Query 030241
Match_columns 181
No_of_seqs 135 out of 737
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 10:44:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030241.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030241hhsearch_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 6.9E-45 1.5E-49 310.4 15.2 163 3-167 11-199 (310)
2 KOG1597 Transcription initiati 100.0 1.7E-42 3.6E-47 287.6 14.3 163 4-167 1-181 (308)
3 COG1405 SUA7 Transcription ini 100.0 3.3E-37 7.2E-42 259.6 11.5 148 4-160 2-159 (285)
4 KOG1598 Transcription initiati 99.8 4.9E-19 1.1E-23 157.5 10.0 121 4-160 1-128 (521)
5 PF08271 TF_Zn_Ribbon: TFIIB z 99.7 7.2E-18 1.6E-22 104.1 3.2 43 4-47 1-43 (43)
6 PF00382 TFIIB: Transcription 99.3 4.3E-12 9.3E-17 86.0 6.8 49 112-160 1-56 (71)
7 PRK00423 tfb transcription ini 98.4 1.2E-06 2.6E-11 75.2 7.1 53 108-160 219-278 (310)
8 cd00043 CYCLIN Cyclin box fold 98.0 4.1E-05 8.8E-10 51.5 7.4 54 107-160 4-64 (88)
9 smart00385 CYCLIN domain prese 97.9 5.4E-05 1.2E-09 50.5 6.5 50 111-160 2-58 (83)
10 COG1405 SUA7 Transcription ini 97.8 5.1E-05 1.1E-09 64.5 6.3 54 107-160 193-253 (285)
11 KOG1597 Transcription initiati 97.3 0.00083 1.8E-08 57.0 6.6 53 108-160 203-262 (308)
12 PF01857 RB_B: Retinoblastoma- 97.3 0.0018 3.9E-08 49.3 7.9 57 104-160 10-75 (135)
13 PF11781 RRN7: RNA polymerase 97.1 0.00038 8.3E-09 41.1 2.2 28 4-34 9-36 (36)
14 PF08792 A2L_zn_ribbon: A2L zi 96.9 0.00084 1.8E-08 38.9 2.6 31 1-33 1-31 (33)
15 PRK00415 rps27e 30S ribosomal 96.9 0.00055 1.2E-08 44.7 1.8 31 4-35 12-42 (59)
16 COG2051 RPS27A Ribosomal prote 96.9 0.00058 1.3E-08 45.5 1.7 31 4-35 20-50 (67)
17 PF01667 Ribosomal_S27e: Ribos 96.8 0.00047 1E-08 44.5 0.9 30 4-34 8-37 (55)
18 PHA00626 hypothetical protein 96.7 0.0014 3.1E-08 42.2 2.6 31 4-35 1-35 (59)
19 TIGR00569 ccl1 cyclin ccl1. Un 96.7 0.007 1.5E-07 52.0 7.3 59 102-160 52-120 (305)
20 PLN00209 ribosomal protein S27 96.3 0.002 4.4E-08 45.1 1.7 31 4-35 37-67 (86)
21 PTZ00083 40S ribosomal protein 96.3 0.0024 5.3E-08 44.6 1.8 31 4-35 36-66 (85)
22 COG5333 CCL1 Cdk activating ki 96.3 0.0046 1E-07 52.7 3.8 53 106-158 46-105 (297)
23 PF13248 zf-ribbon_3: zinc-rib 96.1 0.0031 6.7E-08 34.4 1.3 22 4-31 3-24 (26)
24 PRK00398 rpoP DNA-directed RNA 96.0 0.0051 1.1E-07 38.0 2.2 31 1-33 1-31 (46)
25 PRK00420 hypothetical protein; 96.0 0.005 1.1E-07 45.4 2.5 31 1-34 21-51 (112)
26 PF13240 zinc_ribbon_2: zinc-r 96.0 0.0033 7.1E-08 33.4 1.1 22 5-32 1-22 (23)
27 PF14803 Nudix_N_2: Nudix N-te 95.7 0.0064 1.4E-07 35.4 1.6 26 5-32 2-31 (34)
28 COG1645 Uncharacterized Zn-fin 95.6 0.0057 1.2E-07 46.2 1.4 27 3-33 28-55 (131)
29 PF02150 RNA_POL_M_15KD: RNA p 95.6 0.01 2.3E-07 34.7 2.2 30 4-34 2-31 (35)
30 PF08274 PhnA_Zn_Ribbon: PhnA 95.5 0.011 2.5E-07 33.4 2.0 27 4-33 3-29 (30)
31 KOG0834 CDK9 kinase-activating 95.4 0.032 6.9E-07 48.4 5.4 55 106-160 40-101 (323)
32 PF00134 Cyclin_N: Cyclin, N-t 95.4 0.055 1.2E-06 39.3 5.9 53 105-157 31-90 (127)
33 PRK00432 30S ribosomal protein 95.2 0.013 2.9E-07 37.0 2.0 27 4-33 21-47 (50)
34 PRK11827 hypothetical protein; 95.1 0.017 3.8E-07 37.9 2.3 28 4-33 9-36 (60)
35 smart00778 Prim_Zn_Ribbon Zinc 94.9 0.025 5.4E-07 33.6 2.3 29 3-31 3-33 (37)
36 COG1997 RPL43A Ribosomal prote 94.7 0.03 6.5E-07 39.4 2.7 29 3-33 35-63 (89)
37 PF10571 UPF0547: Uncharacteri 94.6 0.019 4E-07 31.4 1.1 24 5-34 2-25 (26)
38 PRK10220 hypothetical protein; 94.4 0.098 2.1E-06 38.3 4.9 30 1-33 1-30 (111)
39 PF14354 Lar_restr_allev: Rest 94.4 0.041 8.9E-07 35.6 2.7 27 4-31 4-37 (61)
40 PF09538 FYDLN_acid: Protein o 94.4 0.025 5.5E-07 41.4 1.9 31 3-36 9-39 (108)
41 KOG0794 CDK8 kinase-activating 94.3 0.096 2.1E-06 43.4 5.3 53 107-159 43-102 (264)
42 PF06677 Auto_anti-p27: Sjogre 94.3 0.044 9.5E-07 33.2 2.4 26 2-30 16-41 (41)
43 smart00661 RPOL9 RNA polymeras 94.2 0.037 7.9E-07 34.6 2.1 28 5-34 2-31 (52)
44 TIGR02098 MJ0042_CXXC MJ0042 f 94.2 0.021 4.5E-07 33.6 0.9 29 4-34 3-36 (38)
45 PF03966 Trm112p: Trm112p-like 94.1 0.053 1.1E-06 36.2 2.9 17 17-33 47-63 (68)
46 PRK00464 nrdR transcriptional 94.1 0.043 9.3E-07 42.7 2.8 30 4-33 1-38 (154)
47 PF09297 zf-NADH-PPase: NADH p 94.0 0.065 1.4E-06 30.4 2.7 28 3-32 3-30 (32)
48 TIGR01206 lysW lysine biosynth 93.7 0.033 7.2E-07 35.8 1.2 30 4-34 3-33 (54)
49 COG1998 RPS31 Ribosomal protei 93.6 0.043 9.3E-07 34.5 1.6 27 4-32 20-46 (51)
50 COG2835 Uncharacterized conser 93.6 0.055 1.2E-06 35.5 2.0 30 2-33 7-36 (60)
51 TIGR00244 transcriptional regu 93.5 0.081 1.8E-06 40.8 3.1 30 4-33 1-38 (147)
52 KOG1598 Transcription initiati 92.8 0.099 2.1E-06 47.8 3.2 22 139-160 207-228 (521)
53 TIGR02300 FYDLN_acid conserved 92.8 0.071 1.5E-06 40.1 1.9 31 3-36 9-39 (129)
54 PF08273 Prim_Zn_Ribbon: Zinc- 92.6 0.11 2.5E-06 31.3 2.3 29 4-32 4-35 (40)
55 KOG0835 Cyclin L [General func 92.5 0.35 7.5E-06 42.0 5.9 53 108-160 141-202 (367)
56 COG2824 PhnA Uncharacterized Z 92.3 0.31 6.6E-06 35.6 4.6 33 1-36 1-33 (112)
57 TIGR00686 phnA alkylphosphonat 92.3 0.29 6.4E-06 35.7 4.5 28 4-34 3-30 (109)
58 TIGR01384 TFS_arch transcripti 91.9 0.11 2.5E-06 37.2 2.0 28 4-35 1-28 (104)
59 TIGR03655 anti_R_Lar restricti 91.9 0.13 2.8E-06 32.6 2.0 31 4-34 2-37 (53)
60 KOG1779 40s ribosomal protein 91.7 0.089 1.9E-06 36.2 1.2 29 4-33 35-63 (84)
61 PF05191 ADK_lid: Adenylate ki 91.1 0.031 6.7E-07 32.9 -1.4 30 4-33 2-31 (36)
62 smart00834 CxxC_CXXC_SSSS Puta 90.7 0.16 3.5E-06 29.9 1.5 30 4-33 6-36 (41)
63 PF13719 zinc_ribbon_5: zinc-r 90.7 0.099 2.1E-06 30.8 0.6 30 4-33 3-35 (37)
64 KOG2496 Cdk activating kinase 90.6 0.63 1.4E-05 40.0 5.5 41 120-160 73-120 (325)
65 PF12760 Zn_Tnp_IS1595: Transp 90.5 0.35 7.7E-06 29.6 3.0 28 3-31 18-45 (46)
66 PF07282 OrfB_Zn_ribbon: Putat 90.3 0.2 4.3E-06 33.1 1.8 29 4-34 29-57 (69)
67 PF01780 Ribosomal_L37ae: Ribo 90.2 0.18 3.9E-06 35.8 1.6 29 4-34 36-64 (90)
68 COG1594 RPB9 DNA-directed RNA 90.1 0.23 4.9E-06 36.6 2.2 34 3-36 2-35 (113)
69 COG2888 Predicted Zn-ribbon RN 90.0 0.2 4.4E-06 32.7 1.6 26 5-32 11-36 (61)
70 PRK05654 acetyl-CoA carboxylas 89.8 0.38 8.3E-06 41.1 3.6 43 4-48 28-77 (292)
71 smart00659 RPOLCX RNA polymera 89.6 0.27 5.9E-06 30.2 1.9 27 4-33 3-29 (44)
72 smart00440 ZnF_C2C2 C2C2 Zinc 89.5 0.32 7E-06 29.1 2.1 27 5-32 2-37 (40)
73 PF09862 DUF2089: Protein of u 89.4 0.31 6.7E-06 36.0 2.4 26 6-37 1-26 (113)
74 KOG0835 Cyclin L [General func 89.2 1.5 3.2E-05 38.2 6.7 59 102-160 20-85 (367)
75 PRK05978 hypothetical protein; 89.2 0.32 6.9E-06 37.6 2.4 35 4-39 34-68 (148)
76 COG1327 Predicted transcriptio 89.2 0.27 5.9E-06 38.0 2.1 30 4-33 1-38 (156)
77 PRK12495 hypothetical protein; 89.1 0.26 5.7E-06 40.4 2.0 32 1-36 40-71 (226)
78 PTZ00255 60S ribosomal protein 89.1 0.3 6.4E-06 34.7 2.0 30 3-34 36-65 (90)
79 COG4888 Uncharacterized Zn rib 89.0 0.26 5.6E-06 35.6 1.7 29 5-34 24-57 (104)
80 PF03604 DNA_RNApol_7kD: DNA d 88.1 0.29 6.4E-06 28.0 1.3 25 5-32 2-26 (32)
81 PRK14892 putative transcriptio 88.1 0.28 6.1E-06 35.4 1.5 42 4-46 22-71 (99)
82 PF03119 DNA_ligase_ZBD: NAD-d 88.0 0.54 1.2E-05 26.0 2.2 22 5-28 1-22 (28)
83 TIGR00280 L37a ribosomal prote 87.6 0.38 8.3E-06 34.2 1.8 30 3-34 35-64 (91)
84 PF12773 DZR: Double zinc ribb 87.0 0.39 8.4E-06 29.6 1.5 12 23-34 12-23 (50)
85 COG5349 Uncharacterized protei 86.9 0.31 6.7E-06 36.4 1.1 39 4-43 22-60 (126)
86 PF05129 Elf1: Transcription e 86.8 0.24 5.2E-06 34.4 0.4 32 5-36 24-59 (81)
87 PRK03976 rpl37ae 50S ribosomal 86.5 0.46 1E-05 33.7 1.8 30 3-34 36-65 (90)
88 PRK09710 lar restriction allev 86.4 0.73 1.6E-05 30.6 2.5 28 4-32 7-36 (64)
89 COG3478 Predicted nucleic-acid 86.3 0.52 1.1E-05 31.3 1.8 14 5-19 6-19 (68)
90 PRK14890 putative Zn-ribbon RN 85.6 0.71 1.5E-05 30.1 2.1 29 2-32 6-34 (59)
91 PF01096 TFIIS_C: Transcriptio 85.3 0.61 1.3E-05 27.7 1.6 27 5-32 2-37 (39)
92 PF09855 DUF2082: Nucleic-acid 85.1 0.83 1.8E-05 30.3 2.3 27 5-32 2-45 (64)
93 PRK09678 DNA-binding transcrip 84.6 1 2.2E-05 30.6 2.6 31 3-34 1-40 (72)
94 PRK06266 transcription initiat 84.0 0.27 5.8E-06 39.1 -0.5 31 4-35 118-148 (178)
95 PF14255 Cys_rich_CPXG: Cystei 84.0 0.76 1.7E-05 29.3 1.7 28 5-32 2-33 (52)
96 PRK02935 hypothetical protein; 83.6 0.85 1.8E-05 33.2 2.0 38 4-48 71-108 (110)
97 COG4640 Predicted membrane pro 83.3 0.66 1.4E-05 41.2 1.6 28 3-36 1-28 (465)
98 PF13717 zinc_ribbon_4: zinc-r 82.1 0.54 1.2E-05 27.5 0.4 29 4-33 3-35 (36)
99 COG1996 RPC10 DNA-directed RNA 82.0 0.51 1.1E-05 29.7 0.3 28 4-33 7-34 (49)
100 TIGR02443 conserved hypothetic 82.0 1.5 3.3E-05 28.6 2.5 30 3-32 9-40 (59)
101 PRK12286 rpmF 50S ribosomal pr 82.0 0.85 1.8E-05 29.6 1.4 27 4-37 28-54 (57)
102 TIGR02605 CxxC_CxxC_SSSS putat 81.8 0.9 1.9E-05 28.3 1.4 28 4-31 6-34 (52)
103 KOG4164 Cyclin ik3-1/CABLES [C 81.4 2.7 5.9E-05 37.5 4.7 49 110-158 387-442 (497)
104 cd00350 rubredoxin_like Rubred 81.3 1.3 2.7E-05 25.3 1.8 23 5-31 3-25 (33)
105 PF15616 TerY-C: TerY-C metal 81.3 0.9 1.9E-05 34.4 1.5 7 5-11 79-85 (131)
106 PF14446 Prok-RING_1: Prokaryo 81.0 1.3 2.8E-05 28.5 1.9 27 3-33 5-31 (54)
107 PRK13130 H/ACA RNA-protein com 80.9 0.77 1.7E-05 29.7 0.9 24 2-33 4-27 (56)
108 PF06827 zf-FPG_IleRS: Zinc fi 80.9 0.99 2.1E-05 25.0 1.2 28 4-31 2-29 (30)
109 PF11672 DUF3268: Protein of u 80.8 1.4 3.1E-05 31.9 2.3 31 3-34 2-42 (102)
110 PF11023 DUF2614: Protein of u 80.6 0.51 1.1E-05 34.7 -0.0 39 4-49 70-108 (114)
111 PF05876 Terminase_GpA: Phage 80.3 0.94 2E-05 42.1 1.6 43 4-46 201-255 (557)
112 PRK08402 replication factor A; 80.2 1.4 3E-05 38.8 2.5 27 4-32 213-239 (355)
113 KOG1088 Uncharacterized conser 79.9 0.71 1.5E-05 34.3 0.5 17 17-33 92-108 (124)
114 PF14122 YokU: YokU-like prote 79.8 1.2 2.5E-05 31.3 1.5 23 21-43 33-55 (87)
115 PRK12336 translation initiatio 79.4 1.2 2.7E-05 35.9 1.8 29 4-32 99-128 (201)
116 PRK08351 DNA-directed RNA poly 79.2 1.1 2.3E-05 29.6 1.1 32 1-46 1-32 (61)
117 PF10058 DUF2296: Predicted in 78.4 1.1 2.3E-05 28.7 0.9 29 4-32 23-53 (54)
118 PHA02942 putative transposase; 77.9 1.5 3.2E-05 38.9 2.0 28 4-34 326-353 (383)
119 CHL00174 accD acetyl-CoA carbo 77.6 0.45 9.7E-06 40.8 -1.3 30 4-34 39-68 (296)
120 PF09723 Zn-ribbon_8: Zinc rib 77.5 1.4 3.1E-05 26.5 1.3 28 4-31 6-34 (42)
121 TIGR00515 accD acetyl-CoA carb 77.4 0.47 1E-05 40.5 -1.2 30 4-34 27-56 (285)
122 PF01783 Ribosomal_L32p: Ribos 77.3 1.6 3.5E-05 28.0 1.6 28 4-38 27-54 (56)
123 TIGR03826 YvyF flagellar opero 76.8 0.61 1.3E-05 35.6 -0.6 30 1-35 1-30 (137)
124 PRK00241 nudC NADH pyrophospha 76.1 2 4.3E-05 36.0 2.2 29 3-33 99-127 (256)
125 COG1773 Rubredoxin [Energy pro 76.1 2.1 4.5E-05 27.6 1.8 26 1-30 1-26 (55)
126 PF14952 zf-tcix: Putative tre 76.0 1.7 3.6E-05 26.7 1.3 25 4-34 12-38 (44)
127 COG4068 Uncharacterized protei 75.8 0.53 1.2E-05 30.7 -1.0 26 3-34 8-34 (64)
128 KOG4557 Origin recognition com 75.5 3.9 8.4E-05 33.7 3.6 49 111-159 95-154 (262)
129 PF04161 Arv1: Arv1-like famil 75.5 1.5 3.1E-05 35.6 1.2 34 4-37 1-38 (208)
130 PF08646 Rep_fac-A_C: Replicat 75.3 2.6 5.6E-05 31.8 2.5 27 5-34 20-48 (146)
131 COG3877 Uncharacterized protei 75.2 2.8 6.1E-05 30.7 2.5 28 4-37 7-34 (122)
132 TIGR01031 rpmF_bact ribosomal 75.1 1.9 4.1E-05 27.7 1.4 26 4-36 27-52 (55)
133 smart00401 ZnF_GATA zinc finge 74.7 3.1 6.6E-05 26.3 2.3 32 3-34 3-36 (52)
134 PRK12366 replication factor A; 74.5 2.1 4.5E-05 40.5 2.1 25 4-32 533-557 (637)
135 PF09526 DUF2387: Probable met 74.2 3.6 7.8E-05 27.8 2.7 31 3-33 8-40 (71)
136 PF06397 Desulfoferrod_N: Desu 74.1 2 4.3E-05 25.3 1.2 22 4-26 7-28 (36)
137 PF00301 Rubredoxin: Rubredoxi 73.7 1.8 3.9E-05 26.9 1.0 16 24-39 2-17 (47)
138 COG1656 Uncharacterized conser 73.3 1.5 3.3E-05 34.5 0.8 29 3-33 97-140 (165)
139 cd00730 rubredoxin Rubredoxin; 73.2 2.8 6E-05 26.4 1.8 13 24-36 2-14 (50)
140 KOG2906 RNA polymerase III sub 73.0 2.8 6.1E-05 30.2 2.0 30 4-34 2-32 (105)
141 cd04476 RPA1_DBD_C RPA1_DBD_C: 72.6 3 6.5E-05 32.1 2.3 27 4-33 35-61 (166)
142 COG1326 Uncharacterized archae 72.5 1.5 3.3E-05 35.3 0.6 31 4-35 7-42 (201)
143 PRK12380 hydrogenase nickel in 72.5 2.3 5E-05 31.2 1.6 6 25-30 88-93 (113)
144 COG2093 DNA-directed RNA polym 72.3 2.2 4.8E-05 28.2 1.2 34 2-47 3-36 (64)
145 KOG1010 Rb (Retinoblastoma tum 71.1 9.4 0.0002 37.2 5.6 51 109-159 35-91 (920)
146 TIGR00100 hypA hydrogenase nic 70.5 2.8 6.1E-05 30.8 1.6 18 14-31 61-78 (115)
147 PRK14559 putative protein seri 70.4 2.7 5.8E-05 39.8 1.9 7 5-11 3-9 (645)
148 PF13453 zf-TFIIB: Transcripti 70.0 3.8 8.2E-05 24.3 1.8 28 5-33 1-29 (41)
149 PF10122 Mu-like_Com: Mu-like 70.0 1.2 2.6E-05 28.2 -0.3 31 2-33 3-34 (51)
150 TIGR03830 CxxCG_CxxCG_HTH puta 70.0 3.6 7.7E-05 29.9 2.1 11 23-33 31-41 (127)
151 PF12172 DUF35_N: Rubredoxin-l 69.6 2.6 5.6E-05 24.4 1.0 21 4-30 12-32 (37)
152 TIGR01384 TFS_arch transcripti 68.5 4.8 0.0001 28.6 2.5 28 4-32 63-99 (104)
153 PF07754 DUF1610: Domain of un 68.0 4.2 9.1E-05 21.7 1.5 23 6-31 1-24 (24)
154 COG0777 AccD Acetyl-CoA carbox 67.2 1.5 3.2E-05 37.3 -0.5 30 4-34 29-58 (294)
155 PF04606 Ogr_Delta: Ogr/Delta- 67.0 4.2 9.1E-05 25.0 1.7 28 5-33 1-37 (47)
156 KOG0402 60S ribosomal protein 67.0 1.8 3.8E-05 30.3 -0.1 30 3-34 36-65 (92)
157 PRK03824 hypA hydrogenase nick 66.5 3.8 8.2E-05 31.0 1.6 21 14-34 61-81 (135)
158 COG4530 Uncharacterized protei 65.6 3.4 7.4E-05 30.5 1.2 33 3-38 9-41 (129)
159 TIGR00155 pqiA_fam integral me 65.2 4.9 0.00011 35.9 2.4 30 5-34 15-44 (403)
160 TIGR00569 ccl1 cyclin ccl1. Un 64.8 27 0.00058 30.1 6.7 23 139-161 204-226 (305)
161 KOG3134 Predicted membrane pro 64.8 1.9 4.1E-05 35.4 -0.3 34 4-37 1-38 (225)
162 PF06044 DRP: Dam-replacing fa 64.5 4.1 8.8E-05 34.1 1.6 30 4-34 32-64 (254)
163 PRK05508 methionine sulfoxide 64.2 6.3 0.00014 29.4 2.4 33 18-50 28-62 (119)
164 PF01155 HypA: Hydrogenase exp 64.1 1.8 4E-05 31.6 -0.5 24 5-32 72-95 (113)
165 KOG2593 Transcription initiati 64.0 3.5 7.6E-05 37.0 1.2 32 3-34 128-164 (436)
166 TIGR00319 desulf_FeS4 desulfof 63.5 5.7 0.00012 22.5 1.7 23 4-27 8-30 (34)
167 PF08063 PADR1: PADR1 (NUC008) 63.5 4.4 9.6E-05 25.9 1.3 21 4-27 15-35 (55)
168 cd00729 rubredoxin_SM Rubredox 63.5 6.5 0.00014 22.6 1.9 8 24-31 19-26 (34)
169 TIGR00595 priA primosomal prot 63.5 6.1 0.00013 36.2 2.7 29 4-34 223-251 (505)
170 cd00974 DSRD Desulforedoxin (D 63.4 5.7 0.00012 22.6 1.6 24 4-28 5-28 (34)
171 PF01599 Ribosomal_S27: Riboso 63.4 9.1 0.0002 23.8 2.6 26 4-31 19-46 (47)
172 PF14768 RPA_interact_C: Repli 62.9 5.9 0.00013 27.3 2.0 26 5-34 1-26 (82)
173 PRK03564 formate dehydrogenase 62.9 6.9 0.00015 33.8 2.8 10 24-33 253-262 (309)
174 PRK14559 putative protein seri 62.8 4.3 9.2E-05 38.5 1.6 24 5-34 29-52 (645)
175 PRK05580 primosome assembly pr 62.5 6.5 0.00014 37.4 2.8 29 4-34 391-419 (679)
176 KOG1010 Rb (Retinoblastoma tum 62.1 15 0.00033 35.8 5.1 54 107-160 679-741 (920)
177 PRK03681 hypA hydrogenase nick 60.9 5.3 0.00012 29.3 1.5 16 15-30 62-77 (114)
178 PF14206 Cys_rich_CPCC: Cystei 60.9 8.8 0.00019 26.4 2.5 26 4-32 2-29 (78)
179 TIGR01562 FdhE formate dehydro 60.8 7.6 0.00016 33.5 2.6 32 3-34 224-263 (305)
180 PRK06393 rpoE DNA-directed RNA 60.8 3.6 7.8E-05 27.3 0.5 20 4-31 6-25 (64)
181 PF14353 CpXC: CpXC protein 60.4 8 0.00017 28.5 2.4 12 23-34 38-49 (128)
182 KOG2907 RNA polymerase I trans 60.2 3.6 7.9E-05 30.3 0.5 32 3-36 7-38 (116)
183 cd00202 ZnF_GATA Zinc finger D 60.1 3.3 7.2E-05 26.4 0.3 29 6-34 2-32 (54)
184 PRK15103 paraquat-inducible me 59.8 6.1 0.00013 35.5 2.0 32 4-36 11-43 (419)
185 PRK14873 primosome assembly pr 59.4 7.2 0.00016 37.1 2.5 27 4-32 393-419 (665)
186 PRK07218 replication factor A; 59.2 4.2 9E-05 36.6 0.8 21 4-32 298-318 (423)
187 PF04502 DUF572: Family of unk 59.1 4.7 0.0001 34.9 1.1 25 4-28 78-102 (324)
188 PRK04023 DNA polymerase II lar 59.0 7.1 0.00015 38.8 2.4 11 24-34 664-674 (1121)
189 PF04810 zf-Sec23_Sec24: Sec23 58.9 12 0.00026 22.1 2.6 30 3-32 2-33 (40)
190 PF13824 zf-Mss51: Zinc-finger 58.7 7.3 0.00016 25.1 1.7 24 5-33 1-24 (55)
191 PF10080 DUF2318: Predicted me 58.1 9.2 0.0002 27.7 2.3 30 4-36 36-65 (102)
192 PF14471 DUF4428: Domain of un 57.6 3.3 7.1E-05 26.1 -0.1 28 5-33 1-30 (51)
193 COG0333 RpmF Ribosomal protein 57.1 6.7 0.00014 25.4 1.3 25 4-35 28-52 (57)
194 PF02984 Cyclin_C: Cyclin, C-t 57.1 26 0.00057 24.4 4.6 19 139-157 41-59 (118)
195 TIGR03829 YokU_near_AblA uncha 56.6 8.8 0.00019 27.1 1.9 34 5-38 1-50 (89)
196 PF01485 IBR: IBR domain; Int 56.3 6.5 0.00014 24.7 1.2 28 4-33 19-50 (64)
197 PF13790 DUF4182: Domain of un 56.2 5.8 0.00013 23.6 0.8 13 22-34 2-14 (38)
198 KOG3507 DNA-directed RNA polym 55.9 6.4 0.00014 25.7 1.0 25 5-33 22-47 (62)
199 PF03833 PolC_DP2: DNA polymer 55.6 3.8 8.3E-05 39.8 0.0 11 24-34 681-691 (900)
200 PRK00222 methionine sulfoxide 54.7 11 0.00024 28.9 2.4 34 17-50 37-72 (142)
201 PF08772 NOB1_Zn_bind: Nin one 54.7 6.4 0.00014 26.8 1.0 11 1-11 22-32 (73)
202 PF01807 zf-CHC2: CHC2 zinc fi 54.6 12 0.00025 26.5 2.4 27 5-31 35-62 (97)
203 PRK00564 hypA hydrogenase nick 54.5 5.5 0.00012 29.3 0.7 19 14-32 62-80 (117)
204 PRK14714 DNA polymerase II lar 54.5 7.7 0.00017 39.4 1.8 6 5-10 669-674 (1337)
205 smart00290 ZnF_UBP Ubiquitin C 54.5 11 0.00024 22.8 2.0 23 5-35 1-23 (50)
206 COG1198 PriA Primosomal protei 54.2 11 0.00023 36.4 2.7 27 4-32 445-471 (730)
207 PRK06260 threonine synthase; V 54.1 5.6 0.00012 35.2 0.8 30 1-34 1-30 (397)
208 PF01412 ArfGap: Putative GTPa 54.0 5 0.00011 29.3 0.4 30 4-33 14-43 (116)
209 PRK00085 recO DNA repair prote 53.4 9.3 0.0002 31.1 1.9 27 4-30 150-177 (247)
210 cd07973 Spt4 Transcription elo 53.2 9 0.00019 27.5 1.6 27 4-33 4-30 (98)
