4 5.3E-05 31.0 0.5 30 3-34 7-36 (116)
171 TIGR00569 ccl1 cyclin ccl1. Un 65.8 19 0.00041 30.9 5.9 18 139-156 204-221 (305)
172 TIGR00595 priA primosomal prot 65.7 5.2 0.00011 36.6 2.7 29 4-34 223-251 (505)
173 COG2093 DNA-directed RNA polym 65.6 3.7 8E-05 26.9 1.2 26 1-32 2-27 (64)
174 PF14205 Cys_rich_KTR: Cystein 65.6 4.9 0.00011 25.6 1.7 27 5-31 6-36 (55)
175 PF04606 Ogr_Delta: Ogr/Delta- 65.4 4.9 0.00011 24.5 1.7 28 5-33 1-37 (47)
176 TIGR03829 YokU_near_AblA uncha 65.3 3 6.5E-05 29.3 0.8 36 5-40 1-52 (89)
177 PRK05580 primosome assembly pr 64.9 5.4 0.00012 37.8 2.7 28 4-33 391-418 (679)
178 COG4068 Uncharacterized protei 64.9 0.86 1.9E-05 29.5 -1.8 26 3-34 8-34 (64)
179 PF12172 DUF35_N: Rubredoxin-l 64.8 4.3 9.3E-05 23.3 1.3 21 4-30 12-32 (37)
180 PRK03681 hypA hydrogenase nick 64.7 4.1 8.9E-05 29.7 1.5 17 15-31 62-78 (114)
181 COG4530 Uncharacterized protei 64.6 3.8 8.3E-05 30.0 1.3 32 3-37 9-40 (129)
182 PF14768 RPA_interact_C: Repli 64.5 6.3 0.00014 27.0 2.3 28 5-36 1-28 (82)
183 cd00974 DSRD Desulforedoxin (D 64.5 5.4 0.00012 22.5 1.7 24 4-28 5-28 (34)
184 TIGR01562 FdhE formate dehydro 64.3 5.8 0.00013 34.0 2.5 31 3-33 224-262 (305)
185 cd00202 ZnF_GATA Zinc finger D 64.3 2.3 4.9E-05 27.0 0.1 30 5-34 1-32 (54)
186 PF01485 IBR: IBR domain; Int 64.1 4.5 9.8E-05 25.4 1.5 28 4-33 19-50 (64)
187 PRK15103 paraquat-inducible me 63.9 4.3 9.4E-05 36.3 1.8 31 4-35 11-42 (419)
188 KOG4557 Origin recognition com 63.7 18 0.00038 29.8 5.0 46 110-155 94-150 (262)
189 PF08063 PADR1: PADR1 (NUC008) 63.1 4.5 9.8E-05 25.7 1.3 22 4-28 15-36 (55)
190 PF14471 DUF4428: Domain of un 62.9 2.2 4.8E-05 26.7 -0.2 28 5-33 1-30 (51)
191 PRK14873 primosome assembly pr 62.2 5.9 0.00013 37.6 2.4 27 4-32 393-419 (665)
192 PF04216 FdhE: Protein involve 62.0 8.2 0.00018 32.5 3.0 32 3-34 211-249 (290)
193 KOG3507 DNA-directed RNA polym 61.8 4.8 0.0001 26.1 1.2 23 5-31 22-45 (62)
194 TIGR03831 YgiT_finger YgiT-typ 61.8 6.9 0.00015 23.0 1.9 10 24-33 33-42 (46)
195 KOG3134 Predicted membrane pro 61.7 1.8 4E-05 35.2 -0.9 34 4-37 1-38 (225)
196 PF10080 DUF2318: Predicted me 61.4 8.5 0.00018 27.7 2.6 27 5-34 37-63 (102)
197 PF01807 zf-CHC2: CHC2 zinc fi 61.4 7.9 0.00017 27.2 2.4 27 5-31 35-62 (97)
198 KOG0794 CDK8 kinase-activating 61.3 9.3 0.0002 31.7 3.1 21 139-159 192-212 (264)
199 PRK00750 lysK lysyl-tRNA synth 61.1 6.5 0.00014 36.0 2.4 34 5-39 177-215 (510)
200 COG1779 C4-type Zn-finger prot 61.0 4.8 0.0001 32.4 1.4 37 4-40 15-60 (201)
201 PRK04023 DNA polymerase II lar 60.8 5.8 0.00013 39.2 2.1 11 24-34 664-674 (1121)
202 TIGR00319 desulf_FeS4 desulfof 60.0 6.4 0.00014 22.2 1.4 22 5-27 9-30 (34)
203 PF07191 zinc-ribbons_6: zinc- 60.0 7.9 0.00017 26.0 2.1 26 4-33 2-27 (70)
204 smart00647 IBR In Between Ring 59.9 9 0.0002 24.0 2.3 28 4-33 19-50 (64)
205 PF09082 DUF1922: Domain of un 58.7 9 0.0002 25.5 2.1 26 5-34 5-30 (68)
206 PF01396 zf-C4_Topoisom: Topoi 58.5 21 0.00045 20.9 3.5 29 4-33 2-34 (39)
207 PF08613 Cyclin: Cyclin; Inte 58.5 28 0.0006 26.2 5.2 65 108-172 54-136 (149)
208 cd00729 rubredoxin_SM Rubredox 58.3 9.1 0.0002 21.7 1.9 8 24-31 19-26 (34)
209 PF04810 zf-Sec23_Sec24: Sec23 58.1 14 0.00031 21.6 2.8 30 3-32 2-33 (40)
210 COG2816 NPY1 NTP pyrophosphohy 57.9 6.8 0.00015 33.2 1.8 28 3-34 111-140 (279)
211 COG1198 PriA Primosomal protei 57.8 8.5 0.00018 36.9 2.7 27 4-32 445-471 (730)
212 PF08772 NOB1_Zn_bind: Nin one 57.8 4.8 0.0001 27.2 0.8 12 1-12 22-33 (73)
213 PF14206 Cys_rich_CPCC: Cystei 57.3 11 0.00025 25.7 2.5 26 4-32 2-29 (78)
214 TIGR00310 ZPR1_znf ZPR1 zinc f 57.1 8.2 0.00018 30.9 2.1 29 5-33 2-40 (192)
215 PRK06386 replication factor A; 56.8 4.9 0.00011 35.3 0.8 21 4-32 237-257 (358)
216 COG4643 Uncharacterized protei 56.8 6.4 0.00014 34.2 1.5 26 5-30 34-61 (366)
217 PRK00564 hypA hydrogenase nick 56.5 4.9 0.00011 29.5 0.7 18 14-31 62-79 (117)
218 smart00342 HTH_ARAC helix_turn 56.2 10 0.00022 24.3 2.2 62 112-174 4-72 (84)
219 TIGR00340 zpr1_rel ZPR1-relate 55.6 8 0.00017 30.1 1.8 28 6-33 1-38 (163)
220 PF09889 DUF2116: Uncharacteri 55.5 3.7 8E-05 26.6 -0.1 27 2-34 2-29 (59)
221 COG0333 RpmF Ribosomal protein 54.5 7.3 0.00016 25.1 1.1 24 4-34 28-51 (57)
222 PRK08197 threonine synthase; V 54.5 6.1 0.00013 34.7 1.1 27 3-34 7-33 (394)
223 PRK05508 methionine sulfoxide 54.0 10 0.00022 28.1 2.0 33 18-50 28-62 (119)
224 COG4391 Uncharacterized protei 53.9 8.9 0.00019 25.0 1.5 20 14-33 38-58 (62)
225 PF01921 tRNA-synt_1f: tRNA sy 53.7 4.8 0.0001 35.4 0.3 35 5-39 176-215 (360)
226 PRK14714 DNA polymerase II lar 53.5 7.7 0.00017 39.2 1.7 7 25-31 694-700 (1337)
227 KOG0656 G1/S-specific cyclin D 53.1 55 0.0012 28.5 6.6 51 106-156 79-139 (335)
228 PF01412 ArfGap: Putative GTPa 52.9 4.5 9.8E-05 29.4 0.0 30 4-33 14-43 (116)
229 TIGR01562 FdhE formate dehydro 52.3 11 0.00023 32.4 2.2 28 4-31 185-218 (305)
230 COG1571 Predicted DNA-binding 52.3 8.3 0.00018 34.5 1.5 33 4-39 351-383 (421)
231 PRK06393 rpoE DNA-directed RNA 52.2 5.8 0.00012 26.2 0.4 21 3-31 5-25 (64)
232 TIGR00613 reco DNA repair prot 51.8 10 0.00022 30.6 1.9 28 4-31 148-176 (241)
233 PRK14526 adenylate kinase; Pro 51.8 12 0.00025 30.2 2.2 33 4-36 123-155 (211)
234 smart00290 ZnF_UBP Ubiquitin C 51.1 13 0.00029 22.3 1.9 22 5-34 1-22 (50)
235 PRK00085 recO DNA repair prote 50.9 11 0.00023 30.6 1.9 26 5-30 151-177 (247)
236 cd00674 LysRS_core_class_I cat 50.8 12 0.00027 32.7 2.4 33 4-37 170-206 (353)
237 PRK00222 methionine sulfoxide 50.5 12 0.00026 28.6 2.0 33 18-50 38-72 (142)
238 TIGR00354 polC DNA polymerase, 49.9 5.9 0.00013 39.0 0.3 23 3-33 625-647 (1095)
239 PHA03074 late transcription fa 49.7 8.6 0.00019 31.1 1.1 30 2-34 3-32 (225)
240 COG3809 Uncharacterized protei 49.3 16 0.00034 25.2 2.2 28 4-33 2-31 (88)
241 smart00105 ArfGap Putative GTP 49.3 11 0.00024 27.2 1.6 31 3-33 3-33 (112)
242 TIGR01053 LSD1 zinc finger dom 49.2 26 0.00056 19.6 2.7 28 4-33 2-29 (31)
243 PF13878 zf-C2H2_3: zinc-finge 49.2 8 0.00017 23.0 0.7 16 21-36 11-26 (41)
244 TIGR00357 methionine-R-sulfoxi 48.9 13 0.00028 28.1 1.9 33 18-50 35-69 (134)
245 PF14369 zf-RING_3: zinc-finge 48.7 12 0.00026 21.4 1.4 26 4-31 3-29 (35)
246 PF09334 tRNA-synt_1g: tRNA sy 48.5 9.2 0.0002 33.8 1.2 23 5-34 138-160 (391)
247 PF00320 GATA: GATA zinc finge 48.4 4.6 0.0001 23.2 -0.5 27 6-32 1-29 (36)
248 PF00643 zf-B_box: B-box zinc 47.7 31 0.00067 19.8 3.1 23 3-33 3-25 (42)
249 PRK00448 polC DNA polymerase I 47.7 9.9 0.00021 39.2 1.4 31 3-34 908-944 (1437)
250 PF07295 DUF1451: Protein of u 47.5 10 0.00022 29.0 1.2 15 20-34 109-123 (146)
251 PRK06450 threonine synthase; V 47.3 10 0.00022 32.8 1.2 29 1-34 1-29 (338)
252 PF03367 zf-ZPR1: ZPR1 zinc-fi 47.0 16 0.00034 28.3 2.2 30 4-33 2-40 (161)
253 PRK14714 DNA polymerase II lar 46.2 9.6 0.00021 38.6 1.1 26 6-34 695-720 (1337)
254 TIGR03879 near_KaiC_dom probab 45.9 22 0.00047 24.0 2.4 19 157-175 36-54 (73)
255 PF10005 DUF2248: Uncharacteri 45.9 12 0.00026 32.7 1.5 24 5-34 1-24 (343)
256 COG3677 Transposase and inacti 45.8 16 0.00035 27.2 2.1 30 3-33 30-63 (129)
257 PRK07591 threonine synthase; V 45.1 10 0.00022 33.8 0.9 26 4-34 19-44 (421)
258 PLN02569 threonine synthase 44.5 14 0.0003 33.7 1.7 27 3-34 49-75 (484)
259 COG1545 Predicted nucleic-acid 44.4 13 0.00027 28.2 1.3 24 4-33 30-53 (140)
260 KOG1010 Rb (Retinoblastoma tum 44.0 53 0.0012 32.1 5.5 50 107-156 679-737 (920)
261 PF01641 SelR: SelR domain; I 43.8 16 0.00035 27.2 1.7 32 19-50 33-66 (124)
262 PRK08329 threonine synthase; V 43.6 16 0.00036 31.5 2.0 25 4-34 2-26 (347)
263 smart00709 Zpr1 Duplicated dom 42.9 20 0.00044 27.7 2.3 29 5-33 2-39 (160)
264 PF08421 Methyltransf_13: Puta 42.3 19 0.00041 23.2 1.7 17 24-40 41-57 (62)
265 PF13408 Zn_ribbon_recom: Reco 42.1 13 0.00029 22.8 0.9 14 21-34 3-16 (58)
266 COG5347 GTPase-activating prot 42.1 20 0.00043 31.0 2.3 31 3-33 20-50 (319)
267 PRK01110 rpmF 50S ribosomal pr 42.0 14 0.00031 23.9 1.1 28 4-39 28-55 (60)
268 COG0375 HybF Zn finger protein 41.9 14 0.0003 27.2 1.1 15 19-33 66-80 (115)
269 PF01475 FUR: Ferric uptake re 41.6 17 0.00036 26.1 1.5 13 22-34 79-91 (120)
270 COG2260 Predicted Zn-ribbon RN 41.6 14 0.00031 23.8 1.0 22 4-33 6-27 (59)
271 PRK09462 fur ferric uptake reg 41.1 16 0.00034 27.5 1.4 12 23-34 90-101 (148)
272 cd07973 Spt4 Transcription elo 41.1 17 0.00036 26.0 1.4 27 4-33 4-30 (98)
273 PF14319 Zn_Tnp_IS91: Transpos 40.8 16 0.00036 26.4 1.4 34 4-39 43-76 (111)
274 PF00325 Crp: Bacterial regula 40.5 5 0.00011 22.7 -1.1 18 157-174 6-23 (32)
275 PF14951 DUF4503: Domain of un 40.4 18 0.00039 31.8 1.7 38 5-43 276-314 (389)
276 cd07153 Fur_like Ferric uptake 39.5 17 0.00038 25.7 1.3 13 22-34 72-84 (116)
277 COG1107 Archaea-specific RecJ- 39.4 22 0.00048 33.4 2.2 24 3-30 2-25 (715)
278 TIGR02642 phage_xxxx uncharact 39.4 18 0.0004 28.8 1.5 23 4-30 100-122 (186)
279 smart00400 ZnF_CHCC zinc finge 39.3 40 0.00087 20.8 2.9 27 5-31 4-31 (55)
280 COG1675 TFA1 Transcription ini 39.2 6.3 0.00014 31.1 -1.1 29 5-35 115-144 (176)
281 PF01363 FYVE: FYVE zinc finge 39.1 27 0.00059 22.4 2.1 30 4-37 10-39 (69)
282 PRK04023 DNA polymerase II lar 38.9 19 0.00042 35.8 1.8 11 24-34 652-662 (1121)
283 PF12677 DUF3797: Domain of un 38.8 24 0.00052 21.9 1.6 7 5-11 15-21 (49)
284 COG0735 Fur Fe2+/Zn2+ uptake r 38.7 18 0.00039 27.4 1.3 13 22-34 92-104 (145)
285 TIGR01391 dnaG DNA primase, ca 38.7 31 0.00068 30.7 3.1 27 5-31 36-63 (415)
286 PRK03564 formate dehydrogenase 38.4 20 0.00044 30.8 1.7 29 3-31 187-220 (309)
287 PRK04179 rpl37e 50S ribosomal 38.3 16 0.00034 23.9 0.8 25 2-31 16-40 (62)
288 COG4311 SoxD Sarcosine oxidase 38.1 17 0.00038 25.8 1.1 12 1-12 1-12 (97)
289 TIGR01405 polC_Gram_pos DNA po 37.9 17 0.00037 36.9 1.4 31 3-34 683-719 (1213)
290 PF00356 LacI: Bacterial regul 37.4 6.6 0.00014 24.0 -1.0 18 157-174 3-20 (46)
291 PF14149 YhfH: YhfH-like prote 37.3 4.1 9E-05 23.9 -1.8 16 21-36 11-26 (37)
292 COG5525 Bacteriophage tail ass 37.1 20 0.00042 33.6 1.5 32 5-36 229-272 (611)
293 COG5134 Uncharacterized conser 37.1 32 0.00068 28.3 2.5 25 4-28 80-104 (272)
294 COG2126 RPL37A Ribosomal prote 36.4 19 0.00042 23.3 1.0 25 3-32 16-40 (61)
295 PF02945 Endonuclease_7: Recom 36.4 16 0.00036 25.0 0.7 31 3-33 22-62 (81)
296 PHA02540 61 DNA primase; Provi 36.0 34 0.00074 29.8 2.8 28 5-32 29-64 (337)
297 PRK05638 threonine synthase; V 36.0 21 0.00046 31.9 1.5 25 4-34 2-26 (442)
298 PRK07217 replication factor A; 35.9 17 0.00037 31.3 0.9 21 4-32 189-211 (311)
299 TIGR00467 lysS_arch lysyl-tRNA 35.9 23 0.00049 32.7 1.8 32 5-37 170-204 (515)
300 PF13913 zf-C2HC_2: zinc-finge 35.9 23 0.0005 18.5 1.1 9 3-11 2-10 (25)
301 COG3024 Uncharacterized protei 35.6 18 0.0004 23.8 0.8 28 4-32 8-36 (65)
302 PF00096 zf-C2H2: Zinc finger, 35.4 33 0.00071 16.8 1.6 11 24-34 1-11 (23)
303 PF00130 C1_1: Phorbol esters/ 35.1 61 0.0013 19.5 3.2 35 3-40 11-45 (53)
304 PF02591 DUF164: Putative zinc 35.1 21 0.00045 22.4 1.0 30 4-33 23-56 (56)
305 COG2176 PolC DNA polymerase II 34.9 22 0.00048 36.1 1.6 31 3-34 914-950 (1444)
306 KOG0856 Predicted pilin-like t 34.5 25 0.00055 26.8 1.5 33 18-50 49-83 (146)
307 COG1499 NMD3 NMD protein affec 34.3 15 0.00032 32.3 0.2 14 106-119 161-174 (355)
308 PRK11639 zinc uptake transcrip 34.0 23 0.0005 27.4 1.3 12 23-34 100-111 (169)
309 PF06689 zf-C4_ClpX: ClpX C4-t 33.8 15 0.00033 21.7 0.2 26 4-29 2-30 (41)
310 PF09779 Ima1_N: Ima1 N-termin 33.6 30 0.00065 25.8 1.8 28 5-32 2-29 (131)
311 PF13613 HTH_Tnp_4: Helix-turn 33.6 14 0.0003 22.8 0.0 36 141-176 7-42 (53)
312 PF00628 PHD: PHD-finger; Int 33.4 32 0.0007 20.6 1.7 30 5-39 1-30 (51)
313 PRK00279 adk adenylate kinase; 33.1 32 0.00069 27.2 2.0 30 4-33 128-157 (215)
314 PF09845 DUF2072: Zn-ribbon co 33.1 18 0.00038 27.3 0.5 13 25-37 3-15 (131)
315 PRK05667 dnaG DNA primase; Val 33.1 43 0.00093 31.3 3.1 27 5-31 38-65 (580)
316 TIGR00617 rpa1 replication fac 32.8 29 0.00062 32.6 1.9 26 5-33 476-503 (608)
317 PRK11032 hypothetical protein; 32.7 24 0.00052 27.5 1.2 15 20-34 121-135 (160)
318 PF13309 HTH_22: HTH domain 32.7 52 0.0011 21.2 2.7 49 110-170 5-59 (64)
319 PF12156 ATPase-cat_bd: Putati 32.7 17 0.00037 25.2 0.4 39 4-43 1-45 (88)
320 PF03685 UPF0147: Uncharacteri 32.5 1.7E+02 0.0037 20.4 5.2 49 101-149 4-55 (85)
321 KOG1010 Rb (Retinoblastoma tum 32.3 93 0.002 30.6 5.2 47 109-155 35-87 (920)
322 COG0229 Conserved domain frequ 32.3 36 0.00079 25.8 2.1 33 18-50 37-71 (140)
323 smart00504 Ubox Modified RING 32.1 23 0.0005 22.1 0.9 29 4-40 2-30 (63)
324 PRK00762 hypA hydrogenase nick 31.9 21 0.00045 26.4 0.7 18 14-32 61-78 (124)
325 PRK14715 DNA polymerase II lar 31.4 20 0.00042 36.8 0.6 24 3-34 674-697 (1627)
326 PF06676 DUF1178: Protein of u 31.1 29 0.00063 26.6 1.4 8 4-11 33-40 (148)
327 PRK08173 DNA topoisomerase III 30.6 31 0.00068 33.8 1.9 26 4-33 625-650 (862)
328 KOG0834 CDK9 kinase-activating 30.5 18 0.00039 31.3 0.2 18 139-156 193-210 (323)
329 PF13384 HTH_23: Homeodomain-l 30.5 12 0.00025 22.5 -0.8 19 156-174 20-38 (50)
330 PF14690 zf-ISL3: zinc-finger 30.4 37 0.0008 20.0 1.5 8 4-11 3-10 (47)
331 smart00064 FYVE Protein presen 30.2 36 0.00079 21.8 1.6 30 4-37 11-40 (68)
332 PF03833 PolC_DP2: DNA polymer 30.0 17 0.00038 35.4 0.0 10 25-34 694-703 (900)
333 PF01907 Ribosomal_L37e: Ribos 29.9 24 0.00052 22.5 0.6 24 4-32 16-39 (55)
334 PRK09263 anaerobic ribonucleos 29.8 28 0.00061 33.4 1.4 26 4-31 642-667 (711)
335 COG1066 Sms Predicted ATP-depe 29.7 26 0.00057 31.6 1.1 31 107-137 130-167 (456)
336 PF08882 Acetone_carb_G: Aceto 29.3 29 0.00063 25.4 1.1 12 23-34 74-85 (112)
337 COG5257 GCD11 Translation init 29.3 26 0.00057 30.8 1.0 25 4-33 58-82 (415)
338 COG0846 SIR2 NAD-dependent pro 29.2 23 0.00051 29.5 0.6 39 3-41 122-165 (250)
339 cd01411 SIR2H SIR2H: Uncharact 29.2 31 0.00067 27.9 1.4 36 4-41 119-154 (225)
340 KOG0706 Predicted GTPase-activ 29.0 32 0.0007 31.0 1.5 31 2-32 22-52 (454)
341 PRK04016 DNA-directed RNA poly 29.0 22 0.00047 23.3 0.3 12 24-35 5-16 (62)
342 PTZ00408 NAD-dependent deacety 28.9 20 0.00043 29.6 0.2 39 3-41 117-157 (242)
343 PHA00689 hypothetical protein 28.7 40 0.00087 21.1 1.5 24 22-46 16-39 (62)
344 PHA02956 hypothetical protein; 28.5 32 0.00069 26.3 1.2 20 13-32 107-126 (189)
345 COG5333 CCL1 Cdk activating ki 28.4 1.3E+02 0.0029 25.8 5.0 18 139-156 190-207 (297)
346 TIGR00320 dfx_rbo desulfoferro 28.3 37 0.00081 25.2 1.6 22 4-26 8-29 (125)
347 PRK00481 NAD-dependent deacety 28.2 33 0.00072 28.0 1.4 38 3-41 122-160 (242)
348 PRK00133 metG methionyl-tRNA s 28.0 28 0.00061 32.9 1.0 10 157-166 495-504 (673)
349 cd00065 FYVE FYVE domain; Zinc 27.9 43 0.00094 20.5 1.6 30 4-37 3-32 (57)
350 PF02701 zf-Dof: Dof domain, z 27.9 33 0.00072 22.5 1.0 28 3-31 5-38 (63)
351 PRK15103 paraquat-inducible me 27.8 39 0.00084 30.3 1.8 24 5-34 223-246 (419)
352 cd01410 SIRT7 SIRT7: Eukaryoti 27.7 37 0.0008 27.2 1.6 38 3-41 95-138 (206)
353 PF10083 DUF2321: Uncharacteri 27.5 36 0.00077 26.4 1.3 14 24-37 40-53 (158)
354 PRK04338 N(2),N(2)-dimethylgua 27.4 35 0.00076 30.1 1.5 35 4-45 245-279 (382)
355 COG3364 Zn-ribbon containing p 27.2 26 0.00056 25.3 0.5 11 25-35 4-14 (112)
356 PLN03165 chaperone protein dna 27.1 27 0.00058 25.5 0.6 7 5-11 54-60 (111)
357 PRK00418 DNA gyrase inhibitor; 27.1 33 0.00071 22.4 0.9 27 4-32 7-35 (62)
358 PF09567 RE_MamI: MamI restric 26.9 26 0.00056 29.5 0.5 23 4-32 83-105 (314)
359 PRK08116 hypothetical protein; 26.5 52 0.0011 27.4 2.3 28 4-32 17-48 (268)
360 PF06906 DUF1272: Protein of u 26.5 40 0.00086 21.6 1.2 6 25-30 43-48 (57)
361 PF04032 Rpr2: RNAse P Rpr2/Rp 26.2 33 0.00071 22.9 0.9 20 15-34 38-57 (85)
362 PF04981 NMD3: NMD3 family ; 26.1 27 0.00059 28.5 0.5 31 5-35 15-47 (236)
363 PF13542 HTH_Tnp_ISL3: Helix-t 25.9 37 0.0008 20.3 1.0 28 147-174 19-48 (52)
364 PRK05550 bifunctional methioni 25.8 48 0.001 28.2 1.9 33 18-50 31-65 (283)
365 cd00021 BBOX B-Box-type zinc f 25.6 59 0.0013 18.0 1.8 7 5-11 2-8 (39)
366 PRK04330 hypothetical protein; 25.5 2.4E+02 0.0052 19.7 6.0 64 100-168 6-72 (88)
367 KOG0818 GTPase-activating prot 25.2 36 0.00079 31.4 1.2 28 4-32 9-37 (669)
368 COG2344 AT-rich DNA-binding pr 25.2 22 0.00049 28.7 -0.1 49 117-176 3-55 (211)
369 TIGR00155 pqiA_fam integral me 25.0 44 0.00096 29.7 1.7 24 17-40 7-30 (403)
370 PRK07956 ligA NAD-dependent DN 24.0 59 0.0013 31.0 2.4 33 4-38 405-440 (665)
371 cd04762 HTH_MerR-trunc Helix-T 23.6 20 0.00044 20.5 -0.5 17 157-173 4-20 (49)
372 smart00109 C1 Protein kinase C 23.5 48 0.001 19.2 1.1 30 3-36 11-40 (49)
373 COG1110 Reverse gyrase [DNA re 23.4 24 0.00053 35.2 -0.3 25 3-30 8-33 (1187)
374 PRK14704 anaerobic ribonucleos 23.4 43 0.00094 31.6 1.4 21 4-31 560-580 (618)
375 COG4647 AcxC Acetone carboxyla 23.3 30 0.00064 26.2 0.2 13 22-34 119-131 (165)
376 COG0498 ThrC Threonine synthas 23.3 24 0.00052 31.6 -0.3 31 3-37 5-35 (411)
377 KOG0006 E3 ubiquitin-protein l 22.8 40 0.00088 29.3 0.9 32 1-34 313-347 (446)
378 TIGR00570 cdk7 CDK-activating 22.5 56 0.0012 28.1 1.8 11 1-11 1-11 (309)
379 PF08996 zf-DNA_Pol: DNA Polym 22.3 63 0.0014 25.5 1.9 32 5-38 20-60 (188)
380 TIGR00201 comF comF family pro 22.3 38 0.00082 26.5 0.6 23 6-34 1-23 (190)
381 TIGR00382 clpX endopeptidase C 22.2 51 0.0011 29.5 1.5 28 5-32 9-38 (413)
382 KOG1368 Threonine aldolase [Am 22.1 2.3E+02 0.005 24.8 5.3 78 102-180 209-307 (384)
383 PF05377 FlaC_arch: Flagella a 22.1 1.1E+02 0.0023 19.6 2.5 37 101-137 12-50 (55)
384 COG1813 Predicted transcriptio 22.0 40 0.00087 26.4 0.7 36 1-37 1-39 (165)
385 cd01413 SIR2_Af2 SIR2_Af2: Arc 22.0 50 0.0011 26.7 1.3 39 3-41 113-154 (222)
386 COG4307 Uncharacterized protei 21.9 40 0.00086 28.7 0.7 28 1-34 1-28 (349)
387 PRK14018 trifunctional thiored 21.7 63 0.0014 29.9 2.0 33 18-50 413-447 (521)
388 cd01412 SIRT5_Af1_CobB SIRT5_A 21.6 64 0.0014 25.9 1.9 39 3-41 109-148 (224)
389 PTZ00073 60S ribosomal protein 21.6 47 0.001 23.4 0.9 24 3-31 16-39 (91)
390 PLN03131 hypothetical protein; 21.6 66 0.0014 30.5 2.1 30 4-33 24-53 (705)
391 TIGR00575 dnlj DNA ligase, NAD 21.5 70 0.0015 30.4 2.3 33 4-38 393-427 (652)
392 cd01407 SIR2-fam SIR2 family o 21.5 48 0.001 26.5 1.1 39 3-41 109-151 (218)
393 COG1885 Uncharacterized protei 21.5 38 0.00082 24.6 0.4 19 18-36 44-62 (115)
394 KOG3022 Predicted ATPase, nucl 21.1 30 0.00064 29.6 -0.2 31 1-32 220-250 (300)
395 COG2023 RPR2 RNase P subunit R 21.1 62 0.0013 23.4 1.5 31 4-34 57-93 (105)
396 COG5515 Uncharacterized conser 21.0 1.4E+02 0.003 19.6 2.9 30 13-43 35-64 (70)
397 PF13894 zf-C2H2_4: C2H2-type 20.8 74 0.0016 15.1 1.4 9 25-33 2-10 (24)
398 COG1107 Archaea-specific RecJ- 20.8 62 0.0014 30.5 1.8 12 24-35 81-92 (715)
399 PRK01381 Trp operon repressor; 20.6 64 0.0014 23.1 1.5 18 156-173 58-75 (99)
400 PF10276 zf-CHCC: Zinc-finger 20.5 97 0.0021 18.3 2.0 13 21-33 27-39 (40)
401 PRK09709 exonuclease VIII; Rev 20.4 47 0.001 32.5 1.0 27 4-39 526-552 (877)
402 TIGR03060 PS_II_psb29 photosys 20.4 1.4E+02 0.003 24.4 3.5 29 109-137 165-195 (214)
403 COG2995 PqiA Uncharacterized p 20.4 51 0.0011 29.4 1.1 30 4-33 19-48 (418)
404 PRK14067 exodeoxyribonuclease 20.3 1.5E+02 0.0032 20.3 3.2 37 100-136 4-42 (80)
405 COG1644 RPB10 DNA-directed RNA 20.3 29 0.00063 22.7 -0.3 13 24-36 5-17 (63)
406 PRK05342 clpX ATP-dependent pr 20.3 55 0.0012 29.2 1.3 26 3-29 9-37 (412)
407 PLN03119 putative ADP-ribosyla 20.2 82 0.0018 29.6 2.4 30 4-33 24-53 (648)
408 PRK11475 DNA-binding transcrip 20.2 2.1E+02 0.0045 22.7 4.6 36 99-134 136-177 (207)
409 KOG4198 RNA-binding Ran Zn-fin 20.1 70 0.0015 27.2 1.8 27 5-32 117-149 (280)
410 PF05864 Chordopox_RPO7: Chord 20.0 40 0.00087 21.8 0.3 12 24-35 5-16 (63)
No 1
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=9.1e-47 Score=320.66 Aligned_cols=176 Identities=27% Similarity=0.471 Sum_probs=158.2
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcccccccccccCCCCCCCCccccCCCCccccCCCCceEEecCC-C
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPN-G 81 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~sr~G~~~~~~~~~~gl~T~i~~~~-~ 81 (182)
...||+||+ +++++|+.+|++||++||+||+|++||+|||||+|++|+ .++++|+|+|.++++||.||+|.|+++. +
T Consensus 11 ~~~Cp~Cg~-~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~-~~~~~RvG~~~~~~~~~~gl~T~I~~~~~~ 88 (310)
T PRK00423 11 KLVCPECGS-DKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQ-REKRSRVGAPMTYTIHDKGLSTDIDWRNKD 88 (310)
T ss_pred CCcCcCCCC-CCeeEECCCCeEeecccCCcccccccccCCCccCCCccc-cCCccccCCCCCccccCCCCceEeecCCcc
Confidence 357999998 789999999999999999999999999999999999985 5699999999999999999999999643 3
Q ss_pred CCCcccc-------ccccccccCC---CCchHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHH
Q 030129 82 ASGEFLS-------SSLGRWQNRG---SNPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWL 144 (182)
Q Consensus 82 ~~~~~l~-------~~l~~~q~~~---~~~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~ 144 (182)
+.|+.++ .+|++||++. ++.||+|..||++|.++|+.|+||+.++|+ .||+++.++ + ++++++
T Consensus 89 ~~g~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~ 168 (310)
T PRK00423 89 SYGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVV 168 (310)
T ss_pred cccccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHH
Confidence 3455444 2588999875 678999999999999999999999999999 999999887 3 999999
Q ss_pred HHHHHHHHhhCC-----HHHHHhcCCCceeeeceeeehhcc
Q 030129 145 LACTLLVDKKTS-----HALLRKSALSPMELQRRKLAEQKN 180 (182)
Q Consensus 145 AAclY~acr~~~-----~eia~~~~v~~~~i~r~~~~~~~~ 180 (182)
|||||+|||+++ +||++++++++++||+.|..+.|.
T Consensus 169 AAclYiACR~~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~ 209 (310)
T PRK00423 169 AAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRE 209 (310)
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 999999999995 999999999999999998877653
No 2
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=7.9e-44 Score=293.60 Aligned_cols=169 Identities=49% Similarity=0.738 Sum_probs=155.4
Q ss_pred CCCCCCCCCCc-eeEeCCCCceEeCCCceeeeCCCcccccccccccCCCCCCCCccccCCCCccccCCCCceEEecCCCC
Q 030129 4 AFCSDCKKHTE-VVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGA 82 (182)
Q Consensus 4 ~~Cp~Cg~~~~-iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~sr~G~~~~~~~~~~gl~T~i~~~~~~ 82 (182)
++||+|+..+. +|+|+.+|+++|..||+|+++++||+++|||+|++++++.||+|||+|.||++.+.+|+|.|+++.+.
T Consensus 1 ~~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r~Id~~sEwrtfsnd~~~~DPsrvG~~sNPlL~~g~L~T~I~~g~g~ 80 (308)
T KOG1597|consen 1 MTCPDCKRHPENLVEDHSAGDTVCSECGLVLEDRIIDEGSEWRTFSNDDSDADPSRVGASSNPLLDGGDLSTFISKGTGT 80 (308)
T ss_pred CCCCCCCCCCCCeeeeccCCceecccCCeeeccccccccccccccccCCCCCCccccCCCCCCCCCCCCcceeeecCCCC
Confidence 46999998777 99999999999999999999999999999999999988899999999999999999999999988766
Q ss_pred CCccccccccccccC--CCCchHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHh
Q 030129 83 SGEFLSSSLGRWQNR--GSNPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDK 153 (182)
Q Consensus 83 ~~~~l~~~l~~~q~~--~~~~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr 153 (182)
.+..++ .|.++|++ +++.|+.|..||+.|..|++.|+||..|.++ +||+++.+. + +.++++|||||+|||
T Consensus 81 ~s~~~s-~l~~~Q~~~sm~~~d~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACR 159 (308)
T KOG1597|consen 81 SSSFAS-SLGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACR 159 (308)
T ss_pred CHHHHH-HHHHHhcccccCCccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHH
Confidence 554433 48889984 5789999999999999999999999999999 999999976 4 999999999999999
Q ss_pred hCC-----HHHHHhcCCCceeeece
Q 030129 154 KTS-----HALLRKSALSPMELQRR 173 (182)
Q Consensus 154 ~~~-----~eia~~~~v~~~~i~r~ 173 (182)
+.+ +||+.+++|+.+||||.
T Consensus 160 q~~~pRT~kEI~~~anv~kKEIgr~ 184 (308)
T KOG1597|consen 160 QEDVPRTFKEISAVANVSKKEIGRC 184 (308)
T ss_pred hcCCCchHHHHHHHHcCCHHHHHHH
Confidence 985 99999999999999993
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=3.9e-40 Score=275.88 Aligned_cols=169 Identities=28% Similarity=0.496 Sum_probs=150.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcccccccccccCCCCCCCCccccCCCCccccCCCCceEEecCCCC
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGA 82 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~sr~G~~~~~~~~~~gl~T~i~~~~~~ 82 (182)
++.||+||+ ++++.|++.|++||.+||+|++|..||.|||||+| ++ ...+ |+|+|.++.+||.|++|.|+++...
T Consensus 1 ~~~CpeCg~-~~~~~d~~~ge~VC~~CG~Vi~~~~id~gpewr~f-~e--~~~~-r~g~P~t~~~~d~~l~t~i~~~~~~ 75 (285)
T COG1405 1 VMSCPECGS-TNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAF-DE--RHER-RVGAPLTPSIHDKGLSTIIGWGDKD 75 (285)
T ss_pred CCCCCCCCC-ccceeeccCCeEEeccCCEEeccccccCCCCcccc-cc--cccc-cccCCCccccCccchhhhcccchhH
Confidence 367999998 69999999999999999999999999999999999 33 2234 9999999999999999999975422
Q ss_pred CCccccccccccccCC---CCchHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHH
Q 030129 83 SGEFLSSSLGRWQNRG---SNPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVD 152 (182)
Q Consensus 83 ~~~~l~~~l~~~q~~~---~~~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~ac 152 (182)
...+|++||.+. +++||+|..|+.+|.++++.|+||..+.|. .||+++.++ + +.++++|||||+||
T Consensus 76 ----~~~rlr~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~ac 151 (285)
T COG1405 76 ----KMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAAC 151 (285)
T ss_pred ----HHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHH
Confidence 235789999754 479999999999999999999999999999 999999998 5 89999999999999
Q ss_pred hhCC-----HHHHHhcCCCceeeeceeeehhcc
Q 030129 153 KKTS-----HALLRKSALSPMELQRRKLAEQKN 180 (182)
Q Consensus 153 r~~~-----~eia~~~~v~~~~i~r~~~~~~~~ 180 (182)
|+++ .||++++++++++|||+|....++
T Consensus 152 R~~~~prtl~eIa~a~~V~~kei~rtyr~~~~~ 184 (285)
T COG1405 152 RINGVPRTLDEIAKALGVSKKEIGRTYRLLVRE 184 (285)
T ss_pred HHcCCCccHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence 9984 999999999999999999866554
No 4
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=99.85 E-value=1.3e-21 Score=172.89 Aligned_cols=137 Identities=18% Similarity=0.298 Sum_probs=114.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcccccccccccCCCCCCCCccccCCCCccccCCCCceEEecCCCCC
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGAS 83 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~sr~G~~~~~~~~~~gl~T~i~~~~~~~ 83 (182)
+.|++||+ +++..|+.+|+.+|+.||.|+|+++|..+. +|.+. + .|+.|+....+.
T Consensus 1 ~~C~~C~~-s~fe~d~a~g~~~C~~CG~v~E~~~ivsev---~F~e~-----------~---------~G~~v~~~~~g~ 56 (521)
T KOG1598|consen 1 MVCKNCGG-SNFERDEATGNLYCTACGTVLEYNNIVAEV---TFVEG-----------A---------QGQFVRVGQSGA 56 (521)
T ss_pred CcCCCCCC-CCcccccccCCceeccccceeeccceeEEe---eeecc-----------c---------ceeEEeccccCC
Confidence 47999998 799999999999999999999999998754 56532 1 134554322111
Q ss_pred CccccccccccccCCCCchHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC
Q 030129 84 GEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS 156 (182)
Q Consensus 84 ~~~l~~~l~~~q~~~~~~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~ 156 (182)
+. ..+++++++++|.+.|..++.+|+|+. +++. .+|++|.++ | +...|+|||+|++||+++
T Consensus 57 ~~-----------s~e~r~~t~~n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~ 124 (521)
T KOG1598|consen 57 GS-----------SLESREKTIYNARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEK 124 (521)
T ss_pred cc-----------chHHHHHHHHHHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhC
Confidence 10 126789999999999999999999999 7777 999999998 7 899999999999999984
Q ss_pred -----HHHHHhcCCCceeeeceeee
Q 030129 157 -----HALLRKSALSPMELQRRKLA 176 (182)
Q Consensus 157 -----~eia~~~~v~~~~i~r~~~~ 176 (182)
.|+++++.|+++.||++||.
T Consensus 125 t~hlliDfS~~Lqv~Vy~LG~~~l~ 149 (521)
T KOG1598|consen 125 TDHLLIDFSSYLQVSVYDLGSNFLE 149 (521)
T ss_pred CceEEEEeccceEEehhhhhHHHHH
Confidence 89999999999999999874
No 5
>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=99.70 E-value=8.4e-18 Score=103.23 Aligned_cols=43 Identities=51% Similarity=1.076 Sum_probs=38.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcccccccccc
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTF 47 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f 47 (182)
++||+||+ +.+++|+.+|++||+.||+||+|+.|++++|||+|
T Consensus 1 m~Cp~Cg~-~~~~~D~~~g~~vC~~CG~Vl~e~~i~~~~e~r~f 43 (43)
T PF08271_consen 1 MKCPNCGS-KEIVFDPERGELVCPNCGLVLEENIIDEGPEWREF 43 (43)
T ss_dssp ESBTTTSS-SEEEEETTTTEEEETTT-BBEE-TTBSCCCSCCHC
T ss_pred CCCcCCcC-CceEEcCCCCeEECCCCCCEeecccccCCcccccC
Confidence 47999998 56999999999999999999999999999999987
No 6
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=99.55 E-value=1e-14 Score=98.45 Aligned_cols=59 Identities=14% Similarity=0.253 Sum_probs=52.2
Q ss_pred HHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceee
Q 030129 112 IATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMEL 170 (182)
Q Consensus 112 I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i 170 (182)
|++||+.|+||+.+.+. +||+++.+. + +|.+++|||||+|||+++ +||+++++|+++||
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 78999999999999999 999999887 4 899999999999999985 99999999999876
No 7
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.04 E-value=3.3e-10 Score=96.66 Aligned_cols=72 Identities=6% Similarity=0.095 Sum_probs=64.5
Q ss_pred HHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceeeeceee
Q 030129 108 AFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMELQRRKL 175 (182)
Q Consensus 108 a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i~r~~~ 175 (182)
+.++|.++|+.|+||..+.+. +|++++.+. + +|.++||||||+||+.++ +|||++++|++.||.++|-
T Consensus 219 p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~yk 298 (310)
T PRK00423 219 PIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYK 298 (310)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHH
Confidence 568999999999999999888 999999876 4 999999999999999974 9999999999999998885
Q ss_pred ehhc
Q 030129 176 AEQK 179 (182)
Q Consensus 176 ~~~~ 179 (182)
-..+
T Consensus 299 el~~ 302 (310)
T PRK00423 299 ELAE 302 (310)
T ss_pred HHHH
Confidence 5443
No 8
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=98.83 E-value=6.2e-09 Score=87.80 Aligned_cols=69 Identities=12% Similarity=0.157 Sum_probs=63.0
Q ss_pred HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceeeece
Q 030129 106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMELQRR 173 (182)
Q Consensus 106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i~r~ 173 (182)
.+..++|++||+.||||+.+... +|.+++.+. + +|..+||||||+|++.++ +|||.+++|++.||-.+
T Consensus 192 ~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrnr 271 (285)
T COG1405 192 VDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNR 271 (285)
T ss_pred CCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHHH
Confidence 35678999999999999988777 999999887 4 999999999999999985 99999999999999988
Q ss_pred e
Q 030129 174 K 174 (182)
Q Consensus 174 ~ 174 (182)
|
T Consensus 272 y 272 (285)
T COG1405 272 Y 272 (285)
T ss_pred H
Confidence 8
No 9
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.56 E-value=8.3e-08 Score=80.30 Aligned_cols=69 Identities=9% Similarity=0.102 Sum_probs=62.5
Q ss_pred HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhC-----CHHHHHhcCCCceeeece
Q 030129 106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKT-----SHALLRKSALSPMELQRR 173 (182)
Q Consensus 106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~-----~~eia~~~~v~~~~i~r~ 173 (182)
..+-++|.++|+.|+||..+.+. ++.+++.+. + +|.+||||.||++++.. .+||.+++||.+.||-..
T Consensus 201 ~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~s 280 (308)
T KOG1597|consen 201 ISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNS 280 (308)
T ss_pred hhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHH
Confidence 34678999999999999999988 999999887 4 99999999999999987 399999999999999877
Q ss_pred e
Q 030129 174 K 174 (182)
Q Consensus 174 ~ 174 (182)
|
T Consensus 281 Y 281 (308)
T KOG1597|consen 281 Y 281 (308)
T ss_pred H
Confidence 6
No 10
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=98.37 E-value=1e-06 Score=59.43 Aligned_cols=68 Identities=10% Similarity=0.109 Sum_probs=58.2
Q ss_pred HHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC-----HHHHHhcCC-Cceeeece
Q 030129 107 LAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS-----HALLRKSAL-SPMELQRR 173 (182)
Q Consensus 107 ~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~-----~eia~~~~v-~~~~i~r~ 173 (182)
.+++.|.+++..++++..+... .+++++... + ++..+++||||+||+..+ .|+...++. +..+|.+.
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~ 83 (88)
T cd00043 4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEILRM 83 (88)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHHHH
Confidence 5789999999999999998888 888888665 3 999999999999999873 889999888 87777654
Q ss_pred e
Q 030129 174 K 174 (182)
Q Consensus 174 ~ 174 (182)
+
T Consensus 84 e 84 (88)
T cd00043 84 E 84 (88)
T ss_pred H
Confidence 3
No 11
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.32 E-value=1.2e-06 Score=58.51 Aligned_cols=64 Identities=9% Similarity=0.050 Sum_probs=54.4
Q ss_pred HHHHHHHHhCChHHHHHH--HHHHHHHh-c-c---CHHHHHHHHHHHHHhhCC-----HHHHHhcCC-Cceeeecee
Q 030129 111 TIATMSDRIGQMRYIRRW--KIKSLVEA-E-I---KTHYWLLACTLLVDKKTS-----HALLRKSAL-SPMELQRRK 174 (182)
Q Consensus 111 ~I~~i~~~L~L~~~v~~~--~i~k~a~~-~-l---~~~~v~AAclY~acr~~~-----~eia~~~~v-~~~~i~r~~ 174 (182)
.|.+++..+++|+.+... .+++++.. . + ++..++|||||+||+..+ .++...++. ++.+|.+.+
T Consensus 2 ~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~ 78 (83)
T smart00385 2 FLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRME 78 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHH
Confidence 578999999999998888 88888866 3 3 999999999999999884 888998988 877776543
No 12
>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=97.16 E-value=0.00034 Score=41.04 Aligned_cols=27 Identities=30% Similarity=0.554 Sum_probs=23.2
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.|+.|++ . .+....|.++|..||.|++
T Consensus 10 ~C~~C~~-~--~~~~~dG~~yC~~cG~~~E 36 (36)
T PF11781_consen 10 PCPVCGS-R--WFYSDDGFYYCDRCGHQSE 36 (36)
T ss_pred cCCCCCC-e--EeEccCCEEEhhhCceEcC
Confidence 4999997 2 6778999999999999974
No 13
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=97.05 E-value=0.00075 Score=38.81 Aligned_cols=31 Identities=23% Similarity=0.451 Sum_probs=25.6
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
|....|+.|+. +.++..+.+..+|.+||.+.
T Consensus 1 ~~~~~C~~C~~--~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 1 SNLKKCSKCGG--NGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred CCceEcCCCCC--CeEEEecCCeEEcccCCcEe
Confidence 56678999997 35566789999999999985
No 14
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=96.74 E-value=0.00084 Score=43.54 Aligned_cols=30 Identities=37% Similarity=0.780 Sum_probs=27.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.+||.|+. ..+|+++.+-...|..||.+|.
T Consensus 12 VkCp~C~n-~q~vFsha~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 12 VKCPDCGN-EQVVFSHASTVVRCLVCGKTLA 41 (59)
T ss_pred EECCCCCC-eEEEEecCCcEEECcccCCCcc
Confidence 57999997 7899999999999999999985
No 15
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=96.73 E-value=0.0011 Score=43.75 Aligned_cols=31 Identities=35% Similarity=0.778 Sum_probs=28.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (182)
.+||.|+. ..+++++.+-...|..||.+|-+
T Consensus 20 VkCpdC~N-~q~vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 20 VKCPDCGN-EQVVFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred EECCCCCC-EEEEeccCceEEEecccccEEEe
Confidence 47999997 78999999999999999999953
No 16
>PHA00626 hypothetical protein
Probab=96.71 E-value=0.0015 Score=41.80 Aligned_cols=31 Identities=23% Similarity=0.549 Sum_probs=23.2
Q ss_pred CCCCCCCCCCceeEe----CCCCceEeCCCceeeeC
Q 030129 4 AFCSDCKKHTEVVFD----HSAGDTVCSECGLVLES 35 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D----~~~G~~vC~~CG~Vl~e 35 (182)
|.||.||+ .+|+.. -.+..+.|.+||.-...
T Consensus 1 m~CP~CGS-~~Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 1 MSCPKCGS-GNIAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCC-ceeeeeceecccCcceEcCCCCCeech
Confidence 46999998 556542 23689999999998643
No 17
>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=96.66 E-value=0.00081 Score=43.08 Aligned_cols=30 Identities=33% Similarity=0.722 Sum_probs=22.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.+||.|+. ..+|+++++-...|..||.+|-
T Consensus 8 VkCp~C~~-~q~vFSha~t~V~C~~Cg~~L~ 37 (55)
T PF01667_consen 8 VKCPGCYN-IQTVFSHAQTVVKCVVCGTVLA 37 (55)
T ss_dssp EE-TTT-S-EEEEETT-SS-EE-SSSTSEEE
T ss_pred EECCCCCC-eeEEEecCCeEEEcccCCCEec
Confidence 57999997 6899999999999999999995
No 18
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=96.55 E-value=0.0026 Score=36.79 Aligned_cols=28 Identities=25% Similarity=0.666 Sum_probs=15.6
Q ss_pred CCCCCCCCCCceeEeC----CCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDH----SAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~----~~G~~vC~~CG~Vl 33 (182)
.+||.||.. +.... +.-..||+.||.|-
T Consensus 1 kfC~~CG~~--l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 1 KFCPQCGGP--LERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp -B-TTT--B---EEE--TT-SS-EEEETTTTEEE
T ss_pred CccccccCh--hhhhcCCCCCccceECCCCCCEE
Confidence 379999973 44433 34449999999983
No 19
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.
Probab=96.48 E-value=0.013 Score=44.38 Aligned_cols=53 Identities=11% Similarity=0.046 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc---c----CHHHHHHHHHHHHHhhCC
Q 030129 104 GLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE---I----KTHYWLLACTLLVDKKTS 156 (182)
Q Consensus 104 ~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~---l----~~~~v~AAclY~acr~~~ 156 (182)
.+.-|...|..+|++|+|++.+.+. .+|+.+..+ | ..+.++..|+|+.||.+.
T Consensus 10 vy~la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~ 71 (135)
T PF01857_consen 10 VYKLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSK 71 (135)
T ss_dssp HHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhc
Confidence 3455899999999999999998777 888877543 3 899999999999999884
No 20
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=96.46 E-value=0.0037 Score=53.01 Aligned_cols=59 Identities=15% Similarity=0.125 Sum_probs=48.9
Q ss_pred hHHH-HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC--HHHH
Q 030129 102 DRGL-ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS--HALL 160 (182)
Q Consensus 102 er~L-~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~--~eia 160 (182)
+.+| ..++..|..+|.+|+||..+..+ .+|++..-. + ++..++++|||+||+.+. .+|.
T Consensus 41 e~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~ 109 (297)
T COG5333 41 ELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDIS 109 (297)
T ss_pred hhhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhh
Confidence 4444 45789999999999999999999 788887554 3 999999999999999886 5553
No 21
>PLN00209 ribosomal protein S27; Provisional
Probab=96.25 E-value=0.0029 Score=43.97 Aligned_cols=31 Identities=35% Similarity=0.657 Sum_probs=28.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (182)
.+||.|+. ..+|+.+++-...|..||.+|.+
T Consensus 37 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 37 VKCQGCFN-ITTVFSHSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred EECCCCCC-eeEEEecCceEEEccccCCEeec
Confidence 57999997 68999999999999999999953
No 22
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=96.25 E-value=0.0013 Score=59.30 Aligned_cols=70 Identities=11% Similarity=0.022 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHHHhCChHHHHHH--HHHHHHH--hc--c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceee
Q 030129 106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVE--AE--I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMEL 170 (182)
Q Consensus 106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~--~~--l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i 170 (182)
..-.-+|.++++.|-..+.-.+. .-++++. ++ + +|..++.||||+|||.++ .||+.++.|++.||
T Consensus 164 vDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl 243 (521)
T KOG1598|consen 164 VDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTL 243 (521)
T ss_pred cCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHH
Confidence 34445666777666443322222 2222322 22 2 999999999999999996 89999999999999
Q ss_pred eceee
Q 030129 171 QRRKL 175 (182)
Q Consensus 171 ~r~~~ 175 (182)
.++|.
T Consensus 244 ~kRl~ 248 (521)
T KOG1598|consen 244 SKRLK 248 (521)
T ss_pred HHHHH
Confidence 88763
No 23
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=96.16 E-value=0.0035 Score=43.42 Aligned_cols=31 Identities=26% Similarity=0.618 Sum_probs=28.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (182)
.+||.|+. ..+|+++++-...|..||.+|-+
T Consensus 36 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 36 VKCPGCSQ-ITTVFSHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred EECCCCCC-eeEEEecCceEEEccccCCEeec
Confidence 57999997 68999999999999999999953
No 24
>PRK00420 hypothetical protein; Validated
Probab=96.16 E-value=0.0043 Score=45.50 Aligned_cols=31 Identities=29% Similarity=0.600 Sum_probs=23.9
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
|-...||.||. ++ +-...|..+|..||.++.
T Consensus 21 ml~~~CP~Cg~--pL-f~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 21 MLSKHCPVCGL--PL-FELKDGEVVCPVHGKVYI 51 (112)
T ss_pred HccCCCCCCCC--cc-eecCCCceECCCCCCeee
Confidence 34467999996 33 444899999999999874
No 25
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=96.14 E-value=0.018 Score=49.26 Aligned_cols=55 Identities=11% Similarity=0.054 Sum_probs=46.2
Q ss_pred hHHH-HHHHHHHHHHHHHhC--ChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC
Q 030129 102 DRGL-ILAFKTIATMSDRIG--QMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS 156 (182)
Q Consensus 102 er~L-~~a~~~I~~i~~~L~--L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~ 156 (182)
|+.| ...-..|.++|..|+ ||+.++-+ .+|++..-. + .+..|++||||+||+.+.
T Consensus 52 E~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE 116 (305)
T TIGR00569 52 ELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEE 116 (305)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccc
Confidence 5555 347789999999999 99999888 888887554 3 999999999999999873
No 26
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=96.07 E-value=0.005 Score=37.77 Aligned_cols=31 Identities=29% Similarity=0.682 Sum_probs=25.2
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
|-...||.||. .+.+|+..+...|..||.-+
T Consensus 1 ~~~y~C~~CG~--~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 1 MAEYKCARCGR--EVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred CCEEECCCCCC--EEEECCCCCceECCCCCCeE
Confidence 55678999996 57778777799999999754
No 27
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=95.96 E-value=0.0043 Score=46.56 Aligned_cols=29 Identities=24% Similarity=0.704 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCc-eee
Q 030129 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECG-LVL 33 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG-~Vl 33 (182)
|-...||.||. ++. - .+|+++|..|| .+.
T Consensus 26 ML~~hCp~Cg~--PLF-~-KdG~v~CPvC~~~~~ 55 (131)
T COG1645 26 MLAKHCPKCGT--PLF-R-KDGEVFCPVCGYREV 55 (131)
T ss_pred HHHhhCcccCC--cce-e-eCCeEECCCCCceEE
Confidence 33457999996 343 3 89999999999 554
No 28
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=95.86 E-value=0.0046 Score=33.48 Aligned_cols=22 Identities=27% Similarity=0.967 Sum_probs=17.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCce
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (182)
+.||+||. . + +.+..+|..||.
T Consensus 3 ~~Cp~Cg~-~-~----~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGA-E-I----DPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCC-c-C----CcccccChhhCC
Confidence 67999996 2 2 356899999996
No 29
>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=95.83 E-value=0.01 Score=34.50 Aligned_cols=31 Identities=19% Similarity=0.484 Sum_probs=18.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
+..||+||+ -=+......+...|..||++.+
T Consensus 1 m~FCp~C~n-lL~p~~~~~~~~~C~~C~Y~~~ 31 (35)
T PF02150_consen 1 MRFCPECGN-LLYPKEDKEKRVACRTCGYEEP 31 (35)
T ss_dssp --BETTTTS-BEEEEEETTTTEEESSSS-EEE
T ss_pred CeeCCCCCc-cceEcCCCccCcCCCCCCCccC
Confidence 358999996 2222233444457999999964
No 30
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=95.79 E-value=0.0078 Score=37.83 Aligned_cols=28 Identities=25% Similarity=0.707 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
...||.||+ . +..++ .+...|..||+..
T Consensus 20 ~~fCP~Cg~-~-~m~~~-~~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGS-G-FMAEH-LDRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCc-c-hhecc-CCcEECCCcCCEE
Confidence 357999997 4 55554 4899999999874
No 31
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=95.70 E-value=0.0047 Score=32.54 Aligned_cols=22 Identities=27% Similarity=0.963 Sum_probs=16.6
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
+||+||. .+ ..+..+|..||.-
T Consensus 1 ~Cp~CG~--~~----~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGA--EI----EDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCC--CC----CCcCcchhhhCCc
Confidence 5999997 22 2467889999974
No 32
>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=95.61 E-value=0.013 Score=34.56 Aligned_cols=29 Identities=31% Similarity=0.720 Sum_probs=22.2
Q ss_pred CCCCCCCCCCCceeEeC--CCCceEeCCCce
Q 030129 3 DAFCSDCKKHTEVVFDH--SAGDTVCSECGL 31 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~--~~G~~vC~~CG~ 31 (182)
+..||.||+...+-+|. .+|..+|..||.
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 46799999865555555 458999999974
No 33
>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=95.52 E-value=0.011 Score=37.73 Aligned_cols=30 Identities=33% Similarity=0.720 Sum_probs=21.5
Q ss_pred CCCCCCCCCCceeEeCCCCc-eEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGD-TVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~-~vC~~CG~Vl~ 34 (182)
-.||.||.. --+.|...|+ +.|..||.-++
T Consensus 3 ~~CP~CG~~-iev~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAE-IELENPELGELVICDECGAELE 33 (54)
T ss_pred cCCCCCCCE-EecCCCccCCEEeCCCCCCEEE
Confidence 479999973 2233445576 67999999985
No 34
>PRK11827 hypothetical protein; Provisional
Probab=95.27 E-value=0.017 Score=37.73 Aligned_cols=28 Identities=14% Similarity=0.494 Sum_probs=24.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
..||.|++ .+..|....+++|..||++.
T Consensus 9 LaCP~ckg--~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 9 IACPVCNG--KLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred eECCCCCC--cCeEcCCCCeEECCccCeec
Confidence 46999986 57888888899999999985
No 35
>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=95.00 E-value=0.016 Score=33.91 Aligned_cols=29 Identities=28% Similarity=0.653 Sum_probs=20.9
Q ss_pred CCCCCCCCCCceeEeC-----CCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDH-----SAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~-----~~G~~vC~~CG~Vl~ 34 (182)
..||+|+.. +.++. ..+...|..||.++.
T Consensus 3 ~~CP~C~~~--~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTS--FRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCE--EEeCHHHcCCCCCEEECCCCCCEEE
Confidence 569999972 33342 345799999999874
No 36
>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=94.96 E-value=0.032 Score=31.31 Aligned_cols=27 Identities=26% Similarity=0.439 Sum_probs=14.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
-+||.|++. .... +...+||.+||.-+
T Consensus 3 p~Cp~C~se-~~y~--D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSE-YTYE--DGELLVCPECGHEW 29 (30)
T ss_dssp ---TTT------EE---SSSEEETTTTEEE
T ss_pred CCCCCCCCc-ceec--cCCEEeCCcccccC
Confidence 479999983 3333 46779999999754
No 37
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=94.95 E-value=0.11 Score=37.56 Aligned_cols=52 Identities=15% Similarity=0.128 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhC
Q 030129 104 GLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKT 155 (182)
Q Consensus 104 ~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~ 155 (182)
......+.|..++..++++..+.-. .++.+.... + ++..+++||+|+||+.+
T Consensus 30 ~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~ 88 (127)
T PF00134_consen 30 MRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKME 88 (127)
T ss_dssp HHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhh
Confidence 3466889999999999999988777 777777665 3 88999999999999987
No 38
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=94.87 E-value=0.027 Score=39.26 Aligned_cols=29 Identities=28% Similarity=0.563 Sum_probs=25.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
-.||.|++ + .+....+|-..|..||.++.
T Consensus 36 ~~Cp~C~~-~-~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 36 HVCPFCGR-T-TVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred CcCCCCCC-c-ceeeeccCeEEcCCCCCeec
Confidence 46999998 4 67888999999999999863
No 39
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=94.84 E-value=0.019 Score=35.82 Aligned_cols=27 Identities=30% Similarity=0.768 Sum_probs=22.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
..||.||. ..++.|+.. .+.|..||+.
T Consensus 20 ~~CPrCG~-gvfmA~H~d-R~~CGkCgyT 46 (51)
T COG1998 20 RFCPRCGP-GVFMADHKD-RWACGKCGYT 46 (51)
T ss_pred ccCCCCCC-cchhhhcCc-eeEeccccce
Confidence 57999995 677888766 8999999987
No 40
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=94.77 E-value=0.067 Score=44.00 Aligned_cols=49 Identities=10% Similarity=0.046 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-----cCHHHHHHHHHHHHHhhC
Q 030129 107 LAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-----IKTHYWLLACTLLVDKKT 155 (182)
Q Consensus 107 ~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-----l~~~~v~AAclY~acr~~ 155 (182)
-..+.|..++..|+|.+.|+-+ .++|+..-+ +.|..+|+-|||+||+.+
T Consensus 43 ~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvE 98 (264)
T KOG0794|consen 43 FMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVE 98 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhh
Confidence 3568899999999999999888 555665443 399999999999999976
No 41
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=94.69 E-value=0.091 Score=45.31 Aligned_cols=51 Identities=14% Similarity=-0.031 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC
Q 030129 106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS 156 (182)
Q Consensus 106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~ 156 (182)
.++...|.+++.+|++|..-+.. .+|-+..-. | .+..+|+||||+|++.+.
T Consensus 40 ~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEe 97 (323)
T KOG0834|consen 40 QEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEE 97 (323)
T ss_pred HHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhccc
Confidence 67999999999999999876555 666665433 4 778999999999999883
No 42
>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=94.58 E-value=0.062 Score=30.31 Aligned_cols=29 Identities=21% Similarity=0.460 Sum_probs=16.8
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
..+|+.||+ ........-..+|..||...
T Consensus 3 ~rfC~~CG~--~t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGA--PTKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT----BEEE-SSSS-EEESSSS-EE
T ss_pred CcccCcCCc--cccCCCCcCEeECCCCcCEe
Confidence 578999997 33445555669999999863
No 43
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=94.53 E-value=0.038 Score=34.29 Aligned_cols=28 Identities=25% Similarity=0.687 Sum_probs=19.1
Q ss_pred CCCCCCCCCceeEeCC-C-CceEeCCCceeee
Q 030129 5 FCSDCKKHTEVVFDHS-A-GDTVCSECGLVLE 34 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~-~-G~~vC~~CG~Vl~ 34 (182)
+||.||+ - +..... . ..++|..||.+..
T Consensus 2 FCp~Cg~-~-l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGN-M-LIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCC-c-cccccCCCCCEEECCcCCCeEE
Confidence 7999996 2 222222 2 3799999998854
No 44
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=94.52 E-value=0.031 Score=43.22 Aligned_cols=30 Identities=27% Similarity=0.576 Sum_probs=20.5
Q ss_pred CCCCCCCCCCceeEeCC---CCc-----eEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHS---AGD-----TVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~---~G~-----~vC~~CG~Vl 33 (182)
|+||+||+....+.|.. .|. .-|++||.-+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 57999997432566653 454 4599999765
No 45
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=94.46 E-value=0.019 Score=31.15 Aligned_cols=24 Identities=29% Similarity=0.833 Sum_probs=18.3
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.||+|+.. | ......|..||.++.
T Consensus 2 ~CP~C~~~--V----~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAE--V----PESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCC--c----hhhcCcCCCCCCCCc
Confidence 69999972 2 245689999999863
No 46
>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=94.42 E-value=0.024 Score=41.30 Aligned_cols=31 Identities=23% Similarity=0.664 Sum_probs=25.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (182)
...||.||.. .+|-..--+||..||.++.-.
T Consensus 9 KR~Cp~CG~k---FYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAK---FYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcch---hccCCCCCccCCCCCCccCcc
Confidence 4679999972 589888889999999998644
No 47
>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=94.41 E-value=0.041 Score=33.12 Aligned_cols=27 Identities=33% Similarity=0.849 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCc
Q 030129 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECG 30 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG 30 (182)
|-...||.|+. .+.. ..+|.++|..|+
T Consensus 15 ML~~~Cp~C~~--PL~~-~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 15 MLDEHCPDCGT--PLMR-DKDGKIYCVSCG 41 (41)
T ss_pred HhcCccCCCCC--eeEE-ecCCCEECCCCC
Confidence 34568999974 4544 578999999996
No 48
>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=94.39 E-value=0.058 Score=35.77 Aligned_cols=17 Identities=29% Similarity=0.788 Sum_probs=15.6
Q ss_pred EeCCCCceEeCCCceee
Q 030129 17 FDHSAGDTVCSECGLVL 33 (182)
Q Consensus 17 ~D~~~G~~vC~~CG~Vl 33 (182)
++..+|.++|.+||.+.
T Consensus 47 ~~i~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 47 VEIVEGELICPECGREY 63 (68)
T ss_dssp EETTTTEEEETTTTEEE
T ss_pred ccccCCEEEcCCCCCEE
Confidence 68899999999999986
No 49
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=93.87 E-value=0.076 Score=34.15 Aligned_cols=28 Identities=25% Similarity=0.656 Sum_probs=20.2
Q ss_pred CCCCCCCCCCCceeEeCCCC-------ceEeCCCce
Q 030129 3 DAFCSDCKKHTEVVFDHSAG-------DTVCSECGL 31 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G-------~~vC~~CG~ 31 (182)
..-||.||+ ..+.+....+ .+.|.+||.
T Consensus 3 LkPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence 356999987 5666665544 256999999
No 50
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=93.75 E-value=0.056 Score=35.15 Aligned_cols=30 Identities=27% Similarity=0.669 Sum_probs=25.9
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
...-||.|++ .+.+|.+.++++|..|++..
T Consensus 7 eiLaCP~~kg--~L~~~~~~~~L~c~~~~~aY 36 (60)
T COG2835 7 EILACPVCKG--PLVYDEEKQELICPRCKLAY 36 (60)
T ss_pred eeeeccCcCC--cceEeccCCEEEecccCcee
Confidence 3456999997 48999999999999999985
No 51
>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=93.68 E-value=0.065 Score=32.09 Aligned_cols=29 Identities=28% Similarity=0.634 Sum_probs=16.4
Q ss_pred CCCCCCCCCCcee-EeC--CCCceEeCCCcee
Q 030129 4 AFCSDCKKHTEVV-FDH--SAGDTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv-~D~--~~G~~vC~~CG~V 32 (182)
..||.|++...+- ++. .+|..+|..|+-+
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C~~~ 35 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICRQCGGD 35 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEETTTTBE
T ss_pred CCCCCCcCccccccCcCcccCCCEECCCCCCc
Confidence 4699999865554 443 4699999999434
No 52
>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=93.64 E-value=0.072 Score=40.81 Aligned_cols=30 Identities=30% Similarity=0.742 Sum_probs=22.8
Q ss_pred CCCCCCCCCCceeEeC---CCCceE-----eCCCceee
Q 030129 4 AFCSDCKKHTEVVFDH---SAGDTV-----CSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~---~~G~~v-----C~~CG~Vl 33 (182)
|+||.|+....-|.|+ +.|..| |..||.=+
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence 6799999866667786 667655 99998754
No 53
>PRK10220 hypothetical protein; Provisional
Probab=92.94 E-value=0.09 Score=38.19 Aligned_cols=30 Identities=23% Similarity=0.523 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
|+.-.||.|.+ .-.-. +...+||.+||.--
T Consensus 1 m~lP~CP~C~s-eytY~--d~~~~vCpeC~hEW 30 (111)
T PRK10220 1 MSLPHCPKCNS-EYTYE--DNGMYICPECAHEW 30 (111)
T ss_pred CCCCcCCCCCC-cceEc--CCCeEECCcccCcC
Confidence 77889999997 33223 34569999999643
No 54
>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=92.92 E-value=0.067 Score=39.97 Aligned_cols=31 Identities=13% Similarity=0.288 Sum_probs=25.8
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (182)
...||.||.. .+|-..--++|..||.++...
T Consensus 9 Kr~Cp~cg~k---FYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 9 KRICPNTGSK---FYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cccCCCcCcc---ccccCCCCccCCCcCCccCcc
Confidence 4679999972 589888899999999998644
No 55
>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=92.54 E-value=0.08 Score=33.39 Aligned_cols=31 Identities=23% Similarity=0.283 Sum_probs=20.1
Q ss_pred CCCCCCCCCCceeE---eC--CCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVF---DH--SAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~---D~--~~G~~vC~~CG~Vl~ 34 (182)
..||.||+....+. +. ..|...|..||....
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~ 37 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP 37 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence 46999998433132 32 334457999999864
No 56
>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=92.45 E-value=0.08 Score=37.81 Aligned_cols=28 Identities=32% Similarity=0.739 Sum_probs=21.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (182)
..||.||+ .+ .+..+.++|..||.+.+.
T Consensus 1 ~fC~~Cg~--~l--~~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 1 KFCPKCGS--LM--TPKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCCcccCc--cc--ccCCCeEECcCCCCcccc
Confidence 37999996 22 456789999999998653
No 57
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=91.85 E-value=0.16 Score=37.23 Aligned_cols=25 Identities=32% Similarity=0.679 Sum_probs=20.0
Q ss_pred CCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129 6 CSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (182)
Q Consensus 6 Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (182)
||.||+ .-.|+ .+-|.+||+.|+-+
T Consensus 1 CPvCg~-~l~vt-----~l~C~~C~t~i~G~ 25 (113)
T PF09862_consen 1 CPVCGG-ELVVT-----RLKCPSCGTEIEGE 25 (113)
T ss_pred CCCCCC-ceEEE-----EEEcCCCCCEEEee
Confidence 999997 44454 59999999999644
No 58
>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=91.78 E-value=0.13 Score=36.19 Aligned_cols=29 Identities=31% Similarity=0.524 Sum_probs=24.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
..||.||+ .. +.....|-.-|..||.++.
T Consensus 36 y~Cp~Cgk-~~-vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 36 YTCPFCGK-TS-VKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp BEESSSSS-SE-EEEEETTEEEETTTTEEEE
T ss_pred CcCCCCCC-ce-eEEeeeEEeecCCCCCEEe
Confidence 46999997 44 6788999999999999984
No 59
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=91.46 E-value=0.11 Score=35.47 Aligned_cols=29 Identities=34% Similarity=0.751 Sum_probs=26.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
.+||.|-. ...++.++...++|.+|+.|+
T Consensus 35 VkC~gc~~-iT~vfSHaqtvVvc~~c~~il 63 (84)
T KOG1779|consen 35 VKCPGCFK-ITTVFSHAQTVVVCEGCSTIL 63 (84)
T ss_pred EEcCCceE-EEEEeecCceEEEcCCCceEE
Confidence 57999986 567899999999999999997
No 60
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=91.33 E-value=0.15 Score=37.33 Aligned_cols=34 Identities=29% Similarity=0.579 Sum_probs=23.7
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (182)
+..||.||+---.-.|...+.++|..||...+-.
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 5789999972111123356789999999987644
No 61
>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=91.28 E-value=0.18 Score=33.17 Aligned_cols=29 Identities=21% Similarity=0.576 Sum_probs=21.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
..||.||.. . ..+.......|..||...+
T Consensus 29 q~C~~CG~~-~-~~~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 29 QTCPRCGHR-N-KKRRSGRVFTCPNCGFEMD 57 (69)
T ss_pred cCccCcccc-c-ccccccceEEcCCCCCEEC
Confidence 569999963 2 2245667899999999864
No 62
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=90.79 E-value=0.12 Score=30.23 Aligned_cols=28 Identities=21% Similarity=0.665 Sum_probs=20.5
Q ss_pred CCCCCCCCCCceeEeC-----CCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDH-----SAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~-----~~G~~vC~~CG~Vl 33 (182)
..||+|+.. ..+++ ..+..-|..||.++
T Consensus 3 i~CP~C~~~--f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTR--FRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCce--EEcCHHHcccCCcEEECCCCCcEe
Confidence 469999963 33332 46779999999986
No 63
>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=90.43 E-value=0.31 Score=29.70 Aligned_cols=27 Identities=22% Similarity=0.469 Sum_probs=20.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCce
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (182)
..||.||+ ..+..-...+..-|.+|+.
T Consensus 19 ~~CP~Cg~-~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGS-TKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCC-eeeEEeCCCCeEECCCCCC
Confidence 46999998 4544444569999999974
No 64
>PRK12495 hypothetical protein; Provisional
Probab=90.32 E-value=0.19 Score=40.93 Aligned_cols=31 Identities=29% Similarity=0.812 Sum_probs=24.8
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (182)
|....|+.||. + | + -..|.++|..|+.++.+
T Consensus 40 msa~hC~~CG~-P-I-p-a~pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 40 MTNAHCDECGD-P-I-F-RHDGQEFCPTCQQPVTE 70 (226)
T ss_pred cchhhcccccC-c-c-c-CCCCeeECCCCCCcccc
Confidence 56678999997 3 3 3 45899999999999875
No 65
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=90.12 E-value=0.26 Score=34.75 Aligned_cols=29 Identities=28% Similarity=0.528 Sum_probs=24.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
..||.||+ .. +.....|-..|..||.++.