211 smart00647 IBR In Between Ring 53.1 12 0.00027 23.5 2.1 28 4-33 19-50 (64)
212 PF09889 DUF2116: Uncharacteri 52.7 2.8 6.1E-05 27.4 -1.0 27 3-35 3-30 (59)
213 PF07191 zinc-ribbons_6: zinc- 52.4 9.5 0.00021 25.8 1.5 26 4-33 2-27 (70)
214 KOG0656 G1/S-specific cyclin D 52.4 58 0.0013 28.5 6.7 55 106-160 79-145 (335)
215 PRK06386 replication factor A; 52.1 6.9 0.00015 34.5 1.0 21 4-32 237-257 (358)
216 PRK14526 adenylate kinase; Pro 52.1 10 0.00022 30.6 2.0 33 4-36 123-155 (211)
217 PF00320 GATA: GATA zinc finge 51.8 5.4 0.00012 23.1 0.2 27 6-32 1-29 (36)
218 TIGR00613 reco DNA repair prot 51.7 11 0.00023 30.6 2.0 28 4-31 148-176 (241)
219 PF13878 zf-C2H2_3: zinc-finge 51.6 6.1 0.00013 23.7 0.4 16 22-37 12-27 (41)
220 PRK00750 lysK lysyl-tRNA synth 51.3 12 0.00025 34.5 2.4 33 5-38 177-214 (510)
221 TIGR00310 ZPR1_znf ZPR1 zinc f 51.3 11 0.00024 30.3 1.9 30 5-34 2-41 (192)
222 PF09082 DUF1922: Domain of un 50.3 11 0.00024 25.3 1.6 26 5-34 5-30 (68)
223 PF04216 FdhE: Protein involve 50.2 9.6 0.00021 32.2 1.6 29 4-32 173-206 (290)
224 smart00105 ArfGap Putative GTP 49.4 8.6 0.00019 27.9 1.0 31 4-34 4-34 (112)
225 COG2816 NPY1 NTP pyrophosphohy 49.3 11 0.00024 32.1 1.8 30 3-34 111-140 (279)
226 COG5333 CCL1 Cdk activating ki 49.2 46 0.001 28.6 5.5 62 99-160 125-211 (297)
227 PRK08197 threonine synthase; V 47.6 8.2 0.00018 34.1 0.8 27 3-34 7-33 (394)
228 TIGR00357 methionine-R-sulfoxi 47.1 14 0.00031 28.0 1.9 33 18-50 35-69 (134)
229 COG4391 Uncharacterized protei 45.8 12 0.00026 24.7 1.1 20 15-34 39-59 (62)
230 COG4643 Uncharacterized protei 45.2 13 0.00028 32.6 1.6 26 5-30 34-61 (366)
231 PF10005 DUF2248: Uncharacteri 45.1 13 0.00028 32.6 1.6 25 5-35 1-25 (343)
232 TIGR00340 zpr1_rel ZPR1-relate 45.0 18 0.0004 28.3 2.3 29 6-34 1-39 (163)
233 PRK01110 rpmF 50S ribosomal pr 44.3 12 0.00026 24.4 1.0 28 4-39 28-55 (60)
234 cd00674 LysRS_core_class_I cat 44.3 18 0.00038 31.9 2.3 33 4-37 170-206 (353)
235 PHA03074 late transcription fa 43.9 15 0.00032 30.0 1.6 30 2-34 3-32 (225)
236 PF09334 tRNA-synt_1g: tRNA sy 43.8 11 0.00025 33.3 1.1 24 4-34 137-160 (391)
237 COG1571 Predicted DNA-binding 43.6 14 0.00031 33.2 1.7 32 5-39 352-383 (421)
238 PF14369 zf-RING_3: zinc-finge 42.1 17 0.00036 21.0 1.3 26 4-31 3-29 (35)
239 PRK06450 threonine synthase; V 41.2 12 0.00027 32.4 0.9 29 1-34 1-29 (338)
240 COG2260 Predicted Zn-ribbon RN 41.0 15 0.00032 24.0 1.0 22 4-33 6-27 (59)
241 PF01363 FYVE: FYVE zinc finge 40.8 19 0.00041 23.4 1.5 30 4-37 10-39 (69)
242 PRK14714 DNA polymerase II lar 40.6 13 0.00029 37.8 1.1 8 5-12 681-688 (1337)
243 PF14319 Zn_Tnp_IS91: Transpos 40.6 8.9 0.00019 28.0 -0.1 34 4-39 43-76 (111)
244 PF13408 Zn_ribbon_recom: Reco 40.3 15 0.00031 22.7 0.9 14 21-34 3-16 (58)
245 TIGR02642 phage_xxxx uncharact 40.0 18 0.00038 29.1 1.5 23 4-30 100-122 (186)
246 PF14149 YhfH: YhfH-like prote 39.7 5.3 0.00012 23.6 -1.1 16 21-36 11-26 (37)
247 PF12677 DUF3797: Domain of un 39.7 23 0.00049 22.2 1.6 8 4-11 14-21 (49)
248 PRK08329 threonine synthase; V 39.5 19 0.00042 31.2 1.8 25 4-34 2-26 (347)
249 PF14690 zf-ISL3: zinc-finger 39.3 20 0.00044 21.3 1.4 8 4-11 3-10 (47)
250 PF06689 zf-C4_ClpX: ClpX C4-t 39.1 12 0.00027 22.3 0.4 26 4-29 2-30 (41)
251 PF14951 DUF4503: Domain of un 39.0 21 0.00045 31.6 1.9 38 5-43 276-314 (389)
252 KOG0794 CDK8 kinase-activating 38.5 41 0.00089 28.1 3.5 22 139-160 192-213 (264)
253 PRK00133 metG methionyl-tRNA s 38.4 16 0.00034 34.7 1.2 22 5-33 141-162 (673)
254 PF07295 DUF1451: Protein of u 38.4 15 0.00031 28.3 0.8 15 20-34 109-123 (146)
255 COG1779 C4-type Zn-finger prot 38.2 20 0.00044 29.1 1.6 36 4-40 15-60 (201)
256 COG0143 MetG Methionyl-tRNA sy 37.9 18 0.0004 33.7 1.5 25 5-36 144-168 (558)
257 COG2126 RPL37A Ribosomal prote 37.7 18 0.00039 23.6 1.0 25 4-33 17-41 (61)
258 smart00709 Zpr1 Duplicated dom 37.5 28 0.00061 27.1 2.3 29 5-33 2-39 (160)
259 PF01907 Ribosomal_L37e: Ribos 37.5 23 0.0005 22.8 1.5 24 4-32 16-39 (55)
260 COG3677 Transposase and inacti 37.4 24 0.00052 26.5 1.8 30 3-33 30-63 (129)
261 PLN02569 threonine synthase 37.2 19 0.0004 33.0 1.4 27 3-34 49-75 (484)
262 PF01396 zf-C4_Topoisom: Topoi 37.2 33 0.00071 20.2 2.0 29 4-33 2-34 (39)
263 PF14205 Cys_rich_KTR: Cystein 37.1 29 0.00062 22.3 1.8 27 5-31 6-36 (55)
264 smart00064 FYVE Protein presen 37.0 26 0.00056 22.6 1.7 30 4-37 11-40 (68)
265 PF01641 SelR: SelR domain; I 36.9 19 0.00042 27.0 1.2 33 18-50 32-66 (124)
266 PF03367 zf-ZPR1: ZPR1 zinc-fi 36.7 15 0.00033 28.5 0.7 30 4-33 2-40 (161)
267 COG0229 Conserved domain frequ 36.4 27 0.00059 26.7 2.0 33 18-50 37-71 (140)
268 PF08421 Methyltransf_13: Puta 36.3 20 0.00044 23.2 1.1 17 23-39 40-56 (62)
269 PF02236 Viral_DNA_bi: Viral D 36.1 49 0.0011 23.2 3.1 59 105-174 6-70 (86)
270 PRK04179 rpl37e 50S ribosomal 35.8 19 0.0004 23.8 0.9 24 3-31 17-40 (62)
271 PRK00118 putative DNA-binding 35.7 1.2E+02 0.0026 21.9 5.2 40 111-150 35-87 (104)
272 COG5134 Uncharacterized conser 35.3 32 0.0007 28.4 2.3 25 4-28 80-104 (272)
273 PRK07591 threonine synthase; V 35.1 16 0.00034 32.7 0.6 26 4-34 19-44 (421)
274 PRK03564 formate dehydrogenase 34.6 24 0.00053 30.5 1.7 29 3-31 187-220 (309)
275 PHA00689 hypothetical protein 34.2 28 0.00061 22.0 1.5 27 20-47 14-40 (62)
276 PRK00448 polC DNA polymerase I 34.0 22 0.00048 36.9 1.5 31 3-34 908-944 (1437)
277 PRK05638 threonine synthase; V 33.9 22 0.00048 31.9 1.3 25 4-34 2-26 (442)
278 PRK04023 DNA polymerase II lar 33.7 26 0.00056 35.1 1.8 8 4-11 627-634 (1121)
279 PF05460 ORC6: Origin recognit 33.7 14 0.0003 32.5 0.0 46 114-159 3-58 (353)
280 cd00065 FYVE FYVE domain; Zinc 33.6 33 0.00071 21.2 1.8 30 4-37 3-32 (57)
281 PF00130 C1_1: Phorbol esters/ 33.5 36 0.00079 20.7 1.9 35 3-40 11-45 (53)
282 PF02591 DUF164: Putative zinc 33.3 24 0.00052 22.2 1.1 31 3-33 22-56 (56)
283 TIGR03060 PS_II_psb29 photosys 33.2 62 0.0013 26.6 3.7 29 109-137 165-195 (214)
284 PRK11475 DNA-binding transcrip 33.0 86 0.0019 25.1 4.6 56 99-155 136-197 (207)
285 PRK00279 adk adenylate kinase; 32.6 36 0.00077 27.0 2.2 33 4-36 128-160 (215)
286 COG5525 Bacteriophage tail ass 32.6 23 0.0005 33.3 1.2 33 4-36 228-272 (611)
287 TIGR00354 polC DNA polymerase, 32.5 16 0.00034 36.3 0.2 23 3-33 625-647 (1095)
288 smart00400 ZnF_CHCC zinc finge 32.5 60 0.0013 20.1 2.9 26 5-30 4-30 (55)
289 PRK09462 fur ferric uptake reg 32.0 23 0.00049 26.7 1.0 12 23-34 90-101 (148)
290 PRK13266 Thf1-like protein; Re 31.9 66 0.0014 26.6 3.7 29 109-137 167-197 (225)
291 PRK04016 DNA-directed RNA poly 31.7 22 0.00047 23.5 0.7 13 24-36 5-17 (62)
292 PF13913 zf-C2HC_2: zinc-finge 31.5 30 0.00065 18.2 1.1 9 3-11 2-10 (25)
293 TIGR00467 lysS_arch lysyl-tRNA 31.4 29 0.00063 32.1 1.7 33 4-37 169-204 (515)
294 COG3809 Uncharacterized protei 31.4 40 0.00086 23.4 1.9 28 4-33 2-31 (88)
295 COG4311 SoxD Sarcosine oxidase 31.3 26 0.00056 25.1 1.1 12 1-12 1-12 (97)
296 PRK08173 DNA topoisomerase III 31.2 31 0.00066 34.0 1.9 27 4-34 625-651 (862)
297 COG1499 NMD3 NMD protein affec 31.0 18 0.00039 31.9 0.3 12 1-12 4-15 (355)
298 PRK07956 ligA NAD-dependent DN 30.8 37 0.00079 32.5 2.3 34 3-38 404-440 (665)
299 COG0375 HybF Zn finger protein 30.7 27 0.00057 25.9 1.1 19 15-33 62-80 (115)
300 PHA02540 61 DNA primase; Provi 30.7 48 0.001 29.0 2.8 28 5-32 29-64 (337)
301 PRK00762 hypA hydrogenase nick 30.6 22 0.00049 26.3 0.7 18 14-32 61-78 (124)
302 PF03811 Zn_Tnp_IS1: InsA N-te 30.6 27 0.00059 20.3 0.9 10 4-14 6-15 (36)
303 cd07153 Fur_like Ferric uptake 30.6 25 0.00054 24.9 0.9 13 22-34 72-84 (116)
304 PF11264 ThylakoidFormat: Thyl 30.5 78 0.0017 26.0 3.9 30 108-137 161-192 (216)
305 COG0735 Fur Fe2+/Zn2+ uptake r 30.3 25 0.00054 26.7 0.9 13 22-34 92-104 (145)
306 TIGR01391 dnaG DNA primase, ca 30.2 51 0.0011 29.4 3.0 34 5-40 36-70 (415)
307 smart00504 Ubox Modified RING 29.9 17 0.00038 22.8 -0.0 29 4-40 2-30 (63)
308 PF10886 DUF2685: Protein of u 29.7 29 0.00062 22.3 1.0 36 4-40 2-40 (54)
309 TIGR01405 polC_Gram_pos DNA po 29.5 30 0.00064 35.4 1.5 31 3-34 683-719 (1213)
310 cd01410 SIRT7 SIRT7: Eukaryoti 29.4 35 0.00076 27.4 1.7 38 3-41 95-138 (206)
311 PF00488 MutS_V: MutS domain V 29.3 62 0.0013 26.5 3.2 23 114-136 210-234 (235)
312 PF01475 FUR: Ferric uptake re 29.2 27 0.00059 25.1 0.9 13 22-34 79-91 (120)
313 PF01921 tRNA-synt_1f: tRNA sy 29.1 13 0.00028 32.8 -0.9 34 5-38 176-214 (360)
314 cd00021 BBOX B-Box-type zinc f 29.1 47 0.001 18.5 1.8 26 5-30 2-27 (39)
315 COG1885 Uncharacterized protei 29.0 42 0.0009 24.5 1.8 8 4-11 50-57 (115)
316 COG1107 Archaea-specific RecJ- 28.8 40 0.00086 32.0 2.1 28 4-32 3-30 (715)
317 COG2023 RPR2 RNase P subunit R 28.7 46 0.00099 24.3 2.0 31 4-34 57-93 (105)
318 COG4307 Uncharacterized protei 28.7 24 0.00051 30.2 0.6 28 1-34 1-28 (349)
319 COG2979 Uncharacterized protei 28.6 66 0.0014 26.5 3.1 20 109-128 194-213 (225)
320 PF03685 UPF0147: Uncharacteri 28.6 1.9E+02 0.0042 20.2 5.0 50 101-150 4-56 (85)
321 smart00550 Zalpha Z-DNA-bindin 28.3 99 0.0022 20.1 3.5 27 111-137 24-50 (68)
322 PF12651 RHH_3: Ribbon-helix-h 28.2 1.4E+02 0.003 17.9 4.3 22 107-128 12-34 (44)
323 PRK11032 hypothetical protein; 28.2 27 0.0006 27.3 0.8 14 20-33 121-134 (160)
324 COG0846 SIR2 NAD-dependent pro 28.1 27 0.00058 29.3 0.8 39 3-41 122-165 (250)
325 PF00628 PHD: PHD-finger; Int 28.0 38 0.00081 20.4 1.3 26 5-35 1-26 (51)
326 PF09779 Ima1_N: Ima1 N-termin 28.0 43 0.00093 25.1 1.9 28 5-32 2-29 (131)
327 PF06676 DUF1178: Protein of u 27.9 35 0.00077 26.3 1.4 8 4-11 33-40 (148)
328 TIGR00575 dnlj DNA ligase, NAD 27.8 44 0.00095 31.8 2.3 34 3-38 392-427 (652)
329 PTZ00408 NAD-dependent deacety 27.4 24 0.00053 29.2 0.5 39 3-41 117-157 (242)
330 PRK00481 NAD-dependent deacety 27.2 39 0.00083 27.7 1.6 38 3-41 122-160 (242)
331 PRK09263 anaerobic ribonucleos 27.2 34 0.00073 33.0 1.4 26 4-31 642-667 (711)
332 TIGR03831 YgiT_finger YgiT-typ 27.2 44 0.00095 19.5 1.5 14 20-33 29-42 (46)
333 TIGR00320 dfx_rbo desulfoferro 27.1 40 0.00086 25.2 1.5 26 4-32 8-33 (125)
334 KOG0856 Predicted pilin-like t 27.0 49 0.0011 25.4 2.0 33 18-50 49-83 (146)
335 cd01411 SIR2H SIR2H: Uncharact 26.8 34 0.00074 27.8 1.2 37 3-41 118-154 (225)
336 PF09845 DUF2072: Zn-ribbon co 26.7 29 0.00063 26.3 0.7 13 25-37 3-15 (131)
337 PRK11639 zinc uptake transcrip 26.5 31 0.00068 26.8 0.9 12 23-34 100-111 (169)
338 PF10083 DUF2321: Uncharacteri 26.4 38 0.00083 26.4 1.3 27 5-40 30-56 (158)
339 PRK07217 replication factor A; 26.1 33 0.00072 29.7 1.1 21 4-32 189-211 (311)
340 TIGR01053 LSD1 zinc finger dom 25.9 84 0.0018 17.6 2.4 27 4-32 2-28 (31)
341 KOG3251 Golgi SNAP receptor co 25.7 3.3E+02 0.0071 22.4 6.7 27 102-128 156-182 (213)
342 KOG2272 Focal adhesion protein 25.6 20 0.00044 30.3 -0.3 24 21-44 193-217 (332)
343 PLN03060 inositol phosphatase- 25.5 90 0.0019 25.5 3.4 27 111-137 159-187 (206)
344 KOG0006 E3 ubiquitin-protein l 25.4 39 0.00086 29.6 1.4 32 1-34 313-347 (446)
345 PRK00039 ruvC Holliday junctio 25.1 82 0.0018 24.4 3.0 63 102-165 43-106 (164)
346 COG1644 RPB10 DNA-directed RNA 25.0 25 0.00054 23.2 0.1 13 24-36 5-17 (63)
347 COG4393 Predicted membrane pro 25.0 32 0.0007 30.3 0.8 27 5-34 336-362 (405)
348 smart00109 C1 Protein kinase C 25.0 50 0.0011 19.2 1.5 30 3-36 11-40 (49)
349 PRK04338 N(2),N(2)-dimethylgua 25.0 42 0.00091 29.7 1.5 34 5-45 246-279 (382)
350 PRK15103 paraquat-inducible me 24.6 51 0.0011 29.6 2.0 10 24-33 236-245 (419)
351 PRK05667 dnaG DNA primase; Val 24.6 73 0.0016 29.9 3.1 27 5-31 38-65 (580)
352 PF00643 zf-B_box: B-box zinc 24.5 52 0.0011 18.9 1.4 9 3-11 3-11 (42)
353 PHA02956 hypothetical protein; 24.4 49 0.0011 25.5 1.6 20 13-32 107-126 (189)
354 COG5347 GTPase-activating prot 24.3 64 0.0014 28.0 2.5 30 4-33 21-50 (319)
355 PRK14067 exodeoxyribonuclease 24.2 1.3E+02 0.0029 20.6 3.6 37 100-136 4-42 (80)
356 COG0272 Lig NAD-dependent DNA 24.2 50 0.0011 31.6 1.9 36 3-40 404-442 (667)
357 PF13005 zf-IS66: zinc-finger 24.1 45 0.00097 19.9 1.1 8 4-11 3-10 (47)
358 PRK04330 hypothetical protein; 24.0 2.7E+02 0.0057 19.7 5.6 51 100-150 6-59 (88)
359 PRK05550 bifunctional methioni 23.9 56 0.0012 28.0 2.0 33 18-50 31-65 (283)
360 TIGR00617 rpa1 replication fac 23.9 55 0.0012 30.9 2.1 27 4-33 475-503 (608)
361 PF04981 NMD3: NMD3 family ; 23.9 32 0.0007 28.2 0.5 31 5-35 15-47 (236)
362 PF06906 DUF1272: Protein of u 23.9 47 0.001 21.5 1.2 7 25-31 43-49 (57)
363 COG1675 TFA1 Transcription ini 23.7 17 0.00037 28.9 -1.0 31 4-36 114-145 (176)
364 PF11020 DUF2610: Domain of un 23.6 2E+02 0.0044 19.9 4.3 25 120-144 45-72 (82)
365 PRK14715 DNA polymerase II lar 22.9 42 0.00092 34.7 1.2 23 4-34 675-697 (1627)
366 TIGR00155 pqiA_fam integral me 22.8 54 0.0012 29.3 1.8 37 17-63 7-43 (403)
367 COG5319 Uncharacterized protei 22.7 33 0.00072 26.0 0.4 11 22-32 31-41 (142)
368 cd00029 C1 Protein kinase C co 22.4 49 0.0011 19.5 1.0 31 3-36 11-41 (50)
369 TIGR00570 cdk7 CDK-activating 22.4 59 0.0013 28.2 1.9 11 1-11 1-11 (309)
370 PRK14018 trifunctional thiored 22.3 68 0.0015 29.8 2.4 33 18-50 413-447 (521)
371 PLN00047 photosystem II biogen 22.2 1.1E+02 0.0023 26.3 3.4 28 110-137 211-240 (283)
372 COG2176 PolC DNA polymerase II 22.2 52 0.0011 33.8 1.6 31 3-34 914-950 (1444)
373 cd01413 SIR2_Af2 SIR2_Af2: Arc 22.2 51 0.0011 26.7 1.4 38 3-40 113-153 (222)
374 PF08996 zf-DNA_Pol: DNA Polym 21.8 64 0.0014 25.5 1.9 34 4-39 19-61 (188)
375 COG2331 Uncharacterized protei 21.8 15 0.00033 25.2 -1.4 29 5-33 14-43 (82)
376 PF00196 GerE: Bacterial regul 21.6 1.4E+02 0.0031 18.3 3.2 24 111-134 20-46 (58)
377 COG4189 Predicted transcriptio 21.6 89 0.0019 26.4 2.7 18 111-128 39-56 (308)
378 PRK14704 anaerobic ribonucleos 21.6 49 0.0011 31.3 1.3 21 4-31 560-580 (618)
379 TIGR01565 homeo_ZF_HD homeobox 21.3 80 0.0017 20.4 1.9 17 110-126 33-49 (58)
380 PF12156 ATPase-cat_bd: Putati 21.3 46 0.001 23.1 0.8 42 4-48 1-48 (88)
381 cd08313 Death_TNFR1 Death doma 21.2 1.2E+02 0.0026 20.8 2.9 20 109-128 11-30 (80)
382 PF05864 Chordopox_RPO7: Chord 21.1 38 0.00083 22.0 0.4 13 23-35 4-16 (63)
383 PF04031 Las1: Las1-like ; In 21.1 81 0.0018 24.3 2.3 19 110-128 102-120 (154)
384 PHA03082 DNA-dependent RNA pol 21.0 38 0.00082 22.1 0.3 13 23-35 4-16 (63)
385 PF10668 Phage_terminase: Phag 21.0 1.8E+02 0.0038 18.9 3.5 18 111-128 24-41 (60)
386 TIGR00201 comF comF family pro 21.0 42 0.00091 26.3 0.7 23 6-34 1-23 (190)
387 COG3364 Zn-ribbon containing p 20.8 44 0.00095 24.4 0.6 11 25-35 4-14 (112)
388 PHA02325 hypothetical protein 20.7 51 0.0011 21.9 0.9 11 1-11 1-11 (72)
389 PTZ00073 60S ribosomal protein 20.5 47 0.001 23.5 0.7 23 4-31 17-39 (91)
390 cd01407 SIR2-fam SIR2 family o 20.5 55 0.0012 26.3 1.3 39 3-41 109-151 (218)
391 PF06056 Terminase_5: Putative 20.4 92 0.002 19.9 2.1 18 111-128 15-32 (58)
392 PLN03165 chaperone protein dna 20.4 58 0.0013 23.9 1.2 7 5-11 54-60 (111)
393 KOG0653 Cyclin B and related k 20.4 4.5E+02 0.0097 23.2 7.1 65 106-170 159-231 (391)
394 PF04032 Rpr2: RNAse P Rpr2/Rp 20.2 52 0.0011 22.0 0.9 20 15-34 38-57 (85)
395 COG1545 Predicted nucleic-acid 20.1 88 0.0019 23.6 2.2 24 4-33 30-53 (140)
396 smart00547 ZnF_RBZ Zinc finger 20.1 49 0.0011 17.1 0.6 11 22-32 1-11 (26)
397 KOG0818 GTPase-activating prot 20.1 52 0.0011 30.6 1.1 29 4-32 9-37 (669)
398 PF04967 HTH_10: HTH DNA bindi 20.0 1.9E+02 0.0041 18.2 3.4 18 111-128 25-42 (53)
No 1
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=6.9e-45 Score=310.42 Aligned_cols=163 Identities=28% Similarity=0.508 Sum_probs=145.0
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccccCCccccccccccccCCCCCCCccccCCCCccccCCCCceEEeCCC-C
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPN-G 81 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~Ewr~F~~~~~~~d~sr~G~p~~~~l~~~gl~T~i~~~~-~ 81 (181)
..+||+||+ +++++|+++|++||++||+||+|++||+|||||+|++++ .+|++|+|+|.++++||.|++|.|++++ +
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 367999998 789999999999999999999999999999999999875 5699999999999999999999999654 3
Q ss_pred CCCcccc-------ccccccccCC---CCchHHHHHHHHHHHHHHHHhCCchHHHHH--HHHHHHHhh-h----CHHHHH
Q 030241 82 ASGEFLS-------SSLGRWQNRG---SNPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWL 144 (181)
Q Consensus 82 ~~g~~l~-------~~l~~~q~~~---~~~er~l~~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~-l----~~~~v~ 144 (181)
..|+.++ .+|++||++. ++.||+|..|+++|++||+.|+||+.|+|+ .+|+++.++ + +.++++
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 4555443 2488998875 678999999999999999999999999999 899999887 3 899999
Q ss_pred HHHHHHHHHhCCCCcc--------ccChhhh
Q 030241 145 LACTLLVDKKTSHALL--------RVQPKIL 167 (181)
Q Consensus 145 AAclYiACR~~~~p~t--------~~~~~~~ 167 (181)
|||||+|||++++|.| .+.+|.+
T Consensus 169 AAclYiACR~~~~prtl~eI~~~~~v~~k~i 199 (310)
T PRK00423 169 AAALYAACRRCKVPRTLDEIAEVSRVSRKEI 199 (310)
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCCHHHH
Confidence 9999999999999987 4666655
No 2
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=1.7e-42 Score=287.56 Aligned_cols=163 Identities=50% Similarity=0.748 Sum_probs=147.9
Q ss_pred CCCCCCCCCCc-eeEeCCCCceEeCCCccccccCCccccccccccccCCCCCCCccccCCCCccccCCCCceEEeCCCCC
Q 030241 4 AFCSDCKKHTE-VVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGA 82 (181)
Q Consensus 4 ~~Cp~Cg~~~~-iv~D~~~G~~vC~~CG~Vl~e~~id~~~Ewr~F~~~~~~~d~sr~G~p~~~~l~~~gl~T~i~~~~~~ 82 (181)
++||+|+.+++ +|+|+.+|++||.+||+|+++++||.++|||+|++++++.||+|||+|.||++.+.+|.|.|+.+.+.