T Consensus 37 y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 37 YFCPFCGK-HA-VKRQAVGIWRCKGCKKTVA 65 (90)
T ss_pred ccCCCCCC-Cc-eeeeeeEEEEcCCCCCEEe
Confidence 57999997 44 5677889999999999984
No 66
>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=90.12 E-value=0.054 Score=31.63 Aligned_cols=29 Identities=28% Similarity=0.718 Sum_probs=20.3
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
.||.||..-++.+++..-+.+|..||.-|
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred CcCCCCCccccccCCCCCCCccCCCCCee
Confidence 58888875566777777778888888754
No 67
>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=90.09 E-value=0.15 Score=29.83 Aligned_cols=30 Identities=33% Similarity=0.545 Sum_probs=19.2
Q ss_pred CCCCCCCCCCceeEeCC-CCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHS-AGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~-~G~~vC~~CG~Vl 33 (182)
.+|++||..-++..... .....|..||.-+
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 47999996323333322 4567899999843
No 68
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=89.93 E-value=0.3 Score=35.39 Aligned_cols=33 Identities=24% Similarity=0.697 Sum_probs=24.2
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (182)
|+...||.|.+ +.+++ +.+.++|.+|+.--.+.
T Consensus 1 ~~lp~cp~c~s--EytYe-d~~~~~cpec~~ew~~~ 33 (112)
T COG2824 1 MSLPPCPKCNS--EYTYE-DGGQLICPECAHEWNEN 33 (112)
T ss_pred CCCCCCCccCC--ceEEe-cCceEeCchhccccccc
Confidence 56778999996 45554 45589999999765433
No 69
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=89.83 E-value=0.21 Score=35.83 Aligned_cols=29 Identities=34% Similarity=0.865 Sum_probs=22.2
Q ss_pred CCCCCCCCCcee---EeC--CCCceEeCCCceeee
Q 030129 5 FCSDCKKHTEVV---FDH--SAGDTVCSECGLVLE 34 (182)
Q Consensus 5 ~Cp~Cg~~~~iv---~D~--~~G~~vC~~CG~Vl~ 34 (182)
.||.||. ..++ ++- .-|..+|..||+-.+
T Consensus 24 tCp~Cgh-e~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 24 TCPRCGH-EKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred ecCccCC-eeeeEEEEEecCceeEEEcccCcceEE
Confidence 5999997 4444 443 668899999999875
No 70
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=89.53 E-value=0.19 Score=36.10 Aligned_cols=30 Identities=27% Similarity=0.612 Sum_probs=22.3
Q ss_pred CCCCCCCCCCce--eEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEV--VFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~i--v~D~~~G~~vC~~CG~Vl~ 34 (182)
..||+||. ..+ -.|...+..+|..||...+
T Consensus 22 f~CP~Cge-~~v~v~~~k~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 22 FECPRCGK-VSISVKIKKNIAIITCGNCGLYTE 53 (99)
T ss_pred eECCCCCC-eEeeeecCCCcceEECCCCCCccC
Confidence 35999995 332 2455778899999999865
No 71
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=89.07 E-value=0.28 Score=37.73 Aligned_cols=30 Identities=30% Similarity=0.635 Sum_probs=20.5
Q ss_pred CCCCCCCCCCceeEeC---CCCc-----eEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDH---SAGD-----TVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~---~~G~-----~vC~~CG~Vl 33 (182)
|+||.|+....-|.|+ +.|. -.|.+||.=+
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RF 38 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERF 38 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhccccccccc
Confidence 6799999855556675 4454 3588888643
No 72
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=88.99 E-value=0.86 Score=39.39 Aligned_cols=49 Identities=10% Similarity=0.053 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHhCChHHH-HHHHHHHHHHhc-----c---CHHHHHHHHHHHHHhhC
Q 030129 107 LAFKTIATMSDRIGQMRYI-RRWKIKSLVEAE-----I---KTHYWLLACTLLVDKKT 155 (182)
Q Consensus 107 ~a~~~I~~i~~~L~L~~~v-~~~~i~k~a~~~-----l---~~~~v~AAclY~acr~~ 155 (182)
...+.|-.+-..|+||++. +.+..+.-+.+. + +++.||+||+|+|.|..
T Consensus 140 hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~ 197 (367)
T KOG0835|consen 140 HPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNL 197 (367)
T ss_pred ccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhh
Confidence 3446677888888998876 222333333333 2 99999999999999976
No 73
>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=88.99 E-value=0.31 Score=34.36 Aligned_cols=29 Identities=31% Similarity=0.565 Sum_probs=24.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
..||.|+. .. +.....|-..|..||.++.
T Consensus 36 y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 36 YVCPFCGK-KT-VKRGSTGIWTCRKCGAKFA 64 (91)
T ss_pred ccCCCCCC-Cc-eEEEeeEEEEcCCCCCEEe
Confidence 57999997 44 5677999999999999974
No 74
>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=88.53 E-value=0.43 Score=34.68 Aligned_cols=28 Identities=18% Similarity=0.496 Sum_probs=19.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
-.||.|++ .-.-.| ...+||.+||.--.
T Consensus 3 p~CP~C~s-eytY~d--g~~~iCpeC~~EW~ 30 (109)
T TIGR00686 3 PPCPKCNS-EYTYHD--GTQLICPSCLYEWN 30 (109)
T ss_pred CcCCcCCC-cceEec--CCeeECcccccccc
Confidence 46999997 333333 44699999998654
No 75
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=88.44 E-value=0.31 Score=31.64 Aligned_cols=26 Identities=31% Similarity=0.754 Sum_probs=12.7
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
.|..||. .|-.+..--...|.+||.+
T Consensus 11 ~CtSCg~--~i~p~e~~v~F~CPnCGe~ 36 (61)
T COG2888 11 VCTSCGR--EIAPGETAVKFPCPNCGEV 36 (61)
T ss_pred eeccCCC--EeccCCceeEeeCCCCCce
Confidence 5666664 2222322233567777743
No 76
>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=88.14 E-value=0.22 Score=34.33 Aligned_cols=32 Identities=25% Similarity=0.564 Sum_probs=17.6
Q ss_pred CCCCCCCCCce--eEeC--CCCceEeCCCceeeeCC
Q 030129 5 FCSDCKKHTEV--VFDH--SAGDTVCSECGLVLESH 36 (182)
Q Consensus 5 ~Cp~Cg~~~~i--v~D~--~~G~~vC~~CG~Vl~e~ 36 (182)
.||.|+....+ ..|. ..|.+.|..||...+-.
T Consensus 24 ~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 24 DCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp --TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred cCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 59999943333 3344 46789999999998643
No 77
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=87.99 E-value=0.39 Score=33.82 Aligned_cols=29 Identities=24% Similarity=0.559 Sum_probs=24.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
..||.|++ .. +.....|-.-|..||.++.
T Consensus 37 y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 37 HVCPVCGR-PK-VKRVGTGIWECRKCGAKFA 65 (90)
T ss_pred ccCCCCCC-Cc-eEEEEEEEEEcCCCCCEEe
Confidence 57999986 44 5677899999999999985
No 78
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=87.98 E-value=0.43 Score=29.07 Aligned_cols=27 Identities=30% Similarity=0.720 Sum_probs=19.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
..|.+||. ++..+ ..+.+-|.+||.=|
T Consensus 3 Y~C~~Cg~--~~~~~-~~~~irC~~CG~rI 29 (44)
T smart00659 3 YICGECGR--ENEIK-SKDVVRCRECGYRI 29 (44)
T ss_pred EECCCCCC--EeecC-CCCceECCCCCceE
Confidence 46999997 33333 56779999999644
No 79
>COG4640 Predicted membrane protein [Function unknown]
Probab=87.77 E-value=0.28 Score=43.31 Aligned_cols=28 Identities=29% Similarity=0.800 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (182)
|..||.||+. . .+++.-|+.||.-+..+
T Consensus 1 M~fC~kcG~q-k-----~Ed~~qC~qCG~~~t~~ 28 (465)
T COG4640 1 MKFCPKCGSQ-K-----AEDDVQCTQCGHKFTSR 28 (465)
T ss_pred CCcccccccc-c-----ccccccccccCCcCCch
Confidence 4689999973 2 35677799999876533
No 80
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=87.33 E-value=0.62 Score=27.68 Aligned_cols=27 Identities=30% Similarity=0.596 Sum_probs=18.5
Q ss_pred CCCCCCCCCceeEe------CC---CCceEeCCCcee
Q 030129 5 FCSDCKKHTEVVFD------HS---AGDTVCSECGLV 32 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D------~~---~G~~vC~~CG~V 32 (182)
.||.||. .+.++- .+ +-.++|.+||..
T Consensus 2 ~Cp~C~~-~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~ 37 (40)
T smart00440 2 PCPKCGN-REATFFQLQTRSADEPMTVFYVCTKCGHR 37 (40)
T ss_pred cCCCCCC-CeEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence 6999997 455431 12 336899999965
No 81
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=87.26 E-value=0.63 Score=30.67 Aligned_cols=28 Identities=21% Similarity=0.398 Sum_probs=18.8
Q ss_pred CCCCCCCCCCceeEeCCCCc--eEeCCCcee
Q 030129 4 AFCSDCKKHTEVVFDHSAGD--TVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~--~vC~~CG~V 32 (182)
..||.||.. .+..-...|- .+|..||..
T Consensus 7 KPCPFCG~~-~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 7 KPCPFCGCP-SVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred cCCCCCCCc-eeEEEecCceEEEEcCCCCcC
Confidence 469999984 3333333443 689999985
No 82
>PRK05978 hypothetical protein; Provisional
Probab=87.19 E-value=0.42 Score=36.74 Aligned_cols=32 Identities=19% Similarity=0.445 Sum_probs=21.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (182)
.+||.||. ..+..-+-.=..-|..||+-++-.
T Consensus 34 grCP~CG~-G~LF~g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 34 GRCPACGE-GKLFRAFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred CcCCCCCC-CcccccccccCCCccccCCccccC
Confidence 47999997 555332233346799999987533
No 83
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=87.18 E-value=1.5 Score=30.86 Aligned_cols=66 Identities=12% Similarity=0.082 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHhCChHHHHHH--HHHHHH-Hhc-c---CHHHHHHHHHHHHHhhCC------HHHHHhcCCCceeeece
Q 030129 108 AFKTIATMSDRIGQMRYIRRW--KIKSLV-EAE-I---KTHYWLLACTLLVDKKTS------HALLRKSALSPMELQRR 173 (182)
Q Consensus 108 a~~~I~~i~~~L~L~~~v~~~--~i~k~a-~~~-l---~~~~v~AAclY~acr~~~------~eia~~~~v~~~~i~r~ 173 (182)
.+..|+.+....+....+... .+...+ .+. | +|..+||||+|+|.+..+ ..+...++++..+|-..
T Consensus 3 p~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c 81 (118)
T PF02984_consen 3 PYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKEC 81 (118)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHH
Confidence 456777774444444455555 444554 333 3 999999999999998742 45666777766665443
No 84
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=86.91 E-value=0.79 Score=30.96 Aligned_cols=31 Identities=13% Similarity=0.308 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCceeEeC-------CCCceEeC--CCceeee
Q 030129 3 DAFCSDCKKHTEVVFDH-------SAGDTVCS--ECGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~-------~~G~~vC~--~CG~Vl~ 34 (182)
++.||.||. ...|.+. .+=...|+ +||..+-
T Consensus 1 mm~CP~Cg~-~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 1 MFHCPLCQH-AAHARTSRYITDTTKERYHQCQNVNCSATFI 40 (72)
T ss_pred CccCCCCCC-ccEEEEChhcChhhheeeeecCCCCCCCEEE
Confidence 478999998 4566664 22236788 8998764
No 85
>PF12773 DZR: Double zinc ribbon
Probab=86.76 E-value=0.36 Score=29.65 Aligned_cols=11 Identities=27% Similarity=0.863 Sum_probs=5.6
Q ss_pred ceEeCCCceee
Q 030129 23 DTVCSECGLVL 33 (182)
Q Consensus 23 ~~vC~~CG~Vl 33 (182)
..+|..||..+
T Consensus 29 ~~~C~~Cg~~~ 39 (50)
T PF12773_consen 29 KKICPNCGAEN 39 (50)
T ss_pred CCCCcCCcCCC
Confidence 44555555543
No 86
>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=86.71 E-value=0.72 Score=25.30 Aligned_cols=22 Identities=23% Similarity=0.540 Sum_probs=11.8
Q ss_pred CCCCCCCCCceeEeCCCCceEeCC
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSE 28 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~ 28 (182)
.||.||+ .++...+.-.+.|.+
T Consensus 1 ~CP~C~s--~l~~~~~ev~~~C~N 22 (28)
T PF03119_consen 1 TCPVCGS--KLVREEGEVDIRCPN 22 (28)
T ss_dssp B-TTT----BEEE-CCTTCEEE--
T ss_pred CcCCCCC--EeEcCCCCEeEECCC
Confidence 5999996 566666666788864
No 87
>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=86.65 E-value=0.78 Score=27.05 Aligned_cols=27 Identities=33% Similarity=0.607 Sum_probs=15.1
Q ss_pred CCCCCCCCCceeEe-C-----C---CCceEeCCCcee
Q 030129 5 FCSDCKKHTEVVFD-H-----S---AGDTVCSECGLV 32 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D-~-----~---~G~~vC~~CG~V 32 (182)
.||.||.. +.++- . + +-.++|.+||..
T Consensus 2 ~Cp~Cg~~-~a~~~~~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 2 KCPKCGHN-EAVFFQIQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp --SSS-SS-EEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred CCcCCCCC-eEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence 69999974 44332 1 2 224889999975
No 88
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=86.45 E-value=3.4 Score=35.81 Aligned_cols=55 Identities=15% Similarity=0.087 Sum_probs=44.4
Q ss_pred chHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHH-Hhc-c---CHHHHHHHHHHHHHhhC
Q 030129 101 PDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLV-EAE-I---KTHYWLLACTLLVDKKT 155 (182)
Q Consensus 101 ~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a-~~~-l---~~~~v~AAclY~acr~~ 155 (182)
.+--..-+-..|++-+=-|+||+...-+ -||... ... | ..+.++.|||.+|++.+
T Consensus 19 e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiE 80 (367)
T KOG0835|consen 19 EEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIE 80 (367)
T ss_pred HHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhc
Confidence 3444466899999999999999987666 566554 555 5 89999999999999987
No 89
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=85.41 E-value=0.2 Score=39.59 Aligned_cols=29 Identities=31% Similarity=0.796 Sum_probs=20.8
Q ss_pred CCCCCCCCCceeE-eCCCCceEeCCCceeeeC
Q 030129 5 FCSDCKKHTEVVF-DHSAGDTVCSECGLVLES 35 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~-D~~~G~~vC~~CG~Vl~e 35 (182)
.||.|+. ...+ |.-+....|..||.++.+
T Consensus 119 ~Cp~C~~--rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 119 FCPNCHI--RFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred ECCCCCc--EEeHHHHhhcCCcCCCCCCCCee
Confidence 5999986 2333 334567899999999864
No 90
>PRK08402 replication factor A; Reviewed
Probab=85.40 E-value=0.63 Score=40.71 Aligned_cols=27 Identities=30% Similarity=0.767 Sum_probs=22.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
..||.|++ .++.|...|...|..||.|
T Consensus 213 ~aCp~CnK--kv~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 213 DACPECRR--KVDYDPATDTWICPEHGEV 239 (355)
T ss_pred ecCCCCCe--EEEEecCCCCEeCCCCCCc
Confidence 36999986 4555888899999999975
No 91
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=85.24 E-value=0.67 Score=29.30 Aligned_cols=29 Identities=34% Similarity=0.696 Sum_probs=21.4
Q ss_pred CCCCCCCCCceeEeCCCCc----eEeCCCceee
Q 030129 5 FCSDCKKHTEVVFDHSAGD----TVCSECGLVL 33 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~----~vC~~CG~Vl 33 (182)
.||+||....+..|.+.|+ -=|.-|-.=+
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI 34 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPI 34 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCcc
Confidence 6999998778888998886 2366666543
No 92
>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=85.21 E-value=0.95 Score=32.63 Aligned_cols=31 Identities=23% Similarity=0.518 Sum_probs=20.3
Q ss_pred CCCCCCCCCCCceeEe------CC--C-Cc-eEeCCCceeee
Q 030129 3 DAFCSDCKKHTEVVFD------HS--A-GD-TVCSECGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D------~~--~-G~-~vC~~CG~Vl~ 34 (182)
...||+||. ..+..+ .. . .. ++|+.|+.-+.
T Consensus 2 p~~CpYCg~-~~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG 42 (102)
T PF11672_consen 2 PIICPYCGG-PAELVDGSEIYGHRYDDGPYLYVCTPCDAYVG 42 (102)
T ss_pred CcccCCCCC-eeEEcccchhcCccCCCCceeEECCCCCceee
Confidence 468999998 344444 11 2 22 78999988775
No 93
>PRK02935 hypothetical protein; Provisional
Probab=85.11 E-value=0.64 Score=33.63 Aligned_cols=38 Identities=26% Similarity=0.581 Sum_probs=24.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCccccccccccc
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFA 48 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~ 48 (182)
..||+|++.+.+.=+ ...|-.|+.-+. +|.+.|-..|+
T Consensus 71 V~CP~C~K~TKmLGr----vD~CM~C~~PLT---Ld~~legkefd 108 (110)
T PRK02935 71 VICPSCEKPTKMLGR----VDACMHCNQPLT---LDRSLEGKEFD 108 (110)
T ss_pred eECCCCCchhhhccc----eeecCcCCCcCC---cCccccccCcC
Confidence 469999986554322 358999998874 45444433444
No 94
>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=85.00 E-value=0.56 Score=26.64 Aligned_cols=24 Identities=29% Similarity=0.715 Sum_probs=15.9
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCce
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (182)
.|.+||.. +.+.....+-|..||.
T Consensus 2 ~C~~Cg~~---~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAE---VELKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSS---E-BSTSSTSSBSSSS-
T ss_pred CCCcCCCe---eEcCCCCcEECCcCCC
Confidence 58899862 2244556688999985
No 95
>PF15616 TerY-C: TerY-C metal binding domain
Probab=83.84 E-value=0.71 Score=34.77 Aligned_cols=9 Identities=22% Similarity=0.733 Sum_probs=6.9
Q ss_pred CCCCCCCCC
Q 030129 4 AFCSDCKKH 12 (182)
Q Consensus 4 ~~Cp~Cg~~ 12 (182)
--||+||..
T Consensus 78 PgCP~CGn~ 86 (131)
T PF15616_consen 78 PGCPHCGNQ 86 (131)
T ss_pred CCCCCCcCh
Confidence 459999973
No 96
>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=83.79 E-value=0.5 Score=43.70 Aligned_cols=43 Identities=21% Similarity=0.596 Sum_probs=28.8
Q ss_pred CCCCCCCCCCcee-----E----eCCCCceEeCCCceeeeCCC---ccccccccc
Q 030129 4 AFCSDCKKHTEVV-----F----DHSAGDTVCSECGLVLESHS---IDETSEWRT 46 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv-----~----D~~~G~~vC~~CG~Vl~e~~---id~~~ewr~ 46 (182)
..||+||....+. . ++.+-.++|..||..++|+- +...-+|+.
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~~~G~Wv~ 255 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRRMVRRGRWVA 255 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhhccCCeEEEe
Confidence 4699999643332 2 24566799999999998753 223457764
No 97
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=83.51 E-value=3.1 Score=35.69 Aligned_cols=45 Identities=7% Similarity=0.060 Sum_probs=35.2
Q ss_pred CChHHHHHH--HHHHHHH-hc--c--CHHHHHHHHHHHHHhhCC-----HHHHHhcC
Q 030129 120 GQMRYIRRW--KIKSLVE-AE--I--KTHYWLLACTLLVDKKTS-----HALLRKSA 164 (182)
Q Consensus 120 ~L~~~v~~~--~i~k~a~-~~--l--~~~~v~AAclY~acr~~~-----~eia~~~~ 164 (182)
.||..|+-+ .+|+++. .. . +|..|+++|+|+||+... .+|+.-..
T Consensus 73 ~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~ 129 (325)
T KOG2496|consen 73 NLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMN 129 (325)
T ss_pred CCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhcc
Confidence 789999888 8899884 33 2 999999999999999763 45555443
No 98
>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=82.92 E-value=0.62 Score=28.85 Aligned_cols=28 Identities=29% Similarity=0.567 Sum_probs=16.4
Q ss_pred CCCCCCCCCCceeEe-CCCCceEeCCCce
Q 030129 4 AFCSDCKKHTEVVFD-HSAGDTVCSECGL 31 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D-~~~G~~vC~~CG~ 31 (182)
.+|++||..-++... .+.....|..||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 468888852232221 1235567888886
No 99
>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=82.80 E-value=1.4 Score=33.20 Aligned_cols=27 Identities=30% Similarity=0.740 Sum_probs=19.4
Q ss_pred CCC--CCCCCCceeEeCCCCceEeCCCceeee
Q 030129 5 FCS--DCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 5 ~Cp--~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.|| .|++ .+..+ ..|.+.|..||..++
T Consensus 20 aC~~~~C~k--Kv~~~-~~~~y~C~~C~~~~~ 48 (146)
T PF08646_consen 20 ACPNEKCNK--KVTEN-GDGSYRCEKCNKTVE 48 (146)
T ss_dssp E-TSTTTS---B-EEE-TTTEEEETTTTEEES
T ss_pred CCCCccCCC--EeecC-CCcEEECCCCCCcCC
Confidence 499 9997 35555 779999999999873
No 100
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=82.70 E-value=0.57 Score=27.20 Aligned_cols=29 Identities=31% Similarity=0.722 Sum_probs=19.2
Q ss_pred CCCCCCCCCCceeEe----CCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFD----HSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D----~~~G~~vC~~CG~Vl 33 (182)
..||+|+..-. |-| .....+-|+.||.++
T Consensus 3 i~Cp~C~~~y~-i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYE-IDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEe-CCHHHCCCCCcEEECCCCCCEe
Confidence 46999996322 222 244568899999875
No 101
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=82.34 E-value=0.99 Score=29.78 Aligned_cols=13 Identities=23% Similarity=0.445 Sum_probs=9.0
Q ss_pred CCCCCCCCCceeEe
Q 030129 5 FCSDCKKHTEVVFD 18 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D 18 (182)
+||.||. ++..++
T Consensus 6 kCpKCgn-~~~~ek 18 (68)
T COG3478 6 KCPKCGN-TNYEEK 18 (68)
T ss_pred cCCCcCC-cchhhc
Confidence 4999997 455444
No 102
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.08 E-value=0.67 Score=34.37 Aligned_cols=36 Identities=22% Similarity=0.483 Sum_probs=23.0
Q ss_pred CCCCCCCCCceeEe-CCCCceEeCCCceeeeCCCccccc
Q 030129 5 FCSDCKKHTEVVFD-HSAGDTVCSECGLVLESHSIDETS 42 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D-~~~G~~vC~~CG~Vl~e~~id~~~ 42 (182)
.||+||. ..+ +| .-.=--.|..||.=+..+--|++|
T Consensus 23 rCP~CGe-GrL-F~gFLK~~p~C~aCG~dyg~~~a~DgP 59 (126)
T COG5349 23 RCPRCGE-GRL-FRGFLKVVPACEACGLDYGFADADDGP 59 (126)
T ss_pred CCCCCCC-chh-hhhhcccCchhhhccccccCCcccCCC
Confidence 6999996 443 33 222336899999887655444444
No 103
>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=82.07 E-value=0.83 Score=25.11 Aligned_cols=28 Identities=18% Similarity=0.372 Sum_probs=15.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCce
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (182)
.+||.|+....-+.....+..+|..|=-
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCcC
Confidence 4799999743334445677799998843
No 104
>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=81.74 E-value=0.37 Score=30.28 Aligned_cols=32 Identities=16% Similarity=0.359 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCCCcee-EeCCCCceEeCCCceee
Q 030129 1 MTDAFCSDCKKHTEVV-FDHSAGDTVCSECGLVL 33 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv-~D~~~G~~vC~~CG~Vl 33 (182)
|....|++|++- =.. -+....++-|..||.+-
T Consensus 2 ~~eiRC~~Cnkl-La~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 2 LKEIRCGHCNKL-LAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred CcceeccchhHH-HhhhcCccEEEEECCCCCccc
Confidence 356789999862 111 24566889999999995
No 105
>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=81.71 E-value=1.1 Score=34.44 Aligned_cols=26 Identities=27% Similarity=0.760 Sum_probs=20.0
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
.||.|++ .+ .+...|.+.|..|+..+
T Consensus 36 aC~~C~k--kv-~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 36 ACPGCNK--KV-VEEGNGTYRCEKCNKSV 61 (166)
T ss_pred cccccCc--cc-EeCCCCcEECCCCCCcC
Confidence 5999997 23 34444899999999886
No 106
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=81.58 E-value=3.6 Score=36.60 Aligned_cols=48 Identities=15% Similarity=0.083 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHhCChHHHHHH--HHHHH-HHhc-c---CHHHHHHHHHHHHHhhC
Q 030129 108 AFKTIATMSDRIGQMRYIRRW--KIKSL-VEAE-I---KTHYWLLACTLLVDKKT 155 (182)
Q Consensus 108 a~~~I~~i~~~L~L~~~v~~~--~i~k~-a~~~-l---~~~~v~AAclY~acr~~ 155 (182)
..+++.++....+|....+-+ -+|.+ +.+. + +....|.|||.+|.+.+
T Consensus 385 lKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmn 439 (497)
T KOG4164|consen 385 LKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMN 439 (497)
T ss_pred HHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhh
Confidence 445666666666776544444 55554 4666 4 88999999999999987
No 107
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=81.37 E-value=0.56 Score=29.30 Aligned_cols=28 Identities=29% Similarity=0.669 Sum_probs=21.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
..|-.||+ .+..|.....+-|+.||.=|
T Consensus 7 Y~C~~Cg~--~~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 7 YKCARCGR--EVELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEhhhcCC--eeehhhccCceeCCCCCcEE
Confidence 46999996 34446688889999999643
No 108
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=81.34 E-value=0.75 Score=29.55 Aligned_cols=24 Identities=21% Similarity=0.522 Sum_probs=18.3
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
.+.+|+.||. ..+ ..+|..||...
T Consensus 4 ~mr~C~~Cgv-YTL-------k~~CP~CG~~t 27 (56)
T PRK13130 4 KIRKCPKCGV-YTL-------KEICPVCGGKT 27 (56)
T ss_pred cceECCCCCC-EEc-------cccCcCCCCCC
Confidence 3568999996 333 57999999775
No 109
>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=81.06 E-value=1.6 Score=28.74 Aligned_cols=9 Identities=33% Similarity=1.147 Sum_probs=7.7
Q ss_pred eEeCCCcee
Q 030129 24 TVCSECGLV 32 (182)
Q Consensus 24 ~vC~~CG~V 32 (182)
++|++||..
T Consensus 37 v~C~~CGYT 45 (64)
T PF09855_consen 37 VSCTNCGYT 45 (64)
T ss_pred EECCCCCCE
Confidence 689999987
No 110
>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=81.01 E-value=1.3 Score=25.10 Aligned_cols=23 Identities=30% Similarity=0.807 Sum_probs=14.1
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCce
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (182)
.|+.||- ++|.......|..||.
T Consensus 3 ~C~~CGy----~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGY----IYDGEEAPWVCPVCGA 25 (33)
T ss_pred ECCCCCC----EECCCcCCCcCcCCCC
Confidence 4777763 3455556667777765
No 111
>PHA02942 putative transposase; Provisional
Probab=80.98 E-value=1.2 Score=39.30 Aligned_cols=28 Identities=18% Similarity=0.480 Sum_probs=20.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
..||.||.. . .+.......|..||.+.+
T Consensus 326 q~Cs~CG~~-~--~~l~~r~f~C~~CG~~~d 353 (383)
T PHA02942 326 VSCPKCGHK-M--VEIAHRYFHCPSCGYEND 353 (383)
T ss_pred ccCCCCCCc-c--CcCCCCEEECCCCCCEeC
Confidence 569999962 2 244456799999999974
No 112
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=80.91 E-value=1.3 Score=36.99 Aligned_cols=29 Identities=17% Similarity=0.450 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
..+||.||+. +......-...|..||.+.
T Consensus 99 ~~fC~~CG~~--~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 99 HRFCGYCGHP--MHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred CccccccCCC--CeecCCceeEECCCCCCEE
Confidence 4689999973 3334444558899999765
No 113
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=80.65 E-value=1.4 Score=31.49 Aligned_cols=31 Identities=23% Similarity=0.515 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCceeEeCC-CCceEeCCCceeee
Q 030129 3 DAFCSDCKKHTEVVFDHS-AGDTVCSECGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~-~G~~vC~~CG~Vl~ 34 (182)
+..||.||+ .-+|+--+ -....|..|++|..
T Consensus 1 m~FCP~Cgn-~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 1 MLFCPTCGN-MLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred CcccCCCCC-EEEEecCCeEeeEEcCCCCceee
Confidence 358999996 32332222 25578999999964
No 114
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=80.47 E-value=0.9 Score=29.23 Aligned_cols=26 Identities=23% Similarity=0.646 Sum_probs=17.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (182)
..||+||. .. .--.+|..||+--+..
T Consensus 28 ~~C~~CG~-~~------~~H~vC~~CG~Y~gr~ 53 (57)
T PRK12286 28 VECPNCGE-PK------LPHRVCPSCGYYKGRE 53 (57)
T ss_pred eECCCCCC-cc------CCeEECCCCCcCCCEE
Confidence 46999996 22 1248999999765433
No 115
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.44 E-value=1.5 Score=31.84 Aligned_cols=27 Identities=22% Similarity=0.589 Sum_probs=21.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (182)
..||.||. ..||+ ++-|..|++-+.-+
T Consensus 7 ~~cPvcg~-~~iVT-----eL~c~~~etTVrg~ 33 (122)
T COG3877 7 NRCPVCGR-KLIVT-----ELKCSNCETTVRGN 33 (122)
T ss_pred CCCCcccc-cceeE-----EEecCCCCceEecc
Confidence 47999998 56776 59999999998644
No 116
>PRK12366 replication factor A; Reviewed
Probab=80.16 E-value=1.1 Score=42.18 Aligned_cols=25 Identities=36% Similarity=0.954 Sum_probs=19.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
..||.|++ .++ + ..|.+.|..||.+
T Consensus 533 ~aCp~Cnk--Kv~-~-~~g~~~C~~c~~~ 557 (637)
T PRK12366 533 YLCPNCRK--RVE-E-VDGEYICEFCGEV 557 (637)
T ss_pred ecccccCe--EeE-c-CCCcEECCCCCCC
Confidence 36999986 333 3 5799999999988
No 117
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=80.11 E-value=0.68 Score=37.06 Aligned_cols=31 Identities=32% Similarity=0.587 Sum_probs=19.8
Q ss_pred CCCCCCCCCCce--eEeCCCC---ceEeCCCceeeeC
Q 030129 4 AFCSDCKKHTEV--VFDHSAG---DTVCSECGLVLES 35 (182)
Q Consensus 4 ~~Cp~Cg~~~~i--v~D~~~G---~~vC~~CG~Vl~e 35 (182)
+.||.|+. .++ .+=-..| .+-|.+||+|-.+
T Consensus 7 ~~Cp~Cg~-eev~hEVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 7 IECPSCGS-EEVSHEVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred EECCCCCc-chhhHHHHHhcCCceEEEccCCCcEeec
Confidence 46999994 333 1111223 4789999999855
No 118
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=79.82 E-value=0.88 Score=35.54 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=9.2
Q ss_pred ceEeCCCceee
Q 030129 23 DTVCSECGLVL 33 (182)
Q Consensus 23 ~~vC~~CG~Vl 33 (182)
.+.|+.||.+.
T Consensus 130 f~~C~~CgkiY 140 (165)
T COG1656 130 FYRCPKCGKIY 140 (165)
T ss_pred eeECCCCcccc
Confidence 46799999985
No 119
>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=78.73 E-value=1 Score=28.63 Aligned_cols=29 Identities=24% Similarity=0.566 Sum_probs=20.8
Q ss_pred CCCCCCCCCCcee--EeCCCCceEeCCCcee
Q 030129 4 AFCSDCKKHTEVV--FDHSAGDTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv--~D~~~G~~vC~~CG~V 32 (182)
..|++|..++-.. .+.+.=.++|..||..
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred EECcccchhhcccccccCCceEEEcCCCCCc
Confidence 4699998754443 5566667999999863
No 120
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=78.42 E-value=0.97 Score=33.34 Aligned_cols=18 Identities=39% Similarity=0.696 Sum_probs=15.0
Q ss_pred EeCCCCceEeCCCceeee
Q 030129 17 FDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 17 ~D~~~G~~vC~~CG~Vl~ 34 (182)
+|-.+|+++|.+||.|..
T Consensus 92 ~~v~EG~l~CpetG~vfp 109 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVFP 109 (124)
T ss_pred hhhccceEecCCCCcEee
Confidence 355789999999999973
No 121
>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=78.37 E-value=0.41 Score=40.61 Aligned_cols=30 Identities=17% Similarity=0.429 Sum_probs=21.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.+||.|+. .-...|-.....||..||.-..
T Consensus 27 ~~c~~c~~-~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 27 TKCPKCGQ-VLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred eECCCCcc-hhhHHHHHhhCCCCCCCCCcCc
Confidence 47999996 3333345667799999998754
No 122
>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=78.33 E-value=1.2 Score=27.51 Aligned_cols=16 Identities=31% Similarity=0.665 Sum_probs=10.7
Q ss_pred eEeCCCceeeeCCCcc
Q 030129 24 TVCSECGLVLESHSID 39 (182)
Q Consensus 24 ~vC~~CG~Vl~e~~id 39 (182)
+.|..||.|.++..=|
T Consensus 2 y~C~~CgyvYd~~~Gd 17 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGD 17 (47)
T ss_dssp EEETTTSBEEETTTBB
T ss_pred cCCCCCCEEEcCCcCC
Confidence 5677777777765543
No 123
>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=77.99 E-value=2.4 Score=27.45 Aligned_cols=29 Identities=24% Similarity=0.582 Sum_probs=19.3
Q ss_pred CCCCCCCCCCceeEeCCCCc--eEeCCCcee
Q 030129 4 AFCSDCKKHTEVVFDHSAGD--TVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~--~vC~~CG~V 32 (182)
-.||.|+.-..++.=.+.|. .-|..||.-
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 46999997444433223333 789999987
No 124
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=77.97 E-value=0.42 Score=40.80 Aligned_cols=30 Identities=20% Similarity=0.470 Sum_probs=22.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.+||.|+. .-...+-.....||..||.-+.
T Consensus 39 ~kc~~C~~-~~~~~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 39 VQCENCYG-LNYKKFLKSKMNICEQCGYHLK 68 (296)
T ss_pred eECCCccc-hhhHHHHHHcCCCCCCCCCCcC
Confidence 47999996 3334455677899999998764
No 125
>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=77.71 E-value=0.73 Score=33.70 Aligned_cols=39 Identities=26% Similarity=0.516 Sum_probs=25.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcccccccccccC
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFAN 49 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~ 49 (182)
..||+|++.+...=. ..-|-.|+.-+- +|...|-..|++
T Consensus 70 V~CP~C~K~TKmLGr----~D~CM~C~~pLT---Ld~~legkef~~ 108 (114)
T PF11023_consen 70 VECPNCGKQTKMLGR----VDACMHCKEPLT---LDPSLEGKEFDE 108 (114)
T ss_pred eECCCCCChHhhhch----hhccCcCCCcCc---cCchhhcchhhH
Confidence 469999985433221 248999998874 555555445554
No 126
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=77.37 E-value=1.4 Score=41.61 Aligned_cols=7 Identities=29% Similarity=1.118 Sum_probs=3.5
Q ss_pred CCCCCCC
Q 030129 5 FCSDCKK 11 (182)
Q Consensus 5 ~Cp~Cg~ 11 (182)
+||.||.
T Consensus 3 ~Cp~Cg~ 9 (645)
T PRK14559 3 ICPQCQF 9 (645)
T ss_pred cCCCCCC
Confidence 4555553
No 127
>PF14122 YokU: YokU-like protein
Probab=76.61 E-value=2 Score=29.93 Aligned_cols=24 Identities=25% Similarity=0.634 Sum_probs=18.2
Q ss_pred CCCceEeCCCceeeeCCCcccccc
Q 030129 20 SAGDTVCSECGLVLESHSIDETSE 43 (182)
Q Consensus 20 ~~G~~vC~~CG~Vl~e~~id~~~e 43 (182)
++=-++|.+||.|..+..+..+.|
T Consensus 32 ~tP~i~C~~CgmvYq~d~vi~EIE 55 (87)
T PF14122_consen 32 DTPAIICSNCGMVYQDDEVIKEIE 55 (87)
T ss_pred CCceeeecCCCcEEehhHHHHHHh
Confidence 344589999999998777766554
No 128
>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=76.25 E-value=2 Score=27.41 Aligned_cols=24 Identities=25% Similarity=0.721 Sum_probs=15.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
..||+||. .. .---+|..||.--+
T Consensus 27 ~~C~~cG~-~~------~~H~vc~~cG~Y~g 50 (55)
T TIGR01031 27 VVCPNCGE-FK------LPHRVCPSCGYYKG 50 (55)
T ss_pred eECCCCCC-cc------cCeeECCccCeECC
Confidence 35888886 22 12478999997644
No 129
>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=76.19 E-value=2.1 Score=26.73 Aligned_cols=14 Identities=21% Similarity=0.679 Sum_probs=9.4
Q ss_pred eEeCCCceeeeCCC
Q 030129 24 TVCSECGLVLESHS 37 (182)
Q Consensus 24 ~vC~~CG~Vl~e~~ 37 (182)
++|..||+|.++..
T Consensus 2 y~C~~CgyiYd~~~ 15 (50)
T cd00730 2 YECRICGYIYDPAE 15 (50)
T ss_pred cCCCCCCeEECCCC
Confidence 46777777776543
No 130
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=75.76 E-value=1.4 Score=39.32 Aligned_cols=32 Identities=31% Similarity=0.721 Sum_probs=23.7
Q ss_pred CCCCCCCCCC-C----ceeEeCCCCceEeCCCceeee
Q 030129 3 DAFCSDCKKH-T----EVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~-~----~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
...||.|.+. + .-++|..+|...|..||.=|.
T Consensus 128 ~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelv 164 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELV 164 (436)
T ss_pred cccCCccccchhhhHHHHhhcccCceEEEecCCCchh
Confidence 3579999973 1 124578899999999986554
No 131
>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=75.72 E-value=0.5 Score=35.86 Aligned_cols=30 Identities=30% Similarity=0.510 Sum_probs=23.2
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (182)
|....||.||+ -+ .+ +|..+|..|....++
T Consensus 1 m~l~nC~~Cgk--lF--~~-~~~~iCp~C~~~~e~ 30 (137)
T TIGR03826 1 MELANCPKCGR--LF--VK-TGRDVCPSCYEEEER 30 (137)
T ss_pred CCCccccccch--hh--hh-cCCccCHHHhHHHHH
Confidence 77789999997 23 33 488999999987643
No 132
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=75.58 E-value=0.55 Score=40.00 Aligned_cols=30 Identities=23% Similarity=0.519 Sum_probs=21.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.+||.|+. .-...|-.....||..||.-..
T Consensus 28 ~~c~~c~~-~~~~~~l~~~~~vc~~c~~h~r 57 (292)
T PRK05654 28 TKCPSCGQ-VLYRKELEANLNVCPKCGHHMR 57 (292)
T ss_pred eECCCccc-hhhHHHHHhcCCCCCCCCCCee
Confidence 47999996 3333445566789999999765
No 133
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=75.57 E-value=0.99 Score=31.31 Aligned_cols=29 Identities=31% Similarity=0.499 Sum_probs=23.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
..|+.||+ . -+-...-|-..|..|..|+.
T Consensus 37 y~CsfCGK-~-~vKR~AvGiW~C~~C~kv~a 65 (92)
T KOG0402|consen 37 YTCSFCGK-K-TVKRKAVGIWKCGSCKKVVA 65 (92)
T ss_pred hhhhhcch-h-hhhhhceeEEecCCccceec
Confidence 46999997 3 35677889999999999974
No 134
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=75.35 E-value=1.4 Score=35.44 Aligned_cols=34 Identities=26% Similarity=0.598 Sum_probs=23.6
Q ss_pred CCCCCCCCCC-ceeEeCCCCc---eEeCCCceeeeCCC
Q 030129 4 AFCSDCKKHT-EVVFDHSAGD---TVCSECGLVLESHS 37 (182)
Q Consensus 4 ~~Cp~Cg~~~-~iv~D~~~G~---~vC~~CG~Vl~e~~ 37 (182)
+.|-+||... .+-.++..|. +.|.+||.|.|.-+
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~vaDkYi 38 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVADKYI 38 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCccccee
Confidence 4699999731 2334565554 89999999986544
No 135
>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=75.20 E-value=2.3 Score=22.54 Aligned_cols=23 Identities=26% Similarity=0.787 Sum_probs=13.9
Q ss_pred CCCCCCCCceeEeCC-CCceEeCCCce
Q 030129 6 CSDCKKHTEVVFDHS-AGDTVCSECGL 31 (182)
Q Consensus 6 Cp~Cg~~~~iv~D~~-~G~~vC~~CG~ 31 (182)
|..|+. .| ...+ .-.+.|.+||.
T Consensus 1 C~sC~~--~i-~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGR--PI-APREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCC--cc-cCcccCceEeCCCCCC
Confidence 667775 22 3333 34588999983
No 136
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=74.61 E-value=2.8 Score=26.24 Aligned_cols=32 Identities=28% Similarity=0.768 Sum_probs=20.2
Q ss_pred CCCCCCCCCCCceeE-eCCCCc-eEeCCCceeee
Q 030129 3 DAFCSDCKKHTEVVF-DHSAGD-TVCSECGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~-D~~~G~-~vC~~CG~Vl~ 34 (182)
...|.+|+.....+. +...|. ++|..||+-..
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~ 36 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYK 36 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHH
Confidence 356888886433333 235555 88999988753
No 137
>PF14353 CpXC: CpXC protein
Probab=74.60 E-value=3 Score=30.71 Aligned_cols=12 Identities=25% Similarity=0.758 Sum_probs=9.8
Q ss_pred ceEeCCCceeee
Q 030129 23 DTVCSECGLVLE 34 (182)
Q Consensus 23 ~~vC~~CG~Vl~ 34 (182)
..+|..||....
T Consensus 38 ~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 38 SFTCPSCGHKFR 49 (128)
T ss_pred EEECCCCCCcee
Confidence 489999998763
No 138
>COG1773 Rubredoxin [Energy production and conversion]
Probab=74.28 E-value=2.5 Score=27.03 Aligned_cols=11 Identities=45% Similarity=0.924 Sum_probs=5.2
Q ss_pred eEeCCCceeee
Q 030129 24 TVCSECGLVLE 34 (182)
Q Consensus 24 ~vC~~CG~Vl~ 34 (182)
..|..||.|.+
T Consensus 4 ~~C~~CG~vYd 14 (55)
T COG1773 4 WRCSVCGYVYD 14 (55)
T ss_pred eEecCCceEec
Confidence 34555555543
No 139
>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=74.14 E-value=3.9 Score=25.30 Aligned_cols=26 Identities=23% Similarity=0.668 Sum_probs=18.6
Q ss_pred CCCC--CCCCCCceeEeCCCCceEeCCCce
Q 030129 4 AFCS--DCKKHTEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 4 ~~Cp--~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (182)
..|| .||. ..++-++. ....|..||+
T Consensus 19 k~CP~~~CG~-GvFMA~H~-dR~~CGKCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGA-GVFMAEHK-DRHYCGKCGY 46 (47)
T ss_dssp EE-TSTTTTS-SSEEEE-S-SEEEETTTSS
T ss_pred hcCCCcccCC-ceEeeecC-CCccCCCccc
Confidence 4699 8996 56676665 4799999996
No 140
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=74.11 E-value=2 Score=31.32 Aligned_cols=6 Identities=33% Similarity=1.160 Sum_probs=3.1
Q ss_pred EeCCCc
Q 030129 25 VCSECG 30 (182)
Q Consensus 25 vC~~CG 30 (182)
.|+.||
T Consensus 88 ~CP~Cg 93 (113)
T PRK12380 88 QCPHCH 93 (113)
T ss_pred cCcCCC
Confidence 355555
No 141
>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=73.99 E-value=1.4 Score=26.29 Aligned_cols=28 Identities=32% Similarity=0.640 Sum_probs=16.0
Q ss_pred CCCCCCCCCCceeEeCC-CCceEeCCCce
Q 030129 4 AFCSDCKKHTEVVFDHS-AGDTVCSECGL 31 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~-~G~~vC~~CG~ 31 (182)
-+|+.||..-++..... .....|..||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 46888875223332222 35677888886
No 142
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=73.94 E-value=2.2 Score=27.19 Aligned_cols=26 Identities=35% Similarity=0.678 Sum_probs=18.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
.+|+.||. .+ .| ..--+||..||.+.
T Consensus 6 ~~C~~Cg~--~~-~~-~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 6 CKCPVCGK--KF-KD-GDDIVVCPECGAPY 31 (54)
T ss_pred ccChhhCC--cc-cC-CCCEEECCCCCCcc
Confidence 57999996 22 22 23358999999985
No 143
>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=73.60 E-value=2 Score=27.38 Aligned_cols=24 Identities=25% Similarity=0.706 Sum_probs=15.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
..||+||. .. ..-.+|..||+.=.
T Consensus 27 ~~c~~cg~-~~------~~H~vc~~cG~y~~ 50 (56)
T PF01783_consen 27 VKCPNCGE-PK------LPHRVCPSCGYYKG 50 (56)
T ss_dssp EESSSSSS-EE------STTSBCTTTBBSSS
T ss_pred eeeccCCC-Ee------cccEeeCCCCeECC
Confidence 46889985 11 23489999996543
No 144
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=72.25 E-value=3.2 Score=24.46 Aligned_cols=26 Identities=31% Similarity=0.742 Sum_probs=15.9
Q ss_pred CCCCCCCCCceeEeCCCCc---eEeCCCceee
Q 030129 5 FCSDCKKHTEVVFDHSAGD---TVCSECGLVL 33 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~---~vC~~CG~Vl 33 (182)
+||.|+.. +. ...-++ ..|..||=+-
T Consensus 1 ~CP~C~~~--l~-~~~~~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTE--LE-PVRLGDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcc--cc-eEEECCEEEEECCCCCeEE
Confidence 59999862 21 211122 5699998774
No 145
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=71.99 E-value=1.1 Score=29.17 Aligned_cols=20 Identities=15% Similarity=0.174 Sum_probs=18.0
Q ss_pred CHHHHHhcCCCceeeeceee
Q 030129 156 SHALLRKSALSPMELQRRKL 175 (182)
Q Consensus 156 ~~eia~~~~v~~~~i~r~~~ 175 (182)
++|||+.+||+..+|.+|+.
T Consensus 25 lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred HHHHHHHHCCCHHHHHHHhh
Confidence 59999999999999998864
No 146
>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=71.85 E-value=3.5 Score=29.85 Aligned_cols=11 Identities=36% Similarity=0.664 Sum_probs=8.5
Q ss_pred eEeCCCceeee
Q 030129 24 TVCSECGLVLE 34 (182)
Q Consensus 24 ~vC~~CG~Vl~ 34 (182)
.+|.+||.++-
T Consensus 32 ~~C~~CGe~~~ 42 (127)
T TIGR03830 32 WYCPACGEELL 42 (127)
T ss_pred eECCCCCCEEE
Confidence 57999988763
No 147
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=71.54 E-value=2.7 Score=33.78 Aligned_cols=29 Identities=28% Similarity=0.560 Sum_probs=19.0
Q ss_pred CCCCCCCCC-CceeEeCCCCceEeCCCcee
Q 030129 4 AFCSDCKKH-TEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~-~~iv~D~~~G~~vC~~CG~V 32 (182)
..||.|++. +.++.+...=.+.|..||..
T Consensus 99 V~C~~C~~pdT~l~k~~~~~~l~C~aCGa~ 128 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVLMLRCDACGAH 128 (201)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 359999983 34444422224689999986
No 148
>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=71.53 E-value=2.6 Score=30.80 Aligned_cols=19 Identities=11% Similarity=0.422 Sum_probs=9.9
Q ss_pred ceeEeCCCCceEeCCCcee
Q 030129 14 EVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 14 ~iv~D~~~G~~vC~~CG~V 32 (182)
.+..+...+...|.+||..
T Consensus 61 ~L~I~~~p~~~~C~~Cg~~ 79 (115)
T TIGR00100 61 KLNIEDEPVECECEDCSEE 79 (115)
T ss_pred EEEEEeeCcEEEcccCCCE
Confidence 3444445555556666544
No 149
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=71.31 E-value=3.8 Score=26.57 Aligned_cols=28 Identities=29% Similarity=0.634 Sum_probs=16.8
Q ss_pred CCCCCCCCCCCCceeEeCC-CCceEeCCCcee
Q 030129 2 TDAFCSDCKKHTEVVFDHS-AGDTVCSECGLV 32 (182)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~D~~-~G~~vC~~CG~V 32 (182)
+..+|..||. .| ...+ .-...|.+||.+
T Consensus 6 ~~~~CtSCg~--~i-~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 6 EPPKCTSCGI--EI-APREKAVKFLCPNCGEV 34 (59)
T ss_pred cCccccCCCC--cc-cCCCccCEeeCCCCCCe
Confidence 3456888885 23 2222 334778888877
No 150
>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=71.24 E-value=4.2 Score=27.31 Aligned_cols=30 Identities=23% Similarity=0.675 Sum_probs=20.7
Q ss_pred CCCCCCCCCCceeE--eCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVF--DHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~--D~~~G~~vC~~CG~Vl 33 (182)
-.||.|+.-..|.. +..--..-|-.||+.-
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e 40 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYTE 40 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCee
Confidence 46999998544442 3344447899999983
No 151
>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=71.12 E-value=2.6 Score=24.55 Aligned_cols=22 Identities=27% Similarity=0.578 Sum_probs=10.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEe
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVC 26 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC 26 (182)
.+|..||. -.-+.+...|.++|
T Consensus 7 YkC~~CGn-iVev~~~g~g~lvC 28 (36)
T PF06397_consen 7 YKCEHCGN-IVEVVHDGGGPLVC 28 (36)
T ss_dssp EE-TTT---EEEEEE--SS-EEE
T ss_pred EEccCCCC-EEEEEECCCCCEEe
Confidence 46888886 23345667777888
No 152
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=71.09 E-value=2.5 Score=27.61 Aligned_cols=23 Identities=30% Similarity=0.811 Sum_probs=16.0
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCce
Q 030129 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (182)
|...-|.+|+. ++ +. ..|..||-
T Consensus 1 M~~kAC~~C~~---i~-~~----~~CP~Cgs 23 (61)
T PRK08351 1 MTEKACRHCHY---IT-TE----DRCPVCGS 23 (61)
T ss_pred CchhhhhhCCc---cc-CC----CcCCCCcC
Confidence 66668999985 22 21 26999997
No 153
>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=70.28 E-value=3.1 Score=36.96 Aligned_cols=29 Identities=28% Similarity=0.652 Sum_probs=17.6
Q ss_pred CCCCCCCCCceeEeC-CCCceEeCCCceeee
Q 030129 5 FCSDCKKHTEVVFDH-SAGDTVCSECGLVLE 34 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~-~~G~~vC~~CG~Vl~ 34 (182)
.||+|+.... +.+. ......|..||.++.
T Consensus 15 ~C~~Cd~l~~-~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 15 LCSQCDMLVA-LPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eCCCCCCccc-ccCCCCCCeeECCCCCCCCc
Confidence 4888886322 2222 333467888888884
No 154
>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=69.90 E-value=3 Score=35.18 Aligned_cols=29 Identities=28% Similarity=0.626 Sum_probs=12.6
Q ss_pred CCCCCCCCCCce-eEeCCC--C--ceEeCCCcee
Q 030129 4 AFCSDCKKHTEV-VFDHSA--G--DTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~i-v~D~~~--G--~~vC~~CG~V 32 (182)
..||.||+.+.+ +..... | ...|.-||+-
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~ 206 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTE 206 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--E
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCe
Confidence 579999985322 223332 5 4899999975
No 155
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=69.21 E-value=2.4 Score=36.58 Aligned_cols=28 Identities=25% Similarity=0.380 Sum_probs=21.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
++||.|++.-.|-+||.+++++|.. |..
T Consensus 78 ~kC~~C~~~i~~kTDPkn~dY~~~~-Ga~ 105 (324)
T PF04502_consen 78 IKCPRCSNEIEFKTDPKNTDYVVES-GAR 105 (324)
T ss_pred EEcCCCCCEEeeecCCCCCCeeeec-Cee
Confidence 4699998755677899988888876 444
No 156
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=68.91 E-value=3 Score=24.60 Aligned_cols=13 Identities=31% Similarity=0.925 Sum_probs=11.7
Q ss_pred CceEeCCCceeee
Q 030129 22 GDTVCSECGLVLE 34 (182)
Q Consensus 22 G~~vC~~CG~Vl~ 34 (182)
|.+||+.|..+|+
T Consensus 2 GtIvCq~C~~~Id 14 (38)
T PF13790_consen 2 GTIVCQHCNETID 14 (38)
T ss_pred CEEEeccccceee
Confidence 7899999999985
No 157
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=68.63 E-value=3.2 Score=31.20 Aligned_cols=21 Identities=24% Similarity=0.629 Sum_probs=14.5
Q ss_pred ceeEeCCCCceEeCCCceeee
Q 030129 14 EVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 14 ~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.+......+...|.+||.+..
T Consensus 61 ~L~i~~~p~~~~C~~CG~~~~ 81 (135)
T PRK03824 61 EIIFEEEEAVLKCRNCGNEWS 81 (135)
T ss_pred EEEEEecceEEECCCCCCEEe
Confidence 455556667788888887654
No 158
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=68.25 E-value=3.1 Score=39.26 Aligned_cols=24 Identities=21% Similarity=0.632 Sum_probs=14.8
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.||+||.. ...|..+|.+||.-+.
T Consensus 29 ~Cp~CG~~------~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 29 PCPQCGTE------VPVDEAHCPNCGAETG 52 (645)
T ss_pred cCCCCCCC------CCcccccccccCCccc
Confidence 46666641 2356678888887654
No 159
>PRK06260 threonine synthase; Validated
Probab=68.18 E-value=2.5 Score=37.21 Aligned_cols=30 Identities=37% Similarity=0.630 Sum_probs=22.6
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
|...+|+.||.. ++...-...|..||-.++
T Consensus 1 ~~~~~C~~cg~~----~~~~~~~~~Cp~cg~~l~ 30 (397)
T PRK06260 1 MYWLKCIECGKE----YDPDEIIYTCPECGGLLE 30 (397)
T ss_pred CCEEEECCCCCC----CCCCCccccCCCCCCeEE
Confidence 677899999972 344555678999998765
No 160
>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=67.91 E-value=5.8 Score=23.02 Aligned_cols=25 Identities=32% Similarity=0.796 Sum_probs=15.1
Q ss_pred CCCCCCCCCCc-eeEeC--CCC--ceEeCCC
Q 030129 4 AFCSDCKKHTE-VVFDH--SAG--DTVCSEC 29 (182)
Q Consensus 4 ~~Cp~Cg~~~~-iv~D~--~~G--~~vC~~C 29 (182)
..||.|++ +. ++-.= ..| .+.|.+|
T Consensus 6 v~CP~C~s-~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQS-TEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCC-CCcceeCCCCCCCCEeEecCcC
Confidence 57999998 45 43321 223 3677777
No 161
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=67.39 E-value=2.8 Score=25.47 Aligned_cols=25 Identities=24% Similarity=0.666 Sum_probs=16.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCC--Cceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSE--CGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~--CG~Vl~ 34 (182)
.+||.||.. +-.+| +.|.+ |+.|+.
T Consensus 12 rkCp~CGt~-----NG~R~-~~CKN~~C~~~~~ 38 (44)
T PF14952_consen 12 RKCPKCGTY-----NGTRG-LSCKNKSCPQVFN 38 (44)
T ss_pred ccCCcCcCc-----cCccc-ccccCCccchhhh
Confidence 579999952 22333 77874 988874
No 162
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=67.22 E-value=1.5 Score=37.13 Aligned_cols=30 Identities=20% Similarity=0.490 Sum_probs=22.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.+||.|+. .-...|-.+...||..||.-..
T Consensus 29 ~KCp~c~~-~~y~~eL~~n~~vcp~c~~h~r 58 (294)
T COG0777 29 TKCPSCGE-MLYRKELESNLKVCPKCGHHMR 58 (294)
T ss_pred eECCCccc-eeeHHHHHhhhhcccccCcccc
Confidence 47999996 3223355777899999998754
No 163
>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=67.02 E-value=3.9 Score=33.96 Aligned_cols=30 Identities=20% Similarity=0.610 Sum_probs=11.4
Q ss_pred CCCCCCCCCCceeE---eCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVF---DHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~---D~~~G~~vC~~CG~Vl~ 34 (182)
++||+||+ ..+-. +..-.+..|..|+.-.|
T Consensus 32 ~yCP~Cg~-~~L~~f~NN~PVaDF~C~~C~eeyE 64 (254)
T PF06044_consen 32 MYCPNCGS-KPLSKFENNRPVADFYCPNCNEEYE 64 (254)
T ss_dssp ---TTT---SS-EE--------EEE-TTT--EEE
T ss_pred CcCCCCCC-hhHhhccCCCccceeECCCCchHHh
Confidence 57999997 33321 22345699999997665
No 164
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=67.02 E-value=4 Score=26.10 Aligned_cols=24 Identities=29% Similarity=0.755 Sum_probs=18.0
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
.||.|+... +..=.+.|.+||...
T Consensus 1 ~Cpv~~~~~-----~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKDL-----PAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCcccc-----ccccCCcCCCCCCcC
Confidence 499998721 445568999999986
No 165
>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=66.51 E-value=1.5 Score=31.86 Aligned_cols=24 Identities=38% Similarity=0.823 Sum_probs=10.2
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
+|+.||. . +++......|+.||.-
T Consensus 72 ~C~~Cg~--~--~~~~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 72 RCRDCGH--E--FEPDEFDFSCPRCGSP 95 (113)
T ss_dssp EETTTS---E--EECHHCCHH-SSSSSS
T ss_pred ECCCCCC--E--EecCCCCCCCcCCcCC
Confidence 4666654 1 2222333556666653
No 166
>PRK07218 replication factor A; Provisional
Probab=66.48 E-value=2.6 Score=37.78 Aligned_cols=21 Identities=24% Similarity=0.689 Sum_probs=16.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
..||+|++. + + ...|..||.|
T Consensus 298 ~rCP~C~r~--v--~----~~~C~~hG~v 318 (423)
T PRK07218 298 ERCPECGRV--I--Q----KGQCRSHGAV 318 (423)
T ss_pred ecCcCcccc--c--c----CCcCCCCCCc
Confidence 469999972 2 2 2799999988
No 167
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=66.34 E-value=5.5 Score=34.24 Aligned_cols=10 Identities=40% Similarity=1.105 Sum_probs=5.8
Q ss_pred eEeCCCceee
Q 030129 24 TVCSECGLVL 33 (182)
Q Consensus 24 ~vC~~CG~Vl 33 (182)
.+|..|+.-+
T Consensus 253 e~C~~C~~Yl 262 (309)
T PRK03564 253 ESCGDCGTYL 262 (309)
T ss_pred eecccccccc
Confidence 4566666554
No 168
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=65.96 E-value=2 Score=41.56 Aligned_cols=11 Identities=45% Similarity=1.226 Sum_probs=0.0
Q ss_pred eEeCCCceeee
Q 030129 24 TVCSECGLVLE 34 (182)
Q Consensus 24 ~vC~~CG~Vl~ 34 (182)
+.|..||..+.
T Consensus 681 ~~Cp~C~~~~~ 691 (900)
T PF03833_consen 681 YVCPDCGIEVE 691 (900)
T ss_dssp -----------
T ss_pred eeccccccccC
Confidence 56666666654
No 169
>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=65.83 E-value=6.9 Score=27.64 Aligned_cols=29 Identities=24% Similarity=0.555 Sum_probs=19.3
Q ss_pred CCCCCCCCCCCceeEe---------CCCCceEeCCCcee
Q 030129 3 DAFCSDCKKHTEVVFD---------HSAGDTVCSECGLV 32 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D---------~~~G~~vC~~CG~V 32 (182)
...||.||. ...++= +.+=.++|.+||..
T Consensus 62 ~~~Cp~Cg~-~~a~f~~~Q~RsadE~~T~fy~C~~C~~~ 99 (104)
T TIGR01384 62 RVECPKCGH-KEAYYWLLQTRRADEPETRFYKCTKCGYV 99 (104)
T ss_pred cCCCCCCCC-CeeEEEEeccCCCCCCcEEEEEeCCCCCe
Confidence 357999997 454332 23335899999975
No 170
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=65.83 E-value=2.4 Score=31.01 Aligned_cols=30 Identities=23% Similarity=0.533 Sum_probs=21.9
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
...|+.||+ -+..-...+..+|..|+.+..
T Consensus 7 ~~FC~~CG~--ll~~~~~~~~~~C~~Ck~~~~ 36 (116)
T KOG2907|consen 7 LDFCSDCGS--LLEEPSAQSTVLCIRCKIEYP 36 (116)
T ss_pred cchhhhhhh--hcccccccCceEeccccccCC
Confidence 367999996 234445777788999998764
No 171
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=65.75 E-value=19 Score=30.88 Aligned_cols=18 Identities=17% Similarity=0.135 Sum_probs=16.9
Q ss_pred CHHHHHHHHHHHHHhhCC
Q 030129 139 KTHYWLLACTLLVDKKTS 156 (182)
Q Consensus 139 ~~~~v~AAclY~acr~~~ 156 (182)
.|..||+||||+|++..+
T Consensus 204 ~Ps~IAlAAI~lA~~~~~ 221 (305)
T TIGR00569 204 TPSQIALAAILHTASRAG 221 (305)
T ss_pred CHHHHHHHHHHHHHHHhC
Confidence 999999999999999875
No 172
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=65.65 E-value=5.2 Score=36.56 Aligned_cols=29 Identities=21% Similarity=0.647 Sum_probs=22.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
..||+|+. .+++....+.+.|..||....
T Consensus 223 ~~C~~C~~--~l~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 223 LCCPNCDV--SLTYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred cCCCCCCC--ceEEecCCCeEEcCCCcCcCC
Confidence 46999985 567777888899999998753
No 173
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=65.64 E-value=3.7 Score=26.92 Aligned_cols=26 Identities=27% Similarity=0.714 Sum_probs=16.8
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
|...-|.+|+.. +. ...-+|..||.-
T Consensus 2 ~~~kAC~~Ck~l---~~---~d~e~CP~Cgs~ 27 (64)
T COG2093 2 STEKACKNCKRL---TP---EDTEICPVCGST 27 (64)
T ss_pred chhHHHhhcccc---CC---CCCccCCCCCCc
Confidence 445669999862 21 235689999864
No 174
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=65.59 E-value=4.9 Score=25.62 Aligned_cols=27 Identities=19% Similarity=0.492 Sum_probs=15.4
Q ss_pred CCCCCCCCCceeEeCC----CCceEeCCCce
Q 030129 5 FCSDCKKHTEVVFDHS----AGDTVCSECGL 31 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~----~G~~vC~~CG~ 31 (182)
.||.||+.+.+-...+ +=-+.|..|-.
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~ 36 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLYCPKCKQ 36 (55)
T ss_pred ECCCCCCccceeeecCceeccccccCCCCCc
Confidence 5999997543322222 22267888863
No 175
>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=65.38 E-value=4.9 Score=24.50 Aligned_cols=28 Identities=18% Similarity=0.484 Sum_probs=17.1
Q ss_pred CCCCCCCCCceeEeC-------CCCceEeCC--Cceee
Q 030129 5 FCSDCKKHTEVVFDH-------SAGDTVCSE--CGLVL 33 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~-------~~G~~vC~~--CG~Vl 33 (182)
+||+||+. ..+.-. .+=...|++ ||.-.
T Consensus 1 ~CP~Cg~~-a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tf 37 (47)
T PF04606_consen 1 RCPHCGSK-ARIRTSRQLSPLTRELYCQCTNPECGHTF 37 (47)
T ss_pred CcCCCCCe-eEEEEchhhCcceEEEEEEECCCcCCCEE
Confidence 59999973 333321 222367887 98765
No 176
>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=65.32 E-value=3 Score=29.30 Aligned_cols=36 Identities=25% Similarity=0.607 Sum_probs=22.7
Q ss_pred CCCCCCC------CCceeEeCCCCc----------eEeCCCceeeeCCCccc
Q 030129 5 FCSDCKK------HTEVVFDHSAGD----------TVCSECGLVLESHSIDE 40 (182)
Q Consensus 5 ~Cp~Cg~------~~~iv~D~~~G~----------~vC~~CG~Vl~e~~id~ 40 (182)
.|+-|++ .+.+.+|...|. ++|..||.+.-+.-+-.
T Consensus 1 ~C~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~dev~~ 52 (89)
T TIGR03829 1 KCRWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQDDTTVK 52 (89)
T ss_pred CCcccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEeecHHHHH
Confidence 4888953 133455555553 68999999875554443
No 177
>PRK05580 primosome assembly protein PriA; Validated
Probab=64.89 E-value=5.4 Score=37.80 Aligned_cols=28 Identities=21% Similarity=0.540 Sum_probs=22.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
..||+|+. .+++....+.+.|..||...
T Consensus 391 ~~C~~C~~--~l~~h~~~~~l~Ch~Cg~~~ 418 (679)
T PRK05580 391 AECPHCDA--SLTLHRFQRRLRCHHCGYQE 418 (679)
T ss_pred cCCCCCCC--ceeEECCCCeEECCCCcCCC
Confidence 46999985 57777788889999999874
No 178
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=64.87 E-value=0.86 Score=29.50 Aligned_cols=26 Identities=38% Similarity=0.888 Sum_probs=18.9
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCC-Cceeee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSE-CGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~-CG~Vl~ 34 (182)
+.-|+.||. .|- .++.+|++ ||.+++
T Consensus 8 H~HC~VCg~--aIp----~de~~CSe~C~eil~ 34 (64)
T COG4068 8 HRHCVVCGK--AIP----PDEQVCSEECGEILN 34 (64)
T ss_pred CccccccCC--cCC----CccchHHHHHHHHHH
Confidence 456999996 343 45889985 998774
No 179
>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=64.81 E-value=4.3 Score=23.27 Aligned_cols=21 Identities=43% Similarity=1.054 Sum_probs=10.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCc
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECG 30 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG 30 (182)
.+|+.||. +.+.+. .+|..||
T Consensus 12 ~rC~~Cg~---~~~pPr---~~Cp~C~ 32 (37)
T PF12172_consen 12 QRCRDCGR---VQFPPR---PVCPHCG 32 (37)
T ss_dssp EE-TTT-----EEES-----SEETTTT
T ss_pred EEcCCCCC---EecCCC---cCCCCcC
Confidence 36888885 334333 7888887
No 180
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=64.73 E-value=4.1 Score=29.74 Aligned_cols=17 Identities=12% Similarity=0.505 Sum_probs=7.8
Q ss_pred eeEeCCCCceEeCCCce
Q 030129 15 VVFDHSAGDTVCSECGL 31 (182)
Q Consensus 15 iv~D~~~G~~vC~~CG~ 31 (182)
+......+...|.+||.
T Consensus 62 L~i~~~p~~~~C~~Cg~ 78 (114)
T PRK03681 62 LHLEEQEAECWCETCQQ 78 (114)
T ss_pred EEEEeeCcEEEcccCCC
Confidence 33344444455555553
No 181
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.59 E-value=3.8 Score=29.97 Aligned_cols=32 Identities=13% Similarity=0.122 Sum_probs=25.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCCC
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~ 37 (182)
.+.||+||+. .+|-.+--+||.-||.-.....
T Consensus 9 KridPetg~K---FYDLNrdPiVsPytG~s~P~s~ 40 (129)
T COG4530 9 KRIDPETGKK---FYDLNRDPIVSPYTGKSYPRSY 40 (129)
T ss_pred cccCccccch---hhccCCCccccCcccccchHHH
Confidence 4679999973 5788899999999998764443
No 182
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=64.52 E-value=6.3 Score=26.98 Aligned_cols=28 Identities=29% Similarity=0.705 Sum_probs=20.1
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (182)
.||.|.. .++.. ..+.+.| .||+-|.-.
T Consensus 1 iCPVC~~-~~L~~--~~~~i~C-~Cgl~l~~~ 28 (82)
T PF14768_consen 1 ICPVCQK-GNLRE--NSNVISC-SCGLRLNTQ 28 (82)
T ss_pred CCCccCC-Ccccc--cCCeEEC-CCccEEecC
Confidence 4999997 56655 5777888 677776533
No 183
>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=64.47 E-value=5.4 Score=22.50 Aligned_cols=24 Identities=25% Similarity=0.490 Sum_probs=13.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCC
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSE 28 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~ 28 (182)
.+|..||. -..+.+...|+++|-.
T Consensus 5 ykC~~CGn-iv~v~~~~~~~l~Ccg 28 (34)
T cd00974 5 YKCEICGN-IVEVLNVGGGTLVCCG 28 (34)
T ss_pred EEcCCCCc-EEEEEECCCcceeecC
Confidence 45777775 2334455566666643
No 184
>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=64.32 E-value=5.8 Score=34.05 Aligned_cols=31 Identities=26% Similarity=0.611 Sum_probs=17.1
Q ss_pred CCCCCCCCCCCceeE---eC---CCCc--eEeCCCceee
Q 030129 3 DAFCSDCKKHTEVVF---DH---SAGD--TVCSECGLVL 33 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~---D~---~~G~--~vC~~CG~Vl 33 (182)
..+||+||+...+.+ +. ..+. .+|.+|+.-+
T Consensus 224 R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~Yl 262 (305)
T TIGR01562 224 RVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYL 262 (305)
T ss_pred CccCCCCCCCCceeeEeecCCCCCcceEEeeccccccch
Confidence 456888886433321 21 1112 3788888776
No 185
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=64.30 E-value=2.3 Score=26.96 Aligned_cols=30 Identities=37% Similarity=0.853 Sum_probs=16.8
Q ss_pred CCCCCCCCCceeE--eCCCCceEeCCCceeee
Q 030129 5 FCSDCKKHTEVVF--DHSAGDTVCSECGLVLE 34 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~--D~~~G~~vC~~CG~Vl~ 34 (182)
.|.+|+....... .+..+.+.|..||+-..
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~ 32 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWK 32 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHH
Confidence 3777775322222 22366677777777653
No 186
>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=64.06 E-value=4.5 Score=25.38 Aligned_cols=28 Identities=21% Similarity=0.700 Sum_probs=15.4
Q ss_pred CCCCC--CCCCCceeEeCCCCc--eEeCCCceee
Q 030129 4 AFCSD--CKKHTEVVFDHSAGD--TVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~--Cg~~~~iv~D~~~G~--~vC~~CG~Vl 33 (182)
..||. |+. .+..+..... +.|..||..+
T Consensus 19 ~~Cp~~~C~~--~~~~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 19 RWCPNPDCEY--IIEKDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp C--TTSST-----ECS-SSTTS--CCTTSCCSEE
T ss_pred cCCCCCCCcc--cEEecCCCCCCeeECCCCCCcC
Confidence 57988 986 3555555555 8899998765
No 187
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=63.89 E-value=4.3 Score=36.28 Aligned_cols=31 Identities=23% Similarity=0.621 Sum_probs=19.4
Q ss_pred CCCCCCCCCCceeEeCCCC-ceEeCCCceeeeC
Q 030129 4 AFCSDCKKHTEVVFDHSAG-DTVCSECGLVLES 35 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G-~~vC~~CG~Vl~e 35 (182)
..||+|+.... +.+-..| ...|..||.++..
T Consensus 11 ~~C~~Cd~l~~-~~~l~~g~~a~CpRCg~~L~~ 42 (419)
T PRK15103 11 ILCPQCDMLVA-LPRLEHGQKAACPRCGTTLTV 42 (419)
T ss_pred ccCCCCCceee-cCCCCCCCeeECCCCCCCCcC
Confidence 45999996221 1222334 4779999999843
No 188
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=63.67 E-value=18 Score=29.76 Aligned_cols=46 Identities=15% Similarity=0.156 Sum_probs=30.1
Q ss_pred HHHHHHHHHhCChHHHHHH-HHHHHHHh------c----cCHHHHHHHHHHHHHhhC
Q 030129 110 KTIATMSDRIGQMRYIRRW-KIKSLVEA------E----IKTHYWLLACTLLVDKKT 155 (182)
Q Consensus 110 ~~I~~i~~~L~L~~~v~~~-~i~k~a~~------~----l~~~~v~AAclY~acr~~ 155 (182)
-.|+.+|=+||+.+.+... .+.+...+ . |+....++|++|.||+..
T Consensus 94 ~~VrdlaVQfgc~evi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~l 150 (262)
T KOG4557|consen 94 LNVRDLAVQFGCVEVIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKL 150 (262)
T ss_pred cCHHHHHHHHhHHHHHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHH
Confidence 3456677777776655444 33333222 1 277789999999999976
No 189
>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=63.14 E-value=4.5 Score=25.72 Aligned_cols=22 Identities=32% Similarity=0.677 Sum_probs=14.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCC
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSE 28 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~ 28 (182)
..||.|++ ..+++|.. .+.|+.
T Consensus 15 ~~Cp~C~~-~~l~~~~~--~Y~C~G 36 (55)
T PF08063_consen 15 EPCPKCKG-GQLYFDGS--GYKCTG 36 (55)
T ss_dssp ---SSSSE--EEEEETT--EEEEES
T ss_pred CCCCCCCC-CeEEecCC--ccEeCc
Confidence 46999997 67888755 788873
No 190
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=62.91 E-value=2.2 Score=26.74 Aligned_cols=28 Identities=29% Similarity=0.652 Sum_probs=18.4
Q ss_pred CCCCCCCCCcee--EeCCCCceEeCCCceee
Q 030129 5 FCSDCKKHTEVV--FDHSAGDTVCSECGLVL 33 (182)
Q Consensus 5 ~Cp~Cg~~~~iv--~D~~~G~~vC~~CG~Vl 33 (182)
.|+-||..-.+. +..+.| +||.+|--=+
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 499999632221 225778 8999998554
No 191
>PRK14873 primosome assembly protein PriA; Provisional
Probab=62.17 E-value=5.9 Score=37.56 Aligned_cols=27 Identities=26% Similarity=0.615 Sum_probs=21.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
..||+|+. .+.+....+...|.-||..