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 47999998777 99999999999999999999999999999999999987899999999999999999999999988765
Q ss_pred CCccccccccccccC--CCCchHHHHHHHHHHHHHHHHhCCchHHHHH--HHHHHHHhh--h---CHHHHHHHHHHHHHH
Q 030241 83 SGEFLSSSLGRWQNR--GSNPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDK 153 (181)
Q Consensus 83 ~g~~l~~~l~~~q~~--~~~~er~l~~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~--l---~~~~v~AAclYiACR 153 (181)
++..+ ..|.++|++ +++.|+.+..||++|..|+++|+||..|.|+ ++||++++. + +.++++|||||+|||
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 SSSFA-SSLGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACR 159 (308)
T ss_pred CHHHH-HHHHHHhcccccCCccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHH
Confidence 54433 347788974 4789999999999999999999999999999 999999876 4 899999999999999
Q ss_pred hCCCCcc--------ccChhhh
Q 030241 154 KTSHALL--------RVQPKIL 167 (181)
Q Consensus 154 ~~~~p~t--------~~~~~~~ 167 (181)
+++.|.| .||||+.
T Consensus 160 q~~~pRT~kEI~~~anv~kKEI 181 (308)
T KOG1597|consen 160 QEDVPRTFKEISAVANVSKKEI 181 (308)
T ss_pred hcCCCchHHHHHHHHcCCHHHH
Confidence 9999987 6888874
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=3.3e-37 Score=259.55 Aligned_cols=148 Identities=30% Similarity=0.542 Sum_probs=132.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccCCccccccccccccCCCCCCCccccCCCCccccCCCCceEEeCCCCCC
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGAS 83 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~Ewr~F~~~~~~~d~sr~G~p~~~~l~~~gl~T~i~~~~~~~ 83 (181)
+.||+||+ ++++.|++.|++||.+||+|++|+.||.|||||+| ++ ...+ |+|+|.++.+||.|++|.|+++...
T Consensus 2 ~~CpeCg~-~~~~~d~~~ge~VC~~CG~Vi~~~~id~gpewr~f-~e--~~~~-r~g~P~t~~~~d~~l~t~i~~~~~~- 75 (285)
T COG1405 2 MSCPECGS-TNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAF-DE--RHER-RVGAPLTPSIHDKGLSTIIGWGDKD- 75 (285)
T ss_pred CCCCCCCC-ccceeeccCCeEEeccCCEEeccccccCCCCcccc-cc--cccc-cccCCCccccCccchhhhcccchhH-
Confidence 57999998 79999999999999999999999999999999999 33 2334 9999999999999999999876421
Q ss_pred CccccccccccccCC---CCchHHHHHHHHHHHHHHHHhCCchHHHHH--HHHHHHHhh-h----CHHHHHHHHHHHHHH
Q 030241 84 GEFLSSSLGRWQNRG---SNPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDK 153 (181)
Q Consensus 84 g~~l~~~l~~~q~~~---~~~er~l~~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~-l----~~~~v~AAclYiACR 153 (181)
...+|++||.+. +++||++..++.+|+.+++.|+||.+|.|+ .||+++.++ + +.+.++|||+|+|||
T Consensus 76 ---~~~rlr~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR 152 (285)
T COG1405 76 ---KMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACR 152 (285)
T ss_pred ---HHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHH
Confidence 235688999754 579999999999999999999999999999 999999988 5 899999999999999
Q ss_pred hCCCCcc
Q 030241 154 KTSHALL 160 (181)
Q Consensus 154 ~~~~p~t 160 (181)
+++.|.|
T Consensus 153 ~~~~prt 159 (285)
T COG1405 153 INGVPRT 159 (285)
T ss_pred HcCCCcc
Confidence 9999987
No 4
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=99.78 E-value=4.9e-19 Score=157.51 Aligned_cols=121 Identities=19% Similarity=0.338 Sum_probs=99.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccCCccccccccccccCCCCCCCccccCCCCccccCCCCceEEeCCCCCC
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGAS 83 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~Ewr~F~~~~~~~d~sr~G~p~~~~l~~~gl~T~i~~~~~~~ 83 (181)
+.|++||+ +++..|..+|+.+|+.||.|+|+++|+.+. +|... + .|+.|+....+.
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 899999999999999999999999999754 46522 1 134554322111
Q ss_pred CccccccccccccCCCCchHHHHHHHHHHHHHHHHhCCchHHHHH--HHHHHHHhh-h----CHHHHHHHHHHHHHHhCC
Q 030241 84 GEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS 156 (181)
Q Consensus 84 g~~l~~~l~~~q~~~~~~er~l~~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~-l----~~~~v~AAclYiACR~~~ 156 (181)
+. ..+++++++++|++.|++++.+|+|+. ++|. .+|++|.++ | +...|+|||+|++||+++
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 116889999999999999999999999 8888 999999999 7 899999999999999999
Q ss_pred CCcc
Q 030241 157 HALL 160 (181)
Q Consensus 157 ~p~t 160 (181)
++..
T Consensus 125 t~hl 128 (521)
T KOG1598|consen 125 TDHL 128 (521)
T ss_pred CceE
Confidence 9953
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=7.2e-18 Score=104.15 Aligned_cols=43 Identities=51% Similarity=1.076 Sum_probs=38.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccCCcccccccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTF 47 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~Ewr~F 47 (181)
++||+||+ +.+++|+.+|++||++||+||+|+.|++++|||+|
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 67999999999999999999999999999999987
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=99.33 E-value=4.3e-12 Score=85.98 Aligned_cols=49 Identities=14% Similarity=0.210 Sum_probs=43.2
Q ss_pred HHHHHHHhCCchHHHHH--HHHHHHHhh-h----CHHHHHHHHHHHHHHhCCCCcc
Q 030241 112 IATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTSHALL 160 (181)
Q Consensus 112 I~~ia~~L~Lp~~v~e~--~i~k~a~~~-l----~~~~v~AAclYiACR~~~~p~t 160 (181)
|++||++|+||++|+++ ++|+++.+. + ++..++|||||+|||+++.|+|
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t 56 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRT 56 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSS
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcC
Confidence 68999999999999999 999999877 4 7899999999999999999987
No 7
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=98.35 E-value=1.2e-06 Score=75.17 Aligned_cols=53 Identities=6% Similarity=0.054 Sum_probs=48.4
Q ss_pred HHHHHHHHHHHhCCchHHHHH--HHHHHHHhh-h----CHHHHHHHHHHHHHHhCCCCcc
Q 030241 108 AFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTSHALL 160 (181)
Q Consensus 108 a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~-l----~~~~v~AAclYiACR~~~~p~t 160 (181)
....|.++|++|+||..+.++ +|++++.+. + ++..++|||||+|||.++.|.|
T Consensus 219 p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t 278 (310)
T PRK00423 219 PIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRT 278 (310)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCC
Confidence 457889999999999999999 899999776 4 8999999999999999999976
No 8
>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=97.99 E-value=4.1e-05 Score=51.55 Aligned_cols=54 Identities=7% Similarity=0.014 Sum_probs=47.1
Q ss_pred HHHHHHHHHHHHhCCchHHHHH--HHHHHHHhh--h---CHHHHHHHHHHHHHHhCCCCcc
Q 030241 107 LAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTSHALL 160 (181)
Q Consensus 107 ~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~--l---~~~~v~AAclYiACR~~~~p~t 160 (181)
.+++.|.+++..+++|..+... .++.++... + +...+++||||+||+.++.|.+
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~ 64 (88)
T cd00043 4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPW 64 (88)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCC
Confidence 4778999999999999999888 788888655 3 8999999999999999998654
No 9
>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=97.89 E-value=5.4e-05 Score=50.48 Aligned_cols=50 Identities=6% Similarity=-0.068 Sum_probs=43.0
Q ss_pred HHHHHHHHhCCchHHHHH--HHHHHHHh-h-h---CHHHHHHHHHHHHHHhCCCCcc
Q 030241 111 TIATMSDRIGQMRYIRRW--KIKSLVEA-E-I---KTHYWLLACTLLVDKKTSHALL 160 (181)
Q Consensus 111 ~I~~ia~~L~Lp~~v~e~--~i~k~a~~-~-l---~~~~v~AAclYiACR~~~~p~t 160 (181)
.|.+++..+++|+.+... .+++.+.. . + +...++|||||+|||.++.+.+
T Consensus 2 ~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~ 58 (83)
T smart00385 2 FLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPW 58 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCC
Confidence 478899999999999888 78888865 3 3 8999999999999999998743
No 10
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=97.80 E-value=5.1e-05 Score=64.51 Aligned_cols=54 Identities=13% Similarity=0.064 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHhCCchHHHHH--HHHHHHHhh-h----CHHHHHHHHHHHHHHhCCCCcc
Q 030241 107 LAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTSHALL 160 (181)
Q Consensus 107 ~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~-l----~~~~v~AAclYiACR~~~~p~t 160 (181)
+-..+|.++|+.||||+.|... ++.+++.+. + +...++|||||+|+++++.+.|
T Consensus 193 ~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~t 253 (285)
T COG1405 193 DPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRT 253 (285)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchH
Confidence 4567899999999999888777 899999877 4 8999999999999999998876
No 11
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=97.26 E-value=0.00083 Score=56.96 Aligned_cols=53 Identities=9% Similarity=0.063 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHhCCchHHHHH--HHHHHHHhh-h----CHHHHHHHHHHHHHHhCCCCcc
Q 030241 108 AFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTSHALL 160 (181)
Q Consensus 108 a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~-l----~~~~v~AAclYiACR~~~~p~t 160 (181)
.-..|.++|+.|+||..+++. ++-+++.+. + ++-.++||.||++++....+.|
T Consensus 203 t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt 262 (308)
T KOG1597|consen 203 TGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKT 262 (308)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCccc
Confidence 567889999999999999999 899999887 4 8899999999999999887755
No 12
>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=97.26 E-value=0.0018 Score=49.31 Aligned_cols=57 Identities=12% Similarity=0.057 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHHHHhCCchHHHHH--HHHHHHHhh---h----CHHHHHHHHHHHHHHhCCCCcc
Q 030241 104 GLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE---I----KTHYWLLACTLLVDKKTSHALL 160 (181)
Q Consensus 104 ~l~~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~---l----~~~~v~AAclYiACR~~~~p~t 160 (181)
.+.-|..+|+++|++|+|++.+.+. .+|+.+... | ..+.++..|+|+.||.++.++|
T Consensus 10 vy~la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~s 75 (135)
T PF01857_consen 10 VYKLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELS 75 (135)
T ss_dssp HHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--
T ss_pred HHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCC
Confidence 3455889999999999999999888 788876543 3 7899999999999999998876
No 13
>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=97.10 E-value=0.00038 Score=41.11 Aligned_cols=28 Identities=29% Similarity=0.534 Sum_probs=23.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
..|+.|++ . .+...+|..+|..||.|++
T Consensus 9 ~~C~~C~~-~--~~~~~dG~~yC~~cG~~~E 36 (36)
T PF11781_consen 9 EPCPVCGS-R--WFYSDDGFYYCDRCGHQSE 36 (36)
T ss_pred CcCCCCCC-e--EeEccCCEEEhhhCceEcC
Confidence 34999997 3 6778899999999999874
No 14
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=96.94 E-value=0.00084 Score=38.90 Aligned_cols=31 Identities=23% Similarity=0.451 Sum_probs=25.6
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
|....|+.||. +.++..+++..+|.+||.+.
T Consensus 1 ~~~~~C~~C~~--~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 1 SNLKKCSKCGG--NGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred CCceEcCCCCC--CeEEEecCCeEEcccCCcEe
Confidence 55678999996 45666789999999999875
No 15
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=96.91 E-value=0.00055 Score=44.71 Aligned_cols=31 Identities=35% Similarity=0.757 Sum_probs=28.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (181)
.+||+|+. ..+||++++-.+.|..||.+|.+
T Consensus 12 VkCp~C~n-~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 12 VKCPDCGN-EQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EECCCCCC-eEEEEecCCcEEECcccCCCccc
Confidence 57999997 78999999999999999999953
No 16
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=96.87 E-value=0.00058 Score=45.46 Aligned_cols=31 Identities=35% Similarity=0.778 Sum_probs=28.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (181)
.+||+|+. ..++|++.+-.+.|..||.+|-+
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 57999997 78999999999999999999853
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=96.81 E-value=0.00047 Score=44.51 Aligned_cols=30 Identities=33% Similarity=0.722 Sum_probs=23.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.+||.|+. ..+|+++++-.+.|..||.+|-
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 67999997 7899999999999999999995
No 18
>PHA00626 hypothetical protein
Probab=96.72 E-value=0.0014 Score=42.19 Aligned_cols=31 Identities=23% Similarity=0.570 Sum_probs=23.7
Q ss_pred CCCCCCCCCCceeEeC----CCCceEeCCCcccccc
Q 030241 4 AFCSDCKKHTEVVFDH----SAGDTVCSECGLVLES 35 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~----~~G~~vC~~CG~Vl~e 35 (181)
+.||.||+ .+++... .+..++|.+||+-...
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 5666532 3689999999998643
No 19
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=96.66 E-value=0.007 Score=52.01 Aligned_cols=59 Identities=10% Similarity=0.046 Sum_probs=49.6
Q ss_pred hHHH-HHHHHHHHHHHHHhC--CchHHHHH--HHHHHHHhh--h---CHHHHHHHHHHHHHHhCCCCcc
Q 030241 102 DRGL-ILAFKTIATMSDRIG--QMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTSHALL 160 (181)
Q Consensus 102 er~l-~~a~~~I~~ia~~L~--Lp~~v~e~--~i~k~a~~~--l---~~~~v~AAclYiACR~~~~p~t 160 (181)
|+.| ...-..|.++|..|+ ||+.|+-+ .+|+...-+ + ....+++||||+||+.+..|++
T Consensus 52 E~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~s 120 (305)
T TIGR00569 52 ELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVS 120 (305)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcC
Confidence 5555 447789999999999 99999999 788876443 4 8999999999999999999874
No 20
>PLN00209 ribosomal protein S27; Provisional
Probab=96.35 E-value=0.002 Score=45.05 Aligned_cols=31 Identities=35% Similarity=0.657 Sum_probs=28.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (181)
.+||.|+. ..+||++++-.+.|..||.+|-+
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 78999999999999999999953
No 21
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=96.27 E-value=0.0024 Score=44.55 Aligned_cols=31 Identities=26% Similarity=0.618 Sum_probs=28.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (181)
.+||.|+. ..+||++++-.+.|..||.+|-+
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 22
>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=96.27 E-value=0.0046 Score=52.68 Aligned_cols=53 Identities=15% Similarity=0.101 Sum_probs=46.4
Q ss_pred HHHHHHHHHHHHHhCCchHHHHH--HHHHHHHhh--h---CHHHHHHHHHHHHHHhCCCC
Q 030241 106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTSHA 158 (181)
Q Consensus 106 ~~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~--l---~~~~v~AAclYiACR~~~~p 158 (181)
..++..|..+|.+|+||..+.++ .+|++..-+ + +...++++|||+||+-+..|
T Consensus 46 i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~ 105 (297)
T COG5333 46 IYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTP 105 (297)
T ss_pred HHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeeccccc
Confidence 55789999999999999999999 788876444 3 89999999999999999965
No 23
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=96.12 E-value=0.0031 Score=34.41 Aligned_cols=22 Identities=27% Similarity=0.967 Sum_probs=17.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (181)
+.||+||. . + +.+..+|..||.
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 78999996 2 2 357899999996
No 24
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=96.04 E-value=0.0051 Score=37.97 Aligned_cols=31 Identities=29% Similarity=0.682 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
|...+||+||. .+.+|+..+...|..||.-+
T Consensus 1 ~~~y~C~~CG~--~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 1 MAEYKCARCGR--EVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred CCEEECCCCCC--EEEECCCCCceECCCCCCeE
Confidence 55678999996 57788877799999999644
No 25
>PRK00420 hypothetical protein; Validated
Probab=96.02 E-value=0.005 Score=45.41 Aligned_cols=31 Identities=29% Similarity=0.600 Sum_probs=24.0
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
|-...||.||. ++ +-..+|..+|..||.++.
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 33467999996 34 444899999999999873
No 26
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=96.01 E-value=0.0033 Score=33.42 Aligned_cols=22 Identities=23% Similarity=0.915 Sum_probs=16.9
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
+||+||.. + ..+..+|..||.-
T Consensus 1 ~Cp~CG~~--~----~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAE--I----EDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCC--C----CCcCcchhhhCCc
Confidence 59999972 2 2467899999974
No 27
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=95.74 E-value=0.0064 Score=35.42 Aligned_cols=26 Identities=27% Similarity=0.779 Sum_probs=15.4
Q ss_pred CCCCCCCCCceeEe----CCCCceEeCCCccc
Q 030241 5 FCSDCKKHTEVVFD----HSAGDTVCSECGLV 32 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D----~~~G~~vC~~CG~V 32 (181)
+||.||.. +... ...--.||+.||.|
T Consensus 2 fC~~CG~~--l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGP--LERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B---EEE--TT-SS-EEEETTTTEE
T ss_pred ccccccCh--hhhhcCCCCCccceECCCCCCE
Confidence 69999973 4443 34556899999998
No 28
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=95.60 E-value=0.0057 Score=46.21 Aligned_cols=27 Identities=26% Similarity=0.803 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCc-ccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECG-LVL 33 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG-~Vl 33 (181)
...||.||. ++ |- .+|+++|..|| .+.
T Consensus 28 ~~hCp~Cg~--PL-F~-KdG~v~CPvC~~~~~ 55 (131)
T COG1645 28 AKHCPKCGT--PL-FR-KDGEVFCPVCGYREV 55 (131)
T ss_pred HhhCcccCC--cc-ee-eCCeEECCCCCceEE
Confidence 457999997 34 33 89999999999 443
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=95.59 E-value=0.01 Score=34.69 Aligned_cols=30 Identities=20% Similarity=0.533 Sum_probs=19.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
..||+||+ --+......+...|..||++.+
T Consensus 2 ~FCp~C~n-lL~p~~~~~~~~~C~~C~Y~~~ 31 (35)
T PF02150_consen 2 RFCPECGN-LLYPKEDKEKRVACRTCGYEEP 31 (35)
T ss_dssp -BETTTTS-BEEEEEETTTTEEESSSS-EEE
T ss_pred eeCCCCCc-cceEcCCCccCcCCCCCCCccC
Confidence 57999997 3333333455557999999864
No 30
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=95.50 E-value=0.011 Score=33.41 Aligned_cols=27 Identities=30% Similarity=0.485 Sum_probs=14.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
-+||.|++ .....| ...+||.+||.-.
T Consensus 3 p~Cp~C~s-e~~y~D--~~~~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGS-EYTYED--GELLVCPECGHEW 29 (30)
T ss_dssp ---TTT------EE---SSSEEETTTTEEE
T ss_pred CCCCCCCC-cceecc--CCEEeCCcccccC
Confidence 47999998 444444 7889999999643
No 31
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=95.40 E-value=0.032 Score=48.35 Aligned_cols=55 Identities=13% Similarity=-0.055 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHHHhCCchHHHHH--HHHHHHHhh--h---CHHHHHHHHHHHHHHhCCCCcc
Q 030241 106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTSHALL 160 (181)
Q Consensus 106 ~~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~--l---~~~~v~AAclYiACR~~~~p~t 160 (181)
.++.+-|.+++.+|++|..-+.+ .+|....-. | ....+++||||+|++.++.|+.
T Consensus 40 ~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~k 101 (323)
T KOG0834|consen 40 QEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRK 101 (323)
T ss_pred HHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCccc
Confidence 66999999999999999876666 677665443 4 5678999999999999999964
No 32
>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=95.35 E-value=0.055 Score=39.30 Aligned_cols=53 Identities=15% Similarity=0.151 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHHHHhCCchHHHHH--HHHHHHHhh--h---CHHHHHHHHHHHHHHhCCC
Q 030241 105 LILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTSH 157 (181)
Q Consensus 105 l~~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~--l---~~~~v~AAclYiACR~~~~ 157 (181)
-....+.|.+++..++++..+.-. .++...... + +...+++||+++||+.+..
T Consensus 31 r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~ 90 (127)
T PF00134_consen 31 RQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEED 90 (127)
T ss_dssp HHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhcc
Confidence 356888999999999999998777 677776555 3 7889999999999999876
No 33
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=95.23 E-value=0.013 Score=36.99 Aligned_cols=27 Identities=26% Similarity=0.695 Sum_probs=21.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
..||.||+ . +..++. +...|..||+..
T Consensus 21 ~fCP~Cg~-~-~m~~~~-~r~~C~~Cgyt~ 47 (50)
T PRK00432 21 KFCPRCGS-G-FMAEHL-DRWHCGKCGYTE 47 (50)
T ss_pred CcCcCCCc-c-hheccC-CcEECCCcCCEE
Confidence 57999997 5 555544 899999999864
No 34
>PRK11827 hypothetical protein; Provisional
Probab=95.11 E-value=0.017 Score=37.89 Aligned_cols=28 Identities=14% Similarity=0.494 Sum_probs=24.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
..||.|+. .+..|....+++|..||++.
T Consensus 9 LaCP~ckg--~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 9 IACPVCNG--KLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred eECCCCCC--cCeEcCCCCeEECCccCeec
Confidence 56999986 57888888899999999986
No 35
>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=94.86 E-value=0.025 Score=33.56 Aligned_cols=29 Identities=31% Similarity=0.720 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCceeEeC--CCCceEeCCCcc
Q 030241 3 DAFCSDCKKHTEVVFDH--SAGDTVCSECGL 31 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~--~~G~~vC~~CG~ 31 (181)
..-||.||+....-+|. .+|..+|..||.
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 35699999854455555 559999999984
No 36
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=94.68 E-value=0.03 Score=39.36 Aligned_cols=29 Identities=28% Similarity=0.568 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
...||.||+ + .+.-..+|-..|..||.++
T Consensus 35 ~~~Cp~C~~-~-~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 35 KHVCPFCGR-T-TVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CCcCCCCCC-c-ceeeeccCeEEcCCCCCee
Confidence 356999998 4 6788899999999999986
No 37
>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=94.57 E-value=0.019 Score=31.43 Aligned_cols=24 Identities=29% Similarity=0.833 Sum_probs=18.5
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.||+|+.. | ......|..||+++.
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 346789999999863
No 38
>PRK10220 hypothetical protein; Provisional
Probab=94.43 E-value=0.098 Score=38.26 Aligned_cols=30 Identities=27% Similarity=0.569 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
|+.-.||.|++ .....| ...+||.+||.--
T Consensus 1 m~lP~CP~C~s-eytY~d--~~~~vCpeC~hEW 30 (111)
T PRK10220 1 MSLPHCPKCNS-EYTYED--NGMYICPECAHEW 30 (111)
T ss_pred CCCCcCCCCCC-cceEcC--CCeEECCcccCcC
Confidence 67778999998 344344 5679999999743
No 39
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=94.40 E-value=0.041 Score=35.60 Aligned_cols=27 Identities=26% Similarity=0.709 Sum_probs=20.0
Q ss_pred CCCCCCCCCCceeEeCCCCc-------eEeCCCcc
Q 030241 4 AFCSDCKKHTEVVFDHSAGD-------TVCSECGL 31 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~-------~vC~~CG~ 31 (181)
.-||.||+ ..+.++...+. +.|.+||.
T Consensus 4 kPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence 46999997 56666665542 56999999
No 40
>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=94.39 E-value=0.025 Score=41.44 Aligned_cols=31 Identities=23% Similarity=0.664 Sum_probs=25.9
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccccC
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (181)
++.||.||.. .+|-..--+||..||.++.-.
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 4789999973 588888889999999998644
No 41
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=94.33 E-value=0.096 Score=43.36 Aligned_cols=53 Identities=8% Similarity=0.048 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHHhCCchHHHHH--HHHHHHHhh--h---CHHHHHHHHHHHHHHhCCCCc
Q 030241 107 LAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTSHAL 159 (181)
Q Consensus 107 ~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~--l---~~~~v~AAclYiACR~~~~p~ 159 (181)
-..+.|..++..|+|.+.|+-+ -+||...-+ + ....+++-|||+||+.+..|+
T Consensus 43 ~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i 102 (264)
T KOG0794|consen 43 FMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPI 102 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcch
Confidence 3567899999999999999888 566665433 3 899999999999999999983
No 42
>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=94.29 E-value=0.044 Score=33.25 Aligned_cols=26 Identities=31% Similarity=0.827 Sum_probs=20.2
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCc
Q 030241 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECG 30 (181)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG 30 (181)
-...||.||. ++.. ..+|.++|..|+
T Consensus 16 L~~~Cp~C~~--PL~~-~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 16 LDEHCPDCGT--PLMR-DKDGKIYCVSCG 41 (41)
T ss_pred hcCccCCCCC--eeEE-ecCCCEECCCCC
Confidence 3467999985 4545 578999999996
No 43
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=94.23 E-value=0.037 Score=34.56 Aligned_cols=28 Identities=25% Similarity=0.670 Sum_probs=19.3
Q ss_pred CCCCCCCCCceeEeCC-C-CceEeCCCccccc
Q 030241 5 FCSDCKKHTEVVFDHS-A-GDTVCSECGLVLE 34 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~-~-G~~vC~~CG~Vl~ 34 (181)
.||+||+ -+..... . ...+|..||.+..
T Consensus 2 FCp~Cg~--~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGN--MLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCC--ccccccCCCCCEEECCcCCCeEE
Confidence 6999997 2333322 2 3799999998754
No 44
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=94.23 E-value=0.021 Score=33.59 Aligned_cols=29 Identities=28% Similarity=0.653 Sum_probs=20.7
Q ss_pred CCCCCCCCCCceeEeC-----CCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDH-----SAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~-----~~G~~vC~~CG~Vl~ 34 (181)
..||+|+.. ..++. ..+.+.|..||.++.
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 33332 345799999999874
No 45
>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=94.14 E-value=0.053 Score=36.16 Aligned_cols=17 Identities=29% Similarity=0.788 Sum_probs=15.6
Q ss_pred EeCCCCceEeCCCcccc
Q 030241 17 FDHSAGDTVCSECGLVL 33 (181)
Q Consensus 17 ~D~~~G~~vC~~CG~Vl 33 (181)
++..+|.++|.+||.+.
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 46
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=94.13 E-value=0.043 Score=42.68 Aligned_cols=30 Identities=27% Similarity=0.576 Sum_probs=20.6
Q ss_pred CCCCCCCCCCceeEeCC---CCc-----eEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHS---AGD-----TVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~---~G~-----~vC~~CG~Vl 33 (181)
|+||+||++...+.|.. .|. .-|.+||.-.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 57999998433566653 453 3499999764
No 47
>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=94.05 E-value=0.065 Score=30.43 Aligned_cols=28 Identities=21% Similarity=0.498 Sum_probs=17.0
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
..+|+.||+ ..+.....-..+|.+||..
T Consensus 3 ~rfC~~CG~--~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGA--PTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT----BEEE-SSSS-EEESSSS-E
T ss_pred CcccCcCCc--cccCCCCcCEeECCCCcCE
Confidence 368999997 3455666778999999975
No 48
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=93.73 E-value=0.033 Score=35.79 Aligned_cols=30 Identities=33% Similarity=0.720 Sum_probs=20.5
Q ss_pred CCCCCCCCCCceeEeCCCCc-eEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGD-TVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~-~vC~~CG~Vl~ 34 (181)
-.||.||.. --+.|...|+ +.|.+||.-++
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 2223434455 56999999885
No 49
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=93.64 E-value=0.043 Score=34.53 Aligned_cols=27 Identities=30% Similarity=0.768 Sum_probs=23.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
..||.||. ..+..|+.+ -+.|..||+.
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 56999995 678888876 8999999986
No 50
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=93.59 E-value=0.055 Score=35.45 Aligned_cols=30 Identities=27% Similarity=0.669 Sum_probs=26.2
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
+...||.|+. .+.+|.+.++++|..||+..
T Consensus 7 eiLaCP~~kg--~L~~~~~~~~L~c~~~~~aY 36 (60)
T COG2835 7 EILACPVCKG--PLVYDEEKQELICPRCKLAY 36 (60)
T ss_pred eeeeccCcCC--cceEeccCCEEEecccCcee
Confidence 3457999996 49999999999999999986
No 51
>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=93.45 E-value=0.081 Score=40.76 Aligned_cols=30 Identities=30% Similarity=0.742 Sum_probs=23.7
Q ss_pred CCCCCCCCCCceeEeC---CCCceE-----eCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDH---SAGDTV-----CSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~---~~G~~v-----C~~CG~Vl 33 (181)
|+||.||....-|.|. +.|..| |..||.=.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence 6799999866678887 677777 99999754
No 52
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=92.83 E-value=0.099 Score=47.76 Aligned_cols=22 Identities=9% Similarity=-0.037 Sum_probs=21.0
Q ss_pred CHHHHHHHHHHHHHHhCCCCcc
Q 030241 139 KTHYWLLACTLLVDKKTSHALL 160 (181)
Q Consensus 139 ~~~~v~AAclYiACR~~~~p~t 160 (181)
++..++.||||+|||+||+++|
T Consensus 207 RPsglcGAaLliAar~h~~~rs 228 (521)
T KOG1598|consen 207 RPSGLCGAALLIAARMHGFRRT 228 (521)
T ss_pred CccchhHHHHHHHHHHcCcccc
Confidence 8899999999999999999987
No 53
>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=92.79 E-value=0.071 Score=40.07 Aligned_cols=31 Identities=13% Similarity=0.288 Sum_probs=26.2
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccccC
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (181)
++.||.||.. .+|-..--+||..||.++...
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 4789999973 588889999999999998654
No 54
>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=92.59 E-value=0.11 Score=31.25 Aligned_cols=29 Identities=28% Similarity=0.634 Sum_probs=15.9
Q ss_pred CCCCCCCCCCcee-EeC--CCCceEeCCCccc
Q 030241 4 AFCSDCKKHTEVV-FDH--SAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv-~D~--~~G~~vC~~CG~V 32 (181)
.-||.||+....- ++. .+|..+|..|+-+
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 4599999854443 443 5699999999434
No 55
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=92.50 E-value=0.35 Score=42.01 Aligned_cols=53 Identities=11% Similarity=0.061 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHhCCchHH-HHHHHHHHHHhh-----h---CHHHHHHHHHHHHHHhCCCCcc
Q 030241 108 AFKTIATMSDRIGQMRYI-RRWKIKSLVEAE-----I---KTHYWLLACTLLVDKKTSHALL 160 (181)
Q Consensus 108 a~~~I~~ia~~L~Lp~~v-~e~~i~k~a~~~-----l---~~~~v~AAclYiACR~~~~p~t 160 (181)
-.+.|-.+-..|+||++. +.+..+.-+.+. + +.+.+++||+|+|.|..++||.
T Consensus 141 Phklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp 202 (367)
T KOG0835|consen 141 PHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLP 202 (367)
T ss_pred cHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCC
Confidence 345666777788888876 333333333333 2 8999999999999999999885
No 56
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=92.35 E-value=0.31 Score=35.57 Aligned_cols=33 Identities=24% Similarity=0.697 Sum_probs=23.5
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCccccccC
Q 030241 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (181)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (181)
|....||.|.+ +.+++ +.+.++|.+|+.--.+.
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 45678999997 34444 35599999999765433
No 57
>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=92.27 E-value=0.29 Score=35.74 Aligned_cols=28 Identities=18% Similarity=0.496 Sum_probs=20.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
-.||.|++ .....| ...+||.+||.--.
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 36999998 444444 55799999997643
No 58
>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=91.87 E-value=0.11 Score=37.19 Aligned_cols=28 Identities=32% Similarity=0.739 Sum_probs=21.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (181)
..||+||+ .+ .+..+.++|..||.+.+.
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 36999997 23 455789999999998654
No 59
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=91.85 E-value=0.13 Score=32.63 Aligned_cols=31 Identities=23% Similarity=0.283 Sum_probs=20.0
Q ss_pred CCCCCCCCCCceeE---eC--CCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVF---DH--SAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~---D~--~~G~~vC~~CG~Vl~ 34 (181)
.-||.||+....+. |. ..|...|..||....
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~ 37 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP 37 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence 35999998433132 32 344557999999864
No 60
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=91.67 E-value=0.089 Score=36.25 Aligned_cols=29 Identities=34% Similarity=0.751 Sum_probs=26.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
.+||.|-. ...++.+++..++|.+|+.|+
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 67999986 678999999999999999997
No 61
>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=91.06 E-value=0.031 Score=32.92 Aligned_cols=30 Identities=27% Similarity=0.688 Sum_probs=22.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
..||.||..-++.+++..-+.+|..||.-|
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCCee
Confidence 369999985577788888889999999754
No 62
>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=90.69 E-value=0.16 Score=29.94 Aligned_cols=30 Identities=33% Similarity=0.545 Sum_probs=19.5
Q ss_pred CCCCCCCCCCceeEeCC-CCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHS-AGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~-~G~~vC~~CG~Vl 33 (181)
-+|++||..-++..... .....|.+||.-+
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 46999997323333332 5567899999843
No 63
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=90.68 E-value=0.099 Score=30.79 Aligned_cols=30 Identities=27% Similarity=0.635 Sum_probs=20.6
Q ss_pred CCCCCCCCCCceeEe---CCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFD---HSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D---~~~G~~vC~~CG~Vl 33 (181)
..||+|+..-.+-.| ...+.+-|..||.+.
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 469999973222111 247789999999885
No 64
>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=90.58 E-value=0.63 Score=39.97 Aligned_cols=41 Identities=7% Similarity=0.011 Sum_probs=35.0
Q ss_pred CCchHHHHH--HHHHHHH-hh-h---CHHHHHHHHHHHHHHhCCCCcc
Q 030241 120 GQMRYIRRW--KIKSLVE-AE-I---KTHYWLLACTLLVDKKTSHALL 160 (181)
Q Consensus 120 ~Lp~~v~e~--~i~k~a~-~~-l---~~~~v~AAclYiACR~~~~p~t 160 (181)
+||.+|+-+ .+||.+. +. . ....+.++|+|+||+.+..-++
T Consensus 73 ~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~IS 120 (325)
T KOG2496|consen 73 NLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYIS 120 (325)
T ss_pred CCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheec
Confidence 789999999 8999873 43 3 8999999999999999877766
No 65
>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=90.48 E-value=0.35 Score=29.64 Aligned_cols=28 Identities=21% Similarity=0.453 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (181)
...||.||+ .....-...+..-|.+|+.
T Consensus 18 g~~CP~Cg~-~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGS-TKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCC-eeeEEeCCCCeEECCCCCC
Confidence 356999998 4544444569999999974
No 66
>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=90.31 E-value=0.2 Score=33.13 Aligned_cols=29 Identities=21% Similarity=0.576 Sum_probs=21.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
+.||.||.. . ..+.......|..||...+
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 579999973 2 2245677889999999864
No 67
>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=90.19 E-value=0.18 Score=35.77 Aligned_cols=29 Identities=31% Similarity=0.524 Sum_probs=24.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
..||.||. +. +.-...|-.-|..||.++.
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 56999997 44 6778999999999999874
No 68
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=90.10 E-value=0.23 Score=36.64 Aligned_cols=34 Identities=29% Similarity=0.579 Sum_probs=24.0
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccccC
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (181)
+..||.||+---.-.|...+.++|..||...+-+
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 5789999972111123367799999999987654
No 69
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.02 E-value=0.2 Score=32.73 Aligned_cols=26 Identities=31% Similarity=0.754 Sum_probs=12.3
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
.|..||. .|..+..--.-.|.+||.+
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 2223333333456666643
No 70
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=89.76 E-value=0.38 Score=41.15 Aligned_cols=43 Identities=23% Similarity=0.454 Sum_probs=28.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc-------cCCccccccccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE-------SHSIDETSEWRTFA 48 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~-------e~~id~~~Ewr~F~ 48 (181)
.+||+|+. .-...|-.....||..||.-.. +.++|.++ |+.+.
T Consensus 28 ~~c~~c~~-~~~~~~l~~~~~vc~~c~~h~rl~areRi~~L~D~gs-F~E~~ 77 (292)
T PRK05654 28 TKCPSCGQ-VLYRKELEANLNVCPKCGHHMRISARERLDLLLDEGS-FVELD 77 (292)
T ss_pred eECCCccc-hhhHHHHHhcCCCCCCCCCCeeCCHHHHHHHHccCCc-cEEec
Confidence 57999997 3333444666789999998765 23466653 44443
No 71
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=89.64 E-value=0.27 Score=30.16 Aligned_cols=27 Identities=30% Similarity=0.720 Sum_probs=19.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
.+|.+||. ++..+ ..+.+-|.+||.=+
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 47999997 33333 56889999999643
No 72
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=89.47 E-value=0.32 Score=29.11 Aligned_cols=27 Identities=30% Similarity=0.568 Sum_probs=19.1
Q ss_pred CCCCCCCCCceeEe---------CCCCceEeCCCccc
Q 030241 5 FCSDCKKHTEVVFD---------HSAGDTVCSECGLV 32 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D---------~~~G~~vC~~CG~V 32 (181)
.||.||. .+.++- +.+-..+|.+||..
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 555542 23447899999964
No 73
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=89.36 E-value=0.31 Score=36.01 Aligned_cols=26 Identities=31% Similarity=0.617 Sum_probs=20.3
Q ss_pred CCCCCCCCceeEeCCCCceEeCCCccccccCC
Q 030241 6 CSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (181)
Q Consensus 6 Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~ 37 (181)
||.||+ .-.|+ .+-|.+||+.++-+.
T Consensus 1 CPvCg~-~l~vt-----~l~C~~C~t~i~G~F 26 (113)
T PF09862_consen 1 CPVCGG-ELVVT-----RLKCPSCGTEIEGEF 26 (113)
T ss_pred CCCCCC-ceEEE-----EEEcCCCCCEEEeee
Confidence 999997 44444 599999999997543
No 74
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=89.21 E-value=1.5 Score=38.23 Aligned_cols=59 Identities=14% Similarity=0.064 Sum_probs=48.2
Q ss_pred hHHHHHHHHHHHHHHHHhCCchHHHHH--HHHHHH-Hhh-h---CHHHHHHHHHHHHHHhCCCCcc
Q 030241 102 DRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLV-EAE-I---KTHYWLLACTLLVDKKTSHALL 160 (181)
Q Consensus 102 er~l~~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a-~~~-l---~~~~v~AAclYiACR~~~~p~t 160 (181)
+--..-+-..|++-+=.|+||+...-+ -+|... ..+ | ..++++.|||.+|.+.+..|.+
T Consensus 20 ~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr 85 (367)
T KOG0835|consen 20 EELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRR 85 (367)
T ss_pred HHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhcccccc
Confidence 334456889999999999999998777 555554 555 5 8999999999999999999865
No 75
>PRK05978 hypothetical protein; Provisional
Probab=89.18 E-value=0.32 Score=37.63 Aligned_cols=35 Identities=20% Similarity=0.442 Sum_probs=23.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccCCcc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id 39 (181)
.+||.||. ..+..-+-.=..-|..||.-++-..-|
T Consensus 34 grCP~CG~-G~LF~g~Lkv~~~C~~CG~~~~~~~a~ 68 (148)
T PRK05978 34 GRCPACGE-GKLFRAFLKPVDHCAACGEDFTHHRAD 68 (148)
T ss_pred CcCCCCCC-CcccccccccCCCccccCCccccCCcc
Confidence 57999997 665333333446799999988644333
No 76
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=89.16 E-value=0.27 Score=38.04 Aligned_cols=30 Identities=30% Similarity=0.644 Sum_probs=21.6
Q ss_pred CCCCCCCCCCceeEeC---CCCce-----EeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDH---SAGDT-----VCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~---~~G~~-----vC~~CG~Vl 33 (181)
|+||.|+....=|.|+ +.|.. .|.+||.=.
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RF 38 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERF 38 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhccccccccc
Confidence 6799999865667776 45544 488888654
No 77
>PRK12495 hypothetical protein; Provisional
Probab=89.13 E-value=0.26 Score=40.37 Aligned_cols=32 Identities=28% Similarity=0.778 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCccccccC
Q 030241 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (181)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (181)
|....|+.||.+ | + ...|.++|..|+.++.+.
T Consensus 40 msa~hC~~CG~P--I-p-a~pG~~~Cp~CQ~~~~~~ 71 (226)
T PRK12495 40 MTNAHCDECGDP--I-F-RHDGQEFCPTCQQPVTED 71 (226)
T ss_pred cchhhcccccCc--c-c-CCCCeeECCCCCCccccc
Confidence 556789999973 3 3 458999999999998753
No 78
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=89.09 E-value=0.3 Score=34.65 Aligned_cols=30 Identities=27% Similarity=0.516 Sum_probs=24.7
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
...||.||. +. +.-...|-..|..||.++.
T Consensus 36 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 36 KYFCPFCGK-HA-VKRQAVGIWRCKGCKKTVA 65 (90)
T ss_pred CccCCCCCC-Cc-eeeeeeEEEEcCCCCCEEe
Confidence 467999997 44 5667889999999999974
No 79
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=88.97 E-value=0.26 Score=35.57 Aligned_cols=29 Identities=34% Similarity=0.865 Sum_probs=22.3
Q ss_pred CCCCCCCCCcee---EeC--CCCceEeCCCccccc
Q 030241 5 FCSDCKKHTEVV---FDH--SAGDTVCSECGLVLE 34 (181)
Q Consensus 5 ~Cp~Cg~~~~iv---~D~--~~G~~vC~~CG~Vl~ 34 (181)
.||.||. -.++ +|- .-|.++|..||+=.+
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 5999996 4555 443 678999999998765
No 80
>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=88.15 E-value=0.29 Score=28.00 Aligned_cols=25 Identities=28% Similarity=0.660 Sum_probs=16.8
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
.|.+||.. +.+.....+-|.+||.=
T Consensus 2 ~C~~Cg~~---~~~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAE---VELKPGDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSS---E-BSTSSTSSBSSSS-S
T ss_pred CCCcCCCe---eEcCCCCcEECCcCCCe
Confidence 58899972 23455667889999963
No 81
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=88.14 E-value=0.28 Score=35.38 Aligned_cols=42 Identities=24% Similarity=0.480 Sum_probs=28.2
Q ss_pred CCCCCCCCCCc--eeEeCCCCceEeCCCccccccC------Cccccccccc
Q 030241 4 AFCSDCKKHTE--VVFDHSAGDTVCSECGLVLESH------SIDETSEWRT 46 (181)
Q Consensus 4 ~~Cp~Cg~~~~--iv~D~~~G~~vC~~CG~Vl~e~------~id~~~Ewr~ 46 (181)
..||+||. .. +-.|...+..+|..||+--+-. .||--.+|..
T Consensus 22 f~CP~Cge-~~v~v~~~k~~~h~~C~~CG~y~~~~V~~l~epIDVY~~wiD 71 (99)
T PRK14892 22 FECPRCGK-VSISVKIKKNIAIITCGNCGLYTEFEVPSVYDEVDVYNKFID 71 (99)
T ss_pred eECCCCCC-eEeeeecCCCcceEECCCCCCccCEECCccccchhhHHHHHH
Confidence 35999995 32 3345678899999999986532 2444456643
No 82
>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=87.97 E-value=0.54 Score=26.00 Aligned_cols=22 Identities=23% Similarity=0.540 Sum_probs=12.2
Q ss_pred CCCCCCCCCceeEeCCCCceEeCC
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSE 28 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~ 28 (181)
.||.||+ .++.+..+-.+.|.+
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 4999997 577776777788875
No 83
>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=87.57 E-value=0.38 Score=34.15 Aligned_cols=30 Identities=30% Similarity=0.552 Sum_probs=24.9
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
...||.||. +. +.-...|-..|..||.++.
T Consensus 35 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 35 KYVCPFCGK-KT-VKRGSTGIWTCRKCGAKFA 64 (91)
T ss_pred CccCCCCCC-Cc-eEEEeeEEEEcCCCCCEEe
Confidence 467999997 44 5677899999999999974
No 84
>PF12773 DZR: Double zinc ribbon
Probab=87.02 E-value=0.39 Score=29.65 Aligned_cols=12 Identities=33% Similarity=0.852 Sum_probs=5.6
Q ss_pred ceEeCCCccccc
Q 030241 23 DTVCSECGLVLE 34 (181)
Q Consensus 23 ~~vC~~CG~Vl~ 34 (181)
..+|..||..|.
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 444444444443
No 85
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.93 E-value=0.31 Score=36.38 Aligned_cols=39 Identities=18% Similarity=0.368 Sum_probs=25.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccCCcccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSE 43 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~E 43 (181)
-.||+||. ..+.--.-.=.-.|..||+=+...--|++|-
T Consensus 22 grCP~CGe-GrLF~gFLK~~p~C~aCG~dyg~~~a~DgPa 60 (126)
T COG5349 22 GRCPRCGE-GRLFRGFLKVVPACEACGLDYGFADADDGPA 60 (126)
T ss_pred CCCCCCCC-chhhhhhcccCchhhhccccccCCcccCCCc
Confidence 46999997 5543223444568999999876555555543
No 86
>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=86.83 E-value=0.24 Score=34.40 Aligned_cols=32 Identities=25% Similarity=0.571 Sum_probs=17.7
Q ss_pred CCCCCCCCCcee--EeC--CCCceEeCCCccccccC
Q 030241 5 FCSDCKKHTEVV--FDH--SAGDTVCSECGLVLESH 36 (181)
Q Consensus 5 ~Cp~Cg~~~~iv--~D~--~~G~~vC~~CG~Vl~e~ 36 (181)
.||.|+....+. .|. ..|.+.|..||...+-.
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 599999434433 443 57899999999987643
No 87
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=86.52 E-value=0.46 Score=33.67 Aligned_cols=30 Identities=23% Similarity=0.546 Sum_probs=24.7
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
...||.||. +. +.-...|-.-|..||.++.
T Consensus 36 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 36 KHVCPVCGR-PK-VKRVGTGIWECRKCGAKFA 65 (90)
T ss_pred CccCCCCCC-Cc-eEEEEEEEEEcCCCCCEEe
Confidence 467999997 44 5667899999999999974
No 88
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=86.36 E-value=0.73 Score=30.59 Aligned_cols=28 Identities=21% Similarity=0.398 Sum_probs=19.0
Q ss_pred CCCCCCCCCCceeEeCCCCc--eEeCCCccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGD--TVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~--~vC~~CG~V 32 (181)
.-||.||.. .+..-...|- .+|..||..
T Consensus 7 KPCPFCG~~-~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 7 KPCPFCGCP-SVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred cCCCCCCCc-eeEEEecCceEEEEcCCCCcC
Confidence 459999984 4444333443 589999985
No 89
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=86.31 E-value=0.52 Score=31.31 Aligned_cols=14 Identities=21% Similarity=0.422 Sum_probs=10.0
Q ss_pred CCCCCCCCCceeEeC
Q 030241 5 FCSDCKKHTEVVFDH 19 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~ 19 (181)
+||.||. ++.+++.