T Consensus 393 ~~C~~C~~--~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 393 ARCRHCTG--PLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred eECCCCCC--ceeEecCCCeeECCCCcCC
Confidence 46999985 4666666788999999984
No 192
>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=62.00 E-value=8.2 Score=32.53 Aligned_cols=32 Identities=22% Similarity=0.472 Sum_probs=16.6
Q ss_pred CCCCCCCCCCCceeEeC-------CCCceEeCCCceeee
Q 030129 3 DAFCSDCKKHTEVVFDH-------SAGDTVCSECGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~-------~~G~~vC~~CG~Vl~ 34 (182)
...||+||+....-..+ .-.-.+|..||.-+.
T Consensus 211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp TTS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred CCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 45799999743322221 122379999999873
No 193
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=61.85 E-value=4.8 Score=26.06 Aligned_cols=23 Identities=39% Similarity=1.068 Sum_probs=12.5
Q ss_pred CCCCCCCCCceeEeCCCCc-eEeCCCce
Q 030129 5 FCSDCKKHTEVVFDHSAGD-TVCSECGL 31 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~-~vC~~CG~ 31 (182)
.|-+|+.. +.+ ..|+ +-|.+||.
T Consensus 22 iCgdC~~e-n~l---k~~D~irCReCG~ 45 (62)
T KOG3507|consen 22 ICGDCGQE-NTL---KRGDVIRCRECGY 45 (62)
T ss_pred Eecccccc-ccc---cCCCcEehhhcch
Confidence 47777752 322 2344 55777775
No 194
>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=61.82 E-value=6.9 Score=22.98 Aligned_cols=10 Identities=40% Similarity=0.969 Sum_probs=7.4
Q ss_pred eEeCCCceee
Q 030129 24 TVCSECGLVL 33 (182)
Q Consensus 24 ~vC~~CG~Vl 33 (182)
.+|..||..+
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 3588888775
No 195
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=61.72 E-value=1.8 Score=35.25 Aligned_cols=34 Identities=24% Similarity=0.518 Sum_probs=25.9
Q ss_pred CCCCCCCCC-CceeEeCCCCc---eEeCCCceeeeCCC
Q 030129 4 AFCSDCKKH-TEVVFDHSAGD---TVCSECGLVLESHS 37 (182)
Q Consensus 4 ~~Cp~Cg~~-~~iv~D~~~G~---~vC~~CG~Vl~e~~ 37 (182)
+.|-+||.. ..+-.+++.|. +.|.+|+.|+|+-+
T Consensus 1 ~~CVeCg~~vksLy~~Ys~g~irlt~C~nC~e~vDkYi 38 (225)
T KOG3134|consen 1 YRCVECGSEVKSLYTQYSPGNIRLTKCPNCQEVVDKYI 38 (225)
T ss_pred CcccccCchHHHHHHhcCCCcEEEeeCCchhhHHHhHe
Confidence 469999973 34566788884 88999999987554
No 196
>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=61.42 E-value=8.5 Score=27.69 Aligned_cols=27 Identities=22% Similarity=0.628 Sum_probs=20.4
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.|--|+. .... ...+.+||..||.++.
T Consensus 37 aCeiC~~-~GY~--q~g~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 37 ACEICGP-KGYY--QEGDQLVCKNCGVRFN 63 (102)
T ss_pred eccccCC-CceE--EECCEEEEecCCCEEe
Confidence 5889986 3433 3567899999999985
No 197
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 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 CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=61.40 E-value=7.9 Score=27.24 Aligned_cols=27 Identities=15% Similarity=0.389 Sum_probs=17.1
Q ss_pred CCCCCCCC-CceeEeCCCCceEeCCCce
Q 030129 5 FCSDCKKH-TEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 5 ~Cp~Cg~~-~~iv~D~~~G~~vC~~CG~ 31 (182)
.||.|+.. +.+.+++..|...|-.||.
T Consensus 35 ~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~ 62 (97)
T PF01807_consen 35 LCPFHDDKTPSFSINPDKNRFKCFGCGK 62 (97)
T ss_dssp --SSS--SS--EEEETTTTEEEETTT--
T ss_pred ECcCCCCCCCceEEECCCCeEEECCCCC
Confidence 59999853 4678899999999999994
No 198
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=61.29 E-value=9.3 Score=31.70 Aligned_cols=21 Identities=19% Similarity=0.265 Sum_probs=19.0
Q ss_pred CHHHHHHHHHHHHHhhCCHHH
Q 030129 139 KTHYWLLACTLLVDKKTSHAL 159 (182)
Q Consensus 139 ~~~~v~AAclY~acr~~~~ei 159 (182)
.|..+|-||||+||-..++++
T Consensus 192 PPh~IalAcl~Ia~~~~~k~~ 212 (264)
T KOG0794|consen 192 PPHQIALACLYIACVIDEKDI 212 (264)
T ss_pred CHHHHHHHHHHHHHhhcCCCh
Confidence 999999999999999887665
No 199
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=61.06 E-value=6.5 Score=36.00 Aligned_cols=34 Identities=32% Similarity=0.591 Sum_probs=22.7
Q ss_pred CCCCCCCCCcee---EeCCCC--ceEeCCCceeeeCCCcc
Q 030129 5 FCSDCKKHTEVV---FDHSAG--DTVCSECGLVLESHSID 39 (182)
Q Consensus 5 ~Cp~Cg~~~~iv---~D~~~G--~~vC~~CG~Vl~e~~id 39 (182)
.||+||+....+ +|.+.| .+.| .||.-.+-.+-.
T Consensus 177 ic~~cg~~~~~~~~~~d~~~~~v~y~~-~cG~~~~~~~~~ 215 (510)
T PRK00750 177 ICPKCGKVLTTPVISYDAEAGTVTYDC-ECGHEGEVPVTG 215 (510)
T ss_pred eCCCCCccceEEEEEEeCCCCEEEEEc-CCCCEEEEecCC
Confidence 599999864433 477777 4566 499986655443
No 200
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=60.96 E-value=4.8 Score=32.38 Aligned_cols=37 Identities=24% Similarity=0.487 Sum_probs=22.9
Q ss_pred CCCCCCCCCCce-e--Ee-CCCCc-----eEeCCCceeeeCCCccc
Q 030129 4 AFCSDCKKHTEV-V--FD-HSAGD-----TVCSECGLVLESHSIDE 40 (182)
Q Consensus 4 ~~Cp~Cg~~~~i-v--~D-~~~G~-----~vC~~CG~Vl~e~~id~ 40 (182)
..||.||+.-.. . +| |-.|+ ++|..||+=..|-...+
T Consensus 15 ~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~~e 60 (201)
T COG1779 15 IDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKTLE 60 (201)
T ss_pred ecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcccceeecc
Confidence 569999972111 1 11 35565 78999999765554443
No 201
>PRK04023 DNA polymerase II large subunit; Validated
Probab=60.84 E-value=5.8 Score=39.20 Aligned_cols=11 Identities=27% Similarity=0.685 Sum_probs=5.7
Q ss_pred eEeCCCceeee
Q 030129 24 TVCSECGLVLE 34 (182)
Q Consensus 24 ~vC~~CG~Vl~ 34 (182)
..|..||..+.
T Consensus 664 y~CPKCG~El~ 674 (1121)
T PRK04023 664 DECEKCGREPT 674 (1121)
T ss_pred CcCCCCCCCCC
Confidence 44555555543
No 202
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=60.03 E-value=6.4 Score=22.16 Aligned_cols=22 Identities=27% Similarity=0.597 Sum_probs=11.4
Q ss_pred CCCCCCCCCceeEeCCCCceEeC
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCS 27 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~ 27 (182)
+|..||. -..+.+...|+++|-
T Consensus 9 kC~~Cgn-iv~v~~~~~~~l~Cc 30 (34)
T TIGR00319 9 KCEVCGN-IVEVLHAGGGQLVCC 30 (34)
T ss_pred EcCCCCc-EEEEEECCCcceecc
Confidence 5666664 233344455555554
No 203
>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=59.99 E-value=7.9 Score=25.99 Aligned_cols=26 Identities=23% Similarity=0.676 Sum_probs=15.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
..||.|.. ++ +...|.+.|..|+.-+
T Consensus 2 ~~CP~C~~--~L--~~~~~~~~C~~C~~~~ 27 (70)
T PF07191_consen 2 NTCPKCQQ--EL--EWQGGHYHCEACQKDY 27 (70)
T ss_dssp -B-SSS-S--BE--EEETTEEEETTT--EE
T ss_pred CcCCCCCC--cc--EEeCCEEECccccccc
Confidence 46999996 34 4556999999999865
No 204
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=59.93 E-value=9 Score=23.99 Aligned_cols=28 Identities=21% Similarity=0.867 Sum_probs=19.6
Q ss_pred CCCC--CCCCCCceeEe--CCCCceEeCCCceee
Q 030129 4 AFCS--DCKKHTEVVFD--HSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp--~Cg~~~~iv~D--~~~G~~vC~~CG~Vl 33 (182)
.+|| .|+. .+..+ .....+.|..||..+
T Consensus 19 ~~CP~~~C~~--~~~~~~~~~~~~v~C~~C~~~f 50 (64)
T smart00647 19 KWCPAPDCSA--AIIVTEEEGCNRVTCPKCGFSF 50 (64)
T ss_pred cCCCCCCCcc--eEEecCCCCCCeeECCCCCCeE
Confidence 5699 8985 33343 366779999998765
No 205
>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=58.69 E-value=9 Score=25.54 Aligned_cols=26 Identities=31% Similarity=0.687 Sum_probs=19.5
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.| .||. .+..|...-..-| .||..+.
T Consensus 5 rC-~Cgr--~lya~e~~kTkkC-~CG~~l~ 30 (68)
T PF09082_consen 5 RC-DCGR--YLYAKEGAKTKKC-VCGKTLK 30 (68)
T ss_dssp EE-TTS----EEEETT-SEEEE-TTTEEEE
T ss_pred Ee-cCCC--EEEecCCcceeEe-cCCCeee
Confidence 58 7997 4778888888999 9999984
No 206
>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=58.54 E-value=21 Score=20.88 Aligned_cols=29 Identities=24% Similarity=0.465 Sum_probs=17.9
Q ss_pred CCCCCCCCCCceeEeCCCCc-eEeCC---Cceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGD-TVCSE---CGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~-~vC~~---CG~Vl 33 (182)
..||.||+ .-++-....|. +-|++ |....
T Consensus 2 ~~CP~Cg~-~lv~r~~k~g~F~~Cs~yP~C~~~~ 34 (39)
T PF01396_consen 2 EKCPKCGG-PLVLRRGKKGKFLGCSNYPECKYTE 34 (39)
T ss_pred cCCCCCCc-eeEEEECCCCCEEECCCCCCcCCeE
Confidence 57999996 33344444443 56776 76654
No 207
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=58.48 E-value=28 Score=26.25 Aligned_cols=65 Identities=14% Similarity=0.092 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHhCChHHHHHH---HHHHHHH---hc-c-----CHHHHHHHHHHHHHhhC------CHHHHHhcCCCcee
Q 030129 108 AFKTIATMSDRIGQMRYIRRW---KIKSLVE---AE-I-----KTHYWLLACTLLVDKKT------SHALLRKSALSPME 169 (182)
Q Consensus 108 a~~~I~~i~~~L~L~~~v~~~---~i~k~a~---~~-l-----~~~~v~AAclY~acr~~------~~eia~~~~v~~~~ 169 (182)
..++|.++.....++..+.-. .|.|... .. + +..-+..+||-+|.+.. ++..|++.|++..+
T Consensus 54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~e 133 (149)
T PF08613_consen 54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLKE 133 (149)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHH
T ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHHH
Confidence 567888888888888766544 4444444 12 2 77889999999999875 48899999999887
Q ss_pred eec
Q 030129 170 LQR 172 (182)
Q Consensus 170 i~r 172 (182)
+.+
T Consensus 134 ln~ 136 (149)
T PF08613_consen 134 LNE 136 (149)
T ss_dssp HHH
T ss_pred HHH
Confidence 753
No 208
>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=58.26 E-value=9.1 Score=21.75 Aligned_cols=8 Identities=38% Similarity=1.012 Sum_probs=3.9
Q ss_pred eEeCCCce
Q 030129 24 TVCSECGL 31 (182)
Q Consensus 24 ~vC~~CG~ 31 (182)
..|..||.
T Consensus 19 ~~CP~Cg~ 26 (34)
T cd00729 19 EKCPICGA 26 (34)
T ss_pred CcCcCCCC
Confidence 35555554
No 209
>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=58.10 E-value=14 Score=21.62 Aligned_cols=30 Identities=23% Similarity=0.541 Sum_probs=17.6
Q ss_pred CCCCCCCCCC--CceeEeCCCCceEeCCCcee
Q 030129 3 DAFCSDCKKH--TEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 3 ~~~Cp~Cg~~--~~iv~D~~~G~~vC~~CG~V 32 (182)
..+|..|+.. +-..+|......+|.-|+..
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 4579999862 33456777778999999986
No 210
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=57.91 E-value=6.8 Score=33.19 Aligned_cols=28 Identities=32% Similarity=0.707 Sum_probs=19.8
Q ss_pred CCCCCCCCCCCceeEeCCCCc--eEeCCCceeee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGD--TVCSECGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~--~vC~~CG~Vl~ 34 (182)
+.+|+.||..+ .+..|. .+|.+||...=
T Consensus 111 ~RFCg~CG~~~----~~~~~g~~~~C~~cg~~~f 140 (279)
T COG2816 111 HRFCGRCGTKT----YPREGGWARVCPKCGHEHF 140 (279)
T ss_pred CcCCCCCCCcC----ccccCceeeeCCCCCCccC
Confidence 57899999732 233333 89999998763
No 211
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=57.83 E-value=8.5 Score=36.91 Aligned_cols=27 Identities=26% Similarity=0.742 Sum_probs=22.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
..||+|.. .+++--.+|.+.|--||..
T Consensus 445 ~~Cp~Cd~--~lt~H~~~~~L~CH~Cg~~ 471 (730)
T COG1198 445 AECPNCDS--PLTLHKATGQLRCHYCGYQ 471 (730)
T ss_pred ccCCCCCc--ceEEecCCCeeEeCCCCCC
Confidence 46999985 5777778899999999988
No 212
>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=57.83 E-value=4.8 Score=27.21 Aligned_cols=12 Identities=42% Similarity=1.024 Sum_probs=5.1
Q ss_pred CCCCCCCCCCCC
Q 030129 1 MTDAFCSDCKKH 12 (182)
Q Consensus 1 m~~~~Cp~Cg~~ 12 (182)
|....||.||..
T Consensus 22 ~~k~FCp~CGn~ 33 (73)
T PF08772_consen 22 MTKQFCPKCGNA 33 (73)
T ss_dssp SS--S-SSS--S
T ss_pred CCceeCcccCCC
Confidence 566789999863
No 213
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=57.33 E-value=11 Score=25.74 Aligned_cols=26 Identities=15% Similarity=0.356 Sum_probs=18.0
Q ss_pred CCCCCCCCCCceeEeCCCC--ceEeCCCcee
Q 030129 4 AFCSDCKKHTEVVFDHSAG--DTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G--~~vC~~CG~V 32 (182)
..||-||- . +++...+ .-||.-|+=-
T Consensus 2 ~~CPCCg~-~--Tl~~~~~~~ydIC~VC~WE 29 (78)
T PF14206_consen 2 YPCPCCGY-Y--TLEERGEGTYDICPVCFWE 29 (78)
T ss_pred ccCCCCCc-E--EeccCCCcCceECCCCCcc
Confidence 46999996 3 3343333 7899999854
No 214
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=57.09 E-value=8.2 Score=30.89 Aligned_cols=29 Identities=28% Similarity=0.675 Sum_probs=17.6
Q ss_pred CCCCCCCCCce---eEe--CCCCc-----eEeCCCceee
Q 030129 5 FCSDCKKHTEV---VFD--HSAGD-----TVCSECGLVL 33 (182)
Q Consensus 5 ~Cp~Cg~~~~i---v~D--~~~G~-----~vC~~CG~Vl 33 (182)
.||+||..... .++ |--|+ ..|..||.=-
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~ 40 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRS 40 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCcc
Confidence 59999863211 122 33454 5799999863
No 215
>PRK06386 replication factor A; Reviewed
Probab=56.82 E-value=4.9 Score=35.26 Aligned_cols=21 Identities=33% Similarity=0.558 Sum_probs=14.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
..||+|++. +.+ ..|.+||.|
T Consensus 237 ~rCP~C~R~---l~~-----g~C~~HG~v 257 (358)
T PRK06386 237 TKCSVCNKI---IED-----GVCKDHPDA 257 (358)
T ss_pred ecCcCCCeE---ccC-----CcCCCCCCC
Confidence 469999862 222 389999975
No 216
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.79 E-value=6.4 Score=34.25 Aligned_cols=26 Identities=31% Similarity=0.717 Sum_probs=21.7
Q ss_pred CCCCCCCCCceeEeCC--CCceEeCCCc
Q 030129 5 FCSDCKKHTEVVFDHS--AGDTVCSECG 30 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~--~G~~vC~~CG 30 (182)
-||.||+...+-+|.. .|..+|.-||
T Consensus 34 ~cpvcg~k~RFr~dD~kGrGtw~c~y~~ 61 (366)
T COG4643 34 PCPVCGGKDRFRFDDRKGRGTWFCNYCG 61 (366)
T ss_pred CCCccCCccccccCCccCCccEEEEeec
Confidence 5999998777777663 6899999999
No 217
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.48 E-value=4.9 Score=29.46 Aligned_cols=18 Identities=11% Similarity=0.279 Sum_probs=10.3
Q ss_pred ceeEeCCCCceEeCCCce
Q 030129 14 EVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 14 ~iv~D~~~G~~vC~~CG~ 31 (182)
.+..+...+...|.+||.
T Consensus 62 ~L~Ie~vp~~~~C~~Cg~ 79 (117)
T PRK00564 62 ILDIVDEKVELECKDCSH 79 (117)
T ss_pred EEEEEecCCEEEhhhCCC
Confidence 444555556666666663
No 218
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=56.17 E-value=10 Score=24.32 Aligned_cols=62 Identities=11% Similarity=0.072 Sum_probs=37.5
Q ss_pred HHHHHHHhCChHHHHHHHHHHHHHhc----c-CHHHHHHHHHHHHHh-hCCHHHHHhcCC-Cceeeecee
Q 030129 112 IATMSDRIGQMRYIRRWKIKSLVEAE----I-KTHYWLLACTLLVDK-KTSHALLRKSAL-SPMELQRRK 174 (182)
Q Consensus 112 I~~i~~~L~L~~~v~~~~i~k~a~~~----l-~~~~v~AAclY~acr-~~~~eia~~~~v-~~~~i~r~~ 174 (182)
|.++|..+|++.....+ +|+..... + ...-+..|.-|+... ....|||..+|+ +...+-|.|
T Consensus 4 ~~~la~~~~~s~~~l~~-~f~~~~~~s~~~~~~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~F 72 (84)
T smart00342 4 LEDLAEALGMSPRHLQR-LFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAF 72 (84)
T ss_pred HHHHHHHhCCCHHHHHH-HHHHHhCcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHH
Confidence 67888889887654333 33333222 1 444455666666554 234899999998 776665544
No 219
>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=55.60 E-value=8 Score=30.14 Aligned_cols=28 Identities=25% Similarity=0.589 Sum_probs=17.1
Q ss_pred CCCCCCCCcee----E-eCCCCc-----eEeCCCceee
Q 030129 6 CSDCKKHTEVV----F-DHSAGD-----TVCSECGLVL 33 (182)
Q Consensus 6 Cp~Cg~~~~iv----~-D~~~G~-----~vC~~CG~Vl 33 (182)
||.||..+... + -|--|+ ..|..||.=-
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~ 38 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRS 38 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCch
Confidence 99999631111 1 134454 5799999864
No 220
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=55.49 E-value=3.7 Score=26.62 Aligned_cols=27 Identities=22% Similarity=0.557 Sum_probs=18.5
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeC-CCceeee
Q 030129 2 TDAFCSDCKKHTEVVFDHSAGDTVCS-ECGLVLE 34 (182)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~-~CG~Vl~ 34 (182)
.+.-||.||. +|-. .+..|. +|+....
T Consensus 2 ~HkHC~~CG~--~Ip~----~~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 2 PHKHCPVCGK--PIPP----DESFCSPKCREEYR 29 (59)
T ss_pred CCCcCCcCCC--cCCc----chhhhCHHHHHHHH
Confidence 3567999996 3322 388995 7987653
No 221
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=54.54 E-value=7.3 Score=25.09 Aligned_cols=24 Identities=25% Similarity=0.760 Sum_probs=15.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
..||+||. ..+ ---||..||.--+
T Consensus 28 ~~c~~cG~-~~l------~Hrvc~~cg~Y~g 51 (57)
T COG0333 28 SVCPNCGE-YKL------PHRVCLKCGYYKG 51 (57)
T ss_pred eeccCCCC-ccc------CceEcCCCCCccC
Confidence 46888886 222 2378999996543
No 222
>PRK08197 threonine synthase; Validated
Probab=54.49 E-value=6.1 Score=34.74 Aligned_cols=27 Identities=33% Similarity=0.746 Sum_probs=19.2
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
..+|+.||. . ++.+.-...| .||-.++
T Consensus 7 ~~~C~~Cg~-~---~~~~~~~~~C-~cg~~l~ 33 (394)
T PRK08197 7 HLECSKCGE-T---YDADQVHNLC-KCGKPLL 33 (394)
T ss_pred EEEECCCCC-C---CCCCCcceec-CCCCeeE
Confidence 357999996 2 3444556889 8997764
No 223
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=53.96 E-value=10 Score=28.07 Aligned_cols=33 Identities=27% Similarity=0.616 Sum_probs=26.7
Q ss_pred eCCCCceEeCCCceeee--CCCcccccccccccCC
Q 030129 18 DHSAGDTVCSECGLVLE--SHSIDETSEWRTFANE 50 (182)
Q Consensus 18 D~~~G~~vC~~CG~Vl~--e~~id~~~ewr~f~~~ 50 (182)
..+.|.++|..||.-|= +.-.|.|.-|.+|.+-
T Consensus 28 ~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~ 62 (119)
T PRK05508 28 FFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDDE 62 (119)
T ss_pred cCCCeEEEecCCCCccccccccccCCCCCcccCcc
Confidence 35899999999998874 4457889999999753
No 224
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.86 E-value=8.9 Score=25.04 Aligned_cols=20 Identities=30% Similarity=0.672 Sum_probs=15.3
Q ss_pred ceeEeC-CCCceEeCCCceee
Q 030129 14 EVVFDH-SAGDTVCSECGLVL 33 (182)
Q Consensus 14 ~iv~D~-~~G~~vC~~CG~Vl 33 (182)
.+..|- ++|+.+|.-||++.
T Consensus 38 rV~L~mg~~gev~CPYC~t~y 58 (62)
T COG4391 38 RVFLDMGDEGEVVCPYCSTRY 58 (62)
T ss_pred EEEEEcCCCCcEecCccccEE
Confidence 333443 79999999999986
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=53.65 E-value=4.8 Score=35.35 Aligned_cols=35 Identities=29% Similarity=0.558 Sum_probs=18.0
Q ss_pred CCCCCCC-CCceeEeCC--CCc--eEeCCCceeeeCCCcc
Q 030129 5 FCSDCKK-HTEVVFDHS--AGD--TVCSECGLVLESHSID 39 (182)
Q Consensus 5 ~Cp~Cg~-~~~iv~D~~--~G~--~vC~~CG~Vl~e~~id 39 (182)
.|+.||+ .+..+++.+ .+. +.|..||...+-.+-.
T Consensus 176 iC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~i~~ 215 (360)
T PF01921_consen 176 ICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVDITG 215 (360)
T ss_dssp EETTTEE--EEEEEEE--SSSEEEEE--TTS---EEETTT
T ss_pred eccccCCcccceeeEeecCCCEEEEEecCCCCEEEEecCC
Confidence 5999998 333334433 444 8999999997655543
No 226
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=53.50 E-value=7.7 Score=39.24 Aligned_cols=7 Identities=57% Similarity=1.659 Sum_probs=2.8
Q ss_pred EeCCCce
Q 030129 25 VCSECGL 31 (182)
Q Consensus 25 vC~~CG~ 31 (182)
.|.+||.
T Consensus 694 ~CPsCGa 700 (1337)
T PRK14714 694 VCPDCGA 700 (1337)
T ss_pred eCccCCC
Confidence 3444444
No 227
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=53.07 E-value=55 Score=28.52 Aligned_cols=51 Identities=14% Similarity=0.105 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHh-c-c---C---HHHHHHHHHHHHHhhCC
Q 030129 106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEA-E-I---K---THYWLLACTLLVDKKTS 156 (182)
Q Consensus 106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~-~-l---~---~~~v~AAclY~acr~~~ 156 (182)
..|++.|-+.|...+....+.=. .++.+... . + + .+.+|+|||.+|++.+-
T Consensus 79 ~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE 139 (335)
T KOG0656|consen 79 KQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEE 139 (335)
T ss_pred HHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcC
Confidence 46999999999999997765444 55555433 2 4 5 78999999999999873
No 228
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=52.92 E-value=4.5 Score=29.41 Aligned_cols=30 Identities=23% Similarity=0.473 Sum_probs=18.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
..|-+||...+.-.+..-|-.+|..|.-|-
T Consensus 14 ~~CaDCg~~~p~w~s~~~GiflC~~Cag~H 43 (116)
T PF01412_consen 14 KVCADCGAPNPTWASLNYGIFLCLECAGIH 43 (116)
T ss_dssp TB-TTT-SBS--EEETTTTEEE-HHHHHHH
T ss_pred CcCCCCCCCCCCEEEeecChhhhHHHHHHH
Confidence 579999875444556678999999998774
No 229
>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=52.29 E-value=11 Score=32.41 Aligned_cols=28 Identities=25% Similarity=0.560 Sum_probs=17.9
Q ss_pred CCCCCCCCCCc--eeEeC--CCC--ceEeCCCce
Q 030129 4 AFCSDCKKHTE--VVFDH--SAG--DTVCSECGL 31 (182)
Q Consensus 4 ~~Cp~Cg~~~~--iv~D~--~~G--~~vC~~CG~ 31 (182)
..||.||+.+. ++... ..| .+.|.-|+.
T Consensus 185 ~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~t 218 (305)
T TIGR01562 185 TLCPACGSPPVASMVRQGGKETGLRYLSCSLCAT 218 (305)
T ss_pred CcCCCCCChhhhhhhcccCCCCCceEEEcCCCCC
Confidence 47999998532 22221 345 488888875
No 230
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=52.28 E-value=8.3 Score=34.53 Aligned_cols=33 Identities=18% Similarity=0.457 Sum_probs=23.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcc
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id 39 (182)
-.||.||.. +.--..|.+-|..||+-..+..+-
T Consensus 351 p~Cp~Cg~~---m~S~G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 351 PVCPRCGGR---MKSAGRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCCccCCc---hhhcCCCCcccccccccCCccccc
Confidence 369999973 233344469999999998766654
No 231
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=52.19 E-value=5.8 Score=26.17 Aligned_cols=21 Identities=24% Similarity=0.619 Sum_probs=14.0
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCce
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (182)
.+-|.+|+. ++ + ..+|..||-
T Consensus 5 ~~AC~~C~~---i~-~----~~~Cp~Cgs 25 (64)
T PRK06393 5 YRACKKCKR---LT-P----EKTCPVHGD 25 (64)
T ss_pred hhhHhhCCc---cc-C----CCcCCCCCC
Confidence 356888985 22 2 238999987
No 232
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=51.79 E-value=10 Score=30.64 Aligned_cols=28 Identities=25% Similarity=0.705 Sum_probs=20.5
Q ss_pred CCCCCCCCCC-ceeEeCCCCceEeCCCce
Q 030129 4 AFCSDCKKHT-EVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 4 ~~Cp~Cg~~~-~iv~D~~~G~~vC~~CG~ 31 (182)
..|..||... ...+++..|-.+|.+|+.
T Consensus 148 ~~C~~cg~~~~~~~fs~~~gg~~C~~c~~ 176 (241)
T TIGR00613 148 DKCAVCGSKEDLIYFSMTYGGALCRQCGE 176 (241)
T ss_pred CccCCCCCcCCCceEchhcCeEEChhhCc
Confidence 3688888521 246778899999999965
No 233
>PRK14526 adenylate kinase; Provisional
Probab=51.78 E-value=12 Score=30.19 Aligned_cols=33 Identities=15% Similarity=0.354 Sum_probs=21.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (182)
..||.||..-++.+++..-..+|..||--+.-+
T Consensus 123 ~~~~~~g~~y~~~~~pp~~~~~~~~~~~~l~~R 155 (211)
T PRK14526 123 RICKSCNNIFNIYTLPTKEKGICDVCKGDLYQR 155 (211)
T ss_pred CcccccCCccccccCCCCccCcCCCCCCeeecc
Confidence 458888875566666666666787777554433
No 234
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=51.08 E-value=13 Score=22.34 Aligned_cols=22 Identities=36% Similarity=0.546 Sum_probs=16.7
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
+|..|+.. . ...+|-.||.|.-
T Consensus 1 ~C~~C~~~-~-------~l~~CL~C~~~~c 22 (50)
T smart00290 1 RCSVCGTI-E-------NLWLCLTCGQVGC 22 (50)
T ss_pred CcccCCCc-C-------CeEEecCCCCccc
Confidence 58899862 2 2689999999964
No 235
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=50.87 E-value=11 Score=30.59 Aligned_cols=26 Identities=38% Similarity=0.892 Sum_probs=20.8
Q ss_pred CCCCCCCCCc-eeEeCCCCceEeCCCc
Q 030129 5 FCSDCKKHTE-VVFDHSAGDTVCSECG 30 (182)
Q Consensus 5 ~Cp~Cg~~~~-iv~D~~~G~~vC~~CG 30 (182)
.|-.||+..+ ..+++..|-.+|..|+
T Consensus 151 ~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 151 HCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hHhcCCCCCCceEEecccCCccccccc
Confidence 6999997322 4577899999999997
No 236
>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=50.80 E-value=12 Score=32.68 Aligned_cols=33 Identities=36% Similarity=0.768 Sum_probs=21.1
Q ss_pred CCCCCCCCCCcee--EeCCCC--ceEeCCCceeeeCCC
Q 030129 4 AFCSDCKKHTEVV--FDHSAG--DTVCSECGLVLESHS 37 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv--~D~~~G--~~vC~~CG~Vl~e~~ 37 (182)
..||+||..+..+ +|.+.| .+.| .||.--+-.+
T Consensus 170 p~c~~cg~~~~~v~~~d~~~~~v~y~c-~cG~~g~~~~ 206 (353)
T cd00674 170 PYCEKCGKDTTTVEAYDAKAGTVTYKC-ECGHEETVDI 206 (353)
T ss_pred eecCCcCcceeEEEEEeCCCCeEEEEc-CCCCEEEEee
Confidence 3699999643334 454455 5788 5998865444
No 237
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=50.47 E-value=12 Score=28.56 Aligned_cols=33 Identities=27% Similarity=0.560 Sum_probs=26.7
Q ss_pred eCCCCceEeCCCceeee--CCCcccccccccccCC
Q 030129 18 DHSAGDTVCSECGLVLE--SHSIDETSEWRTFANE 50 (182)
Q Consensus 18 D~~~G~~vC~~CG~Vl~--e~~id~~~ewr~f~~~ 50 (182)
..+.|.++|..||.-|= +.-.|.|.-|.+|.+.
T Consensus 38 ~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~ 72 (142)
T PRK00222 38 NKEKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTKP 72 (142)
T ss_pred CCCCeEEEecCCCchhcCCcccccCCCCCcCcCcc
Confidence 45899999999999875 4447888999999864
No 238
>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=49.89 E-value=5.9 Score=38.97 Aligned_cols=23 Identities=26% Similarity=0.537 Sum_probs=17.1
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
..+||.||.. .+ ...|..||.-.
T Consensus 625 ~RKCPkCG~y-Tl-------k~rCP~CG~~T 647 (1095)
T TIGR00354 625 IRKCPQCGKE-SF-------WLKCPVCGELT 647 (1095)
T ss_pred EEECCCCCcc-cc-------cccCCCCCCcc
Confidence 4689999973 22 47999999663
No 239
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=49.67 E-value=8.6 Score=31.13 Aligned_cols=30 Identities=23% Similarity=0.542 Sum_probs=24.2
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
....|..|++ ..++. +.|-..|-.|+.|+.
T Consensus 3 ~l~~C~~C~~-ngiv~--~k~~efC~fC~~~f~ 32 (225)
T PHA03074 3 NLKLCSGCRH-NGIVS--EKDYEFCIFCESVFQ 32 (225)
T ss_pred chhhcCCCCC-CCeee--ecCEEEeecHHHHHh
Confidence 3467999997 67765 588999999999974
No 240
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.31 E-value=16 Score=25.20 Aligned_cols=28 Identities=29% Similarity=0.609 Sum_probs=18.5
Q ss_pred CCCCCCCCCCceeEeCCCCc--eEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGD--TVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~--~vC~~CG~Vl 33 (182)
+.||.|+- +++.-...|- -.|..|+=|-
T Consensus 2 llCP~C~v--~l~~~~rs~vEiD~CPrCrGVW 31 (88)
T COG3809 2 LLCPICGV--ELVMSVRSGVEIDYCPRCRGVW 31 (88)
T ss_pred cccCcCCc--eeeeeeecCceeeeCCccccEe
Confidence 57999994 3433333333 5799999885
No 241
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=49.29 E-value=11 Score=27.19 Aligned_cols=31 Identities=23% Similarity=0.425 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
...|-+|+....--....-|-.+|..|.-|-
T Consensus 3 N~~CaDC~~~~p~w~s~~~GifvC~~CsgiH 33 (112)
T smart00105 3 NKKCFDCGAPNPTWASVNLGVFLCIECSGIH 33 (112)
T ss_pred CCcccCCCCCCCCcEEeccceeEhHHhHHHH
Confidence 3568899874333345567889999998774
No 242
>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=49.22 E-value=26 Score=19.59 Aligned_cols=28 Identities=21% Similarity=0.634 Sum_probs=21.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
+.|..|+. .+.+.+..-..-|.-|..|-
T Consensus 2 ~~C~~C~t--~L~yP~gA~~vrCs~C~~vt 29 (31)
T TIGR01053 2 VVCGGCRT--LLMYPRGASSVRCALCQTVN 29 (31)
T ss_pred cCcCCCCc--EeecCCCCCeEECCCCCeEe
Confidence 56899984 56666677778899998773
No 243
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=49.22 E-value=8 Score=22.97 Aligned_cols=16 Identities=31% Similarity=0.837 Sum_probs=12.6
Q ss_pred CCceEeCCCceeeeCC
Q 030129 21 AGDTVCSECGLVLESH 36 (182)
Q Consensus 21 ~G~~vC~~CG~Vl~e~ 36 (182)
-|.+.|..||++....
T Consensus 11 ~~~~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 11 FGATTCPTCGMLYSPG 26 (41)
T ss_pred cCCcCCCCCCCEECCC
Confidence 3678999999997544
No 244
>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=48.89 E-value=13 Score=28.08 Aligned_cols=33 Identities=24% Similarity=0.410 Sum_probs=26.6
Q ss_pred eCCCCceEeCCCceeee--CCCcccccccccccCC
Q 030129 18 DHSAGDTVCSECGLVLE--SHSIDETSEWRTFANE 50 (182)
Q Consensus 18 D~~~G~~vC~~CG~Vl~--e~~id~~~ewr~f~~~ 50 (182)
..+.|.++|..||.-|= +.-.|.|.-|.+|.+.
T Consensus 35 ~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~ 69 (134)
T TIGR00357 35 NKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKP 69 (134)
T ss_pred CCCCeEEEccCCCCccccccchhcCCCCCcCcCcc
Confidence 45889999999999875 4457889999999754
No 245
>PF14369 zf-RING_3: zinc-finger
Probab=48.70 E-value=12 Score=21.44 Aligned_cols=26 Identities=23% Similarity=0.684 Sum_probs=15.5
Q ss_pred CCCCCCCCCCceeE-eCCCCceEeCCCce
Q 030129 4 AFCSDCKKHTEVVF-DHSAGDTVCSECGL 31 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~-D~~~G~~vC~~CG~ 31 (182)
.+|-.|... |.. .....+..|..|+-
T Consensus 3 ywCh~C~~~--V~~~~~~~~~~~CP~C~~ 29 (35)
T PF14369_consen 3 YWCHQCNRF--VRIAPSPDSDVACPRCHG 29 (35)
T ss_pred EeCccCCCE--eEeCcCCCCCcCCcCCCC
Confidence 468889862 322 23344445999974
No 246
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 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. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=48.46 E-value=9.2 Score=33.77 Aligned_cols=23 Identities=39% Similarity=0.907 Sum_probs=13.7
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.||.|+. +...| ..|..||..++
T Consensus 138 ~CP~C~~------~~a~g-~~Ce~cG~~~~ 160 (391)
T PF09334_consen 138 TCPYCGS------DKARG-DQCENCGRPLE 160 (391)
T ss_dssp EETTT--------SSCTT-TEETTTSSBEE
T ss_pred cccCcCc------cccCC-CcccCCCCCcc
Confidence 5788874 12233 56788888876
No 247
>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=48.40 E-value=4.6 Score=23.23 Aligned_cols=27 Identities=30% Similarity=0.760 Sum_probs=12.1
Q ss_pred CCCCCCCCcee-EeCCCCce-EeCCCcee
Q 030129 6 CSDCKKHTEVV-FDHSAGDT-VCSECGLV 32 (182)
Q Consensus 6 Cp~Cg~~~~iv-~D~~~G~~-vC~~CG~V 32 (182)
|-+|+...... -....|.. +|..||+-
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~ 29 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLY 29 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHH
Confidence 56676532222 22235665 78887753
No 248
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=47.74 E-value=31 Score=19.84 Aligned_cols=23 Identities=17% Similarity=0.577 Sum_probs=14.9
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
...|+.|+. ..+ .++|.+|+..|
T Consensus 3 ~~~C~~H~~-~~~-------~~~C~~C~~~~ 25 (42)
T PF00643_consen 3 EPKCPEHPE-EPL-------SLFCEDCNEPL 25 (42)
T ss_dssp SSB-SSTTT-SBE-------EEEETTTTEEE
T ss_pred CccCccCCc-cce-------EEEecCCCCcc
Confidence 567999986 322 37788887765
No 249
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=47.66 E-value=9.9 Score=39.23 Aligned_cols=31 Identities=35% Similarity=0.768 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCceeEeCCCCc------eEeCCCceeee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGD------TVCSECGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~------~vC~~CG~Vl~ 34 (182)
+..||+|+- .+++.|.+-|. -.|+.||.-+.
T Consensus 908 hy~C~~C~~-~ef~~~~~~~sG~Dlpdk~Cp~Cg~~~~ 944 (1437)
T PRK00448 908 HYVCPNCKY-SEFFTDGSVGSGFDLPDKDCPKCGTKLK 944 (1437)
T ss_pred cccCccccc-ccccccccccccccCccccCcccccccc
Confidence 567999985 78888765453 56999998775
No 250
>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=47.48 E-value=10 Score=29.02 Aligned_cols=15 Identities=40% Similarity=0.926 Sum_probs=13.2
Q ss_pred CCCceEeCCCceeee
Q 030129 20 SAGDTVCSECGLVLE 34 (182)
Q Consensus 20 ~~G~~vC~~CG~Vl~ 34 (182)
.-|.++|.+||..+.
T Consensus 109 g~G~l~C~~Cg~~~~ 123 (146)
T PF07295_consen 109 GPGTLVCENCGHEVE 123 (146)
T ss_pred cCceEecccCCCEEE
Confidence 579999999999874
No 251
>PRK06450 threonine synthase; Validated
Probab=47.27 E-value=10 Score=32.83 Aligned_cols=29 Identities=28% Similarity=0.620 Sum_probs=20.4
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
|...+|+.||. . +++ .-...|..||-.++
T Consensus 1 ~~~~~C~~Cg~-~---~~~-~~~~~C~~cg~~l~ 29 (338)
T PRK06450 1 MVKEVCMKCGK-E---RES-IYEIRCKKCGGPFE 29 (338)
T ss_pred CceeEECCcCC-c---CCC-cccccCCcCCCEeE
Confidence 45678999997 2 233 33578999998765
No 252
>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=47.01 E-value=16 Score=28.35 Aligned_cols=30 Identities=17% Similarity=0.425 Sum_probs=15.2
Q ss_pred CCCCCCCCCCce----eEeCCCCc-----eEeCCCceee
Q 030129 4 AFCSDCKKHTEV----VFDHSAGD-----TVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~i----v~D~~~G~-----~vC~~CG~Vl 33 (182)
..||.||..... +.-|--|+ ..|..||.=-
T Consensus 2 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~ 40 (161)
T PF03367_consen 2 SLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKN 40 (161)
T ss_dssp EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EE
T ss_pred CcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEe
Confidence 469999974221 11244555 4799999863
No 253
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=46.16 E-value=9.6 Score=38.59 Aligned_cols=26 Identities=38% Similarity=0.850 Sum_probs=15.5
Q ss_pred CCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 6 CSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 6 Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
||.||. .+..|. +|.+.|..||.-+.
T Consensus 695 CPsCGa--ev~~de-s~a~~CP~CGtplv 720 (1337)
T PRK14714 695 CPDCGA--EVPPDE-SGRVECPRCDVELT 720 (1337)
T ss_pred CccCCC--ccCCCc-cccccCCCCCCccc
Confidence 555553 223343 34789999996554
No 254
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=45.90 E-value=22 Score=24.04 Aligned_cols=19 Identities=0% Similarity=-0.013 Sum_probs=13.2
Q ss_pred HHHHHhcCCCceeeeceee
Q 030129 157 HALLRKSALSPMELQRRKL 175 (182)
Q Consensus 157 ~eia~~~~v~~~~i~r~~~ 175 (182)
.|||+.+++|+.+|-.+..
T Consensus 36 kEIAe~LGIS~~TVk~~l~ 54 (73)
T TIGR03879 36 SEIAEELGRTEQTVRNHLK 54 (73)
T ss_pred HHHHHHHCcCHHHHHHHHh
Confidence 6777777777777665543
No 255
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=45.87 E-value=12 Score=32.65 Aligned_cols=24 Identities=38% Similarity=0.945 Sum_probs=18.5
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.|+.||. . +-++ .+.|..||.-|.
T Consensus 1 ~C~~Cg~-~-v~Fe----Nt~C~~Cg~~LG 24 (343)
T PF10005_consen 1 SCPNCGQ-P-VFFE----NTRCLSCGSALG 24 (343)
T ss_pred CCCCCCC-c-ceeC----CCccccCCcccc
Confidence 4999996 3 4443 589999999886
No 256
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.81 E-value=16 Score=27.23 Aligned_cols=30 Identities=27% Similarity=0.540 Sum_probs=19.6
Q ss_pred CCCCCCCCCCCceeEe-C-C--CCceEeCCCceee
Q 030129 3 DAFCSDCKKHTEVVFD-H-S--AGDTVCSECGLVL 33 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D-~-~--~G~~vC~~CG~Vl 33 (182)
+..||.|++ ..++.- . . .-.+.|..||.-+
T Consensus 30 ~~~cP~C~s-~~~~k~g~~~~~~qRyrC~~C~~tf 63 (129)
T COG3677 30 KVNCPRCKS-SNVVKIGGIRRGHQRYKCKSCGSTF 63 (129)
T ss_pred cCcCCCCCc-cceeeECCccccccccccCCcCcce
Confidence 468999998 443322 1 2 2248999999765
No 257
>PRK07591 threonine synthase; Validated
Probab=45.06 E-value=10 Score=33.79 Aligned_cols=26 Identities=31% Similarity=0.574 Sum_probs=19.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.+|+.||.. ++...- +.|..||-.|+
T Consensus 19 l~C~~Cg~~----~~~~~~-~~C~~cg~~l~ 44 (421)
T PRK07591 19 LKCRECGAE----YPLGPI-HVCEECFGPLE 44 (421)
T ss_pred EEeCCCCCc----CCCCCC-ccCCCCCCeEE
Confidence 579999972 343333 88999998775
No 258
>PLN02569 threonine synthase
Probab=44.50 E-value=14 Score=33.73 Aligned_cols=27 Identities=11% Similarity=0.054 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
...|+.||. . ++.+.-.+.| .||-.|+
T Consensus 49 ~l~C~~Cg~-~---y~~~~~~~~C-~cgg~l~ 75 (484)
T PLN02569 49 FLECPLTGE-K---YSLDEVVYRS-KSGGLLD 75 (484)
T ss_pred ccEeCCCCC-c---CCCccccccC-CCCCeEE
Confidence 467999996 2 4556667899 7998885
No 259
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=44.40 E-value=13 Score=28.18 Aligned_cols=24 Identities=29% Similarity=0.765 Sum_probs=16.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
.+|+.||+ +.+-+ ...|..||.-.
T Consensus 30 ~kC~~CG~---v~~PP---r~~Cp~C~~~~ 53 (140)
T COG1545 30 TKCKKCGR---VYFPP---RAYCPKCGSET 53 (140)
T ss_pred EEcCCCCe---EEcCC---cccCCCCCCCC
Confidence 46999996 23333 37899998774
No 260
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=43.98 E-value=53 Score=32.12 Aligned_cols=50 Identities=14% Similarity=0.139 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc---c----CHHHHHHHHHHHHHhhCC
Q 030129 107 LAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE---I----KTHYWLLACTLLVDKKTS 156 (182)
Q Consensus 107 ~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~---l----~~~~v~AAclY~acr~~~ 156 (182)
-|...|+.+|.+|.|.+...+. .+|.-...+ | ..+.++-.|+|+.+|...
T Consensus 679 LAavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~ 737 (920)
T KOG1010|consen 679 LAAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKK 737 (920)
T ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhc
Confidence 3888999999999999988777 777765443 3 889999999999999873
No 261
>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=43.83 E-value=16 Score=27.24 Aligned_cols=32 Identities=31% Similarity=0.578 Sum_probs=24.6
Q ss_pred CCCCceEeCCCceeeeC--CCcccccccccccCC
Q 030129 19 HSAGDTVCSECGLVLES--HSIDETSEWRTFANE 50 (182)
Q Consensus 19 ~~~G~~vC~~CG~Vl~e--~~id~~~ewr~f~~~ 50 (182)
.+.|.++|..||.-|=. .-.|.+.-|.+|.+.
T Consensus 33 ~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~ 66 (124)
T PF01641_consen 33 KEEGIYVCAVCGTPLFSSDTKFDSGCGWPSFWQP 66 (124)
T ss_dssp TSSEEEEETTTS-EEEEGGGEETSSSSSSEESSC
T ss_pred CCCEEEEcCCCCCccccCcccccCCcCCccccCc
Confidence 47899999999998853 335778899998754
No 262
>PRK08329 threonine synthase; Validated
Probab=43.64 E-value=16 Score=31.48 Aligned_cols=25 Identities=24% Similarity=0.701 Sum_probs=17.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.+|+.||.. ++.... +.| .||-.|+
T Consensus 2 l~C~~Cg~~----~~~~~~-~~C-~c~~~l~ 26 (347)
T PRK08329 2 LRCTKCGRT----YEEKFK-LRC-DCGGTLL 26 (347)
T ss_pred cCcCCCCCC----cCCCCc-eec-CCCCcEE
Confidence 689999972 233333 789 7987664
No 263
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=42.93 E-value=20 Score=27.74 Aligned_cols=29 Identities=17% Similarity=0.370 Sum_probs=17.4
Q ss_pred CCCCCCCCCc--e-eE-eCCCCc-----eEeCCCceee
Q 030129 5 FCSDCKKHTE--V-VF-DHSAGD-----TVCSECGLVL 33 (182)
Q Consensus 5 ~Cp~Cg~~~~--i-v~-D~~~G~-----~vC~~CG~Vl 33 (182)
.||.|+.... + .+ -|.-|+ ..|..||.=-
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~ 39 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYRN 39 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCcc
Confidence 5999985322 1 11 133444 5799999863
No 264
>PF08421 Methyltransf_13: Putative zinc binding domain; InterPro: IPR013630 This domain is found at the N terminus of bacterial methyltransferases. ; PDB: 4E2X_A 3NDJ_A 3NDI_A 4E32_A 4E33_A 4E31_A 4E2Y_A 4E2W_A 4E2Z_A 4E30_A.
Probab=42.30 E-value=19 Score=23.22 Aligned_cols=17 Identities=35% Similarity=0.755 Sum_probs=10.1
Q ss_pred eEeCCCceeeeCCCccc
Q 030129 24 TVCSECGLVLESHSIDE 40 (182)
Q Consensus 24 ~vC~~CG~Vl~e~~id~ 40 (182)
.+|.+||+|.=++.++.
T Consensus 41 ~~C~~CglvQl~~~v~p 57 (62)
T PF08421_consen 41 YVCEDCGLVQLEEVVPP 57 (62)
T ss_dssp EEETTT--EEESS---H
T ss_pred EECCCCCchhcCCcCCH
Confidence 79999999987777653
No 265
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=42.10 E-value=13 Score=22.81 Aligned_cols=14 Identities=29% Similarity=0.707 Sum_probs=11.9
Q ss_pred CCceEeCCCceeee
Q 030129 21 AGDTVCSECGLVLE 34 (182)
Q Consensus 21 ~G~~vC~~CG~Vl~ 34 (182)
+|.++|..||.-+-
T Consensus 3 ~g~l~C~~CG~~m~ 16 (58)
T PF13408_consen 3 SGLLRCGHCGSKMT 16 (58)
T ss_pred CCcEEcccCCcEeE
Confidence 58899999998763
No 266
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=42.10 E-value=20 Score=31.00 Aligned_cols=31 Identities=23% Similarity=0.461 Sum_probs=22.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
..+|-+||...+.-.-..-|-.+|.+|.-|-
T Consensus 20 Nk~CaDCga~~P~W~S~nlGvfiCi~CagvH 50 (319)
T COG5347 20 NKKCADCGAPNPTWASVNLGVFLCIDCAGVH 50 (319)
T ss_pred cCccccCCCCCCceEecccCeEEEeecchhh
Confidence 4579999984433334578999999998774
No 267
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=42.00 E-value=14 Score=23.87 Aligned_cols=28 Identities=7% Similarity=0.011 Sum_probs=16.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcc
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id 39 (182)
..||+||. . .. ---+|. ||.--+..+++
T Consensus 28 ~~c~~cg~-~--~~----pH~vc~-cG~Y~gr~v~~ 55 (60)
T PRK01110 28 SVDKTTGE-Y--HL----PHHVSP-KGYYKGRKVLK 55 (60)
T ss_pred eEcCCCCc-e--ec----cceecC-CcccCCeEeec
Confidence 35888885 2 11 136788 88766554443
No 268
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=41.94 E-value=14 Score=27.21 Aligned_cols=15 Identities=20% Similarity=0.656 Sum_probs=6.6
Q ss_pred CCCCceEeCCCceee
Q 030129 19 HSAGDTVCSECGLVL 33 (182)
Q Consensus 19 ~~~G~~vC~~CG~Vl 33 (182)
...+..-|.+|+.++
T Consensus 66 ~~p~~~~C~~C~~~~ 80 (115)
T COG0375 66 EEPAECWCLDCGQEV 80 (115)
T ss_pred EeccEEEeccCCCee
Confidence 344444444444433
No 269
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=41.62 E-value=17 Score=26.14 Aligned_cols=13 Identities=31% Similarity=1.012 Sum_probs=10.1
Q ss_pred CceEeCCCceeee
Q 030129 22 GDTVCSECGLVLE 34 (182)
Q Consensus 22 G~~vC~~CG~Vl~ 34 (182)
.-.+|..||.|++
T Consensus 79 ~h~iC~~Cg~v~~ 91 (120)
T PF01475_consen 79 HHFICTQCGKVID 91 (120)
T ss_dssp EEEEETTTS-EEE
T ss_pred eEEEECCCCCEEE
Confidence 3499999999985
No 270
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=41.59 E-value=14 Score=23.85 Aligned_cols=22 Identities=27% Similarity=0.505 Sum_probs=13.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
.+||.||..+--. .|..||-+.
T Consensus 6 rkC~~cg~YTLke--------~Cp~CG~~t 27 (59)
T COG2260 6 RKCPKCGRYTLKE--------KCPVCGGDT 27 (59)
T ss_pred hcCcCCCceeecc--------cCCCCCCcc
Confidence 4688888643112 388888765
No 271
>PRK09462 fur ferric uptake regulator; Provisional
Probab=41.15 E-value=16 Score=27.49 Aligned_cols=12 Identities=42% Similarity=1.113 Sum_probs=10.8
Q ss_pred ceEeCCCceeee
Q 030129 23 DTVCSECGLVLE 34 (182)
Q Consensus 23 ~~vC~~CG~Vl~ 34 (182)
-.+|..||.|++
T Consensus 90 H~iC~~Cg~i~~ 101 (148)
T PRK09462 90 HLICLDCGKVIE 101 (148)
T ss_pred ceEECCCCCEEE
Confidence 499999999986
No 272
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=41.12 E-value=17 Score=26.01 Aligned_cols=27 Identities=19% Similarity=0.369 Sum_probs=17.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
.-|..|+- |..+..--...|.+||.++
T Consensus 4 rAC~~C~~---I~~~~qf~~~gCpnC~~~l 30 (98)
T cd07973 4 RACLLCSL---IKTEDQFERDGCPNCEGYL 30 (98)
T ss_pred chhccCCc---ccccccccCCCCCCCcchh
Confidence 45888875 3333333356799998666
No 273
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=40.79 E-value=16 Score=26.41 Aligned_cols=34 Identities=21% Similarity=0.578 Sum_probs=23.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcc
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id 39 (182)
..|++||- ..++..+= +.-.|+.||..-.+..++
T Consensus 43 ~~C~~Cg~-~~~~~~SC-k~R~CP~C~~~~~~~W~~ 76 (111)
T PF14319_consen 43 YRCEDCGH-EKIVYNSC-KNRHCPSCQAKATEQWIE 76 (111)
T ss_pred eecCCCCc-eEEecCcc-cCcCCCCCCChHHHHHHH
Confidence 46999996 55555443 444999999987654443
No 274
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=40.53 E-value=5 Score=22.72 Aligned_cols=18 Identities=11% Similarity=0.062 Sum_probs=15.1
Q ss_pred HHHHHhcCCCceeeecee
Q 030129 157 HALLRKSALSPMELQRRK 174 (182)
Q Consensus 157 ~eia~~~~v~~~~i~r~~ 174 (182)
.|||+.+|++..++.|.+
T Consensus 6 ~diA~~lG~t~ETVSR~l 23 (32)
T PF00325_consen 6 QDIADYLGLTRETVSRIL 23 (32)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHhCCcHHHHHHHH
Confidence 699999999999998865
No 275
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=40.41 E-value=18 Score=31.84 Aligned_cols=38 Identities=21% Similarity=0.468 Sum_probs=28.7
Q ss_pred CCCCCCCCCceeEeC-CCCceEeCCCceeeeCCCcccccc
Q 030129 5 FCSDCKKHTEVVFDH-SAGDTVCSECGLVLESHSIDETSE 43 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~-~~G~~vC~~CG~Vl~e~~id~~~e 43 (182)
.|..||+ ..+...+ ++|..-|.+|-.|+.+-.+-...|
T Consensus 276 vCd~CGn-~rLe~~pe~rg~~~C~~Cs~~V~sP~~r~~Le 314 (389)
T PF14951_consen 276 VCDRCGN-GRLEQSPEDRGAFSCGDCSRVVTSPVLRMHLE 314 (389)
T ss_pred cccccCC-ccceeCccCCCceeccchhhhccCcceeeeEE
Confidence 5999997 6776555 577799999999997766554444
No 276
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=39.52 E-value=17 Score=25.66 Aligned_cols=13 Identities=31% Similarity=1.022 Sum_probs=11.3
Q ss_pred CceEeCCCceeee
Q 030129 22 GDTVCSECGLVLE 34 (182)
Q Consensus 22 G~~vC~~CG~Vl~ 34 (182)
.-.+|..||.|.+
T Consensus 72 ~H~~C~~Cg~i~~ 84 (116)
T cd07153 72 HHLICTKCGKVID 84 (116)
T ss_pred CceEeCCCCCEEE
Confidence 3599999999986
No 277
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=39.42 E-value=22 Score=33.36 Aligned_cols=24 Identities=25% Similarity=0.710 Sum_probs=15.2
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCc
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECG 30 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG 30 (182)
.++||.|++...++. |...|.-|+
T Consensus 2 ~~~C~~C~g~G~i~v----~~e~c~vc~ 25 (715)
T COG1107 2 IKKCPECGGKGKIVV----GEEECPVCH 25 (715)
T ss_pred CccccccCCCceEee----eeeeccccc
Confidence 367999998655543 445555553
No 278
>TIGR02642 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q.
Probab=39.40 E-value=18 Score=28.81 Aligned_cols=23 Identities=17% Similarity=0.559 Sum_probs=14.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCc
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECG 30 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG 30 (182)
..||.|++...++.+ .-.|..|+
T Consensus 100 ~~C~~C~G~G~~i~~----~~~C~~C~ 122 (186)
T TIGR02642 100 CKCPRCRGTGLIQRR----QRECDTCA 122 (186)
T ss_pred CcCCCCCCeeEEecC----CCCCCCCC
Confidence 579999984333321 25688884
No 279
>smart00400 ZnF_CHCC zinc finger.
Probab=39.34 E-value=40 Score=20.84 Aligned_cols=27 Identities=15% Similarity=0.273 Sum_probs=21.1
Q ss_pred CCCCCCC-CCceeEeCCCCceEeCCCce
Q 030129 5 FCSDCKK-HTEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 5 ~Cp~Cg~-~~~iv~D~~~G~~vC~~CG~ 31 (182)
.||-+.. .+.+.+++..+...|-.||.
T Consensus 4 ~cPfh~d~~pSf~v~~~kn~~~Cf~cg~ 31 (55)
T smart00400 4 LCPFHGEKTPSFSVSPDKQFFHCFGCGA 31 (55)
T ss_pred cCcCCCCCCCCEEEECCCCEEEEeCCCC
Confidence 5999875 34677788888899999973
No 280
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=39.18 E-value=6.3 Score=31.15 Aligned_cols=29 Identities=31% Similarity=0.704 Sum_probs=19.5
Q ss_pred CCCCCCCCCceeEeC-CCCceEeCCCceeeeC
Q 030129 5 FCSDCKKHTEVVFDH-SAGDTVCSECGLVLES 35 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~-~~G~~vC~~CG~Vl~e 35 (182)
.||.|.. ..-+|. -.-...|+.||-++++
T Consensus 115 ~C~~~~~--r~sfdeA~~~~F~Cp~Cg~~L~~ 144 (176)
T COG1675 115 VCPNCHV--KYSFDEAMELGFTCPKCGEDLEE 144 (176)
T ss_pred eCCCCCC--cccHHHHHHhCCCCCCCCchhhh
Confidence 5999885 344554 1223889999999864
No 281
>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=39.05 E-value=27 Score=22.44 Aligned_cols=30 Identities=30% Similarity=0.557 Sum_probs=15.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCC
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~ 37 (182)
..|..|++ . +..-....-|..||.|+=..-
T Consensus 10 ~~C~~C~~--~--F~~~~rrhhCr~CG~~vC~~C 39 (69)
T PF01363_consen 10 SNCMICGK--K--FSLFRRRHHCRNCGRVVCSSC 39 (69)
T ss_dssp SB-TTT----B---BSSS-EEE-TTT--EEECCC
T ss_pred CcCcCcCC--c--CCCceeeEccCCCCCEECCch
Confidence 56999986 2 244567788999998886444
No 282
>PRK04023 DNA polymerase II large subunit; Validated
Probab=38.94 E-value=19 Score=35.79 Aligned_cols=11 Identities=36% Similarity=0.993 Sum_probs=6.3
Q ss_pred eEeCCCceeee
Q 030129 24 TVCSECGLVLE 34 (182)
Q Consensus 24 ~vC~~CG~Vl~ 34 (182)
..|..||....
T Consensus 652 ~fCP~CG~~~~ 662 (1121)
T PRK04023 652 YRCPRCGIEVE 662 (1121)
T ss_pred eeCccccCcCC
Confidence 56666666543
No 283
>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=38.79 E-value=24 Score=21.94 Aligned_cols=7 Identities=29% Similarity=0.966 Sum_probs=6.2
Q ss_pred CCCCCCC
Q 030129 5 FCSDCKK 11 (182)
Q Consensus 5 ~Cp~Cg~ 11 (182)
.||.||+
T Consensus 15 ~Cp~CGN 21 (49)
T PF12677_consen 15 KCPKCGN 21 (49)
T ss_pred cCcccCC
Confidence 6999996
No 284
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=38.69 E-value=18 Score=27.38 Aligned_cols=13 Identities=38% Similarity=0.991 Sum_probs=11.2
Q ss_pred CceEeCCCceeee
Q 030129 22 GDTVCSECGLVLE 34 (182)
Q Consensus 22 G~~vC~~CG~Vl~ 34 (182)
.-++|.+||.|++
T Consensus 92 ~HliC~~CG~v~e 104 (145)
T COG0735 92 HHLICLDCGKVIE 104 (145)
T ss_pred cEEEecCCCCEEE
Confidence 3589999999986
No 285
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=38.67 E-value=31 Score=30.66 Aligned_cols=27 Identities=15% Similarity=0.305 Sum_probs=22.8
Q ss_pred CCCCCCCC-CceeEeCCCCceEeCCCce
Q 030129 5 FCSDCKKH-TEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 5 ~Cp~Cg~~-~~iv~D~~~G~~vC~~CG~ 31 (182)
.||.|+.. +.+.+++..|..-|-.||.
T Consensus 36 ~CPfh~ek~pSf~v~~~k~~~~Cf~Cg~ 63 (415)
T TIGR01391 36 LCPFHHEKTPSFSVSPEKQFYHCFGCGA 63 (415)
T ss_pred eCCCCCCCCCeEEEEcCCCcEEECCCCC
Confidence 59999753 4688899999999999996
No 286
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=38.40 E-value=20 Score=30.83 Aligned_cols=29 Identities=28% Similarity=0.550 Sum_probs=17.6
Q ss_pred CCCCCCCCCCC--ceeE-eCCCCc--eEeCCCce
Q 030129 3 DAFCSDCKKHT--EVVF-DHSAGD--TVCSECGL 31 (182)
Q Consensus 3 ~~~Cp~Cg~~~--~iv~-D~~~G~--~vC~~CG~ 31 (182)
...||.||+.+ .++. ....|. +.|.-||.
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~t 220 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCES 220 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCC
Confidence 35799999853 2221 123443 78888875
No 287
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=38.27 E-value=16 Score=23.93 Aligned_cols=25 Identities=28% Similarity=0.804 Sum_probs=15.9
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCce
Q 030129 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (182)
.+..|..||+. .. .--.-.|..||.
T Consensus 16 tHt~CrRCG~~-sy----h~qK~~CasCGy 40 (62)
T PRK04179 16 THIRCRRCGRH-SY----NVRKKYCAACGF 40 (62)
T ss_pred ccchhcccCcc-cc----cccccchhhcCC
Confidence 34568888873 22 223567888887
No 288
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=38.05 E-value=17 Score=25.76 Aligned_cols=12 Identities=25% Similarity=0.437 Sum_probs=9.7
Q ss_pred CCCCCCCCCCCC
Q 030129 1 MTDAFCSDCKKH 12 (182)
Q Consensus 1 m~~~~Cp~Cg~~ 12 (182)
|....||+||..
T Consensus 1 mlLI~CP~Cg~R 12 (97)
T COG4311 1 MLLIPCPYCGER 12 (97)
T ss_pred CceecCCCCCCC
Confidence 677889999963
No 289
>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=37.88 E-value=17 Score=36.95 Aligned_cols=31 Identities=39% Similarity=0.865 Sum_probs=23.0
Q ss_pred CCCCCCCCCCCceeEeCCCC------ceEeCCCceeee
Q 030129 3 DAFCSDCKKHTEVVFDHSAG------DTVCSECGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G------~~vC~~CG~Vl~ 34 (182)
+..||+|+- .+++.|.+-| +-.|..||.-+.
T Consensus 683 hy~c~~c~~-~ef~~~~~~~sg~dlp~k~cp~c~~~~~ 719 (1213)
T TIGR01405 683 HYLCPNCKY-SEFITDGSVGSGFDLPDKDCPKCGAPLK 719 (1213)
T ss_pred cccCccccc-ccccccccccccccCccccCcccccccc
Confidence 467999985 7888775433 357999998764
No 290
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=37.37 E-value=6.6 Score=23.95 Aligned_cols=18 Identities=17% Similarity=0.259 Sum_probs=15.3
Q ss_pred HHHHHhcCCCceeeecee
Q 030129 157 HALLRKSALSPMELQRRK 174 (182)
Q Consensus 157 ~eia~~~~v~~~~i~r~~ 174 (182)
+|||+.+|||..|+.|.+
T Consensus 3 ~dIA~~agvS~~TVSr~l 20 (46)
T PF00356_consen 3 KDIAREAGVSKSTVSRVL 20 (46)
T ss_dssp HHHHHHHTSSHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 699999999998887753
No 291
>PF14149 YhfH: YhfH-like protein
Probab=37.29 E-value=4.1 Score=23.89 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=11.3
Q ss_pred CCceEeCCCceeeeCC
Q 030129 21 AGDTVCSECGLVLESH 36 (182)
Q Consensus 21 ~G~~vC~~CG~Vl~e~ 36 (182)
-+.-.|+.||..++|.
T Consensus 11 Lp~K~C~~CG~~i~EQ 26 (37)
T PF14149_consen 11 LPPKKCTECGKEIEEQ 26 (37)
T ss_pred CCCcccHHHHHHHHHH
Confidence 3456788898887653
No 292
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=37.12 E-value=20 Score=33.60 Aligned_cols=32 Identities=25% Similarity=0.652 Sum_probs=21.3
Q ss_pred CCCCCCCCCceeEeC------------CCCceEeCCCceeeeCC
Q 030129 5 FCSDCKKHTEVVFDH------------SAGDTVCSECGLVLESH 36 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~------------~~G~~vC~~CG~Vl~e~ 36 (182)
-||+||...-+.++. +.-.+.|..|+.+|.+.
T Consensus 229 pCPHCGe~q~l~~~e~~~~~g~~~~~~~~~~~~c~h~~~~i~~~ 272 (611)
T COG5525 229 PCPHCGEEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVIRPK 272 (611)
T ss_pred eCCCCCchhhccccccCCCcCcccchhhhhhhhccccCceeeee
Confidence 599999643333321 12336899999999883
No 293
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=37.06 E-value=32 Score=28.25 Aligned_cols=25 Identities=20% Similarity=0.304 Sum_probs=18.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCC
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSE 28 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~ 28 (182)
..||.|+..-.+-+||.+|++|=..
T Consensus 80 I~C~~C~n~i~~RTDPkN~~YV~Es 104 (272)
T COG5134 80 IKCHLCSNPIDVRTDPKNTEYVVES 104 (272)
T ss_pred EEccCCCCceeeecCCCCceEEEec
Confidence 3588888755677788888877554
No 294
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=36.44 E-value=19 Score=23.26 Aligned_cols=25 Identities=20% Similarity=0.616 Sum_probs=16.3
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
+..|..||.. ..- --.-.|..||.=
T Consensus 16 H~~CRRCGr~-syh----v~k~~CaaCGfg 40 (61)
T COG2126 16 HIRCRRCGRR-SYH----VRKKYCAACGFG 40 (61)
T ss_pred eehhhhccch-hee----eccceecccCCC
Confidence 4578889873 321 235689999875
No 295
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=36.42 E-value=16 Score=25.04 Aligned_cols=31 Identities=32% Similarity=0.756 Sum_probs=19.7
Q ss_pred CCCCCCCCC-----CCceeEeC--CCCc---eEeCCCceee
Q 030129 3 DAFCSDCKK-----HTEVVFDH--SAGD---TVCSECGLVL 33 (182)
Q Consensus 3 ~~~Cp~Cg~-----~~~iv~D~--~~G~---~vC~~CG~Vl 33 (182)
...|+-|+. ....++|+ .+|. +.|..|-.++
T Consensus 22 ~~~C~iC~~~~~~~~~~~~vDHdH~tG~vRGlLC~~CN~~l 62 (81)
T PF02945_consen 22 GGRCAICGKPLPGESRKLVVDHDHKTGRVRGLLCRSCNTAL 62 (81)
T ss_dssp TTE-TTT-SEEETTCGGCEEEE-TTTTBEEEEEEHHHHHHH
T ss_pred CCcCcCCCCCcccCCCcceecCCCCCCCchhhhhhHHhhhh
Confidence 357999996 45566665 6666 6788887765
No 296
>PHA02540 61 DNA primase; Provisional
Probab=36.03 E-value=34 Score=29.81 Aligned_cols=28 Identities=18% Similarity=0.366 Sum_probs=22.5
Q ss_pred CCCCCCCC------CceeEeCCCC--ceEeCCCcee
Q 030129 5 FCSDCKKH------TEVVFDHSAG--DTVCSECGLV 32 (182)
Q Consensus 5 ~Cp~Cg~~------~~iv~D~~~G--~~vC~~CG~V 32 (182)
.||-|+-. +.+.+.++.| .+-|-+||.=
T Consensus 29 ~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa~ 64 (337)
T PHA02540 29 RCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGYH 64 (337)
T ss_pred cCCCCCCccccCcCCcEEEeccCCceEEEecCCCCC
Confidence 59999852 2477888888 8999999974
No 297
>PRK05638 threonine synthase; Validated
Probab=35.98 E-value=21 Score=31.89 Aligned_cols=25 Identities=28% Similarity=0.784 Sum_probs=17.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.+|+.||. . ++... .+.| .||-.++
T Consensus 2 l~C~~Cg~-~---~~~~~-~~~C-~c~~~l~ 26 (442)
T PRK05638 2 MKCPKCGR-E---YNSYI-PPFC-ICGELLE 26 (442)
T ss_pred eEeCCCCC-C---CCCCC-ceec-CCCCcEE
Confidence 57999997 2 23222 2789 8997765
No 298
>PRK07217 replication factor A; Reviewed
Probab=35.92 E-value=17 Score=31.27 Aligned_cols=21 Identities=33% Similarity=0.748 Sum_probs=15.1
Q ss_pred CCCCC--CCCCCceeEeCCCCceEeCCCcee
Q 030129 4 AFCSD--CKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~--Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
..||+ |++. + ....|..||.|
T Consensus 189 ~rCP~~~C~Rv---l-----~~g~C~~HG~v 211 (311)
T PRK07217 189 KRCPEEDCTRV---L-----QNGRCSEHGKV 211 (311)
T ss_pred ecCCccccCcc---c-----cCCCCCCCCCc
Confidence 46999 9872 2 23689999977
No 299
>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=35.90 E-value=23 Score=32.66 Aligned_cols=32 Identities=28% Similarity=0.602 Sum_probs=20.8
Q ss_pred CCCCCCCCCceeEeCC---CCceEeCCCceeeeCCC
Q 030129 5 FCSDCKKHTEVVFDHS---AGDTVCSECGLVLESHS 37 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~---~G~~vC~~CG~Vl~e~~ 37 (182)
.||.||+....+++.+ +=.+.| +||.-.+-.+
T Consensus 170 ic~~cGrv~~~~~~~~~~~~v~Y~c-~cG~~g~~~~ 204 (515)
T TIGR00467 170 FCENCGRDTTTVNNYDNEYSIEYSC-ECGNQESVDI 204 (515)
T ss_pred ecCCcCccCceEEEecCCceEEEEc-CCCCEEEEee
Confidence 6999998543444443 345778 4998865544
No 300
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=35.89 E-value=23 Score=18.54 Aligned_cols=9 Identities=22% Similarity=0.501 Sum_probs=6.4
Q ss_pred CCCCCCCCC
Q 030129 3 DAFCSDCKK 11 (182)
Q Consensus 3 ~~~Cp~Cg~ 11 (182)
...||.||+
T Consensus 2 l~~C~~CgR 10 (25)
T PF13913_consen 2 LVPCPICGR 10 (25)
T ss_pred CCcCCCCCC
Confidence 356888886
No 301
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.62 E-value=18 Score=23.79 Aligned_cols=28 Identities=32% Similarity=0.566 Sum_probs=15.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeC-CCcee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCS-ECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~-~CG~V 32 (182)
..||.||+ +..-.+.+.=.-+|. .|-+|
T Consensus 8 v~CP~Cgk-pv~w~~~s~frPFCSkRCklI 36 (65)
T COG3024 8 VPCPTCGK-PVVWGEESPFRPFCSKRCKLI 36 (65)
T ss_pred ccCCCCCC-cccccccCCcCcchhHhhhhc
Confidence 57999997 332222233334554 57654
No 302
>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=35.36 E-value=33 Score=16.84 Aligned_cols=11 Identities=27% Similarity=0.691 Sum_probs=7.7
Q ss_pred eEeCCCceeee
Q 030129 24 TVCSECGLVLE 34 (182)
Q Consensus 24 ~vC~~CG~Vl~ 34 (182)
..|..||.+..
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 36888887764
No 303
>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=35.07 E-value=61 Score=19.50 Aligned_cols=35 Identities=26% Similarity=0.601 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCccc
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDE 40 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~ 40 (182)
..+|-.|+. .| .-...--+.|+.|++++-..=++.
T Consensus 11 ~~~C~~C~~--~i-~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 11 PTYCDVCGK--FI-WGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp TEB-TTSSS--BE-CSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCCCcccCc--cc-CCCCCCeEEECCCCChHhhhhhhh
Confidence 457999986 23 223334589999999998776553
No 304
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=35.05 E-value=21 Score=22.35 Aligned_cols=30 Identities=23% Similarity=0.597 Sum_probs=16.9
Q ss_pred CCCCCCCCC--CceeEeC--CCCceEeCCCceee
Q 030129 4 AFCSDCKKH--TEVVFDH--SAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~--~~iv~D~--~~G~~vC~~CG~Vl 33 (182)
..|..|+-. +..+.+- ..+-..|.+||.+|
T Consensus 23 ~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 23 GTCSGCHMELPPQELNEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred CccCCCCEEcCHHHHHHHHcCCCeEECcCCCccC
Confidence 467777631 1111111 23568999999875
No 305
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=34.93 E-value=22 Score=36.09 Aligned_cols=31 Identities=35% Similarity=0.800 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCceeEeCCCCc------eEeCCCceeee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGD------TVCSECGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~------~vC~~CG~Vl~ 34 (182)
+..||+|.- .+++.|..-|. --|..||.=+.