T Consensus 6 kCpKCgn-~~~~eke 19 (68)
T COG3478 6 KCPKCGN-TNYEEKE 19 (68)
T ss_pred cCCCcCC-cchhhce
Confidence 4999997 5655554
No 90
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=85.62 E-value=0.71 Score=30.15 Aligned_cols=29 Identities=28% Similarity=0.597 Sum_probs=15.3
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
...+|..||. .|..-...-.-.|.+||.+
T Consensus 6 ~~~~CtSCg~--~i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 6 EPPKCTSCGI--EIAPREKAVKFLCPNCGEV 34 (59)
T ss_pred cCccccCCCC--cccCCCccCEeeCCCCCCe
Confidence 3456777775 2321111334567777766
No 91
>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=85.34 E-value=0.61 Score=27.72 Aligned_cols=27 Identities=33% Similarity=0.616 Sum_probs=15.2
Q ss_pred CCCCCCCCCceeEeC---------CCCceEeCCCccc
Q 030241 5 FCSDCKKHTEVVFDH---------SAGDTVCSECGLV 32 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~---------~~G~~vC~~CG~V 32 (181)
.||.||. .+.++-. .+-..+|.+||..
T Consensus 2 ~Cp~Cg~-~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 2 KCPKCGH-NEAVFFQIQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp --SSS-S-SEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred CCcCCCC-CeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence 6999997 4443331 2335789999964
No 92
>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=85.11 E-value=0.83 Score=30.35 Aligned_cols=27 Identities=26% Similarity=0.714 Sum_probs=16.9
Q ss_pred CCCCCCCCCceeEeC--CCC---------------ceEeCCCccc
Q 030241 5 FCSDCKKHTEVVFDH--SAG---------------DTVCSECGLV 32 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~--~~G---------------~~vC~~CG~V 32 (181)
.||.||+ .+...+. .+| .++|++||+.
T Consensus 2 ~C~KCg~-~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 2 KCPKCGN-EEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCC-cceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence 6999997 4443332 111 2579999886
No 93
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=84.59 E-value=1 Score=30.65 Aligned_cols=31 Identities=13% Similarity=0.308 Sum_probs=21.9
Q ss_pred CCCCCCCCCCCceeEeC-------CCCceEeC--CCccccc
Q 030241 3 DAFCSDCKKHTEVVFDH-------SAGDTVCS--ECGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~-------~~G~~vC~--~CG~Vl~ 34 (181)
++.||.||. ...+.+. .+-...|+ +||....
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 5666665 22345688 8998764
No 94
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=84.04 E-value=0.27 Score=39.08 Aligned_cols=31 Identities=26% Similarity=0.558 Sum_probs=21.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (181)
-.||.|+.. -...|.-+..-.|..||.+|.+
T Consensus 118 Y~Cp~C~~r-ytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 118 FFCPNCHIR-FTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred EECCCCCcE-EeHHHHhhcCCcCCCCCCCCee
Confidence 359999862 2223345667889999999864
No 95
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=83.98 E-value=0.76 Score=29.25 Aligned_cols=28 Identities=36% Similarity=0.688 Sum_probs=20.2
Q ss_pred CCCCCCCCCceeEeCCCCce----EeCCCccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDT----VCSECGLV 32 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~----vC~~CG~V 32 (181)
.||+||....+..|...|+. =|.-|-.=
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~P 33 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRP 33 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCc
Confidence 59999987778899887752 25555543
No 96
>PRK02935 hypothetical protein; Provisional
Probab=83.64 E-value=0.85 Score=33.23 Aligned_cols=38 Identities=26% Similarity=0.575 Sum_probs=24.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccCCccccccccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFA 48 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~Ewr~F~ 48 (181)
..||+|++.+.+.= -...|..|+.-|. +|.+.|-..|+
T Consensus 71 V~CP~C~K~TKmLG----rvD~CM~C~~PLT---Ld~~legkefd 108 (110)
T PRK02935 71 VICPSCEKPTKMLG----RVDACMHCNQPLT---LDRSLEGKEFD 108 (110)
T ss_pred eECCCCCchhhhcc----ceeecCcCCCcCC---cCccccccCcC
Confidence 56999998654432 2348999999885 45444433343
No 97
>COG4640 Predicted membrane protein [Function unknown]
Probab=83.31 E-value=0.66 Score=41.25 Aligned_cols=28 Identities=29% Similarity=0.800 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccccC
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (181)
|..||.||+. . .+++.-|+.||.=+..+
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 4589999973 2 35667799999877544
No 98
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=82.11 E-value=0.54 Score=27.50 Aligned_cols=29 Identities=28% Similarity=0.650 Sum_probs=19.5
Q ss_pred CCCCCCCCCCceeEe----CCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFD----HSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D----~~~G~~vC~~CG~Vl 33 (181)
..||+|+.. --+-| .....+-|+.||.+.
T Consensus 3 i~Cp~C~~~-y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAK-YEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCE-EeCCHHHCCCCCcEEECCCCCCEe
Confidence 469999973 22222 245568899999874
No 99
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=82.04 E-value=0.51 Score=29.71 Aligned_cols=28 Identities=29% Similarity=0.669 Sum_probs=21.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
.+|-.||. .+..|.....+.|..||.=+
T Consensus 7 Y~C~~Cg~--~~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 7 YKCARCGR--EVELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEhhhcCC--eeehhhccCceeCCCCCcEE
Confidence 46999997 35557788999999999643
No 100
>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=82.03 E-value=1.5 Score=28.63 Aligned_cols=30 Identities=23% Similarity=0.562 Sum_probs=19.8
Q ss_pred CCCCCCCCCCCceeEeCCCC--ceEeCCCccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAG--DTVCSECGLV 32 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G--~~vC~~CG~V 32 (181)
.-.||.|+.-..+..=.+.| ..-|.+||+-
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred cccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 35799999743343322333 3779999987
No 101
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=81.97 E-value=0.85 Score=29.56 Aligned_cols=27 Identities=22% Similarity=0.596 Sum_probs=18.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccCC
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~ 37 (181)
..||+||+. . .--.+|.+||+--+..+
T Consensus 28 ~~C~~CG~~-~------~~H~vC~~CG~Y~gr~v 54 (57)
T PRK12286 28 VECPNCGEP-K------LPHRVCPSCGYYKGREV 54 (57)
T ss_pred eECCCCCCc-c------CCeEECCCCCcCCCEEe
Confidence 469999972 2 23589999997654443
No 102
>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=81.79 E-value=0.9 Score=28.26 Aligned_cols=28 Identities=29% Similarity=0.567 Sum_probs=16.8
Q ss_pred CCCCCCCCCCceeEe-CCCCceEeCCCcc
Q 030241 4 AFCSDCKKHTEVVFD-HSAGDTVCSECGL 31 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D-~~~G~~vC~~CG~ 31 (181)
.+|++||..-++... .+...+.|..||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 468888852232222 1245677999987
No 103
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=81.37 E-value=2.7 Score=37.54 Aligned_cols=49 Identities=14% Similarity=0.099 Sum_probs=33.0
Q ss_pred HHHHHHHHHhCCchHHHHH--HHHHH-HHhh-h---CHHHHHHHHHHHHHHhCCCC
Q 030241 110 KTIATMSDRIGQMRYIRRW--KIKSL-VEAE-I---KTHYWLLACTLLVDKKTSHA 158 (181)
Q Consensus 110 ~~I~~ia~~L~Lp~~v~e~--~i~k~-a~~~-l---~~~~v~AAclYiACR~~~~p 158 (181)
++++++...-+|-...+-+ -+|.| +.+. + +++..+.|||.+|.++++..
T Consensus 387 REMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~K 442 (497)
T KOG4164|consen 387 REMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLK 442 (497)
T ss_pred HHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhh
Confidence 3555555555554443444 56666 4666 4 88999999999999998654
No 104
>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=81.31 E-value=1.3 Score=25.28 Aligned_cols=23 Identities=30% Similarity=0.807 Sum_probs=14.6
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGL 31 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (181)
.|+.||- +.|.......|..||.
T Consensus 3 ~C~~CGy----~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGY----IYDGEEAPWVCPVCGA 25 (33)
T ss_pred ECCCCCC----EECCCcCCCcCcCCCC
Confidence 4777773 3455556667777775
No 105
>PF15616 TerY-C: TerY-C metal binding domain
Probab=81.25 E-value=0.9 Score=34.43 Aligned_cols=7 Identities=29% Similarity=0.871 Sum_probs=6.1
Q ss_pred CCCCCCC
Q 030241 5 FCSDCKK 11 (181)
Q Consensus 5 ~Cp~Cg~ 11 (181)
-||+||.
T Consensus 79 gCP~CGn 85 (131)
T PF15616_consen 79 GCPHCGN 85 (131)
T ss_pred CCCCCcC
Confidence 5999997
No 106
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=80.99 E-value=1.3 Score=28.46 Aligned_cols=27 Identities=30% Similarity=0.594 Sum_probs=19.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
..+|+.||.. + . +..--+||.+||.+.
T Consensus 5 ~~~C~~Cg~~--~-~-~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 5 GCKCPVCGKK--F-K-DGDDIVVCPECGAPY 31 (54)
T ss_pred CccChhhCCc--c-c-CCCCEEECCCCCCcc
Confidence 3679999962 2 2 234568999999986
No 107
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=80.93 E-value=0.77 Score=29.71 Aligned_cols=24 Identities=21% Similarity=0.522 Sum_probs=18.4
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
-+.+|+.||. ..+ ..+|..||...
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 3578999996 333 57999999775
No 108
>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=80.86 E-value=0.99 Score=24.98 Aligned_cols=28 Identities=18% Similarity=0.372 Sum_probs=16.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (181)
.+||.|+....-+....++..+|..|=-
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 5799999743334445777889988843
No 109
>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=80.79 E-value=1.4 Score=31.93 Aligned_cols=31 Identities=23% Similarity=0.513 Sum_probs=19.4
Q ss_pred CCCCCCCCCCCceeEe------C--CC-Cc-eEeCCCccccc
Q 030241 3 DAFCSDCKKHTEVVFD------H--SA-GD-TVCSECGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D------~--~~-G~-~vC~~CG~Vl~ 34 (181)
+.+||.||.+ ....+ . .. .. .+|+.|+.=++
T Consensus 2 p~~CpYCg~~-~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG 42 (102)
T PF11672_consen 2 PIICPYCGGP-AELVDGSEIYGHRYDDGPYLYVCTPCDAYVG 42 (102)
T ss_pred CcccCCCCCe-eEEcccchhcCccCCCCceeEECCCCCceee
Confidence 5789999983 44444 1 11 22 68888877664
No 110
>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=80.55 E-value=0.51 Score=34.74 Aligned_cols=39 Identities=26% Similarity=0.516 Sum_probs=24.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccCCcccccccccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFAN 49 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~Ewr~F~~ 49 (181)
..||+|+..+.+.=. ...|..|+.-+. +|.+.|-..|++
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 569999985433221 248999999885 555555444543
No 111
>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=80.29 E-value=0.94 Score=42.06 Aligned_cols=43 Identities=21% Similarity=0.596 Sum_probs=29.5
Q ss_pred CCCCCCCCCCcee-----E----eCCCCceEeCCCccccccCC---ccccccccc
Q 030241 4 AFCSDCKKHTEVV-----F----DHSAGDTVCSECGLVLESHS---IDETSEWRT 46 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv-----~----D~~~G~~vC~~CG~Vl~e~~---id~~~Ewr~ 46 (181)
..||+||....+. . ++.+--++|..||..++|+. ....-+|+.
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 4699999743332 2 24567899999999999853 233457775
No 112
>PRK08402 replication factor A; Reviewed
Probab=80.20 E-value=1.4 Score=38.79 Aligned_cols=27 Identities=30% Similarity=0.767 Sum_probs=22.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
..||.|++ .++.|...|...|.+||.|
T Consensus 213 ~aCp~CnK--kv~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 213 DACPECRR--KVDYDPATDTWICPEHGEV 239 (355)
T ss_pred ecCCCCCe--EEEEecCCCCEeCCCCCCc
Confidence 46999986 3555888899999999975
No 113
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=79.87 E-value=0.71 Score=34.28 Aligned_cols=17 Identities=41% Similarity=0.747 Sum_probs=14.9
Q ss_pred EeCCCCceEeCCCcccc
Q 030241 17 FDHSAGDTVCSECGLVL 33 (181)
Q Consensus 17 ~D~~~G~~vC~~CG~Vl 33 (181)
+|-.+|+++|.+||.|.
T Consensus 92 ~~v~EG~l~CpetG~vf 108 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVF 108 (124)
T ss_pred hhhccceEecCCCCcEe
Confidence 45678999999999997
No 114
>PF14122 YokU: YokU-like protein
Probab=79.76 E-value=1.2 Score=31.32 Aligned_cols=23 Identities=26% Similarity=0.654 Sum_probs=17.7
Q ss_pred CCceEeCCCccccccCCcccccc
Q 030241 21 AGDTVCSECGLVLESHSIDETSE 43 (181)
Q Consensus 21 ~G~~vC~~CG~Vl~e~~id~~~E 43 (181)
+=.++|.+||.|.-+..+..+-|
T Consensus 33 tP~i~C~~CgmvYq~d~vi~EIE 55 (87)
T PF14122_consen 33 TPAIICSNCGMVYQDDEVIKEIE 55 (87)
T ss_pred CceeeecCCCcEEehhHHHHHHh
Confidence 34489999999998777766555
No 115
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=79.41 E-value=1.2 Score=35.95 Aligned_cols=29 Identities=28% Similarity=0.560 Sum_probs=20.9
Q ss_pred CCCCCCCCC-CceeEeCCCCceEeCCCccc
Q 030241 4 AFCSDCKKH-TEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~-~~iv~D~~~G~~vC~~CG~V 32 (181)
..||.|+++ |.++.+...=.+.|..||..
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 469999985 44655544445689999986
No 116
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=79.22 E-value=1.1 Score=29.58 Aligned_cols=32 Identities=31% Similarity=0.755 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCccccccCCccccccccc
Q 030241 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRT 46 (181)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~Ewr~ 46 (181)
|....|.+|+. ++ +. ..|..||-. +.+.+|..
T Consensus 1 M~~kAC~~C~~---i~-~~----~~CP~Cgs~------~~T~~W~G 32 (61)
T PRK08351 1 MTEKACRHCHY---IT-TE----DRCPVCGSR------DLSDEWFD 32 (61)
T ss_pred CchhhhhhCCc---cc-CC----CcCCCCcCC------cccccccc
Confidence 66678999986 22 32 269999973 24456643
No 117
>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=78.35 E-value=1.1 Score=28.74 Aligned_cols=29 Identities=24% Similarity=0.566 Sum_probs=21.4
Q ss_pred CCCCCCCCCCcee--EeCCCCceEeCCCccc
Q 030241 4 AFCSDCKKHTEVV--FDHSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv--~D~~~G~~vC~~CG~V 32 (181)
.+|++|.+++-+. .+.+.-..+|..||..
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred EECcccchhhcccccccCCceEEEcCCCCCc
Confidence 5699998754343 6667778999999863
No 118
>PHA02942 putative transposase; Provisional
Probab=77.89 E-value=1.5 Score=38.93 Aligned_cols=28 Identities=18% Similarity=0.474 Sum_probs=20.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
..||.||. .. .+.......|.+||.+.+
T Consensus 326 q~Cs~CG~-~~--~~l~~r~f~C~~CG~~~d 353 (383)
T PHA02942 326 VSCPKCGH-KM--VEIAHRYFHCPSCGYEND 353 (383)
T ss_pred ccCCCCCC-cc--CcCCCCEEECCCCCCEeC
Confidence 57999996 22 244456789999999864
No 119
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=77.60 E-value=0.45 Score=40.83 Aligned_cols=30 Identities=20% Similarity=0.470 Sum_probs=22.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.+||.|+. .-...|-.....||..||.-..
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 57999997 3334455778899999998765
No 120
>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=77.52 E-value=1.4 Score=26.48 Aligned_cols=28 Identities=32% Similarity=0.640 Sum_probs=16.9
Q ss_pred CCCCCCCCCCceeEeCC-CCceEeCCCcc
Q 030241 4 AFCSDCKKHTEVVFDHS-AGDTVCSECGL 31 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~-~G~~vC~~CG~ 31 (181)
-+|++||..-++..... .....|..||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 35888885223333222 46788888887
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=77.41 E-value=0.47 Score=40.47 Aligned_cols=30 Identities=17% Similarity=0.429 Sum_probs=22.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.+||+|+. .-...|-.....||..||.-..
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 57999997 3333345677899999998765
No 122
>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=77.26 E-value=1.6 Score=27.97 Aligned_cols=28 Identities=25% Similarity=0.653 Sum_probs=18.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccCCc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSI 38 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~i 38 (181)
..||+||. .. ..-.+|.+||+.=+..+|
T Consensus 27 ~~c~~cg~-~~------~~H~vc~~cG~y~~r~v~ 54 (56)
T PF01783_consen 27 VKCPNCGE-PK------LPHRVCPSCGYYKGRQVI 54 (56)
T ss_dssp EESSSSSS-EE------STTSBCTTTBBSSSSSSS
T ss_pred eeeccCCC-Ee------cccEeeCCCCeECCEEEe
Confidence 46999996 11 345899999966444433
No 123
>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=76.82 E-value=0.61 Score=35.61 Aligned_cols=30 Identities=33% Similarity=0.586 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcccccc
Q 030241 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (181)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (181)
|....||.||+ - |.. +|..+|.+|....++
T Consensus 1 m~l~nC~~Cgk--l--F~~-~~~~iCp~C~~~~e~ 30 (137)
T TIGR03826 1 MELANCPKCGR--L--FVK-TGRDVCPSCYEEEER 30 (137)
T ss_pred CCCccccccch--h--hhh-cCCccCHHHhHHHHH
Confidence 77889999997 2 333 488999999988654
No 124
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=76.14 E-value=2 Score=35.98 Aligned_cols=29 Identities=17% Similarity=0.450 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
..+||.||+. +......-...|..||.+.
T Consensus 99 ~~fC~~CG~~--~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 99 HRFCGYCGHP--MHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred CccccccCCC--CeecCCceeEECCCCCCEE
Confidence 4689999984 3344455668899999764
No 125
>COG1773 Rubredoxin [Energy production and conversion]
Probab=76.12 E-value=2.1 Score=27.62 Aligned_cols=26 Identities=35% Similarity=0.588 Sum_probs=13.0
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCc
Q 030241 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECG 30 (181)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG 30 (181)
|...+|..||= |+|++.|+-.|.-|+
T Consensus 1 m~~~~C~~CG~----vYd~e~Gdp~~gi~p 26 (55)
T COG1773 1 MKRWRCSVCGY----VYDPEKGDPRCGIAP 26 (55)
T ss_pred CCceEecCCce----EeccccCCccCCCCC
Confidence 33445555552 455555555554443
No 126
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=76.04 E-value=1.7 Score=26.68 Aligned_cols=25 Identities=24% Similarity=0.660 Sum_probs=17.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeC--CCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCS--ECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~--~CG~Vl~ 34 (181)
.+||.||. . +-.+| +.|. +|+.|+.
T Consensus 12 rkCp~CGt-~----NG~R~-~~CKN~~C~~~~~ 38 (44)
T PF14952_consen 12 RKCPKCGT-Y----NGTRG-LSCKNKSCPQVFN 38 (44)
T ss_pred ccCCcCcC-c----cCccc-ccccCCccchhhh
Confidence 57999996 2 33444 7787 4998874
No 127
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=75.84 E-value=0.53 Score=30.71 Aligned_cols=26 Identities=38% Similarity=0.888 Sum_probs=19.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCC-Cccccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSE-CGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~-CG~Vl~ 34 (181)
...|+.||. .|- .++.+|++ ||.+++
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 467999996 342 46889985 998874
No 128
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=75.51 E-value=3.9 Score=33.73 Aligned_cols=49 Identities=14% Similarity=0.158 Sum_probs=32.1
Q ss_pred HHHHHHHHhCCchHHHHH-HHHHHHHhh----------hCHHHHHHHHHHHHHHhCCCCc
Q 030241 111 TIATMSDRIGQMRYIRRW-KIKSLVEAE----------IKTHYWLLACTLLVDKKTSHAL 159 (181)
Q Consensus 111 ~I~~ia~~L~Lp~~v~e~-~i~k~a~~~----------l~~~~v~AAclYiACR~~~~p~ 159 (181)
.|+++|=++|+.+-+.-. ++.+...++ |++-.+.+|++|.|||..+..+
T Consensus 95 ~VrdlaVQfgc~evi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKV 154 (262)
T KOG4557|consen 95 NVRDLAVQFGCVEVIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLKV 154 (262)
T ss_pred CHHHHHHHHhHHHHHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhh
Confidence 456666667666655444 333333322 2788999999999999886543
No 129
>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=75.46 E-value=1.5 Score=35.58 Aligned_cols=34 Identities=26% Similarity=0.537 Sum_probs=23.4
Q ss_pred CCCCCCCCCC-ceeEeCCCC---ceEeCCCccccccCC
Q 030241 4 AFCSDCKKHT-EVVFDHSAG---DTVCSECGLVLESHS 37 (181)
Q Consensus 4 ~~Cp~Cg~~~-~iv~D~~~G---~~vC~~CG~Vl~e~~ 37 (181)
++|-+||.+. .+..++..| -..|.+||.|.|+-+
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 5799999742 234555544 378999999986443
No 130
>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=75.31 E-value=2.6 Score=31.82 Aligned_cols=27 Identities=30% Similarity=0.740 Sum_probs=19.3
Q ss_pred CCC--CCCCCCceeEeCCCCceEeCCCccccc
Q 030241 5 FCS--DCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 5 ~Cp--~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.|| .|++ .+..+ .+|...|..||..++
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 779999999998863
No 131
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.21 E-value=2.8 Score=30.68 Aligned_cols=28 Identities=21% Similarity=0.535 Sum_probs=22.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccCC
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~ 37 (181)
.+||.||. ..||+ ++-|..||.-+..+.
T Consensus 7 ~~cPvcg~-~~iVT-----eL~c~~~etTVrg~F 34 (122)
T COG3877 7 NRCPVCGR-KLIVT-----ELKCSNCETTVRGNF 34 (122)
T ss_pred CCCCcccc-cceeE-----EEecCCCCceEecce
Confidence 57999997 57777 599999999986543
No 132
>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=75.05 E-value=1.9 Score=27.67 Aligned_cols=26 Identities=23% Similarity=0.705 Sum_probs=16.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccC
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (181)
..||+||.. . .---||..||+--+..
T Consensus 27 ~~C~~cG~~-~------~~H~vc~~cG~Y~gr~ 52 (55)
T TIGR01031 27 VVCPNCGEF-K------LPHRVCPSCGYYKGRQ 52 (55)
T ss_pred eECCCCCCc-c------cCeeECCccCeECCEE
Confidence 458888862 2 2347899999654433
No 133
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=74.71 E-value=3.1 Score=26.25 Aligned_cols=32 Identities=28% Similarity=0.697 Sum_probs=20.2
Q ss_pred CCCCCCCCCCCcee-EeCCCCc-eEeCCCccccc
Q 030241 3 DAFCSDCKKHTEVV-FDHSAGD-TVCSECGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv-~D~~~G~-~vC~~CG~Vl~ 34 (181)
...|.+|+.....+ -+...|. ++|..||+-..
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~ 36 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYK 36 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHH
Confidence 45788888632222 2335565 88888888754
No 134
>PRK12366 replication factor A; Reviewed
Probab=74.52 E-value=2.1 Score=40.48 Aligned_cols=25 Identities=36% Similarity=0.927 Sum_probs=19.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
..||.|++ .+ .+ ..|...|..||.+
T Consensus 533 ~aCp~Cnk--Kv-~~-~~g~~~C~~c~~~ 557 (637)
T PRK12366 533 YLCPNCRK--RV-EE-VDGEYICEFCGEV 557 (637)
T ss_pred ecccccCe--Ee-Ec-CCCcEECCCCCCC
Confidence 46999986 23 33 5799999999988
No 135
>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=74.21 E-value=3.6 Score=27.84 Aligned_cols=31 Identities=23% Similarity=0.603 Sum_probs=21.4
Q ss_pred CCCCCCCCCCCcee--EeCCCCceEeCCCcccc
Q 030241 3 DAFCSDCKKHTEVV--FDHSAGDTVCSECGLVL 33 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv--~D~~~G~~vC~~CG~Vl 33 (181)
+-.||.|++-..|. .+...-..-|.+||+.-
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e 40 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENGVEYVECVECGYTE 40 (71)
T ss_pred CccCCCCcCccEEEEEEeCCceEEEecCCCCee
Confidence 45799999843333 34445566799999984
No 136
>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=74.09 E-value=2 Score=25.27 Aligned_cols=22 Identities=27% Similarity=0.578 Sum_probs=11.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEe
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVC 26 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC 26 (181)
.+|..||. ---+.+...|.++|
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 46888986 34456667788888
No 137
>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=73.69 E-value=1.8 Score=26.92 Aligned_cols=16 Identities=31% Similarity=0.665 Sum_probs=10.5
Q ss_pred eEeCCCccccccCCcc
Q 030241 24 TVCSECGLVLESHSID 39 (181)
Q Consensus 24 ~vC~~CG~Vl~e~~id 39 (181)
..|..||.|.++..=|
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 4677777777665533
No 138
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=73.33 E-value=1.5 Score=34.45 Aligned_cols=29 Identities=21% Similarity=0.447 Sum_probs=18.7
Q ss_pred CCCCCCCCCCCceeEe---------------CCCCceEeCCCcccc
Q 030241 3 DAFCSDCKKHTEVVFD---------------HSAGDTVCSECGLVL 33 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D---------------~~~G~~vC~~CG~Vl 33 (181)
...||+|+. .++.= ..+-...|..||.+.
T Consensus 97 ~~RCp~CN~--~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 97 FSRCPECNG--ELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred cccCcccCC--EeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 368999986 22221 122356799999985
No 139
>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=73.22 E-value=2.8 Score=26.40 Aligned_cols=13 Identities=23% Similarity=0.726 Sum_probs=8.7
Q ss_pred eEeCCCccccccC
Q 030241 24 TVCSECGLVLESH 36 (181)
Q Consensus 24 ~vC~~CG~Vl~e~ 36 (181)
.+|..||+|.++.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 4677777777654
No 140
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=73.01 E-value=2.8 Score=30.20 Aligned_cols=30 Identities=23% Similarity=0.572 Sum_probs=20.1
Q ss_pred CCCCCCCCCCceeEeCCC-CceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSA-GDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~-G~~vC~~CG~Vl~ 34 (181)
..||.||+ -=+|+..+. ....|..|++|..
T Consensus 2 ~FCP~Cgn-~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 2 LFCPTCGN-MLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred cccCCCCC-EEEEecCCeEeeEEcCCCCceee
Confidence 57999997 333332222 5678999999964
No 141
>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=72.61 E-value=3 Score=32.12 Aligned_cols=27 Identities=26% Similarity=0.722 Sum_probs=20.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
..||.|++ . + .+...|...|..|+..+
T Consensus 35 ~aC~~C~k-k-v-~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 35 PACPGCNK-K-V-VEEGNGTYRCEKCNKSV 61 (166)
T ss_pred ccccccCc-c-c-EeCCCCcEECCCCCCcC
Confidence 35999997 3 3 34444999999999886
No 142
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=72.48 E-value=1.5 Score=35.31 Aligned_cols=31 Identities=32% Similarity=0.596 Sum_probs=19.6
Q ss_pred CCCCCCCCCCcee--EeCCCC---ceEeCCCcccccc
Q 030241 4 AFCSDCKKHTEVV--FDHSAG---DTVCSECGLVLES 35 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv--~D~~~G---~~vC~~CG~Vl~e 35 (181)
..||.||+ -++. .=-..| .+-|.+||+|-.+
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 46999995 3320 001234 4779999999854
No 143
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=72.48 E-value=2.3 Score=31.17 Aligned_cols=6 Identities=33% Similarity=1.160 Sum_probs=3.2
Q ss_pred EeCCCc
Q 030241 25 VCSECG 30 (181)
Q Consensus 25 vC~~CG 30 (181)
.|..||
T Consensus 88 ~CP~Cg 93 (113)
T PRK12380 88 QCPHCH 93 (113)
T ss_pred cCcCCC
Confidence 355555
No 144
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=72.30 E-value=2.2 Score=28.18 Aligned_cols=34 Identities=32% Similarity=0.793 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCccccccCCcccccccccc
Q 030241 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTF 47 (181)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~Ewr~F 47 (181)
....|.+|+. ++. ...-+|..||.- +...||+.+
T Consensus 3 ~~kAC~~Ck~---l~~---~d~e~CP~Cgs~------~~te~W~G~ 36 (64)
T COG2093 3 TEKACKNCKR---LTP---EDTEICPVCGST------DLTEEWFGL 36 (64)
T ss_pred hhHHHhhccc---cCC---CCCccCCCCCCc------ccchhhccE
Confidence 3456889986 222 345689999864 334567543
No 145
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=71.08 E-value=9.4 Score=37.24 Aligned_cols=51 Identities=8% Similarity=0.070 Sum_probs=42.6
Q ss_pred HHHHHHHHHHhCCchHHHHH--HHHHHHHhh--h--CHHHHHHHHHHHHHHhCCCCc
Q 030241 109 FKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I--KTHYWLLACTLLVDKKTSHAL 159 (181)
Q Consensus 109 ~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~--l--~~~~v~AAclYiACR~~~~p~ 159 (181)
.+.....|..|+++.....+ +.|..+.++ + +-.++.|.+||.|||..+.|-
T Consensus 35 ~q~~~~~c~~lnld~~~~~ea~d~yta~~q~~slegs~~hW~~cAlY~~~r~S~~~~ 91 (920)
T KOG1010|consen 35 EQDSDELCRPLNLDEQTETEAWDTYTAVSQRLSLEGSESHWLACALYTACRRSSVPT 91 (920)
T ss_pred hhhhhhhhhhhcccchhhhhhHHHHHHHHhHhCCCccHHHHHHHHHHHHHHhccCCc
Confidence 45677788999999876555 899999888 4 778999999999999998873
No 146
>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=70.54 E-value=2.8 Score=30.79 Aligned_cols=18 Identities=11% Similarity=0.481 Sum_probs=9.3
Q ss_pred ceeEeCCCCceEeCCCcc
Q 030241 14 EVVFDHSAGDTVCSECGL 31 (181)
Q Consensus 14 ~iv~D~~~G~~vC~~CG~ 31 (181)
.+..+...+...|.+||.
T Consensus 61 ~L~I~~~p~~~~C~~Cg~ 78 (115)
T TIGR00100 61 KLNIEDEPVECECEDCSE 78 (115)
T ss_pred EEEEEeeCcEEEcccCCC
Confidence 344444555555555553
No 147
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=70.40 E-value=2.7 Score=39.85 Aligned_cols=7 Identities=29% Similarity=1.118 Sum_probs=3.4
Q ss_pred CCCCCCC
Q 030241 5 FCSDCKK 11 (181)
Q Consensus 5 ~Cp~Cg~ 11 (181)
+||+||.
T Consensus 3 ~Cp~Cg~ 9 (645)
T PRK14559 3 ICPQCQF 9 (645)
T ss_pred cCCCCCC
Confidence 4555553
No 148
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=70.04 E-value=3.8 Score=24.32 Aligned_cols=28 Identities=21% Similarity=0.456 Sum_probs=15.6
Q ss_pred CCCCCCCCCceeEeC-CCCceEeCCCcccc
Q 030241 5 FCSDCKKHTEVVFDH-SAGDTVCSECGLVL 33 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~-~~G~~vC~~CG~Vl 33 (181)
+||.|+.. -..... .---.+|..||=+-
T Consensus 1 ~CP~C~~~-l~~~~~~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTE-LEPVRLGDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcc-cceEEECCEEEEECCCCCeEE
Confidence 59999862 111111 11224699998774
No 149
>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=70.02 E-value=1.2 Score=28.19 Aligned_cols=31 Identities=16% Similarity=0.340 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCCcee-EeCCCCceEeCCCcccc
Q 030241 2 TDAFCSDCKKHTEVV-FDHSAGDTVCSECGLVL 33 (181)
Q Consensus 2 ~~~~Cp~Cg~~~~iv-~D~~~G~~vC~~CG~Vl 33 (181)
...+|++|+.- =.. -+....++-|.-||.+-
T Consensus 3 ~eiRC~~Cnkl-La~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 3 KEIRCGHCNKL-LAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred cceeccchhHH-HhhhcCccEEEEECCCCCccc
Confidence 45789999862 111 24567899999999995
No 150
>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=70.02 E-value=3.6 Score=29.92 Aligned_cols=11 Identities=36% Similarity=0.752 Sum_probs=8.2
Q ss_pred ceEeCCCcccc
Q 030241 23 DTVCSECGLVL 33 (181)
Q Consensus 23 ~~vC~~CG~Vl 33 (181)
-.+|.+||.++
T Consensus 31 ~~~C~~CGe~~ 41 (127)
T TIGR03830 31 GWYCPACGEEL 41 (127)
T ss_pred eeECCCCCCEE
Confidence 34788898875
No 151
>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=69.60 E-value=2.6 Score=24.39 Aligned_cols=21 Identities=43% Similarity=1.054 Sum_probs=11.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECG 30 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG 30 (181)
.+|++||. +.+-+. .+|..||
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 46888886 334333 7888887
No 152
>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=68.47 E-value=4.8 Score=28.60 Aligned_cols=28 Identities=25% Similarity=0.578 Sum_probs=19.5
Q ss_pred CCCCCCCCCCceeEe---------CCCCceEeCCCccc
Q 030241 4 AFCSDCKKHTEVVFD---------HSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D---------~~~G~~vC~~CG~V 32 (181)
..||.||. ...++- +.+=..+|.+||..
T Consensus 63 ~~Cp~Cg~-~~a~f~~~Q~RsadE~~T~fy~C~~C~~~ 99 (104)
T TIGR01384 63 VECPKCGH-KEAYYWLLQTRRADEPETRFYKCTKCGYV 99 (104)
T ss_pred CCCCCCCC-CeeEEEEeccCCCCCCcEEEEEeCCCCCe
Confidence 57999997 555443 23346789999974
No 153
>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=68.00 E-value=4.2 Score=21.73 Aligned_cols=23 Identities=26% Similarity=0.787 Sum_probs=13.0
Q ss_pred CCCCCCCCceeEeCC-CCceEeCCCcc
Q 030241 6 CSDCKKHTEVVFDHS-AGDTVCSECGL 31 (181)
Q Consensus 6 Cp~Cg~~~~iv~D~~-~G~~vC~~CG~ 31 (181)
|..||. .| ...+ .-...|.+||.
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 566764 22 2222 44577888883
No 154
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=67.19 E-value=1.5 Score=37.30 Aligned_cols=30 Identities=20% Similarity=0.490 Sum_probs=22.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.+||.||. .-..-|-.+...||..||.-..
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 3333345778899999998754
No 155
>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=67.00 E-value=4.2 Score=24.96 Aligned_cols=28 Identities=18% Similarity=0.484 Sum_probs=17.1
Q ss_pred CCCCCCCCCceeEeC-------CCCceEeCC--Ccccc
Q 030241 5 FCSDCKKHTEVVFDH-------SAGDTVCSE--CGLVL 33 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~-------~~G~~vC~~--CG~Vl 33 (181)
+||+||+. ..+.-. .+-...|++ ||.-.
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 334457777 88764
No 156
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=66.97 E-value=1.8 Score=30.32 Aligned_cols=30 Identities=30% Similarity=0.488 Sum_probs=24.3
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
...|+.||. . -+-...-|-.-|..|..|+.
T Consensus 36 ky~CsfCGK-~-~vKR~AvGiW~C~~C~kv~a 65 (92)
T KOG0402|consen 36 KYTCSFCGK-K-TVKRKAVGIWKCGSCKKVVA 65 (92)
T ss_pred hhhhhhcch-h-hhhhhceeEEecCCccceec
Confidence 357999997 3 45667889999999999974
No 157
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=66.53 E-value=3.8 Score=31.01 Aligned_cols=21 Identities=24% Similarity=0.629 Sum_probs=14.4
Q ss_pred ceeEeCCCCceEeCCCccccc
Q 030241 14 EVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 14 ~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.++++...+...|.+||.+..
T Consensus 61 ~L~i~~~p~~~~C~~CG~~~~ 81 (135)
T PRK03824 61 EIIFEEEEAVLKCRNCGNEWS 81 (135)
T ss_pred EEEEEecceEEECCCCCCEEe
Confidence 455566667788888886653
No 158
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.56 E-value=3.4 Score=30.46 Aligned_cols=33 Identities=12% Similarity=0.128 Sum_probs=26.2
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccccCCc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSI 38 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~i 38 (181)
+++||+||++ .+|-.+--+||.-||.-.-.+.+
T Consensus 9 KridPetg~K---FYDLNrdPiVsPytG~s~P~s~f 41 (129)
T COG4530 9 KRIDPETGKK---FYDLNRDPIVSPYTGKSYPRSYF 41 (129)
T ss_pred cccCccccch---hhccCCCccccCcccccchHHHH
Confidence 4789999983 47888999999999987654443
No 159
>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=65.22 E-value=4.9 Score=35.87 Aligned_cols=30 Identities=27% Similarity=0.607 Sum_probs=15.4
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.||+|+.-.....-.......|..||.++.
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 477777521111111333456777777773
No 160
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=64.83 E-value=27 Score=30.11 Aligned_cols=23 Identities=13% Similarity=0.072 Sum_probs=20.6
Q ss_pred CHHHHHHHHHHHHHHhCCCCccc
Q 030241 139 KTHYWLLACTLLVDKKTSHALLR 161 (181)
Q Consensus 139 ~~~~v~AAclYiACR~~~~p~t~ 161 (181)
.+..+++||||+|+|..+.++.+
T Consensus 204 ~Ps~IAlAAI~lA~~~~~~~l~~ 226 (305)
T TIGR00569 204 TPSQIALAAILHTASRAGLNMES 226 (305)
T ss_pred CHHHHHHHHHHHHHHHhCCCCcc
Confidence 89999999999999999987653
No 161
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=64.78 E-value=1.9 Score=35.40 Aligned_cols=34 Identities=24% Similarity=0.458 Sum_probs=26.3
Q ss_pred CCCCCCCCC-CceeEeCCCC---ceEeCCCccccccCC
Q 030241 4 AFCSDCKKH-TEVVFDHSAG---DTVCSECGLVLESHS 37 (181)
Q Consensus 4 ~~Cp~Cg~~-~~iv~D~~~G---~~vC~~CG~Vl~e~~ 37 (181)
++|-+||+. ..+-.++..| -+.|.+|+.|+++-+
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 469999974 3466777888 578999999987554
No 162
>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=64.53 E-value=4.1 Score=34.06 Aligned_cols=30 Identities=20% Similarity=0.610 Sum_probs=11.4
Q ss_pred CCCCCCCCCCceeE---eCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVF---DHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~---D~~~G~~vC~~CG~Vl~ 34 (181)
++||+||+ ..+-. +..-.|-.|.+|+.-.|
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 57999998 43322 22456789999987655
No 163
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=64.17 E-value=6.3 Score=29.39 Aligned_cols=33 Identities=27% Similarity=0.616 Sum_probs=27.1
Q ss_pred eCCCCceEeCCCccccc--cCCccccccccccccC
Q 030241 18 DHSAGDTVCSECGLVLE--SHSIDETSEWRTFANE 50 (181)
Q Consensus 18 D~~~G~~vC~~CG~Vl~--e~~id~~~Ewr~F~~~ 50 (181)
..+.|.++|..||.-|= +.-.|++.-|.+|.+.
T Consensus 28 ~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~ 62 (119)
T PRK05508 28 FFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDDE 62 (119)
T ss_pred cCCCeEEEecCCCCccccccccccCCCCCcccCcc
Confidence 45899999999999874 4557889999999853
No 164
>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=64.07 E-value=1.8 Score=31.63 Aligned_cols=24 Identities=33% Similarity=0.747 Sum_probs=11.1
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
+|+.||. .++.......|+.||.-
T Consensus 72 ~C~~Cg~----~~~~~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 72 RCRDCGH----EFEPDEFDFSCPRCGSP 95 (113)
T ss_dssp EETTTS-----EEECHHCCHH-SSSSSS
T ss_pred ECCCCCC----EEecCCCCCCCcCCcCC
Confidence 4666664 12333333556666654
No 165
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=64.02 E-value=3.5 Score=37.04 Aligned_cols=32 Identities=28% Similarity=0.675 Sum_probs=23.7
Q ss_pred CCCCCCCCCCC-----ceeEeCCCCceEeCCCccccc
Q 030241 3 DAFCSDCKKHT-----EVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~-----~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
...||.|++.- .=++|..+|.-.|..||.=|.
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 35799999731 123577899999999997554
No 166
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=63.53 E-value=5.7 Score=22.52 Aligned_cols=23 Identities=26% Similarity=0.540 Sum_probs=12.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeC
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCS 27 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~ 27 (181)
.+|..||. --.+.+...|+++|-
T Consensus 8 ykC~~Cgn-iv~v~~~~~~~l~Cc 30 (34)
T TIGR00319 8 YKCEVCGN-IVEVLHAGGGQLVCC 30 (34)
T ss_pred EEcCCCCc-EEEEEECCCcceecc
Confidence 35777775 334445555666664
No 167
>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=63.52 E-value=4.4 Score=25.93 Aligned_cols=21 Identities=33% Similarity=0.722 Sum_probs=14.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeC
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCS 27 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~ 27 (181)
..||.|++ ..+++|.. .+.|+
T Consensus 15 ~~Cp~C~~-~~l~~~~~--~Y~C~ 35 (55)
T PF08063_consen 15 EPCPKCKG-GQLYFDGS--GYKCT 35 (55)
T ss_dssp ---SSSSE--EEEEETT--EEEEE
T ss_pred CCCCCCCC-CeEEecCC--ccEeC
Confidence 47999997 78888855 78887
No 168
>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=63.49 E-value=6.5 Score=22.55 Aligned_cols=8 Identities=38% Similarity=1.012 Sum_probs=4.5
Q ss_pred eEeCCCcc
Q 030241 24 TVCSECGL 31 (181)
Q Consensus 24 ~vC~~CG~ 31 (181)
.+|.-||.
T Consensus 19 ~~CP~Cg~ 26 (34)
T cd00729 19 EKCPICGA 26 (34)
T ss_pred CcCcCCCC
Confidence 45666654
No 169
>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=63.48 E-value=6.1 Score=36.23 Aligned_cols=29 Identities=21% Similarity=0.647 Sum_probs=23.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
..||+|+. .+++...++.+.|.-||....
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 577877889999999998864
No 170
>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=63.40 E-value=5.7 Score=22.57 Aligned_cols=24 Identities=25% Similarity=0.490 Sum_probs=14.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCC
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSE 28 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~ 28 (181)
.+|..||. --.+.+...|+++|-.
T Consensus 5 ykC~~CGn-iv~v~~~~~~~l~Ccg 28 (34)
T cd00974 5 YKCEICGN-IVEVLNVGGGTLVCCG 28 (34)
T ss_pred EEcCCCCc-EEEEEECCCcceeecC
Confidence 46777775 3444555666677753
No 171
>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=63.38 E-value=9.1 Score=23.83 Aligned_cols=26 Identities=23% Similarity=0.663 Sum_probs=18.6
Q ss_pred CCCC--CCCCCCceeEeCCCCceEeCCCcc
Q 030241 4 AFCS--DCKKHTEVVFDHSAGDTVCSECGL 31 (181)
Q Consensus 4 ~~Cp--~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (181)
..|| .||. ..+..++.+ -.-|..||+
T Consensus 19 k~CP~~~CG~-GvFMA~H~d-R~~CGKCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGA-GVFMAEHKD-RHYCGKCGY 46 (47)
T ss_dssp EE-TSTTTTS-SSEEEE-SS-EEEETTTSS
T ss_pred hcCCCcccCC-ceEeeecCC-CccCCCccc
Confidence 4699 9997 666777754 788999986
No 172
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=62.88 E-value=5.9 Score=27.27 Aligned_cols=26 Identities=31% Similarity=0.724 Sum_probs=19.8
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.||.|.. .++.. ..+.+.| .||+-|.
T Consensus 1 iCPVC~~-~~L~~--~~~~i~C-~Cgl~l~ 26 (82)
T PF14768_consen 1 ICPVCQK-GNLRE--NSNVISC-SCGLRLN 26 (82)
T ss_pred CCCccCC-Ccccc--cCCeEEC-CCccEEe
Confidence 5999997 67655 5788999 6776664
No 173
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=62.86 E-value=6.9 Score=33.83 Aligned_cols=10 Identities=40% Similarity=1.105 Sum_probs=5.2
Q ss_pred eEeCCCcccc
Q 030241 24 TVCSECGLVL 33 (181)
Q Consensus 24 ~vC~~CG~Vl 33 (181)
.+|.+|+.-+
T Consensus 253 e~C~~C~~Yl 262 (309)
T PRK03564 253 ESCGDCGTYL 262 (309)
T ss_pred eecccccccc
Confidence 4555555544
No 174
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=62.82 E-value=4.3 Score=38.54 Aligned_cols=24 Identities=21% Similarity=0.632 Sum_probs=15.1
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.||+||.. -..|...|.+||.-+.
T Consensus 29 ~Cp~CG~~------~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 29 PCPQCGTE------VPVDEAHCPNCGAETG 52 (645)
T ss_pred cCCCCCCC------CCcccccccccCCccc
Confidence 46666641 2356778888887654
No 175
>PRK05580 primosome assembly protein PriA; Validated
Probab=62.45 E-value=6.5 Score=37.41 Aligned_cols=29 Identities=21% Similarity=0.516 Sum_probs=23.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.+||+|+. .+++....+.+.|..||....
T Consensus 391 ~~C~~C~~--~l~~h~~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 391 AECPHCDA--SLTLHRFQRRLRCHHCGYQEP 419 (679)
T ss_pred cCCCCCCC--ceeEECCCCeEECCCCcCCCC
Confidence 46999985 578888889999999998753
No 176
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=62.07 E-value=15 Score=35.84 Aligned_cols=54 Identities=15% Similarity=0.146 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHhCCchHHHHH--HHHHHHHhh---h----CHHHHHHHHHHHHHHhCCCCcc
Q 030241 107 LAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE---I----KTHYWLLACTLLVDKKTSHALL 160 (181)
Q Consensus 107 ~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~---l----~~~~v~AAclYiACR~~~~p~t 160 (181)
-|..+|+.+|++|.|.+...+. .+|.-.... | ..+.+.-.|+|+.||..+..+|
T Consensus 679 LAavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~lt 741 (920)
T KOG1010|consen 679 LAAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLT 741 (920)
T ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccch
Confidence 4888999999999999987777 677765443 3 7899999999999999987766
No 177
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=60.91 E-value=5.3 Score=29.28 Aligned_cols=16 Identities=13% Similarity=0.569 Sum_probs=7.3
Q ss_pred eeEeCCCCceEeCCCc
Q 030241 15 VVFDHSAGDTVCSECG 30 (181)
Q Consensus 15 iv~D~~~G~~vC~~CG 30 (181)
+..+...+...|.+||
T Consensus 62 L~i~~~p~~~~C~~Cg 77 (114)
T PRK03681 62 LHLEEQEAECWCETCQ 77 (114)
T ss_pred EEEEeeCcEEEcccCC
Confidence 3344444444444444
No 178
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=60.89 E-value=8.8 Score=26.44 Aligned_cols=26 Identities=15% Similarity=0.356 Sum_probs=19.1
Q ss_pred CCCCCCCCCCceeEeCCCC--ceEeCCCccc
Q 030241 4 AFCSDCKKHTEVVFDHSAG--DTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G--~~vC~~CG~V 32 (181)
..||-||. . +++...+ .-||.-|+.-
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 47999996 3 3444444 8899999976
No 179
>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=60.81 E-value=7.6 Score=33.51 Aligned_cols=32 Identities=25% Similarity=0.605 Sum_probs=16.4
Q ss_pred CCCCCCCCCCCceeE---eC---CCCc--eEeCCCccccc
Q 030241 3 DAFCSDCKKHTEVVF---DH---SAGD--TVCSECGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~---D~---~~G~--~vC~~CG~Vl~ 34 (181)
..+||+||+...+.+ |. ..+. .+|.+|+.-+.
T Consensus 224 R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 224 RVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred CccCCCCCCCCceeeEeecCCCCCcceEEeeccccccchh
Confidence 456888876332211 21 0111 27888877663
No 180
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=60.76 E-value=3.6 Score=27.32 Aligned_cols=20 Identities=25% Similarity=0.697 Sum_probs=13.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (181)
..|.+|+. ++ + +.+|..||-
T Consensus 6 ~AC~~C~~---i~-~----~~~Cp~Cgs 25 (64)
T PRK06393 6 RACKKCKR---LT-P----EKTCPVHGD 25 (64)
T ss_pred hhHhhCCc---cc-C----CCcCCCCCC
Confidence 56889986 32 2 238999987
No 181
>PF14353 CpXC: CpXC protein
Probab=60.44 E-value=8 Score=28.48 Aligned_cols=12 Identities=25% Similarity=0.758 Sum_probs=9.6
Q ss_pred ceEeCCCccccc
Q 030241 23 DTVCSECGLVLE 34 (181)
Q Consensus 23 ~~vC~~CG~Vl~ 34 (181)
..+|..||....
T Consensus 38 ~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 38 SFTCPSCGHKFR 49 (128)
T ss_pred EEECCCCCCcee
Confidence 578999998763
No 182
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=60.23 E-value=3.6 Score=30.32 Aligned_cols=32 Identities=22% Similarity=0.487 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccccC
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (181)
...|+.||+ -+..-...+..+|..|+.+..-.
T Consensus 7 ~~FC~~CG~--ll~~~~~~~~~~C~~Ck~~~~v~ 38 (116)
T KOG2907|consen 7 LDFCSDCGS--LLEEPSAQSTVLCIRCKIEYPVS 38 (116)
T ss_pred cchhhhhhh--hcccccccCceEeccccccCCHH
Confidence 467999996 23333467777799999887533
No 183
>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=60.12 E-value=3.3 Score=26.38 Aligned_cols=29 Identities=38% Similarity=0.904 Sum_probs=14.8
Q ss_pred CCCCCCCCceeEe--CCCCceEeCCCccccc
Q 030241 6 CSDCKKHTEVVFD--HSAGDTVCSECGLVLE 34 (181)
Q Consensus 6 Cp~Cg~~~~iv~D--~~~G~~vC~~CG~Vl~ 34 (181)
|.+|+.......- +..+...|..||+-..
T Consensus 2 C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~ 32 (54)
T cd00202 2 CSNCGTTTTPLWRRGPSGGSTLCNACGLYWK 32 (54)
T ss_pred CCCCCCCCCcccccCCCCcchHHHHHHHHHH
Confidence 6666652111111 2356667777776653
No 184
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=59.80 E-value=6.1 Score=35.50 Aligned_cols=32 Identities=22% Similarity=0.608 Sum_probs=19.2
Q ss_pred CCCCCCCCCCceeEeCCCC-ceEeCCCccccccC
Q 030241 4 AFCSDCKKHTEVVFDHSAG-DTVCSECGLVLESH 36 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G-~~vC~~CG~Vl~e~ 36 (181)
..||+|+.... +.+-..| ...|..||.++..+
T Consensus 11 ~~C~~Cd~l~~-~~~l~~g~~a~CpRCg~~L~~~ 43 (419)
T PRK15103 11 ILCPQCDMLVA-LPRLEHGQKAACPRCGTTLTVR 43 (419)
T ss_pred ccCCCCCceee-cCCCCCCCeeECCCCCCCCcCC
Confidence 45999986211 1222333 46799999998533
No 185
>PRK14873 primosome assembly protein PriA; Provisional
Probab=59.37 E-value=7.2 Score=37.15 Aligned_cols=27 Identities=26% Similarity=0.615 Sum_probs=21.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
.+||+|+. .+++...++.+.|.-||..