T Consensus 914 HY~Cp~Cky-~Ef~~d~svgsGfDLpdK~CPkCg~pl~ 950 (1444)
T COG2176 914 HYLCPECKY-SEFIDDGSVGSGFDLPDKDCPKCGTPLK 950 (1444)
T ss_pred cccCCCCce-eeeecCCCcCCCCCCCCCCCCcCCCccc
Confidence 467999995 78888775554 56999998764
No 306
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=34.51 E-value=25 Score=26.77 Aligned_cols=33 Identities=27% Similarity=0.593 Sum_probs=27.0
Q ss_pred eCCCCceEeCCCceeee--CCCcccccccccccCC
Q 030129 18 DHSAGDTVCSECGLVLE--SHSIDETSEWRTFANE 50 (182)
Q Consensus 18 D~~~G~~vC~~CG~Vl~--e~~id~~~ewr~f~~~ 50 (182)
..+.|-++|..||.-|= +.-.|.|--|.+|.+.
T Consensus 49 ~~e~GvY~C~~C~~pLykS~tKfdsgcGWPAF~e~ 83 (146)
T KOG0856|consen 49 HFEEGVYVCAGCGTPLYKSTTKFDSGCGWPAFFEA 83 (146)
T ss_pred ccCCceEEEeecCCccccccccccCCCCCchhhhc
Confidence 34889999999998875 3447889999999865
No 307
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=34.28 E-value=15 Score=32.31 Aligned_cols=14 Identities=14% Similarity=0.012 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHh
Q 030129 106 ILAFKTIATMSDRI 119 (182)
Q Consensus 106 ~~a~~~I~~i~~~L 119 (182)
.+++..+.++..++
T Consensus 161 e~~~~~ve~~v~k~ 174 (355)
T COG1499 161 EEAFLFVEEIVLKR 174 (355)
T ss_pred HHHHHHHHHHHHhh
Confidence 56788888877766
No 308
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=33.99 E-value=23 Score=27.43 Aligned_cols=12 Identities=42% Similarity=0.891 Sum_probs=10.8
Q ss_pred ceEeCCCceeee
Q 030129 23 DTVCSECGLVLE 34 (182)
Q Consensus 23 ~~vC~~CG~Vl~ 34 (182)
-.+|..||.|++
T Consensus 100 H~iC~~CGki~~ 111 (169)
T PRK11639 100 MFICDRCGAVKE 111 (169)
T ss_pred eEEeCCCCCEEE
Confidence 489999999986
No 309
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=33.76 E-value=15 Score=21.73 Aligned_cols=26 Identities=27% Similarity=0.658 Sum_probs=12.7
Q ss_pred CCCCCCCCCC---ceeEeCCCCceEeCCC
Q 030129 4 AFCSDCKKHT---EVVFDHSAGDTVCSEC 29 (182)
Q Consensus 4 ~~Cp~Cg~~~---~iv~D~~~G~~vC~~C 29 (182)
.+|.-||+.. ..++.-..|-.||.+|
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~C 30 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDEC 30 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHH
Confidence 4689998732 1233334467888887
No 310
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=33.61 E-value=30 Score=25.79 Aligned_cols=28 Identities=21% Similarity=0.571 Sum_probs=20.9
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
.|-.||..+.+-.+...-...|..|+.+
T Consensus 2 ~C~fC~~~s~~~~~~~~~~w~C~~C~q~ 29 (131)
T PF09779_consen 2 NCWFCGQNSKVPYDNRNSNWTCPHCEQY 29 (131)
T ss_pred eeccCCCCCCCCCCCCCCeeECCCCCCc
Confidence 5999998655555544445999999988
No 311
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=33.58 E-value=14 Score=22.84 Aligned_cols=36 Identities=19% Similarity=0.054 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhhCCHHHHHhcCCCceeeeceeee
Q 030129 141 HYWLLACTLLVDKKTSHALLRKSALSPMELQRRKLA 176 (182)
Q Consensus 141 ~~v~AAclY~acr~~~~eia~~~~v~~~~i~r~~~~ 176 (182)
+.+....+|+-.-....++|..+||++.++.|++-+
T Consensus 7 d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~ 42 (53)
T PF13613_consen 7 DQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHE 42 (53)
T ss_pred HHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHH
Confidence 456777788777777799999999999999887644
No 312
>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=33.44 E-value=32 Score=20.58 Aligned_cols=30 Identities=17% Similarity=0.533 Sum_probs=21.7
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcc
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id 39 (182)
+|+.|++ .+.....+.|..|+..+--.=+.
T Consensus 1 ~C~vC~~-----~~~~~~~i~C~~C~~~~H~~C~~ 30 (51)
T PF00628_consen 1 YCPVCGQ-----SDDDGDMIQCDSCNRWYHQECVG 30 (51)
T ss_dssp EBTTTTS-----SCTTSSEEEBSTTSCEEETTTST
T ss_pred eCcCCCC-----cCCCCCeEEcCCCChhhCcccCC
Confidence 4888986 24566779999999887554443
No 313
>PRK00279 adk adenylate kinase; Reviewed
Probab=33.15 E-value=32 Score=27.21 Aligned_cols=30 Identities=27% Similarity=0.636 Sum_probs=17.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
..||.||..-++.+++......|..||.-+
T Consensus 128 ~~~~~~g~~~~~~~~~p~~~~~~~~~~~~l 157 (215)
T PRK00279 128 RICPACGRTYHVKFNPPKVEGKCDVCGEEL 157 (215)
T ss_pred cccCccCCcccccCCCCCCcCcCcCCCCcc
Confidence 356777664455555554555666666443
No 314
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=33.14 E-value=18 Score=27.27 Aligned_cols=13 Identities=46% Similarity=0.997 Sum_probs=10.7
Q ss_pred EeCCCceeeeCCC
Q 030129 25 VCSECGLVLESHS 37 (182)
Q Consensus 25 vC~~CG~Vl~e~~ 37 (182)
-|+.||.|+++.-
T Consensus 3 ~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 3 QCTKCGRVFEDGS 15 (131)
T ss_pred ccCcCCCCcCCCc
Confidence 4999999998665
No 315
>PRK05667 dnaG DNA primase; Validated
Probab=33.13 E-value=43 Score=31.28 Aligned_cols=27 Identities=15% Similarity=0.320 Sum_probs=23.0
Q ss_pred CCCCCCCC-CceeEeCCCCceEeCCCce
Q 030129 5 FCSDCKKH-TEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 5 ~Cp~Cg~~-~~iv~D~~~G~~vC~~CG~ 31 (182)
.||.|+.. +.+.+++..|.+-|-.||.
T Consensus 38 ~CPfH~ektpSf~V~~~k~~~~CF~Cg~ 65 (580)
T PRK05667 38 LCPFHDEKTPSFTVSPDKQFYHCFGCGA 65 (580)
T ss_pred cCCCCCCCCCceEEECCCCeEEECCCCC
Confidence 59999864 4778899999999999996
No 316
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.81 E-value=29 Score=32.63 Aligned_cols=26 Identities=31% Similarity=0.781 Sum_probs=20.1
Q ss_pred CCCC--CCCCCceeEeCCCCceEeCCCceee
Q 030129 5 FCSD--CKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 5 ~Cp~--Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
.||. |++. +.+...|.+.|..|+...
T Consensus 476 ACp~~~CnKK---V~~~~~g~~~CekC~~~~ 503 (608)
T TIGR00617 476 ACPSEDCNKK---VVDQGDGTYRCEKCNKNF 503 (608)
T ss_pred cCChhhCCCc---cccCCCCCEECCCCCCCC
Confidence 5987 9873 345567999999999765
No 317
>PRK11032 hypothetical protein; Provisional
Probab=32.71 E-value=24 Score=27.46 Aligned_cols=15 Identities=33% Similarity=0.738 Sum_probs=12.7
Q ss_pred CCCceEeCCCceeee
Q 030129 20 SAGDTVCSECGLVLE 34 (182)
Q Consensus 20 ~~G~~vC~~CG~Vl~ 34 (182)
.-|.++|..||.-+.
T Consensus 121 g~G~LvC~~Cg~~~~ 135 (160)
T PRK11032 121 GLGNLVCEKCHHHLA 135 (160)
T ss_pred ecceEEecCCCCEEE
Confidence 468999999999873
No 318
>PF13309 HTH_22: HTH domain
Probab=32.71 E-value=52 Score=21.22 Aligned_cols=49 Identities=10% Similarity=0.043 Sum_probs=30.7
Q ss_pred HHHHHHHHHhCChHHH---HHH-HHHHHHHhc--cCHHHHHHHHHHHHHhhCCHHHHHhcCCCceee
Q 030129 110 KTIATMSDRIGQMRYI---RRW-KIKSLVEAE--IKTHYWLLACTLLVDKKTSHALLRKSALSPMEL 170 (182)
Q Consensus 110 ~~I~~i~~~L~L~~~v---~~~-~i~k~a~~~--l~~~~v~AAclY~acr~~~~eia~~~~v~~~~i 170 (182)
+.|..+....+.|... .++ ++.+...+. |.... .-..+|+.+|||+.||
T Consensus 5 ~~i~~~~~~~~~~~~~l~~~~k~~iV~~L~~~G~F~lKg------------av~~vA~~L~iS~~TV 59 (64)
T PF13309_consen 5 SIIEEVIAEVGKPPSRLSKEEKKEIVRQLYEKGIFLLKG------------AVEYVAEKLGISRATV 59 (64)
T ss_pred HHHHHHHHHhCCChhhCCHHHHHHHHHHHHHCCCcccCc------------HHHHHHHHHCCCHHHH
Confidence 5677788888887654 333 888888776 42111 0134677777777664
No 319
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=32.68 E-value=17 Score=25.16 Aligned_cols=39 Identities=21% Similarity=0.317 Sum_probs=24.6
Q ss_pred CCCCCCCCCCc------eeEeCCCCceEeCCCceeeeCCCcccccc
Q 030129 4 AFCSDCKKHTE------VVFDHSAGDTVCSECGLVLESHSIDETSE 43 (182)
Q Consensus 4 ~~Cp~Cg~~~~------iv~D~~~G~~vC~~CG~Vl~e~~id~~~e 43 (182)
|.|-+||...+ +..+..+-..+|..|-.|. +-+.+.|.+
T Consensus 1 ~~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~-~~i~~~gL~ 45 (88)
T PF12156_consen 1 MKCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVY-QLIHENGLE 45 (88)
T ss_pred CCCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHH-HHHHHcchH
Confidence 56999996321 1223344589999999996 445555543
No 320
>PF03685 UPF0147: Uncharacterised protein family (UPF0147); InterPro: IPR005354 The proteins in this entry are functionally uncharacterised.; PDB: 2QZG_C 2QSB_A.
Probab=32.52 E-value=1.7e+02 Score=20.37 Aligned_cols=49 Identities=14% Similarity=0.143 Sum_probs=32.1
Q ss_pred chHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-cCHHHHHHHHHH
Q 030129 101 PDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-IKTHYWLLACTL 149 (182)
Q Consensus 101 ~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l~~~~v~AAclY 149 (182)
.+..+.++...+.+|.+.-.+|.+|+.. +..+...+. .++..=||.+++
T Consensus 4 ~e~~i~~~~~~L~~I~~D~sVPRNIRr~a~ea~~~L~~e~~~~~vRaataIs 55 (85)
T PF03685_consen 4 NEEKIKQAIQMLERIINDTSVPRNIRRAAEEAKEILNNEEESPGVRAATAIS 55 (85)
T ss_dssp HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHCT-TTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHhCCCcchhHhHHHHHH
Confidence 3667889999999999999999999887 555544443 344444455544
No 321
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=32.27 E-value=93 Score=30.56 Aligned_cols=47 Identities=6% Similarity=0.082 Sum_probs=38.4
Q ss_pred HHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c--CHHHHHHHHHHHHHhhC
Q 030129 109 FKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I--KTHYWLLACTLLVDKKT 155 (182)
Q Consensus 109 ~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l--~~~~v~AAclY~acr~~ 155 (182)
.......|..|+++...... +.|..+... + +-.++.|.+||.+||..
T Consensus 35 ~q~~~~~c~~lnld~~~~~ea~d~yta~~q~~slegs~~hW~~cAlY~~~r~S 87 (920)
T KOG1010|consen 35 EQDSDELCRPLNLDEQTETEAWDTYTAVSQRLSLEGSESHWLACALYTACRRS 87 (920)
T ss_pred hhhhhhhhhhhcccchhhhhhHHHHHHHHhHhCCCccHHHHHHHHHHHHHHhc
Confidence 35556778889998766555 999988887 4 78999999999999987
No 322
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=32.26 E-value=36 Score=25.82 Aligned_cols=33 Identities=27% Similarity=0.564 Sum_probs=26.2
Q ss_pred eCCCCceEeCCCceeee--CCCcccccccccccCC
Q 030129 18 DHSAGDTVCSECGLVLE--SHSIDETSEWRTFANE 50 (182)
Q Consensus 18 D~~~G~~vC~~CG~Vl~--e~~id~~~ewr~f~~~ 50 (182)
..+.|-++|..||.-|= +.-.|.|--|.+|.+-
T Consensus 37 ~~~~GiY~c~~cg~pLF~S~~KfdSgcGWPSF~~p 71 (140)
T COG0229 37 NKEKGIYVCIVCGEPLFSSEDKFDSGCGWPSFTKP 71 (140)
T ss_pred ccCCceEEeecCCCccccccccccCCCCCcccccc
Confidence 34889999999998774 4457888899998754
No 323
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=32.08 E-value=23 Score=22.05 Aligned_cols=29 Identities=24% Similarity=0.347 Sum_probs=21.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCccc
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDE 40 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~ 40 (182)
..||-|+. ++.|+ +...||.|++...|..
T Consensus 2 ~~Cpi~~~---~~~~P-----v~~~~G~v~~~~~i~~ 30 (63)
T smart00504 2 FLCPISLE---VMKDP-----VILPSGQTYERRAIEK 30 (63)
T ss_pred cCCcCCCC---cCCCC-----EECCCCCEEeHHHHHH
Confidence 46999986 34453 7789999998777753
No 324
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.88 E-value=21 Score=26.40 Aligned_cols=18 Identities=22% Similarity=0.663 Sum_probs=10.6
Q ss_pred ceeEeCCCCceEeCCCcee
Q 030129 14 EVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 14 ~iv~D~~~G~~vC~~CG~V 32 (182)
.+......+...| +||..
T Consensus 61 ~L~I~~vp~~~~C-~Cg~~ 78 (124)
T PRK00762 61 DLIVEMIPVEIEC-ECGYE 78 (124)
T ss_pred EEEEEecCeeEEe-eCcCc
Confidence 4555556666666 66643
No 325
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=31.44 E-value=20 Score=36.83 Aligned_cols=24 Identities=33% Similarity=0.603 Sum_probs=17.9
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
..+||.||.. .+ ...|..||.-.+
T Consensus 674 ~~~Cp~Cg~~-~~-------~~~Cp~CG~~~~ 697 (1627)
T PRK14715 674 FFKCPKCGKV-GL-------YHVCPFCGTRVE 697 (1627)
T ss_pred eeeCCCCCCc-cc-------cccCcccCCccc
Confidence 3579999963 22 479999998754
No 326
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=31.15 E-value=29 Score=26.65 Aligned_cols=8 Identities=25% Similarity=0.700 Sum_probs=4.7
Q ss_pred CCCCCCCC
Q 030129 4 AFCSDCKK 11 (182)
Q Consensus 4 ~~Cp~Cg~ 11 (182)
..||.||+
T Consensus 33 v~CP~Cgs 40 (148)
T PF06676_consen 33 VSCPVCGS 40 (148)
T ss_pred ccCCCCCC
Confidence 45666665
No 327
>PRK08173 DNA topoisomerase III; Validated
Probab=30.60 E-value=31 Score=33.78 Aligned_cols=26 Identities=19% Similarity=0.526 Sum_probs=18.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
..||.||+ .++. ..+.+.|++|+..+
T Consensus 625 ~~CP~Cg~--~~~~--~~~~~~Cs~C~f~~ 650 (862)
T PRK08173 625 TPCPNCGG--VVKE--NYRRFACTKCDFSI 650 (862)
T ss_pred ccCCcccc--cccc--cCceeEcCCCCccc
Confidence 36999997 2322 23349999999776
No 328
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=30.54 E-value=18 Score=31.33 Aligned_cols=18 Identities=28% Similarity=0.344 Sum_probs=16.7
Q ss_pred CHHHHHHHHHHHHHhhCC
Q 030129 139 KTHYWLLACTLLVDKKTS 156 (182)
Q Consensus 139 ~~~~v~AAclY~acr~~~ 156 (182)
++..||+||||+||...+
T Consensus 193 ~p~~IAva~i~lA~~~~~ 210 (323)
T KOG0834|consen 193 SPHSIAVACIHLAAKLLG 210 (323)
T ss_pred cCcEEEeehhhHHHHHcC
Confidence 999999999999999775
No 329
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=30.47 E-value=12 Score=22.45 Aligned_cols=19 Identities=11% Similarity=0.123 Sum_probs=15.6
Q ss_pred CHHHHHhcCCCceeeecee
Q 030129 156 SHALLRKSALSPMELQRRK 174 (182)
Q Consensus 156 ~~eia~~~~v~~~~i~r~~ 174 (182)
..+||+.+|||..|+.++.
T Consensus 20 ~~~ia~~lgvs~~Tv~~w~ 38 (50)
T PF13384_consen 20 IREIAKRLGVSRSTVYRWI 38 (50)
T ss_dssp HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4899999999999988864
No 330
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=30.37 E-value=37 Score=20.01 Aligned_cols=8 Identities=25% Similarity=0.829 Sum_probs=5.2
Q ss_pred CCCCCCCC
Q 030129 4 AFCSDCKK 11 (182)
Q Consensus 4 ~~Cp~Cg~ 11 (182)
..||.||+
T Consensus 3 ~~Cp~Cg~ 10 (47)
T PF14690_consen 3 PRCPHCGS 10 (47)
T ss_pred ccCCCcCC
Confidence 45777775
No 331
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=29.98 E-value=17 Score=35.37 Aligned_cols=10 Identities=30% Similarity=0.793 Sum_probs=0.0
Q ss_pred EeCCCceeee
Q 030129 25 VCSECGLVLE 34 (182)
Q Consensus 25 vC~~CG~Vl~ 34 (182)
.|..||.-..
T Consensus 694 ~C~~C~~~~~ 703 (900)
T PF03833_consen 694 ECPKCGRETT 703 (900)
T ss_dssp ----------
T ss_pred ccccccccCc
Confidence 7888887653
No 333
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 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 consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=29.93 E-value=24 Score=22.53 Aligned_cols=24 Identities=21% Similarity=0.834 Sum_probs=13.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
..|..||+ .. +. --.-.|..||.=
T Consensus 16 ~~CrRCG~-~s--yH--~qK~~CasCGyp 39 (55)
T PF01907_consen 16 TLCRRCGR-RS--YH--IQKKTCASCGYP 39 (55)
T ss_dssp EE-TTTSS-EE--EE--TTTTEETTTBTT
T ss_pred eeecccCC-ee--ee--cCCCcccccCCC
Confidence 45888886 22 22 235678888864
No 334
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.83 E-value=28 Score=33.35 Aligned_cols=26 Identities=27% Similarity=0.606 Sum_probs=14.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCce
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (182)
..|+.||-...+..+ ..| ..|+.||-
T Consensus 642 ~~C~~CG~~Ge~~~~-~~~-~~CP~CG~ 667 (711)
T PRK09263 642 DECYECGFTGEFECT-EKG-FTCPKCGN 667 (711)
T ss_pred cccCCCCCCccccCC-CCC-CcCcCCCC
Confidence 468888852222111 223 67888884
No 335
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=29.73 E-value=26 Score=31.56 Aligned_cols=31 Identities=23% Similarity=0.214 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHhCChHHH----HHH---HHHHHHHhc
Q 030129 107 LAFKTIATMSDRIGQMRYI----RRW---KIKSLVEAE 137 (182)
Q Consensus 107 ~a~~~I~~i~~~L~L~~~v----~~~---~i~k~a~~~ 137 (182)
+....|.--+++|+++..- .+. .|++.+.+.
T Consensus 130 ES~~QiklRA~RL~~~~~~l~l~aEt~~e~I~~~l~~~ 167 (456)
T COG1066 130 ESLQQIKLRADRLGLPTNNLYLLAETNLEDIIAELEQE 167 (456)
T ss_pred cCHHHHHHHHHHhCCCccceEEehhcCHHHHHHHHHhc
Confidence 4557788889999987532 333 777777665
No 336
>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=29.35 E-value=29 Score=25.38 Aligned_cols=12 Identities=42% Similarity=0.935 Sum_probs=10.8
Q ss_pred ceEeCCCceeee
Q 030129 23 DTVCSECGLVLE 34 (182)
Q Consensus 23 ~~vC~~CG~Vl~ 34 (182)
++.|..||+.++
T Consensus 74 EyyCP~Cgt~le 85 (112)
T PF08882_consen 74 EYYCPGCGTQLE 85 (112)
T ss_pred EEECCCCcceeE
Confidence 589999999986
No 337
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=29.31 E-value=26 Score=30.79 Aligned_cols=25 Identities=24% Similarity=0.651 Sum_probs=17.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
.+||+|.. ++ ...-+..|..||.-.
T Consensus 58 ~kC~~c~~-~~----~y~~~~~C~~cg~~~ 82 (415)
T COG5257 58 YKCPECYR-PE----CYTTEPKCPNCGAET 82 (415)
T ss_pred EeCCCCCC-Cc----ccccCCCCCCCCCCc
Confidence 47999996 32 233467899999754
No 338
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=29.23 E-value=23 Score=29.47 Aligned_cols=39 Identities=26% Similarity=0.371 Sum_probs=24.4
Q ss_pred CCCCCCCCCCCc---eeEeCCCC-ceEeCCCce-eeeCCCcccc
Q 030129 3 DAFCSDCKKHTE---VVFDHSAG-DTVCSECGL-VLESHSIDET 41 (182)
Q Consensus 3 ~~~Cp~Cg~~~~---iv~D~~~G-~~vC~~CG~-Vl~e~~id~~ 41 (182)
..+|..|+.... +......+ -..|..||- +|.-+++-.|
T Consensus 122 ~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~~lrP~VV~fG 165 (250)
T COG0846 122 RVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGPVLRPDVVWFG 165 (250)
T ss_pred eeEeCCCcCccchhhhhhhcccCCCCcCccCCCccccCCEEEeC
Confidence 357999985221 11112233 367999999 9988887554
No 339
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=29.21 E-value=31 Score=27.95 Aligned_cols=36 Identities=19% Similarity=0.434 Sum_probs=23.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcccc
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDET 41 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~ 41 (182)
..|..|+.. ...+.......|..||-++..+++..|
T Consensus 119 ~~C~~C~~~--~~~~~~~~~p~C~~Cgg~lrP~vv~fg 154 (225)
T cd01411 119 IYCTVCGKT--VDWEEYLKSPYHAKCGGVIRPDIVLYE 154 (225)
T ss_pred eEeCCCCCc--cchhhcCCCCCCCCCCCEeCCCEEEcC
Confidence 569999752 111222223679999999988887554
No 340
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=29.00 E-value=32 Score=31.02 Aligned_cols=31 Identities=23% Similarity=0.513 Sum_probs=22.6
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
....|=.|+..++.-.--.=|-.+|.+|-.|
T Consensus 22 ~NKvCFDCgAknPtWaSVTYGIFLCiDCSAv 52 (454)
T KOG0706|consen 22 ENKVCFDCGAKNPTWASVTYGIFLCIDCSAV 52 (454)
T ss_pred CCceecccCCCCCCceeecceEEEEEecchh
Confidence 3457999997544433345699999999887
No 341
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=29.00 E-value=22 Score=23.31 Aligned_cols=12 Identities=33% Similarity=0.805 Sum_probs=10.2
Q ss_pred eEeCCCceeeeC
Q 030129 24 TVCSECGLVLES 35 (182)
Q Consensus 24 ~vC~~CG~Vl~e 35 (182)
+.|-.||.|+.+
T Consensus 5 vRCFTCGkvi~~ 16 (62)
T PRK04016 5 VRCFTCGKVIAE 16 (62)
T ss_pred eEecCCCCChHH
Confidence 679999999964
No 342
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=28.93 E-value=20 Score=29.56 Aligned_cols=39 Identities=21% Similarity=0.282 Sum_probs=23.1
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCc--eeeeCCCcccc
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECG--LVLESHSIDET 41 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG--~Vl~e~~id~~ 41 (182)
.+.|..|+..-+.-.+...+...|..|| -++..+++-.|
T Consensus 117 ~~~C~~C~~~~~~~~~~~~~~p~C~~Cg~~g~lrP~vV~FG 157 (242)
T PTZ00408 117 KVRCTATGHVFDWTEDVVHGSSRCKCCGCVGTLRPHIVWFG 157 (242)
T ss_pred eEEECCCCcccCchhhhhcCCCccccCCCCCCCCCCEEEcC
Confidence 3579999862221112223446799998 46777776544
No 343
>PHA00689 hypothetical protein
Probab=28.69 E-value=40 Score=21.12 Aligned_cols=24 Identities=25% Similarity=0.551 Sum_probs=15.9
Q ss_pred CceEeCCCceeeeCCCccccccccc
Q 030129 22 GDTVCSECGLVLESHSIDETSEWRT 46 (182)
Q Consensus 22 G~~vC~~CG~Vl~e~~id~~~ewr~ 46 (182)
--..|..||.. .-+.-|.|-||.-
T Consensus 16 ravtckrcgkt-glrweddggewvl 39 (62)
T PHA00689 16 RAVTCKRCGKT-GLRWEDDGGEWVL 39 (62)
T ss_pred ceeehhhcccc-CceeecCCCcEEE
Confidence 34678888875 4566677778853
No 344
>PHA02956 hypothetical protein; Provisional
Probab=28.52 E-value=32 Score=26.34 Aligned_cols=20 Identities=25% Similarity=0.793 Sum_probs=18.0
Q ss_pred CceeEeCCCCceEeCCCcee
Q 030129 13 TEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 13 ~~iv~D~~~G~~vC~~CG~V 32 (182)
+.++.|+.+|.++|..=|.+
T Consensus 107 nsiiidsssgkiicegigii 126 (189)
T PHA02956 107 NSIIIDSSSGKIICEGIGII 126 (189)
T ss_pred ceEEEecCCCcEEeecchHH
Confidence 57899999999999998876
No 345
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=28.40 E-value=1.3e+02 Score=25.76 Aligned_cols=18 Identities=22% Similarity=0.181 Sum_probs=16.8
Q ss_pred CHHHHHHHHHHHHHhhCC
Q 030129 139 KTHYWLLACTLLVDKKTS 156 (182)
Q Consensus 139 ~~~~v~AAclY~acr~~~ 156 (182)
.|..||.||+++||+..+
T Consensus 190 pphiIA~a~l~ia~~~~~ 207 (297)
T COG5333 190 PPHIIALAALLIACEVLG 207 (297)
T ss_pred ChHHHHHHHHHHHHHhcC
Confidence 999999999999999874
No 346
>TIGR00320 dfx_rbo desulfoferrodoxin. This protein is described in some articles as rubredoxin oxidoreductase (rbo), and its gene shares an operon with the rubredoxin gene in Desulfovibrio vulgaris Hildenborough.
Probab=28.33 E-value=37 Score=25.18 Aligned_cols=22 Identities=27% Similarity=0.570 Sum_probs=15.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEe
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVC 26 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC 26 (182)
.+|+.||. --.+.+...|+++|
T Consensus 8 YkC~~CGn-iv~v~~~g~~~l~C 29 (125)
T TIGR00320 8 YKCEVCGN-IVEVLNAGIGQLVC 29 (125)
T ss_pred EECCCCCc-EEEEEECCCcceee
Confidence 46999996 23335666777777
No 347
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=28.24 E-value=33 Score=27.97 Aligned_cols=38 Identities=18% Similarity=0.420 Sum_probs=22.5
Q ss_pred CCCCCCCCCCCceeEeC-CCCceEeCCCceeeeCCCcccc
Q 030129 3 DAFCSDCKKHTEVVFDH-SAGDTVCSECGLVLESHSIDET 41 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~-~~G~~vC~~CG~Vl~e~~id~~ 41 (182)
...|..|+..-. ..+. ......|..||-++..+++-.+
T Consensus 122 ~~~C~~C~~~~~-~~~~~~~~~p~C~~Cgg~lrP~Vv~fg 160 (242)
T PRK00481 122 RARCTKCGQTYD-LDEYLKPEPPRCPKCGGILRPDVVLFG 160 (242)
T ss_pred ceeeCCCCCCcC-hhhhccCCCCCCCCCCCccCCCeEECC
Confidence 356999975211 1111 1123349999999888877443
No 348
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=28.05 E-value=28 Score=32.92 Aligned_cols=10 Identities=10% Similarity=-0.207 Sum_probs=7.3
Q ss_pred HHHHHhcCCC
Q 030129 157 HALLRKSALS 166 (182)
Q Consensus 157 ~eia~~~~v~ 166 (182)
.+|.+.+|++
T Consensus 495 e~i~~~Lg~~ 504 (673)
T PRK00133 495 ERAEAFLNLE 504 (673)
T ss_pred HHHHHHhCCC
Confidence 6777777775
No 349
>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=27.94 E-value=43 Score=20.47 Aligned_cols=30 Identities=27% Similarity=0.628 Sum_probs=20.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCC
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~ 37 (182)
..|+.|+.. +..-....-|..||.|+=..-
T Consensus 3 ~~C~~C~~~----F~~~~rk~~Cr~Cg~~~C~~C 32 (57)
T cd00065 3 SSCMGCGKP----FTLTRRRHHCRNCGRIFCSKC 32 (57)
T ss_pred CcCcccCcc----ccCCccccccCcCcCCcChHH
Confidence 568999862 344566788999998875433
No 350
>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=27.89 E-value=33 Score=22.46 Aligned_cols=28 Identities=25% Similarity=0.473 Sum_probs=17.8
Q ss_pred CCCCCCCCCCCceeEeC------CCCceEeCCCce
Q 030129 3 DAFCSDCKKHTEVVFDH------SAGDTVCSECGL 31 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~------~~G~~vC~~CG~ 31 (182)
...||.|++ .+.-+.+ .+=...|..|-.
T Consensus 5 ~~~CPRC~S-~nTKFcYyNNy~~~QPR~~Ck~C~r 38 (63)
T PF02701_consen 5 PLPCPRCDS-TNTKFCYYNNYNLSQPRYFCKSCRR 38 (63)
T ss_pred CCCCCCcCC-CCCEEEeecCCCCCCcchhhHHHHH
Confidence 467999998 5555554 233466777754
No 351
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=27.81 E-value=39 Score=30.27 Aligned_cols=24 Identities=29% Similarity=0.530 Sum_probs=14.7
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
.||+|+-. . ..+...|..||.++.
T Consensus 223 ~C~~Cd~l---~---~~~~a~CpRC~~~L~ 246 (419)
T PRK15103 223 SCSCCTAI---L---PADQPVCPRCHTKGY 246 (419)
T ss_pred cCCCCCCC---C---CCCCCCCCCCCCcCc
Confidence 48888752 1 123447888888873
No 352
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=27.74 E-value=37 Score=27.16 Aligned_cols=38 Identities=21% Similarity=0.373 Sum_probs=23.6
Q ss_pred CCCCCCCCCCCceeEeC------CCCceEeCCCceeeeCCCcccc
Q 030129 3 DAFCSDCKKHTEVVFDH------SAGDTVCSECGLVLESHSIDET 41 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~------~~G~~vC~~CG~Vl~e~~id~~ 41 (182)
...|+.|+..-. ..+. ..-...|..||-++..+++..|
T Consensus 95 ~~~C~~C~~~~~-~~~~~~~~~~~~~~p~C~~Cgg~lrP~VV~Fg 138 (206)
T cd01410 95 IEVCKSCGPEYV-RDDVVETRGDKETGRRCHACGGILKDTIVDFG 138 (206)
T ss_pred cccCCCCCCccc-hHHHHHHhhcCCCCCcCCCCcCccCCcEEECC
Confidence 457999985211 1111 1123569999999888887665
No 353
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.54 E-value=36 Score=26.43 Aligned_cols=14 Identities=21% Similarity=0.601 Sum_probs=8.0
Q ss_pred eEeCCCceeeeCCC
Q 030129 24 TVCSECGLVLESHS 37 (182)
Q Consensus 24 ~vC~~CG~Vl~e~~ 37 (182)
..|.+|+.=|.-..
T Consensus 40 ~~Cp~C~~~IrG~y 53 (158)
T PF10083_consen 40 TSCPNCSTPIRGDY 53 (158)
T ss_pred HHCcCCCCCCCCce
Confidence 45677766555433
No 354
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=27.43 E-value=35 Score=30.06 Aligned_cols=35 Identities=23% Similarity=0.417 Sum_probs=21.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcccccccc
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWR 45 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr 45 (182)
..|+.|+. ..++.. .....|..||- .....||=|-
T Consensus 245 ~~C~~c~~-~~~~~~--~~~~~C~~c~~----~~~~~GPlW~ 279 (382)
T PRK04338 245 YYCPKCLY-REEVEG--LPPEECPVCGG----KFGTAGPLWL 279 (382)
T ss_pred EECCCCCc-EEEecC--CCCCCCCCCCC----cceecccccc
Confidence 35999996 333322 33456999976 4445778873
No 355
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=27.24 E-value=26 Score=25.33 Aligned_cols=11 Identities=36% Similarity=1.084 Sum_probs=8.5
Q ss_pred EeCCCceeeeC
Q 030129 25 VCSECGLVLES 35 (182)
Q Consensus 25 vC~~CG~Vl~e 35 (182)
.|+.||.|+++
T Consensus 4 ~CtrCG~vf~~ 14 (112)
T COG3364 4 QCTRCGEVFDD 14 (112)
T ss_pred eeccccccccc
Confidence 58888888765
No 356
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=27.12 E-value=27 Score=25.51 Aligned_cols=7 Identities=29% Similarity=0.743 Sum_probs=4.1
Q ss_pred CCCCCCC
Q 030129 5 FCSDCKK 11 (182)
Q Consensus 5 ~Cp~Cg~ 11 (182)
.|+.|++
T Consensus 54 ~C~~C~G 60 (111)
T PLN03165 54 VCRFCVG 60 (111)
T ss_pred CCCCCcC
Confidence 4666655
No 357
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=27.06 E-value=33 Score=22.45 Aligned_cols=27 Identities=33% Similarity=0.700 Sum_probs=14.8
Q ss_pred CCCCCCCCCCceeEeC-CCCceEeCC-Ccee
Q 030129 4 AFCSDCKKHTEVVFDH-SAGDTVCSE-CGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~-~~G~~vC~~-CG~V 32 (182)
..||.|++. ++... ..=.-+|.. |-+|
T Consensus 7 v~CP~C~k~--~~w~~~~~~rPFCS~RCk~I 35 (62)
T PRK00418 7 VNCPTCGKP--VEWGEISPFRPFCSKRCQLI 35 (62)
T ss_pred ccCCCCCCc--ccccCCCCcCCcccHHHHhh
Confidence 579999973 22211 222356664 7554
No 358
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=26.88 E-value=26 Score=29.46 Aligned_cols=23 Identities=22% Similarity=0.660 Sum_probs=14.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
.+|.+||+. .. .=+.-|.+||.-
T Consensus 83 ~~C~~CGa~-V~-----~~e~~Cp~C~St 105 (314)
T PF09567_consen 83 GKCNNCGAN-VS-----RLEESCPNCGST 105 (314)
T ss_pred hhhccccce-ee-----ehhhcCCCCCcc
Confidence 468888862 11 225678888854
No 359
>PRK08116 hypothetical protein; Validated
Probab=26.51 E-value=52 Score=27.38 Aligned_cols=28 Identities=29% Similarity=0.627 Sum_probs=16.7
Q ss_pred CCCCCCCCCCceeEeCCCCce----EeCCCcee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDT----VCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~----vC~~CG~V 32 (182)
..||.||.....+++. .|.. +|..|-.-
T Consensus 17 ~~C~~Cg~~~~~~~~~-~~~~~~~~~~c~C~~~ 48 (268)
T PRK08116 17 EYCEVCGKRIEKVVEL-LGKNRIVPIMCECERE 48 (268)
T ss_pred ccCcCCCCcceeeecc-cCcceecCCCCCChHH
Confidence 5799999854444432 3332 57788553
No 360
>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=26.47 E-value=40 Score=21.65 Aligned_cols=6 Identities=67% Similarity=1.902 Sum_probs=3.0
Q ss_pred EeCCCc
Q 030129 25 VCSECG 30 (182)
Q Consensus 25 vC~~CG 30 (182)
+|.+||
T Consensus 43 ~CPNCg 48 (57)
T PF06906_consen 43 VCPNCG 48 (57)
T ss_pred cCcCCC
Confidence 455554
No 361
>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=26.19 E-value=33 Score=22.94 Aligned_cols=20 Identities=25% Similarity=0.614 Sum_probs=10.1
Q ss_pred eeEeCCCCceEeCCCceeee
Q 030129 15 VVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 15 iv~D~~~G~~vC~~CG~Vl~ 34 (182)
+-.+++-...+|..||.++-
T Consensus 38 ~~l~~~~kr~~Ck~C~~~li 57 (85)
T PF04032_consen 38 IRLPPEIKRTICKKCGSLLI 57 (85)
T ss_dssp ---STTCCCTB-TTT--B--
T ss_pred CCCChHHhcccccCCCCEEe
Confidence 34566777899999999973
No 362
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=26.07 E-value=27 Score=28.50 Aligned_cols=31 Identities=23% Similarity=0.574 Sum_probs=19.0
Q ss_pred CCCCCCCC-CceeE-eCCCCceEeCCCceeeeC
Q 030129 5 FCSDCKKH-TEVVF-DHSAGDTVCSECGLVLES 35 (182)
Q Consensus 5 ~Cp~Cg~~-~~iv~-D~~~G~~vC~~CG~Vl~e 35 (182)
.|+.|--. .+++. +..---.+|..||.....