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 56999985 5777667888999999985
No 186
>PRK07218 replication factor A; Provisional
Probab=59.17 E-value=4.2 Score=36.65 Aligned_cols=21 Identities=24% Similarity=0.689 Sum_probs=16.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
.+||+|+.. + + ..+|.+||.|
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 579999972 2 2 2699999988
No 187
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=59.11 E-value=4.7 Score=34.88 Aligned_cols=25 Identities=24% Similarity=0.380 Sum_probs=19.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCC
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSE 28 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~ 28 (181)
++|+.|+..-.|-+||.+++++|..
T Consensus 78 ~kC~~C~~~i~~kTDPkn~dY~~~~ 102 (324)
T PF04502_consen 78 IKCPRCSNEIEFKTDPKNTDYVVES 102 (324)
T ss_pred EEcCCCCCEEeeecCCCCCCeeeec
Confidence 5799998755677888888888776
No 188
>PRK04023 DNA polymerase II large subunit; Validated
Probab=59.05 E-value=7.1 Score=38.81 Aligned_cols=11 Identities=27% Similarity=0.685 Sum_probs=6.0
Q ss_pred eEeCCCccccc
Q 030241 24 TVCSECGLVLE 34 (181)
Q Consensus 24 ~vC~~CG~Vl~ 34 (181)
..|.+||..+.
T Consensus 664 y~CPKCG~El~ 674 (1121)
T PRK04023 664 DECEKCGREPT 674 (1121)
T ss_pred CcCCCCCCCCC
Confidence 44555665554
No 189
>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=58.87 E-value=12 Score=22.12 Aligned_cols=30 Identities=23% Similarity=0.541 Sum_probs=18.2
Q ss_pred CCCCCCCCCC--CceeEeCCCCceEeCCCccc
Q 030241 3 DAFCSDCKKH--TEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 3 ~~~Cp~Cg~~--~~iv~D~~~G~~vC~~CG~V 32 (181)
+.+|..|+.- .-..+|......+|.-||..
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 5689999863 23567777788999999985
No 190
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=58.70 E-value=7.3 Score=25.08 Aligned_cols=24 Identities=29% Similarity=0.755 Sum_probs=18.2
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
.||.|+... ...-...|.+||...
T Consensus 1 ~Cpv~~~~~-----~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKDL-----PAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCcccc-----ccccCCcCCCCCCcC
Confidence 499999721 455568899999986
No 191
>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=58.06 E-value=9.2 Score=27.68 Aligned_cols=30 Identities=20% Similarity=0.526 Sum_probs=22.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccC
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (181)
..|--|+. .-.. .+.+++||..||.++.-.
T Consensus 36 daCeiC~~-~GY~--q~g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 36 DACEICGP-KGYY--QEGDQLVCKNCGVRFNLP 65 (102)
T ss_pred EeccccCC-CceE--EECCEEEEecCCCEEehh
Confidence 35889986 3333 457899999999998533
No 192
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=57.64 E-value=3.3 Score=26.10 Aligned_cols=28 Identities=29% Similarity=0.652 Sum_probs=18.7
Q ss_pred CCCCCCCCCcee--EeCCCCceEeCCCcccc
Q 030241 5 FCSDCKKHTEVV--FDHSAGDTVCSECGLVL 33 (181)
Q Consensus 5 ~Cp~Cg~~~~iv--~D~~~G~~vC~~CG~Vl 33 (181)
.|+-||..-.+. +..++| +||.+|--=+
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 489999732211 235778 7999998555
No 193
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=57.13 E-value=6.7 Score=25.44 Aligned_cols=25 Identities=24% Similarity=0.727 Sum_probs=16.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (181)
..||+||. .-+ ---||.+||.--+.
T Consensus 28 ~~c~~cG~-~~l------~Hrvc~~cg~Y~g~ 52 (57)
T COG0333 28 SVCPNCGE-YKL------PHRVCLKCGYYKGR 52 (57)
T ss_pred eeccCCCC-ccc------CceEcCCCCCccCe
Confidence 56888886 222 24789999965443
No 194
>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=57.08 E-value=26 Score=24.36 Aligned_cols=19 Identities=21% Similarity=0.088 Sum_probs=16.0
Q ss_pred CHHHHHHHHHHHHHHhCCC
Q 030241 139 KTHYWLLACTLLVDKKTSH 157 (181)
Q Consensus 139 ~~~~v~AAclYiACR~~~~ 157 (181)
+...++|||+|+|.+..+.
T Consensus 41 ~PS~iAaAai~lA~~~~~~ 59 (118)
T PF02984_consen 41 PPSVIAAAAILLARKILGK 59 (118)
T ss_dssp -HHHHHHHHHHHHHHHHHS
T ss_pred CHHHHHHHHHHHHHHHhCc
Confidence 8999999999999998653
No 195
>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=56.56 E-value=8.8 Score=27.14 Aligned_cols=34 Identities=26% Similarity=0.671 Sum_probs=21.3
Q ss_pred CCCCCCCC------CceeEeCCCC----------ceEeCCCccccccCCc
Q 030241 5 FCSDCKKH------TEVVFDHSAG----------DTVCSECGLVLESHSI 38 (181)
Q Consensus 5 ~Cp~Cg~~------~~iv~D~~~G----------~~vC~~CG~Vl~e~~i 38 (181)
.|+-|+.. +.+.+|...| -++|..||.+.-+.-+
T Consensus 1 ~C~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~dev 50 (89)
T TIGR03829 1 KCRWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQDDTT 50 (89)
T ss_pred CCcccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEeecHHH
Confidence 48888541 3345555555 3689999998754443
No 196
>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=56.27 E-value=6.5 Score=24.73 Aligned_cols=28 Identities=21% Similarity=0.700 Sum_probs=15.4
Q ss_pred CCCCC--CCCCCceeEeCCCCc--eEeCCCcccc
Q 030241 4 AFCSD--CKKHTEVVFDHSAGD--TVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~--Cg~~~~iv~D~~~G~--~vC~~CG~Vl 33 (181)
..||. |+. .+..+..... +.|..||...
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 57977 986 3555555555 8899998764
No 197
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=56.15 E-value=5.8 Score=23.58 Aligned_cols=13 Identities=31% Similarity=0.925 Sum_probs=11.6
Q ss_pred CceEeCCCccccc
Q 030241 22 GDTVCSECGLVLE 34 (181)
Q Consensus 22 G~~vC~~CG~Vl~ 34 (181)
|.+||..|+.+|+
T Consensus 2 GtIvCq~C~~~Id 14 (38)
T PF13790_consen 2 GTIVCQHCNETID 14 (38)
T ss_pred CEEEeccccceee
Confidence 7899999999984
No 198
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=55.93 E-value=6.4 Score=25.71 Aligned_cols=25 Identities=36% Similarity=0.987 Sum_probs=14.5
Q ss_pred CCCCCCCCCceeEeCCCCc-eEeCCCcccc
Q 030241 5 FCSDCKKHTEVVFDHSAGD-TVCSECGLVL 33 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~-~vC~~CG~Vl 33 (181)
.|-+||. .+.+ ..|+ +-|.+||.=|
T Consensus 22 iCgdC~~-en~l---k~~D~irCReCG~RI 47 (62)
T KOG3507|consen 22 ICGDCGQ-ENTL---KRGDVIRCRECGYRI 47 (62)
T ss_pred Eeccccc-cccc---cCCCcEehhhcchHH
Confidence 4788886 3322 2344 4588888643
No 199
>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=55.64 E-value=3.8 Score=39.84 Aligned_cols=11 Identities=45% Similarity=1.226 Sum_probs=0.0
Q ss_pred eEeCCCccccc
Q 030241 24 TVCSECGLVLE 34 (181)
Q Consensus 24 ~vC~~CG~Vl~ 34 (181)
..|..||..++
T Consensus 681 ~~Cp~C~~~~~ 691 (900)
T PF03833_consen 681 YVCPDCGIEVE 691 (900)
T ss_dssp -----------
T ss_pred eeccccccccC
Confidence 45666666554
No 200
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=54.70 E-value=11 Score=28.92 Aligned_cols=34 Identities=26% Similarity=0.500 Sum_probs=27.4
Q ss_pred EeCCCCceEeCCCccccc--cCCccccccccccccC
Q 030241 17 FDHSAGDTVCSECGLVLE--SHSIDETSEWRTFANE 50 (181)
Q Consensus 17 ~D~~~G~~vC~~CG~Vl~--e~~id~~~Ewr~F~~~ 50 (181)
...+.|.++|..||.-|= +.-+|+|.-|.+|.+.
T Consensus 37 ~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~ 72 (142)
T PRK00222 37 DNKEKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTKP 72 (142)
T ss_pred CCCCCeEEEecCCCchhcCCcccccCCCCCcCcCcc
Confidence 345899999999999884 4457889999999854
No 201
>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=54.66 E-value=6.4 Score=26.78 Aligned_cols=11 Identities=45% Similarity=1.141 Sum_probs=4.3
Q ss_pred CCCCCCCCCCC
Q 030241 1 MTDAFCSDCKK 11 (181)
Q Consensus 1 m~~~~Cp~Cg~ 11 (181)
|....||.||.
T Consensus 22 ~~k~FCp~CGn 32 (73)
T PF08772_consen 22 MTKQFCPKCGN 32 (73)
T ss_dssp SS--S-SSS--
T ss_pred CCceeCcccCC
Confidence 55677888886
No 202
>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=54.60 E-value=12 Score=26.48 Aligned_cols=27 Identities=15% Similarity=0.389 Sum_probs=17.2
Q ss_pred CCCCCCCC-CceeEeCCCCceEeCCCcc
Q 030241 5 FCSDCKKH-TEVVFDHSAGDTVCSECGL 31 (181)
Q Consensus 5 ~Cp~Cg~~-~~iv~D~~~G~~vC~~CG~ 31 (181)
.||.|+.. +++.++...|...|-.||.
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 49999853 4688899999999999984
No 203
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=54.53 E-value=5.5 Score=29.34 Aligned_cols=19 Identities=16% Similarity=0.324 Sum_probs=11.4
Q ss_pred ceeEeCCCCceEeCCCccc
Q 030241 14 EVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 14 ~iv~D~~~G~~vC~~CG~V 32 (181)
.+..+...+...|.+||..
T Consensus 62 ~L~Ie~vp~~~~C~~Cg~~ 80 (117)
T PRK00564 62 ILDIVDEKVELECKDCSHV 80 (117)
T ss_pred EEEEEecCCEEEhhhCCCc
Confidence 4555556666666666633
No 204
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=54.52 E-value=7.7 Score=39.43 Aligned_cols=6 Identities=33% Similarity=1.088 Sum_probs=2.8
Q ss_pred CCCCCC
Q 030241 5 FCSDCK 10 (181)
Q Consensus 5 ~Cp~Cg 10 (181)
+||+||
T Consensus 669 kCPkCG 674 (1337)
T PRK14714 669 RCPSCG 674 (1337)
T ss_pred ECCCCC
Confidence 344444
No 205
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=54.48 E-value=11 Score=22.80 Aligned_cols=23 Identities=35% Similarity=0.528 Sum_probs=17.3
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcccccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (181)
+|..|+.. + ...+|..||.|.-.
T Consensus 1 ~C~~C~~~-~-------~l~~CL~C~~~~c~ 23 (50)
T smart00290 1 RCSVCGTI-E-------NLWLCLTCGQVGCG 23 (50)
T ss_pred CcccCCCc-C-------CeEEecCCCCcccC
Confidence 58899962 2 26799999999753
No 206
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=54.19 E-value=11 Score=36.40 Aligned_cols=27 Identities=26% Similarity=0.742 Sum_probs=23.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
..||+|.. .+++...+|.+.|--||..
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 46899975 5788889999999999998
No 207
>PRK06260 threonine synthase; Validated
Probab=54.07 E-value=5.6 Score=35.16 Aligned_cols=30 Identities=37% Similarity=0.625 Sum_probs=22.2
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
|-..+|+.||. . ++...-...|..||-.|+
T Consensus 1 ~~~~~C~~cg~-~---~~~~~~~~~Cp~cg~~l~ 30 (397)
T PRK06260 1 MYWLKCIECGK-E---YDPDEIIYTCPECGGLLE 30 (397)
T ss_pred CCEEEECCCCC-C---CCCCCccccCCCCCCeEE
Confidence 55678999997 2 344455678999998764
No 208
>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=54.04 E-value=5 Score=29.30 Aligned_cols=30 Identities=23% Similarity=0.473 Sum_probs=19.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
..|-+||+..+.-.+..-|-.+|..|.-|-
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 569999985455566678999999998774
No 209
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=53.38 E-value=9.3 Score=31.09 Aligned_cols=27 Identities=37% Similarity=0.855 Sum_probs=21.6
Q ss_pred CCCCCCCCCCc-eeEeCCCCceEeCCCc
Q 030241 4 AFCSDCKKHTE-VVFDHSAGDTVCSECG 30 (181)
Q Consensus 4 ~~Cp~Cg~~~~-iv~D~~~G~~vC~~CG 30 (181)
..|-.||+..+ ..++..+|-.+|..|+
T Consensus 150 ~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 150 DHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hhHhcCCCCCCceEEecccCCccccccc
Confidence 36999997422 5678899999999997
No 210
>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=53.24 E-value=9 Score=27.55 Aligned_cols=27 Identities=19% Similarity=0.369 Sum_probs=17.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
..|..|+- |..+..--...|.+||.++
T Consensus 4 rAC~~C~~---I~~~~qf~~~gCpnC~~~l 30 (98)
T cd07973 4 RACLLCSL---IKTEDQFERDGCPNCEGYL 30 (98)
T ss_pred chhccCCc---ccccccccCCCCCCCcchh
Confidence 56888885 3333333457899998766
No 211
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=53.06 E-value=12 Score=23.46 Aligned_cols=28 Identities=21% Similarity=0.867 Sum_probs=19.7
Q ss_pred CCCC--CCCCCCceeEe--CCCCceEeCCCcccc
Q 030241 4 AFCS--DCKKHTEVVFD--HSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp--~Cg~~~~iv~D--~~~G~~vC~~CG~Vl 33 (181)
..|| .|+. .+..+ .....+.|..||...
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 8986 33343 367788999898764
No 212
>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=52.75 E-value=2.8 Score=27.38 Aligned_cols=27 Identities=22% Similarity=0.557 Sum_probs=19.1
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeC-CCcccccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCS-ECGLVLES 35 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~-~CG~Vl~e 35 (181)
...||.||. +|.- .+..|+ +|+.....
T Consensus 3 HkHC~~CG~--~Ip~----~~~fCS~~C~~~~~k 30 (59)
T PF09889_consen 3 HKHCPVCGK--PIPP----DESFCSPKCREEYRK 30 (59)
T ss_pred CCcCCcCCC--cCCc----chhhhCHHHHHHHHH
Confidence 467999996 3422 489995 89887643
No 213
>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=52.44 E-value=9.5 Score=25.77 Aligned_cols=26 Identities=23% Similarity=0.676 Sum_probs=15.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
..||.|.. ++ +...|.+.|..|+.-+
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 44 4456899999998754
No 214
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=52.42 E-value=58 Score=28.54 Aligned_cols=55 Identities=16% Similarity=0.146 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHhCCchHHHHH--HHHHHHH-hh-h---C---HHHHHHHHHHHHHHhCCC--Ccc
Q 030241 106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVE-AE-I---K---THYWLLACTLLVDKKTSH--ALL 160 (181)
Q Consensus 106 ~~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~-~~-l---~---~~~v~AAclYiACR~~~~--p~t 160 (181)
.+|+..|=+.|+..+....+.=- .++-... -. + + ..-+++|||.+|.+.+.. |++
T Consensus 79 ~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll 145 (335)
T KOG0656|consen 79 KQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLL 145 (335)
T ss_pred HHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchh
Confidence 45889999999988887654333 3333321 11 3 4 789999999999999876 765
No 215
>PRK06386 replication factor A; Reviewed
Probab=52.08 E-value=6.9 Score=34.52 Aligned_cols=21 Identities=33% Similarity=0.642 Sum_probs=15.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
.+||+|+. .+.+ -.|.+||.|
T Consensus 237 ~rCP~C~R---~l~~-----g~C~~HG~v 257 (358)
T PRK06386 237 TKCSVCNK---IIED-----GVCKDHPDA 257 (358)
T ss_pred ecCcCCCe---EccC-----CcCCCCCCC
Confidence 47999986 2232 399999975
No 216
>PRK14526 adenylate kinase; Provisional
Probab=52.06 E-value=10 Score=30.62 Aligned_cols=33 Identities=15% Similarity=0.354 Sum_probs=22.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccC
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (181)
..||.||...++.+++.....+|..||--+.-+
T Consensus 123 ~~~~~~g~~y~~~~~pp~~~~~~~~~~~~l~~R 155 (211)
T PRK14526 123 RICKSCNNIFNIYTLPTKEKGICDVCKGDLYQR 155 (211)
T ss_pred CcccccCCccccccCCCCccCcCCCCCCeeecc
Confidence 458888876566777766677888887655433
No 217
>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=51.76 E-value=5.4 Score=23.10 Aligned_cols=27 Identities=33% Similarity=0.778 Sum_probs=13.2
Q ss_pred CCCCCCC-CceeEeCCCCce-EeCCCccc
Q 030241 6 CSDCKKH-TEVVFDHSAGDT-VCSECGLV 32 (181)
Q Consensus 6 Cp~Cg~~-~~iv~D~~~G~~-vC~~CG~V 32 (181)
|-+|+.. +..-.....|.. +|..||+-
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 5677752 222333346666 78888764
No 218
>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=51.74 E-value=11 Score=30.61 Aligned_cols=28 Identities=25% Similarity=0.705 Sum_probs=20.9
Q ss_pred CCCCCCCCCC-ceeEeCCCCceEeCCCcc
Q 030241 4 AFCSDCKKHT-EVVFDHSAGDTVCSECGL 31 (181)
Q Consensus 4 ~~Cp~Cg~~~-~iv~D~~~G~~vC~~CG~ 31 (181)
..|..||... ...++...|-.+|.+|+.
T Consensus 148 ~~C~~cg~~~~~~~fs~~~gg~~C~~c~~ 176 (241)
T TIGR00613 148 DKCAVCGSKEDLIYFSMTYGGALCRQCGE 176 (241)
T ss_pred CccCCCCCcCCCceEchhcCeEEChhhCc
Confidence 4688898621 256778899999999965
No 219
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=51.63 E-value=6.1 Score=23.66 Aligned_cols=16 Identities=38% Similarity=0.931 Sum_probs=12.8
Q ss_pred CceEeCCCccccccCC
Q 030241 22 GDTVCSECGLVLESHS 37 (181)
Q Consensus 22 G~~vC~~CG~Vl~e~~ 37 (181)
|.+.|..||++.....
T Consensus 12 ~~~~C~~CgM~Y~~~~ 27 (41)
T PF13878_consen 12 GATTCPTCGMLYSPGS 27 (41)
T ss_pred CCcCCCCCCCEECCCC
Confidence 6789999999985443
No 220
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=51.31 E-value=12 Score=34.52 Aligned_cols=33 Identities=33% Similarity=0.608 Sum_probs=21.9
Q ss_pred CCCCCCCCCcee---EeCCCC--ceEeCCCccccccCCc
Q 030241 5 FCSDCKKHTEVV---FDHSAG--DTVCSECGLVLESHSI 38 (181)
Q Consensus 5 ~Cp~Cg~~~~iv---~D~~~G--~~vC~~CG~Vl~e~~i 38 (181)
.||+||.....+ +|.+.| .+.| +||.--+-.+-
T Consensus 177 ic~~cg~~~~~~~~~~d~~~~~v~y~~-~cG~~~~~~~~ 214 (510)
T PRK00750 177 ICPKCGKVLTTPVISYDAEAGTVTYDC-ECGHEGEVPVT 214 (510)
T ss_pred eCCCCCccceEEEEEEeCCCCEEEEEc-CCCCEEEEecC
Confidence 699999854433 476776 4556 49988655443
No 221
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=51.28 E-value=11 Score=30.35 Aligned_cols=30 Identities=27% Similarity=0.619 Sum_probs=17.1
Q ss_pred CCCCCCCCCc---eeEe--CCCC-----ceEeCCCccccc
Q 030241 5 FCSDCKKHTE---VVFD--HSAG-----DTVCSECGLVLE 34 (181)
Q Consensus 5 ~Cp~Cg~~~~---iv~D--~~~G-----~~vC~~CG~Vl~ 34 (181)
.||+||.... ..++ +--| ...|.+||+=-.
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ 41 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSN 41 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccc
Confidence 5999986321 1122 1123 346999998643
No 222
>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=50.25 E-value=11 Score=25.26 Aligned_cols=26 Identities=31% Similarity=0.687 Sum_probs=19.7
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
+| .||. -++.|...-.--| .||..+.
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 4788888888999 9999974
No 223
>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=50.21 E-value=9.6 Score=32.21 Aligned_cols=29 Identities=28% Similarity=0.594 Sum_probs=12.1
Q ss_pred CCCCCCCCCCc-eeEeCCC--C--ceEeCCCccc
Q 030241 4 AFCSDCKKHTE-VVFDHSA--G--DTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~-iv~D~~~--G--~~vC~~CG~V 32 (181)
..||.||+.+. -+..... | .+.|.-||.-
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 57999998422 1222222 3 5889999864
No 224
>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=49.41 E-value=8.6 Score=27.91 Aligned_cols=31 Identities=23% Similarity=0.405 Sum_probs=22.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
..|-+||+..+--....-|-.+|.+|.-|-.
T Consensus 4 ~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR 34 (112)
T smart00105 4 KKCFDCGAPNPTWASVNLGVFLCIECSGIHR 34 (112)
T ss_pred CcccCCCCCCCCcEEeccceeEhHHhHHHHH
Confidence 4688999743334455679999999988853
No 225
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=49.26 E-value=11 Score=32.06 Aligned_cols=30 Identities=27% Similarity=0.523 Sum_probs=19.8
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
...|+.||.++. .-...=..+|.+||...=
T Consensus 111 ~RFCg~CG~~~~--~~~~g~~~~C~~cg~~~f 140 (279)
T COG2816 111 HRFCGRCGTKTY--PREGGWARVCPKCGHEHF 140 (279)
T ss_pred CcCCCCCCCcCc--cccCceeeeCCCCCCccC
Confidence 468999998432 122233578999998763
No 226
>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=49.18 E-value=46 Score=28.65 Aligned_cols=62 Identities=13% Similarity=0.164 Sum_probs=40.5
Q ss_pred CCchHHHHHHHHHHHHHHHHhCCchHH--HH-----H---H---HHHHH----Hhh------h--CHHHHHHHHHHHHHH
Q 030241 99 SNPDRGLILAFKTIATMSDRIGQMRYI--RR-----W---K---IKSLV----EAE------I--KTHYWLLACTLLVDK 153 (181)
Q Consensus 99 ~~~er~l~~a~~~I~~ia~~L~Lp~~v--~e-----~---~---i~k~a----~~~------l--~~~~v~AAclYiACR 153 (181)
+++++-+.--+..++.++.-|.++... .+ - . .+..+ .|. + +...+++||+++||+
T Consensus 125 ~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~llypphiIA~a~l~ia~~ 204 (297)
T COG5333 125 SSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACE 204 (297)
T ss_pred ccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceeeeecChHHHHHHHHHHHHH
Confidence 466777777788888887777664321 11 1 1 11111 111 1 889999999999999
Q ss_pred hCCCCcc
Q 030241 154 KTSHALL 160 (181)
Q Consensus 154 ~~~~p~t 160 (181)
..+.|+-
T Consensus 205 ~~~~~~~ 211 (297)
T COG5333 205 VLGMPII 211 (297)
T ss_pred hcCCccc
Confidence 9998864
No 227
>PRK08197 threonine synthase; Validated
Probab=47.61 E-value=8.2 Score=34.06 Aligned_cols=27 Identities=33% Similarity=0.746 Sum_probs=19.4
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
..+|+.||. . ++.+.-...| .||-.++
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 367999997 2 3444556889 8997764
No 228
>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=47.11 E-value=14 Score=28.04 Aligned_cols=33 Identities=24% Similarity=0.410 Sum_probs=27.0
Q ss_pred eCCCCceEeCCCccccc--cCCccccccccccccC
Q 030241 18 DHSAGDTVCSECGLVLE--SHSIDETSEWRTFANE 50 (181)
Q Consensus 18 D~~~G~~vC~~CG~Vl~--e~~id~~~Ewr~F~~~ 50 (181)
..+.|.++|..||.-|= +.-+|+|.-|.+|.+.
T Consensus 35 ~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~ 69 (134)
T TIGR00357 35 NKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKP 69 (134)
T ss_pred CCCCeEEEccCCCCccccccchhcCCCCCcCcCcc
Confidence 45899999999999875 4457889999999754
No 229
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.85 E-value=12 Score=24.65 Aligned_cols=20 Identities=30% Similarity=0.672 Sum_probs=15.4
Q ss_pred eeEeC-CCCceEeCCCccccc
Q 030241 15 VVFDH-SAGDTVCSECGLVLE 34 (181)
Q Consensus 15 iv~D~-~~G~~vC~~CG~Vl~ 34 (181)
+..|. ++|+.+|.-||.+..