T Consensus 15 lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 15 LCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIG 47 (236)
T ss_pred cChHHhcccCCeeecCCccCceECCCCCCEECC
Confidence 47777431 23333 223466999999999854
No 363
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=25.87 E-value=37 Score=20.32 Aligned_cols=28 Identities=14% Similarity=0.076 Sum_probs=20.5
Q ss_pred HHHHHHhhC--CHHHHHhcCCCceeeecee
Q 030129 147 CTLLVDKKT--SHALLRKSALSPMELQRRK 174 (182)
Q Consensus 147 clY~acr~~--~~eia~~~~v~~~~i~r~~ 174 (182)
-++-.|+.. .++||+.+||+..++.|++
T Consensus 19 ~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~ 48 (52)
T PF13542_consen 19 YILKLLRESRSFKDVARELGVSWSTVRRIF 48 (52)
T ss_pred HHHHHHhhcCCHHHHHHHHCCCHHHHHHHH
Confidence 333444444 4899999999999998875
No 364
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=25.83 E-value=48 Score=28.22 Aligned_cols=33 Identities=24% Similarity=0.614 Sum_probs=26.7
Q ss_pred eCCCCceEeCCCceeee--CCCcccccccccccCC
Q 030129 18 DHSAGDTVCSECGLVLE--SHSIDETSEWRTFANE 50 (182)
Q Consensus 18 D~~~G~~vC~~CG~Vl~--e~~id~~~ewr~f~~~ 50 (182)
..+.|.++|..||.-|= +.-.|.|.-|.+|.+-
T Consensus 31 ~~~~G~y~c~~c~~~LF~s~~Kf~sg~GWPsF~~~ 65 (283)
T PRK05550 31 HDEKGVYLCRRCGAPLFRSEDKFNSGCGWPSFDDE 65 (283)
T ss_pred CCCCcEEEcCCCCchhcCChhhccCCCCCcCcCcc
Confidence 45899999999999875 4457889999999763
No 365
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=25.57 E-value=59 Score=17.98 Aligned_cols=7 Identities=14% Similarity=0.738 Sum_probs=5.1
Q ss_pred CCCCCCC
Q 030129 5 FCSDCKK 11 (182)
Q Consensus 5 ~Cp~Cg~ 11 (182)
.|+.++.
T Consensus 2 ~C~~H~~ 8 (39)
T cd00021 2 LCDEHGE 8 (39)
T ss_pred CCCccCC
Confidence 5888875
No 366
>PRK04330 hypothetical protein; Provisional
Probab=25.53 E-value=2.4e+02 Score=19.73 Aligned_cols=64 Identities=11% Similarity=0.115 Sum_probs=44.9
Q ss_pred CchHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-cCHHHHHHHHHHHHHhhCCHHHHHhcCCCce
Q 030129 100 NPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-IKTHYWLLACTLLVDKKTSHALLRKSALSPM 168 (182)
Q Consensus 100 ~~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l~~~~v~AAclY~acr~~~~eia~~~~v~~~ 168 (182)
..|..+.++...+.+|.+--.+|.+|+.. +......+. .++..=||.+|++ +.||+.-=+++.+
T Consensus 6 ~~e~~ik~~~~~L~~I~~D~sVPRNIRraa~ea~~~L~~e~~~~~vRaA~AIs~-----LdeIs~DPNmP~h 72 (88)
T PRK04330 6 DNEEKIKQAIQMLEEIINDTSVPRNIRRAATEAKEILLNEEESPGVRAATAISI-----LDEISNDPNMPLH 72 (88)
T ss_pred chHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHhCcCcchhHHHHHHHHH-----HHHhhcCCCCChH
Confidence 45778899999999999999999999888 666666555 4555555555553 4556655554443
No 367
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=25.25 E-value=36 Score=31.42 Aligned_cols=28 Identities=29% Similarity=0.749 Sum_probs=21.0
Q ss_pred CCCCCCCCCCceeE-eCCCCceEeCCCcee
Q 030129 4 AFCSDCKKHTEVVF-DHSAGDTVCSECGLV 32 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~-D~~~G~~vC~~CG~V 32 (182)
..|-.||+ ++.-. --..|..+|.+|=.|
T Consensus 9 evC~DC~~-~dp~WASvnrGt~lC~eCcsv 37 (669)
T KOG0818|consen 9 EVCADCSG-PDPSWASVNRGTFLCDECCSV 37 (669)
T ss_pred hhhcccCC-CCCcceeecCceEehHhhhHH
Confidence 46999997 43322 338999999999877
No 368
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=25.19 E-value=22 Score=28.67 Aligned_cols=49 Identities=10% Similarity=0.057 Sum_probs=33.0
Q ss_pred HHhCChHHHHHH-HHHHHHHhcc---CHHHHHHHHHHHHHhhCCHHHHHhcCCCceeeeceeee
Q 030129 117 DRIGQMRYIRRW-KIKSLVEAEI---KTHYWLLACTLLVDKKTSHALLRKSALSPMELQRRKLA 176 (182)
Q Consensus 117 ~~L~L~~~v~~~-~i~k~a~~~l---~~~~v~AAclY~acr~~~~eia~~~~v~~~~i~r~~~~ 176 (182)
++-+||..+..+ -+|-+..++| ..+ |...+|||+.++++..+|.|-|.|
T Consensus 3 ~~~~IP~AT~kRL~~YyR~le~l~a~~v~-----------rvsS~els~~~~vdsatIRrDfSY 55 (211)
T COG2344 3 DKKKIPKATAKRLPLYYRVLERLHASGVE-----------RVSSKELSEALGVDSATIRRDFSY 55 (211)
T ss_pred ccccCCHHHHHHhHHHHHHHHHHHHcCCc-----------eecHHHHHHHhCCCHHHHhhhhHH
Confidence 344789888888 6666666652 111 123578888888888888776654
No 369
>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=24.96 E-value=44 Score=29.72 Aligned_cols=24 Identities=21% Similarity=0.558 Sum_probs=17.5
Q ss_pred EeCCCCceEeCCCceeeeCCCccc
Q 030129 17 FDHSAGDTVCSECGLVLESHSIDE 40 (182)
Q Consensus 17 ~D~~~G~~vC~~CG~Vl~e~~id~ 40 (182)
.|+..+...|.+||.|++...+..
T Consensus 7 ~~~~~~~~~C~~Cd~l~~~~~l~~ 30 (403)
T TIGR00155 7 HHPAAKHILCSQCDMLVALPRIES 30 (403)
T ss_pred cCCCCCeeeCCCCCCcccccCCCC
Confidence 355667778999999987655443
No 370
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=24.04 E-value=59 Score=30.96 Aligned_cols=33 Identities=24% Similarity=0.474 Sum_probs=21.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCC---CceeeeCCCc
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSE---CGLVLESHSI 38 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~---CG~Vl~e~~i 38 (182)
..||.||+ .++.+...-.+.|.+ |-.-+..+++
T Consensus 405 ~~CP~Cgs--~l~~~~~~~~~~C~n~~~C~aq~~~~l~ 440 (665)
T PRK07956 405 THCPVCGS--ELVRVEGEAVLRCTNGLSCPAQLKERLI 440 (665)
T ss_pred CCCCCCCC--EeEecCCCeEEECCCCCCCHHHHHHHHH
Confidence 57999997 455444444678873 8655555554
No 371
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=23.58 E-value=20 Score=20.51 Aligned_cols=17 Identities=24% Similarity=0.268 Sum_probs=13.4
Q ss_pred HHHHHhcCCCceeeece
Q 030129 157 HALLRKSALSPMELQRR 173 (182)
Q Consensus 157 ~eia~~~~v~~~~i~r~ 173 (182)
.|+|+.+||+..+|.++
T Consensus 4 ~e~a~~lgvs~~tl~~~ 20 (49)
T cd04762 4 KEAAELLGVSPSTLRRW 20 (49)
T ss_pred HHHHHHHCcCHHHHHHH
Confidence 57888889888887654
No 372
>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=23.50 E-value=48 Score=19.20 Aligned_cols=30 Identities=23% Similarity=0.544 Sum_probs=19.1
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (182)
..+|..|+.. + .....| +.|..|++++-.+
T Consensus 11 ~~~C~~C~~~--i-~~~~~~-~~C~~C~~~~H~~ 40 (49)
T smart00109 11 PTKCCVCRKS--I-WGSFQG-LRCSWCKVKCHKK 40 (49)
T ss_pred CCCccccccc--c-CcCCCC-cCCCCCCchHHHH
Confidence 4579999862 2 222234 7799999887533
No 373
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=23.42 E-value=24 Score=35.23 Aligned_cols=25 Identities=20% Similarity=0.651 Sum_probs=15.8
Q ss_pred CCCCCCCCCCCceeEeC-CCCceEeCCCc
Q 030129 3 DAFCSDCKKHTEVVFDH-SAGDTVCSECG 30 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~-~~G~~vC~~CG 30 (182)
...||+||+ ++--|- ..|.. |..|=
T Consensus 8 ~~~CpNCGG--~isseRL~~glp-Ce~CL 33 (1187)
T COG1110 8 GSSCPNCGG--DISSERLEKGLP-CERCL 33 (1187)
T ss_pred hccCCCCCC--cCcHHHHhcCCC-chhcc
Confidence 457999998 332232 55655 88873
No 374
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=23.39 E-value=43 Score=31.57 Aligned_cols=21 Identities=29% Similarity=0.692 Sum_probs=13.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCce
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (182)
..|+.||- ... . ...|+.||-
T Consensus 560 ~~C~~CGy-~g~-~-----~~~CP~CG~ 580 (618)
T PRK14704 560 DRCKCCSY-HGV-I-----GNECPSCGN 580 (618)
T ss_pred eecCCCCC-CCC-c-----CccCcCCCC
Confidence 46888884 211 1 168888885
No 375
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=23.29 E-value=30 Score=26.17 Aligned_cols=13 Identities=38% Similarity=1.089 Sum_probs=11.0
Q ss_pred CceEeCCCceeee
Q 030129 22 GDTVCSECGLVLE 34 (182)
Q Consensus 22 G~~vC~~CG~Vl~ 34 (182)
-+.+|.+||...+
T Consensus 119 reficpecg~l~e 131 (165)
T COG4647 119 REFICPECGILHE 131 (165)
T ss_pred HHhhCccccceee
Confidence 4689999999875
No 376
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=23.27 E-value=24 Score=31.56 Aligned_cols=31 Identities=29% Similarity=0.735 Sum_probs=22.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCCC
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~ 37 (182)
..+|..|+. . ++...-...|.+||.-++..+
T Consensus 5 ~~rc~~cg~--~--f~~a~~~~~c~~cGl~lp~~~ 35 (411)
T COG0498 5 SLRCLKCGR--E--FSQALLQGLCPDCGLFLPAEY 35 (411)
T ss_pred EeecCCCCc--c--hhhHHhhCcCCcCCccccccc
Confidence 468999996 2 232334689999999998755
No 377
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=22.77 E-value=40 Score=29.34 Aligned_cols=32 Identities=19% Similarity=0.599 Sum_probs=24.4
Q ss_pred CCCCCCCC--CCCCCceeEeCCCCceEeCC-Cceeee
Q 030129 1 MTDAFCSD--CKKHTEVVFDHSAGDTVCSE-CGLVLE 34 (182)
Q Consensus 1 m~~~~Cp~--Cg~~~~iv~D~~~G~~vC~~-CG~Vl~ 34 (182)
|....||. ||. .+...|+.+...|.+ ||.++=
T Consensus 313 ~gGVlCP~pgCG~--gll~EPD~rkvtC~~gCgf~FC 347 (446)
T KOG0006|consen 313 MGGVLCPRPGCGA--GLLPEPDQRKVTCEGGCGFAFC 347 (446)
T ss_pred cCCEecCCCCCCc--ccccCCCCCcccCCCCchhHhH
Confidence 34456877 885 467778999999998 998863
No 378
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.45 E-value=56 Score=28.15 Aligned_cols=11 Identities=45% Similarity=0.908 Sum_probs=9.7
Q ss_pred CCCCCCCCCCC
Q 030129 1 MTDAFCSDCKK 11 (182)
Q Consensus 1 m~~~~Cp~Cg~ 11 (182)
|.+..||.|.+
T Consensus 1 md~~~CP~Ck~ 11 (309)
T TIGR00570 1 MDDQGCPRCKT 11 (309)
T ss_pred CCCCCCCcCCC
Confidence 78889999996
No 379
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 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 DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=22.32 E-value=63 Score=25.46 Aligned_cols=32 Identities=28% Similarity=0.605 Sum_probs=14.6
Q ss_pred CCCCCCCCCceeEeC---------CCCceEeCCCceeeeCCCc
Q 030129 5 FCSDCKKHTEVVFDH---------SAGDTVCSECGLVLESHSI 38 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~---------~~G~~vC~~CG~Vl~e~~i 38 (182)
.||.|+. ...++. ...-..|..|+..+....|
T Consensus 20 ~C~~C~~--~~~f~g~~~~~~~~~~~~~~~C~~C~~~~~~~~l 60 (188)
T PF08996_consen 20 TCPSCGT--EFEFPGVFEEDGDDVSPSGLQCPNCSTPLSPASL 60 (188)
T ss_dssp E-TTT----EEEE-SSS--SSEEEETTEEEETTT--B--HHHH
T ss_pred ECCCCCC--CccccccccCCccccccCcCcCCCCCCcCCHHHH
Confidence 6999996 233322 2335899999997654433
No 380
>TIGR00201 comF comF family protein. This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis.
Probab=22.26 E-value=38 Score=26.48 Aligned_cols=23 Identities=26% Similarity=0.644 Sum_probs=16.3
Q ss_pred CCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 6 CSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 6 Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
|+.|+. .+. .+..+|.+|+.-+.
T Consensus 1 C~~C~~--~~~----~~~~~C~~C~~~~~ 23 (190)
T TIGR00201 1 CSLCGR--PYQ----SVHALCRQCGSWRT 23 (190)
T ss_pred CCcccc--ccc----cccCCchhhCCccc
Confidence 999996 222 23579999987654
No 381
>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
Probab=22.21 E-value=51 Score=29.50 Aligned_cols=28 Identities=32% Similarity=0.649 Sum_probs=17.4
Q ss_pred CCCCCCCCCceeEeC--CCCceEeCCCcee
Q 030129 5 FCSDCKKHTEVVFDH--SAGDTVCSECGLV 32 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D~--~~G~~vC~~CG~V 32 (182)
.|..||+...-+... ..|.++|.+|=..
T Consensus 9 ~c~fc~~~~~~~~~~~~~~~~~ic~~c~~~ 38 (413)
T TIGR00382 9 YCSFCGKSQDEVRKLIAGPGVYICDECIEL 38 (413)
T ss_pred ecCCCCCChhhcccccCCCCCcCCCchHHH
Confidence 799999743222222 2346899999543
No 382
>KOG1368 consensus Threonine aldolase [Amino acid transport and metabolism]
Probab=22.08 E-value=2.3e+02 Score=24.81 Aligned_cols=78 Identities=15% Similarity=0.145 Sum_probs=46.5
Q ss_pred hHHHHHHHHHHHHH-HHHhCC--------hHHHHHH-HHHHHHHhc-cCHHHHHHHHHHHHHhhC----------CHHHH
Q 030129 102 DRGLILAFKTIATM-SDRIGQ--------MRYIRRW-KIKSLVEAE-IKTHYWLLACTLLVDKKT----------SHALL 160 (182)
Q Consensus 102 er~L~~a~~~I~~i-~~~L~L--------~~~v~~~-~i~k~a~~~-l~~~~v~AAclY~acr~~----------~~eia 160 (182)
-+.+.++|+.+.-- +.-||- |...+++ .-||++... ++...+.||+-.+|-... .+++|
T Consensus 209 vk~i~~~fDSVsiCLSKglgAPVGSViVG~k~FI~kA~~~RKalGGGmRQsGvLaaaaLval~~~~~~L~~dHk~A~~lA 288 (384)
T KOG1368|consen 209 VKKICSAFDSVSICLSKGLGAPVGSVIVGSKDFIDKARHFRKALGGGMRQSGVLAAAALVALDENVPLLRADHKRAKELA 288 (384)
T ss_pred HHHHHHhhhhhhhhhhccCCCCcccEEEccHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHhhcchHHHHHHHHHHHHHH
Confidence 34455666665421 222333 3456677 888888887 766666666666665544 27889
Q ss_pred HhcCCCceeeeceeeehhcc
Q 030129 161 RKSALSPMELQRRKLAEQKN 180 (182)
Q Consensus 161 ~~~~v~~~~i~r~~~~~~~~ 180 (182)
+... ...+|--....-|+|
T Consensus 289 e~~~-~~~~i~v~v~a~etN 307 (384)
T KOG1368|consen 289 EYIN-TPEEIRVEVPAVETN 307 (384)
T ss_pred HHhc-cccceeeecchhhcc
Confidence 8887 444455555555555
No 383
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=22.08 E-value=1.1e+02 Score=19.57 Aligned_cols=37 Identities=8% Similarity=0.118 Sum_probs=26.7
Q ss_pred chHHHHHHHHHHHHHHHHh-CChHHHHHH-HHHHHHHhc
Q 030129 101 PDRGLILAFKTIATMSDRI-GQMRYIRRW-KIKSLVEAE 137 (182)
Q Consensus 101 ~er~L~~a~~~I~~i~~~L-~L~~~v~~~-~i~k~a~~~ 137 (182)
-+-.+....+.+..+.+.+ .|.++|++. .||..+...
T Consensus 12 ~~~~i~tvk~en~~i~~~ve~i~envk~ll~lYE~Vs~~ 50 (55)
T PF05377_consen 12 IESSINTVKKENEEISESVEKIEENVKDLLSLYEVVSNQ 50 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 3445666777778887777 567778777 999887654
No 384
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=22.05 E-value=40 Score=26.37 Aligned_cols=36 Identities=25% Similarity=0.474 Sum_probs=22.2
Q ss_pred CCCCCCCCCCCCCc---eeEeCCCCceEeCCCceeeeCCC
Q 030129 1 MTDAFCSDCKKHTE---VVFDHSAGDTVCSECGLVLESHS 37 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~---iv~D~~~G~~vC~~CG~Vl~e~~ 37 (182)
|+.+.|--||+... .|.-...-..||.+|+ -+.-..
T Consensus 1 m~~~~CEiCG~~i~~~~~v~vegsel~VC~~Ca-k~G~~~ 39 (165)
T COG1813 1 MSGMGCELCGREIDKPIKVKVEGAELTVCDDCA-KFGTAA 39 (165)
T ss_pred CCCcceeccccccCCCeeEEeecceeehhHHHH-HhccCc
Confidence 77788999997311 1111234458999999 545333
No 385
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=21.99 E-value=50 Score=26.66 Aligned_cols=39 Identities=15% Similarity=0.388 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCceeE--eCC-CCceEeCCCceeeeCCCcccc
Q 030129 3 DAFCSDCKKHTEVVF--DHS-AGDTVCSECGLVLESHSIDET 41 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~--D~~-~G~~vC~~CG~Vl~e~~id~~ 41 (182)
...|..|+..-.... ... .....|..||-++..+++-.|
T Consensus 113 ~~~C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg~lrP~Vv~fg 154 (222)
T cd01413 113 TAYCVNCGSKYDLEEVKYAKKHEVPRCPKCGGIIRPDVVLFG 154 (222)
T ss_pred cceECCCCCCcchhHHHHhccCCCCcCCCCCCccCCCEEECC
Confidence 357999986211110 011 224679999988887776544
No 386
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.87 E-value=40 Score=28.68 Aligned_cols=28 Identities=36% Similarity=0.940 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (182)
|..-.||+||. .+-++ ...|-.||.-+.
T Consensus 1 mk~FhC~~CgQ--~v~Fe----N~~C~~Cg~~Lg 28 (349)
T COG4307 1 MKDFHCPNCGQ--RVAFE----NSACLSCGSALG 28 (349)
T ss_pred CCcccCCCCCC--eeeec----chHHHhhhhHhh
Confidence 56667999996 34454 578999998775
No 387
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=21.70 E-value=63 Score=29.90 Aligned_cols=33 Identities=21% Similarity=0.233 Sum_probs=26.6
Q ss_pred eCCCCceEeCCCceeee--CCCcccccccccccCC
Q 030129 18 DHSAGDTVCSECGLVLE--SHSIDETSEWRTFANE 50 (182)
Q Consensus 18 D~~~G~~vC~~CG~Vl~--e~~id~~~ewr~f~~~ 50 (182)
..+.|.++|..||.-|= +.-.|.|.-|.+|.+.
T Consensus 413 ~~~~G~y~c~~c~~pLf~s~~Kf~sg~GWPsF~~~ 447 (521)
T PRK14018 413 LFKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTRP 447 (521)
T ss_pred CCCCEEEEecCCCCccccCcccccCCCCCcccCcc
Confidence 35889999999999875 3447889999999853
No 388
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=21.64 E-value=64 Score=25.87 Aligned_cols=39 Identities=21% Similarity=0.261 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCceeEe-CCCCceEeCCCceeeeCCCcccc
Q 030129 3 DAFCSDCKKHTEVVFD-HSAGDTVCSECGLVLESHSIDET 41 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D-~~~G~~vC~~CG~Vl~e~~id~~ 41 (182)
...|..|+.....-.. .......|..||-++..+++-.+
T Consensus 109 ~~~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~lrp~Vv~fg 148 (224)
T cd01412 109 RVRCSSCGYVGENNEEIPEEELPRCPKCGGLLRPGVVWFG 148 (224)
T ss_pred ccccCCCCCCCCcchhhhccCCCCCCCCCCccCCceEECC
Confidence 3579999862111000 12334689999998887776443
No 389
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=21.61 E-value=47 Score=23.38 Aligned_cols=24 Identities=25% Similarity=0.790 Sum_probs=16.0
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCce
Q 030129 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (182)
+..|..||+. .. .--.-.|..||.
T Consensus 16 HtlCrRCG~~-sy----H~qK~~CasCGy 39 (91)
T PTZ00073 16 HTLCRRCGKR-SF----HVQKKRCASCGY 39 (91)
T ss_pred cchhcccCcc-cc----ccccccchhcCC
Confidence 4579999973 32 122466999998
No 390
>PLN03131 hypothetical protein; Provisional
Probab=21.58 E-value=66 Score=30.51 Aligned_cols=30 Identities=13% Similarity=0.295 Sum_probs=22.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
..|-+|+....--....-|-.||..|.-|-
T Consensus 24 k~CADCga~~P~WASiNlGIFICi~CSGIH 53 (705)
T PLN03131 24 RRCINCNSLGPQFVCTNFWTFICMTCSGIH 53 (705)
T ss_pred CccccCCCCCCCeeEeccceEEchhchhhh
Confidence 579999974433445577999999998774
No 391
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=21.55 E-value=70 Score=30.37 Aligned_cols=33 Identities=15% Similarity=0.298 Sum_probs=20.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeC--CCceeeeCCCc
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCS--ECGLVLESHSI 38 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~--~CG~Vl~e~~i 38 (182)
..||.|++ .++.+...-.+.|. .|-.-+..+++
T Consensus 393 ~~CP~C~s--~l~~~~~~~~~~C~n~~C~aq~~~~l~ 427 (652)
T TIGR00575 393 THCPSCGS--PLVKIEEEAVIRCPNLNCPAQRVERIK 427 (652)
T ss_pred CCCCCCCC--EeEecCCcEEEEECCCCCHHHHHHHhH
Confidence 57999997 45554444457786 47655555554
No 392
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=21.55 E-value=48 Score=26.53 Aligned_cols=39 Identities=21% Similarity=0.331 Sum_probs=23.6
Q ss_pred CCCCCCCCCCCceeE---e-CCCCceEeCCCceeeeCCCcccc
Q 030129 3 DAFCSDCKKHTEVVF---D-HSAGDTVCSECGLVLESHSIDET 41 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~---D-~~~G~~vC~~CG~Vl~e~~id~~ 41 (182)
...|..|+.....-. . .......|..||-.+..+++-.|
T Consensus 109 ~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~lrP~Vv~fg 151 (218)
T cd01407 109 RVRCTKCGKEYPRDELQADIDREEVPRCPKCGGLLRPDVVFFG 151 (218)
T ss_pred cceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCccCCCeEECC
Confidence 357999986211100 0 12234689999999888877544
No 393
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.45 E-value=38 Score=24.57 Aligned_cols=19 Identities=37% Similarity=0.754 Sum_probs=13.9
Q ss_pred eCCCCceEeCCCceeeeCC
Q 030129 18 DHSAGDTVCSECGLVLESH 36 (182)
Q Consensus 18 D~~~G~~vC~~CG~Vl~e~ 36 (182)
+-+-|.+.|..||.-++.-
T Consensus 44 ~ie~G~t~CP~Cg~~~e~~ 62 (115)
T COG1885 44 EIEVGSTSCPKCGEPFESA 62 (115)
T ss_pred EEecccccCCCCCCcccee
Confidence 4467888999998776533
No 394
>KOG3022 consensus Predicted ATPase, nucleotide-binding [Cell cycle control, cell division, chromosome partitioning]
Probab=21.14 E-value=30 Score=29.58 Aligned_cols=31 Identities=26% Similarity=0.642 Sum_probs=22.7
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (182)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (182)
|+.-.||+|+. ..-+++..-|+..|..=|+=
T Consensus 220 Ms~f~Cp~C~~-~~~iF~~gGg~~l~~~~glp 250 (300)
T KOG3022|consen 220 MSGFVCPKCGH-STNIFGSGGGERLAEELGLP 250 (300)
T ss_pred cccccCCCCCC-cceeccCccHHHHHHHcCCC
Confidence 66677999987 45577777778888776653
No 395
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=21.06 E-value=62 Score=23.43 Aligned_cols=31 Identities=23% Similarity=0.574 Sum_probs=19.4
Q ss_pred CCCCCCCCC----CceeEeCCCC--ceEeCCCceeee
Q 030129 4 AFCSDCKKH----TEVVFDHSAG--DTVCSECGLVLE 34 (182)
Q Consensus 4 ~~Cp~Cg~~----~~iv~D~~~G--~~vC~~CG~Vl~ 34 (182)
++|+.|.+. .+..+-...| .+.|.+||.+.-
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R 93 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRR 93 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCcEEE
Confidence 479999861 1222233344 478999999863
No 396
>COG5515 Uncharacterized conserved small protein [Function unknown]
Probab=21.05 E-value=1.4e+02 Score=19.61 Aligned_cols=30 Identities=17% Similarity=0.416 Sum_probs=22.2
Q ss_pred CceeEeCCCCceEeCCCceeeeCCCcccccc
Q 030129 13 TEVVFDHSAGDTVCSECGLVLESHSIDETSE 43 (182)
Q Consensus 13 ~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~e 43 (182)
+.-.+|-+++..+|.. ..|.++.-+|-+|+
T Consensus 35 Ptyafn~~~~~m~cgQ-aVVkdvdg~dy~pd 64 (70)
T COG5515 35 PTYAFNAETKTMICGQ-AVVKDVDGIDYGPD 64 (70)
T ss_pred cceeecCCCceEEecc-eEEEeccccccCCC
Confidence 4556777888899887 67777777776664
No 397
>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=20.82 E-value=74 Score=15.07 Aligned_cols=9 Identities=33% Similarity=0.914 Sum_probs=4.4
Q ss_pred EeCCCceee
Q 030129 25 VCSECGLVL 33 (182)
Q Consensus 25 vC~~CG~Vl 33 (182)
.|..||...
T Consensus 2 ~C~~C~~~~ 10 (24)
T PF13894_consen 2 QCPICGKSF 10 (24)
T ss_dssp E-SSTS-EE
T ss_pred CCcCCCCcC
Confidence 466666665
No 398
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=20.80 E-value=62 Score=30.53 Aligned_cols=12 Identities=25% Similarity=0.736 Sum_probs=8.1
Q ss_pred eEeCCCceeeeC
Q 030129 24 TVCSECGLVLES 35 (182)
Q Consensus 24 ~vC~~CG~Vl~e 35 (182)
+.|..||.++..
T Consensus 81 ~~c~~cG~~~~~ 92 (715)
T COG1107 81 LTCDICGDIIVP 92 (715)
T ss_pred EeeccccceecC
Confidence 567777777654
No 399
>PRK01381 Trp operon repressor; Provisional
Probab=20.58 E-value=64 Score=23.09 Aligned_cols=18 Identities=6% Similarity=0.148 Sum_probs=16.4
Q ss_pred CHHHHHhcCCCceeeece
Q 030129 156 SHALLRKSALSPMELQRR 173 (182)
Q Consensus 156 ~~eia~~~~v~~~~i~r~ 173 (182)
.+|||+.+|||.-+|.|.
T Consensus 58 QREIa~~lGvSiaTITRg 75 (99)
T PRK01381 58 QREIKQELGVGIATITRG 75 (99)
T ss_pred HHHHHHHhCCceeeehhh
Confidence 489999999999999885
No 400
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=20.54 E-value=97 Score=18.33 Aligned_cols=13 Identities=38% Similarity=0.861 Sum_probs=10.1
Q ss_pred CCceEeCCCceee
Q 030129 21 AGDTVCSECGLVL 33 (182)
Q Consensus 21 ~G~~vC~~CG~Vl 33 (182)
.|..+|.-||+..
T Consensus 27 ~~~~~CpYCg~~y 39 (40)
T PF10276_consen 27 PGPVVCPYCGTRY 39 (40)
T ss_dssp TCEEEETTTTEEE
T ss_pred CCeEECCCCCCEE
Confidence 3569999999864
No 401
>PRK09709 exonuclease VIII; Reviewed
Probab=20.43 E-value=47 Score=32.49 Aligned_cols=27 Identities=26% Similarity=0.823 Sum_probs=20.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcc
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id 39 (182)
..|+.||. +|--=|.+||.|+.+....
T Consensus 526 ~~~~~~g~---------~~g~~~~d~~a~m~~~t~~ 552 (877)
T PRK09709 526 IVCNACGQ---------TGGDNCPDCGAVMGDATYQ 552 (877)
T ss_pred hhhccccc---------cCCCCCCchhhhccCcccc
Confidence 35888985 3556799999999875544
No 402
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=20.42 E-value=1.4e+02 Score=24.39 Aligned_cols=29 Identities=7% Similarity=-0.036 Sum_probs=24.3
Q ss_pred HHHHHHHHHHhCChHHHHHH--HHHHHHHhc
Q 030129 109 FKTIATMSDRIGQMRYIRRW--KIKSLVEAE 137 (182)
Q Consensus 109 ~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~ 137 (182)
...+.+++..||||..-.++ .+|+.-.++
T Consensus 165 ~~~l~~l~~~L~ls~~kv~KDL~lYrsnLeK 195 (214)
T TIGR03060 165 NEILKELSEALGLSYDRVEKDLDLYKSNLEK 195 (214)
T ss_pred HHHHHHHHHHcCCCHHHHHhhHHHHHhHHHH
Confidence 46789999999999988777 999877665
No 403
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=20.41 E-value=51 Score=29.42 Aligned_cols=30 Identities=23% Similarity=0.579 Sum_probs=16.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
..||+|+-..++-.=...-.-.|..||..+
T Consensus 19 ~~C~eCd~~~~~P~l~~~q~A~CPRC~~~l 48 (418)
T COG2995 19 ILCPECDMLVSLPRLDSGQSAYCPRCGHTL 48 (418)
T ss_pred ecCCCCCceeccccCCCCCcccCCCCCCcc
Confidence 358888853222111122336788888876
No 404
>PRK14067 exodeoxyribonuclease VII small subunit; Provisional
Probab=20.34 E-value=1.5e+02 Score=20.26 Aligned_cols=37 Identities=3% Similarity=-0.112 Sum_probs=25.7
Q ss_pred CchHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHh
Q 030129 100 NPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEA 136 (182)
Q Consensus 100 ~~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~ 136 (182)
+++.+...++..+..|..+|.=++--.+. .+|+....
T Consensus 4 ~k~~sfEeal~~LEeIV~~LE~~~l~Lees~~lyeeG~~ 42 (80)
T PRK14067 4 KKTADFEQQLARLQEIVDALEGGDLPLEESVALYKEGLG 42 (80)
T ss_pred cccCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence 34567788999999999999665533333 66665544
No 405
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=20.30 E-value=29 Score=22.71 Aligned_cols=13 Identities=31% Similarity=0.736 Sum_probs=10.2
Q ss_pred eEeCCCceeeeCC
Q 030129 24 TVCSECGLVLESH 36 (182)
Q Consensus 24 ~vC~~CG~Vl~e~ 36 (182)
+-|-.||.||.+.
T Consensus 5 iRCFsCGkvi~~~ 17 (63)
T COG1644 5 VRCFSCGKVIGHK 17 (63)
T ss_pred eEeecCCCCHHHH
Confidence 4699999999643
No 406
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=20.25 E-value=55 Score=29.21 Aligned_cols=26 Identities=31% Similarity=0.685 Sum_probs=16.6
Q ss_pred CCCCCCCCCCCceeEeC---CCCceEeCCC
Q 030129 3 DAFCSDCKKHTEVVFDH---SAGDTVCSEC 29 (182)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~---~~G~~vC~~C 29 (182)
..+|..||+. .-.+.. ..|..+|.+|
T Consensus 9 ~~~CSFCGr~-~~ev~~li~g~~~~IC~~C 37 (412)
T PRK05342 9 LLYCSFCGKS-QHEVRKLIAGPGVYICDEC 37 (412)
T ss_pred ccccCCCCCC-hhhccccccCCCCcccchH
Confidence 3579999973 222221 2356899999
No 407
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=20.23 E-value=82 Score=29.59 Aligned_cols=30 Identities=17% Similarity=0.293 Sum_probs=21.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (182)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (182)
..|-+|+....--....-|-.||..|.-|-
T Consensus 24 k~CADCgs~~P~WASiNlGIFICi~CSGIH 53 (648)
T PLN03119 24 RRCINCNSLGPQYVCTTFWTFVCMACSGIH 53 (648)
T ss_pred CccccCCCCCCCceeeccceEEeccchhhh
Confidence 579999974333344578889999998774
No 408
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=20.21 E-value=2.1e+02 Score=22.71 Aligned_cols=36 Identities=11% Similarity=0.187 Sum_probs=24.4
Q ss_pred CCchHHHHHHH---HHHHHHHHHhCChHHHHHH---HHHHHH
Q 030129 99 SNPDRGLILAF---KTIATMSDRIGQMRYIRRW---KIKSLV 134 (182)
Q Consensus 99 ~~~er~L~~a~---~~I~~i~~~L~L~~~v~~~---~i~k~a 134 (182)
+.+|+.+.+.+ ...++||+.|+++...++. .||+|.
T Consensus 136 T~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL 177 (207)
T PRK11475 136 SPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKL 177 (207)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 45565554333 2367899999999877766 676665
No 409
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only]
Probab=20.13 E-value=70 Score=27.18 Aligned_cols=27 Identities=22% Similarity=0.598 Sum_probs=15.4
Q ss_pred CCCCCCCCCceeEe------CCCCceEeCCCcee
Q 030129 5 FCSDCKKHTEVVFD------HSAGDTVCSECGLV 32 (182)
Q Consensus 5 ~Cp~Cg~~~~iv~D------~~~G~~vC~~CG~V 32 (182)
.||.|.. ..+-.. -..|+.+|..|+.+
T Consensus 117 ~~~~~~g-~~~~~n~~~~r~~~~GDW~Cp~C~fh 149 (280)
T KOG4198|consen 117 LCPRCPG-LGFSRNNKPKRPWRSGDWECPGCNFH 149 (280)
T ss_pred CCCCCCC-CcccccccccCCccccCcccCCCCce
Confidence 3677764 232222 25677777777766
No 410
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 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. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=20.03 E-value=40 Score=21.77 Aligned_cols=12 Identities=50% Similarity=0.919 Sum_probs=9.6
Q ss_pred eEeCCCceeeeC
Q 030129 24 TVCSECGLVLES 35 (182)
Q Consensus 24 ~vC~~CG~Vl~e 35 (182)
+||..||.=+.|
T Consensus 5 lvCSTCGrDlSe 16 (63)
T PF05864_consen 5 LVCSTCGRDLSE 16 (63)
T ss_pred eeecccCCcchH
Confidence 799999987643
Done!