T Consensus 39 V~L~mg~~gev~CPYC~t~y~ 59 (62)
T COG4391 39 VFLDMGDEGEVVCPYCSTRYR 59 (62)
T ss_pred EEEEcCCCCcEecCccccEEE
Confidence 44443 899999999999863
No 230
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.23 E-value=13 Score=32.64 Aligned_cols=26 Identities=31% Similarity=0.717 Sum_probs=21.8
Q ss_pred CCCCCCCCCceeEeCC--CCceEeCCCc
Q 030241 5 FCSDCKKHTEVVFDHS--AGDTVCSECG 30 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~--~G~~vC~~CG 30 (181)
-||.||...-+-+|.. +|..+|--||
T Consensus 34 ~cpvcg~k~RFr~dD~kGrGtw~c~y~~ 61 (366)
T COG4643 34 PCPVCGGKDRFRFDDRKGRGTWFCNYCG 61 (366)
T ss_pred CCCccCCccccccCCccCCccEEEEeec
Confidence 6999998666777763 6999999999
No 231
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=45.07 E-value=13 Score=32.63 Aligned_cols=25 Identities=36% Similarity=0.862 Sum_probs=19.2
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcccccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (181)
.|+.||. .+.|+ ...|..||.-|+=
T Consensus 1 ~C~~Cg~--~v~Fe----Nt~C~~Cg~~LGf 25 (343)
T PF10005_consen 1 SCPNCGQ--PVFFE----NTRCLSCGSALGF 25 (343)
T ss_pred CCCCCCC--cceeC----CCccccCCccccC
Confidence 4999996 35553 5899999998863
No 232
>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=44.99 E-value=18 Score=28.28 Aligned_cols=29 Identities=28% Similarity=0.665 Sum_probs=16.6
Q ss_pred CCCCCCCCcee----Ee-CCCCc-----eEeCCCccccc
Q 030241 6 CSDCKKHTEVV----FD-HSAGD-----TVCSECGLVLE 34 (181)
Q Consensus 6 Cp~Cg~~~~iv----~D-~~~G~-----~vC~~CG~Vl~ 34 (181)
||.||..+... ++ +--|+ ..|.+||+=-.
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ 39 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRST 39 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchh
Confidence 99999631111 11 12333 46999998754
No 233
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=44.32 E-value=12 Score=24.37 Aligned_cols=28 Identities=7% Similarity=0.007 Sum_probs=17.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccCCcc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id 39 (181)
..||+||.. . . ---||. ||+--+..+++
T Consensus 28 ~~c~~cg~~--~-~----pH~vc~-cG~Y~gr~v~~ 55 (60)
T PRK01110 28 SVDKTTGEY--H-L----PHHVSP-KGYYKGRKVLK 55 (60)
T ss_pred eEcCCCCce--e-c----cceecC-CcccCCeEeec
Confidence 458888862 1 1 236788 99776655554
No 234
>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=44.26 E-value=18 Score=31.87 Aligned_cols=33 Identities=36% Similarity=0.768 Sum_probs=20.3
Q ss_pred CCCCCCCCCCcee--EeCCCC--ceEeCCCccccccCC
Q 030241 4 AFCSDCKKHTEVV--FDHSAG--DTVCSECGLVLESHS 37 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv--~D~~~G--~~vC~~CG~Vl~e~~ 37 (181)
-.||+||..+..+ +|.+.| .+.| +||.--+-.+
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 3699999633333 444444 5678 5998765444
No 235
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=43.92 E-value=15 Score=30.02 Aligned_cols=30 Identities=23% Similarity=0.569 Sum_probs=24.7
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
....|..|++ ..+|.+ .|-..|-.|+.|..
T Consensus 3 ~l~~C~~C~~-ngiv~~--k~~efC~fC~~~f~ 32 (225)
T PHA03074 3 NLKLCSGCRH-NGIVSE--KDYEFCIFCESVFQ 32 (225)
T ss_pred chhhcCCCCC-CCeeee--cCEEEeecHHHHHh
Confidence 4467999997 677664 89999999999975
No 236
>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=43.78 E-value=11 Score=33.32 Aligned_cols=24 Identities=38% Similarity=0.876 Sum_probs=14.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
..||.||. +...| ..|.+||..++
T Consensus 137 g~CP~C~~------~~a~g-~~Ce~cG~~~~ 160 (391)
T PF09334_consen 137 GTCPYCGS------DKARG-DQCENCGRPLE 160 (391)
T ss_dssp CEETTT--------SSCTT-TEETTTSSBEE
T ss_pred ccccCcCc------cccCC-CcccCCCCCcc
Confidence 35888874 22334 56788888876
No 237
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=43.59 E-value=14 Score=33.24 Aligned_cols=32 Identities=19% Similarity=0.430 Sum_probs=24.0
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccccccCCcc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id 39 (181)
.||.||.. . ....++..-|..||+-..+..+.
T Consensus 352 ~Cp~Cg~~-m--~S~G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 352 VCPRCGGR-M--KSAGRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCccCCc-h--hhcCCCCcccccccccCCccccc
Confidence 69999973 2 34445579999999998776654
No 238
>PF14369 zf-RING_3: zinc-finger
Probab=42.12 E-value=17 Score=21.01 Aligned_cols=26 Identities=23% Similarity=0.640 Sum_probs=15.5
Q ss_pred CCCCCCCCCCceeEe-CCCCceEeCCCcc
Q 030241 4 AFCSDCKKHTEVVFD-HSAGDTVCSECGL 31 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D-~~~G~~vC~~CG~ 31 (181)
.+|-.|.. .+... ..+.++.|..|+-
T Consensus 3 ywCh~C~~--~V~~~~~~~~~~~CP~C~~ 29 (35)
T PF14369_consen 3 YWCHQCNR--FVRIAPSPDSDVACPRCHG 29 (35)
T ss_pred EeCccCCC--EeEeCcCCCCCcCCcCCCC
Confidence 46888986 23332 2344445999973
No 239
>PRK06450 threonine synthase; Validated
Probab=41.24 E-value=12 Score=32.38 Aligned_cols=29 Identities=28% Similarity=0.620 Sum_probs=20.4
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
|...+|+.||. . ++. .-...|.+||-.|+
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 3 232 33578999997765
No 240
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=41.02 E-value=15 Score=23.97 Aligned_cols=22 Identities=27% Similarity=0.505 Sum_probs=13.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
.+||+||.-|--. .|..||-+.
T Consensus 6 rkC~~cg~YTLke--------~Cp~CG~~t 27 (59)
T COG2260 6 RKCPKCGRYTLKE--------KCPVCGGDT 27 (59)
T ss_pred hcCcCCCceeecc--------cCCCCCCcc
Confidence 5678887532112 277788765
No 241
>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=40.77 E-value=19 Score=23.35 Aligned_cols=30 Identities=30% Similarity=0.551 Sum_probs=15.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccCC
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~ 37 (181)
..|..|+.. |..-...--|..||.|+=..-
T Consensus 10 ~~C~~C~~~----F~~~~rrhhCr~CG~~vC~~C 39 (69)
T PF01363_consen 10 SNCMICGKK----FSLFRRRHHCRNCGRVVCSSC 39 (69)
T ss_dssp SB-TTT--B-----BSSS-EEE-TTT--EEECCC
T ss_pred CcCcCcCCc----CCCceeeEccCCCCCEECCch
Confidence 569999862 455677888999998875443
No 242
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=40.62 E-value=13 Score=37.78 Aligned_cols=8 Identities=50% Similarity=1.244 Sum_probs=5.1
Q ss_pred CCCCCCCC
Q 030241 5 FCSDCKKH 12 (181)
Q Consensus 5 ~Cp~Cg~~ 12 (181)
+||+||++
T Consensus 681 fCP~CGs~ 688 (1337)
T PRK14714 681 RCPDCGTH 688 (1337)
T ss_pred cCcccCCc
Confidence 57777763
No 243
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=40.60 E-value=8.9 Score=27.97 Aligned_cols=34 Identities=21% Similarity=0.566 Sum_probs=24.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccCCcc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id 39 (181)
..|++||. ..++...=.+- .|..||..-.+..++
T Consensus 43 ~~C~~Cg~-~~~~~~SCk~R-~CP~C~~~~~~~W~~ 76 (111)
T PF14319_consen 43 YRCEDCGH-EKIVYNSCKNR-HCPSCQAKATEQWIE 76 (111)
T ss_pred eecCCCCc-eEEecCcccCc-CCCCCCChHHHHHHH
Confidence 46999996 56666554444 999999997655543
No 244
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=40.28 E-value=15 Score=22.74 Aligned_cols=14 Identities=29% Similarity=0.707 Sum_probs=11.9
Q ss_pred CCceEeCCCccccc
Q 030241 21 AGDTVCSECGLVLE 34 (181)
Q Consensus 21 ~G~~vC~~CG~Vl~ 34 (181)
+|.++|..||.-+-
T Consensus 3 ~g~l~C~~CG~~m~ 16 (58)
T PF13408_consen 3 SGLLRCGHCGSKMT 16 (58)
T ss_pred CCcEEcccCCcEeE
Confidence 58899999998764
No 245
>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=40.00 E-value=18 Score=29.05 Aligned_cols=23 Identities=17% Similarity=0.548 Sum_probs=14.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECG 30 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG 30 (181)
..||.|+....++. +...|.+|+
T Consensus 100 ~~C~~C~G~G~~i~----~~~~C~~C~ 122 (186)
T TIGR02642 100 CKCPRCRGTGLIQR----RQRECDTCA 122 (186)
T ss_pred CcCCCCCCeeEEec----CCCCCCCCC
Confidence 57999987333322 125688885
No 246
>PF14149 YhfH: YhfH-like protein
Probab=39.72 E-value=5.3 Score=23.61 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=12.5
Q ss_pred CCceEeCCCccccccC
Q 030241 21 AGDTVCSECGLVLESH 36 (181)
Q Consensus 21 ~G~~vC~~CG~Vl~e~ 36 (181)
-+.-.|++||..++|.
T Consensus 11 Lp~K~C~~CG~~i~EQ 26 (37)
T PF14149_consen 11 LPPKKCTECGKEIEEQ 26 (37)
T ss_pred CCCcccHHHHHHHHHH
Confidence 4567899999998764
No 247
>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=39.69 E-value=23 Score=22.23 Aligned_cols=8 Identities=25% Similarity=0.866 Sum_probs=6.7
Q ss_pred CCCCCCCC
Q 030241 4 AFCSDCKK 11 (181)
Q Consensus 4 ~~Cp~Cg~ 11 (181)
..||.||+
T Consensus 14 ~~Cp~CGN 21 (49)
T PF12677_consen 14 CKCPKCGN 21 (49)
T ss_pred ccCcccCC
Confidence 46999997
No 248
>PRK08329 threonine synthase; Validated
Probab=39.51 E-value=19 Score=31.17 Aligned_cols=25 Identities=24% Similarity=0.701 Sum_probs=17.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.+|+.||.. ++.... ..| .||-.|+
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 8997764
No 249
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=39.31 E-value=20 Score=21.31 Aligned_cols=8 Identities=25% Similarity=0.829 Sum_probs=5.4
Q ss_pred CCCCCCCC
Q 030241 4 AFCSDCKK 11 (181)
Q Consensus 4 ~~Cp~Cg~ 11 (181)
..||.||+
T Consensus 3 ~~Cp~Cg~ 10 (47)
T PF14690_consen 3 PRCPHCGS 10 (47)
T ss_pred ccCCCcCC
Confidence 46777775
No 250
>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=39.10 E-value=12 Score=22.27 Aligned_cols=26 Identities=27% Similarity=0.658 Sum_probs=13.2
Q ss_pred CCCCCCCCCC---ceeEeCCCCceEeCCC
Q 030241 4 AFCSDCKKHT---EVVFDHSAGDTVCSEC 29 (181)
Q Consensus 4 ~~Cp~Cg~~~---~iv~D~~~G~~vC~~C 29 (181)
.+|..||++. ..++.-..|-.||.+|
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 4799999742 1233334478899887
No 251
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=38.98 E-value=21 Score=31.60 Aligned_cols=38 Identities=21% Similarity=0.468 Sum_probs=29.2
Q ss_pred CCCCCCCCCceeEeC-CCCceEeCCCccccccCCcccccc
Q 030241 5 FCSDCKKHTEVVFDH-SAGDTVCSECGLVLESHSIDETSE 43 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~-~~G~~vC~~CG~Vl~e~~id~~~E 43 (181)
.|..||+ ..++..+ ++|..-|.+|-.|+.+..+--.-|
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 4999998 7787665 577799999999998766544444
No 252
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=38.54 E-value=41 Score=28.14 Aligned_cols=22 Identities=18% Similarity=0.218 Sum_probs=19.8
Q ss_pred CHHHHHHHHHHHHHHhCCCCcc
Q 030241 139 KTHYWLLACTLLVDKKTSHALL 160 (181)
Q Consensus 139 ~~~~v~AAclYiACR~~~~p~t 160 (181)
.+..++.|||||||-..+.+++
T Consensus 192 PPh~IalAcl~Ia~~~~~k~~~ 213 (264)
T KOG0794|consen 192 PPHQIALACLYIACVIDEKDIP 213 (264)
T ss_pred CHHHHHHHHHHHHHhhcCCChH
Confidence 8899999999999999888873
No 253
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=38.36 E-value=16 Score=34.75 Aligned_cols=22 Identities=36% Similarity=0.928 Sum_probs=12.6
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
.||.|+. . | ..|+. |..||..+
T Consensus 141 ~cp~C~~-~----d-~~g~~-ce~cg~~~ 162 (673)
T PRK00133 141 TCPKCGA-E----D-QYGDN-CEVCGATY 162 (673)
T ss_pred ccCCCCC-c----c-cCCch-hhhccccC
Confidence 5888886 2 2 33543 66666544
No 254
>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=38.36 E-value=15 Score=28.34 Aligned_cols=15 Identities=40% Similarity=0.926 Sum_probs=13.1
Q ss_pred CCCceEeCCCccccc
Q 030241 20 SAGDTVCSECGLVLE 34 (181)
Q Consensus 20 ~~G~~vC~~CG~Vl~ 34 (181)
.-|.++|.+||..+.
T Consensus 109 g~G~l~C~~Cg~~~~ 123 (146)
T PF07295_consen 109 GPGTLVCENCGHEVE 123 (146)
T ss_pred cCceEecccCCCEEE
Confidence 579999999999874
No 255
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=38.20 E-value=20 Score=29.06 Aligned_cols=36 Identities=28% Similarity=0.398 Sum_probs=22.3
Q ss_pred CCCCCCCCCCceeE----e-CCCC-----ceEeCCCccccccCCccc
Q 030241 4 AFCSDCKKHTEVVF----D-HSAG-----DTVCSECGLVLESHSIDE 40 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~----D-~~~G-----~~vC~~CG~Vl~e~~id~ 40 (181)
..||.||+ +-... | +--| .++|..||+=..|-...+
T Consensus 15 ~~CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~~e 60 (201)
T COG1779 15 IDCPVCGG-TLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKTLE 60 (201)
T ss_pred ecCCcccc-eeeEEEeeecCCccceEEEEEEEccccCCcccceeecc
Confidence 56999997 21111 1 1233 368999999876665544
No 256
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=37.85 E-value=18 Score=33.75 Aligned_cols=25 Identities=32% Similarity=0.909 Sum_probs=13.9
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccccccC
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (181)
.||.||. +...|+ -|.+||..++..
T Consensus 144 ~cp~cg~------~~arGD-~Ce~Cg~~~~P~ 168 (558)
T COG0143 144 TCPKCGG------EDARGD-QCENCGRTLDPT 168 (558)
T ss_pred cCCCcCc------cccCcc-hhhhccCcCCch
Confidence 4777774 112333 466777776543
No 257
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=37.72 E-value=18 Score=23.59 Aligned_cols=25 Identities=20% Similarity=0.603 Sum_probs=16.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
..|..||. ... . --.-.|+.||.=-
T Consensus 17 ~~CRRCGr-~sy--h--v~k~~CaaCGfgr 41 (61)
T COG2126 17 IRCRRCGR-RSY--H--VRKKYCAACGFGR 41 (61)
T ss_pred ehhhhccc-hhe--e--eccceecccCCCC
Confidence 56999997 332 2 2356899999763
No 258
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=37.52 E-value=28 Score=27.11 Aligned_cols=29 Identities=17% Similarity=0.422 Sum_probs=16.5
Q ss_pred CCCCCCCCCc---eeEe-CCCCc-----eEeCCCcccc
Q 030241 5 FCSDCKKHTE---VVFD-HSAGD-----TVCSECGLVL 33 (181)
Q Consensus 5 ~Cp~Cg~~~~---iv~D-~~~G~-----~vC~~CG~Vl 33 (181)
.||.||.... ..++ +--|+ ..|.+||+=-
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~ 39 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYRN 39 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCcc
Confidence 5999985321 1111 12333 4699999864
No 259
>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=37.50 E-value=23 Score=22.79 Aligned_cols=24 Identities=21% Similarity=0.834 Sum_probs=15.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
..|..||+ .. +. --.-.|..||+=
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 45888987 22 22 235789999875
No 260
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=37.36 E-value=24 Score=26.47 Aligned_cols=30 Identities=27% Similarity=0.546 Sum_probs=19.4
Q ss_pred CCCCCCCCCCCceeEeC----CCCceEeCCCcccc
Q 030241 3 DAFCSDCKKHTEVVFDH----SAGDTVCSECGLVL 33 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~----~~G~~vC~~CG~Vl 33 (181)
+..||.|++ ..++.-- ..--..|.+||.-.
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 4533221 12357899999765
No 261
>PLN02569 threonine synthase
Probab=37.18 E-value=19 Score=33.03 Aligned_cols=27 Identities=11% Similarity=0.054 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
...|+.||. . ++.+.-...| .||-.|+
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 467999997 2 4556667899 8998885
No 262
>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=37.16 E-value=33 Score=20.15 Aligned_cols=29 Identities=24% Similarity=0.408 Sum_probs=16.9
Q ss_pred CCCCCCCCCCceeEeCCCC-ceEeCC---Ccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAG-DTVCSE---CGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G-~~vC~~---CG~Vl 33 (181)
..||.||+ .-++.....| .+.|++ |....
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 3333333443 446765 66554
No 263
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=37.07 E-value=29 Score=22.32 Aligned_cols=27 Identities=22% Similarity=0.476 Sum_probs=14.4
Q ss_pred CCCCCCCCCce--eEeC--CCCceEeCCCcc
Q 030241 5 FCSDCKKHTEV--VFDH--SAGDTVCSECGL 31 (181)
Q Consensus 5 ~Cp~Cg~~~~i--v~D~--~~G~~vC~~CG~ 31 (181)
.||.||+.+.+ -.|. .+=-+.|..|-.
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~ 36 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLYCPKCKQ 36 (55)
T ss_pred ECCCCCCccceeeecCceeccccccCCCCCc
Confidence 58888864322 2221 233467877753
No 264
>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 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=36.91 E-value=19 Score=26.96 Aligned_cols=33 Identities=27% Similarity=0.547 Sum_probs=25.2
Q ss_pred eCCCCceEeCCCccccc--cCCccccccccccccC
Q 030241 18 DHSAGDTVCSECGLVLE--SHSIDETSEWRTFANE 50 (181)
Q Consensus 18 D~~~G~~vC~~CG~Vl~--e~~id~~~Ewr~F~~~ 50 (181)
..+.|.++|..||.-|= +.-+|++.-|.+|.+.
T Consensus 32 ~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~ 66 (124)
T PF01641_consen 32 HKEEGIYVCAVCGTPLFSSDTKFDSGCGWPSFWQP 66 (124)
T ss_dssp TTSSEEEEETTTS-EEEEGGGEETSSSSSSEESSC
T ss_pred CCCCEEEEcCCCCCccccCcccccCCcCCccccCc
Confidence 34789999999999884 3345888899999754
No 266
>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=36.71 E-value=15 Score=28.54 Aligned_cols=30 Identities=20% Similarity=0.589 Sum_probs=14.1
Q ss_pred CCCCCCCCCCce---eEe-CCCCce-----EeCCCcccc
Q 030241 4 AFCSDCKKHTEV---VFD-HSAGDT-----VCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~i---v~D-~~~G~~-----vC~~CG~Vl 33 (181)
..||.||..... .+| +--|++ .|.+||+=-
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 111 233433 799999854
No 267
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=36.44 E-value=27 Score=26.68 Aligned_cols=33 Identities=27% Similarity=0.564 Sum_probs=26.6
Q ss_pred eCCCCceEeCCCccccc--cCCccccccccccccC
Q 030241 18 DHSAGDTVCSECGLVLE--SHSIDETSEWRTFANE 50 (181)
Q Consensus 18 D~~~G~~vC~~CG~Vl~--e~~id~~~Ewr~F~~~ 50 (181)
..+.|-++|..||.-|= +.-.|+|--|.+|.+-
T Consensus 37 ~~~~GiY~c~~cg~pLF~S~~KfdSgcGWPSF~~p 71 (140)
T COG0229 37 NKEKGIYVCIVCGEPLFSSEDKFDSGCGWPSFTKP 71 (140)
T ss_pred ccCCceEEeecCCCccccccccccCCCCCcccccc
Confidence 34899999999998774 4457889999999754
No 268
>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=36.25 E-value=20 Score=23.21 Aligned_cols=17 Identities=35% Similarity=0.687 Sum_probs=9.9
Q ss_pred ceEeCCCccccccCCcc
Q 030241 23 DTVCSECGLVLESHSID 39 (181)
Q Consensus 23 ~~vC~~CG~Vl~e~~id 39 (181)
-.+|.+||+|.=+..++
T Consensus 40 l~~C~~CglvQl~~~v~ 56 (62)
T PF08421_consen 40 LYVCEDCGLVQLEEVVP 56 (62)
T ss_dssp EEEETTT--EEESS---
T ss_pred EEECCCCCchhcCCcCC
Confidence 36899999998777665
No 269
>PF02236 Viral_DNA_bi: Viral DNA-binding protein, all alpha domain; InterPro: IPR003176 This domain represents the N-terminal domain of the viral DNA-binding protein, a multi functional protein involved in DNA replication and transcription control.; GO: 0003677 DNA binding, 0006260 DNA replication, 0006351 transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ADU_A 1ADV_B 2WB0_X 2WAZ_X 1ANV_A.
Probab=36.09 E-value=49 Score=23.17 Aligned_cols=59 Identities=14% Similarity=0.043 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHhCCchH-H---HHH-HHHHHHHhhhCHHHHHHHHHHHHHHhCCCCcc-ccChhhheecccce
Q 030241 105 LILAFKTIATMSDRIGQMRY-I---RRW-KIKSLVEAEIKTHYWLLACTLLVDKKTSHALL-RVQPKILLTSGCFL 174 (181)
Q Consensus 105 l~~a~~~I~~ia~~L~Lp~~-v---~e~-~i~k~a~~~l~~~~v~AAclYiACR~~~~p~t-~~~~~~~~~~~~~~ 174 (181)
-++|+..+..+++.+++-.. + =|. ++|+++... |+-=+....++| +-||....+-|+||
T Consensus 6 wQkaMe~~~~l~e~~kvd~~~~t~lPd~~e~~~Ki~~~-----------~l~~~k~~~~LTFSS~KSf~~~mGRfL 70 (86)
T PF02236_consen 6 WQKAMELAHKLMEKYKVDWKGFTFLPDQGECFRKICQT-----------WLNEEKRGLQLTFSSQKSFTHMMGRFL 70 (86)
T ss_dssp HHHHHHHHHHHHHHTT--HHH--S-TT--HHHHHHHHH-----------HHHHHHTT---SS--HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhccccccCeECCCcHHHHHHHHHH-----------HHHhcCcCCCcceechHHHHHHHHHHH
Confidence 35688999999999988655 1 122 577776554 444445566677 66777777777776
No 270
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=35.83 E-value=19 Score=23.76 Aligned_cols=24 Identities=21% Similarity=0.733 Sum_probs=15.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (181)
...|..||+ ... . --...|..||+
T Consensus 17 Ht~CrRCG~-~sy--h--~qK~~CasCGy 40 (62)
T PRK04179 17 HIRCRRCGR-HSY--N--VRKKYCAACGF 40 (62)
T ss_pred cchhcccCc-ccc--c--ccccchhhcCC
Confidence 356888887 332 2 23578889987
No 271
>PRK00118 putative DNA-binding protein; Validated
Probab=35.68 E-value=1.2e+02 Score=21.92 Aligned_cols=40 Identities=10% Similarity=0.082 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCchHHHHH------HHHHHHHhh--h-----CHHHHHHHHHHH
Q 030241 111 TIATMSDRIGQMRYIRRW------KIKSLVEAE--I-----KTHYWLLACTLL 150 (181)
Q Consensus 111 ~I~~ia~~L~Lp~~v~e~------~i~k~a~~~--l-----~~~~v~AAclYi 150 (181)
.+.+||..+|+|...+.. .-.++++++ | ..+.++|+..|+
T Consensus 35 S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (104)
T PRK00118 35 SLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFIERNELFDKIAYL 87 (104)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHH
Confidence 467788888888765544 233444444 2 456666666554
No 272
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=35.34 E-value=32 Score=28.39 Aligned_cols=25 Identities=20% Similarity=0.304 Sum_probs=17.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCC
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSE 28 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~ 28 (181)
.+||.|+..-.+-+|+.+|++|=..
T Consensus 80 I~C~~C~n~i~~RTDPkN~~YV~Es 104 (272)
T COG5134 80 IKCHLCSNPIDVRTDPKNTEYVVES 104 (272)
T ss_pred EEccCCCCceeeecCCCCceEEEec
Confidence 4588888755677788888877554
No 273
>PRK07591 threonine synthase; Validated
Probab=35.08 E-value=16 Score=32.70 Aligned_cols=26 Identities=31% Similarity=0.574 Sum_probs=18.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.+|+.||.. ++...- ..|.+||-.|+
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 333333 88999998775
No 274
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=34.64 E-value=24 Score=30.49 Aligned_cols=29 Identities=28% Similarity=0.519 Sum_probs=17.0
Q ss_pred CCCCCCCCCCC--ceeEe-CCCC--ceEeCCCcc
Q 030241 3 DAFCSDCKKHT--EVVFD-HSAG--DTVCSECGL 31 (181)
Q Consensus 3 ~~~Cp~Cg~~~--~iv~D-~~~G--~~vC~~CG~ 31 (181)
...||.||+.+ .++.. ...| .+.|.-||.
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~t 220 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCES 220 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCC
Confidence 36799999843 22211 1233 567777764
No 275
>PHA00689 hypothetical protein
Probab=34.18 E-value=28 Score=21.98 Aligned_cols=27 Identities=22% Similarity=0.516 Sum_probs=17.5
Q ss_pred CCCceEeCCCccccccCCcccccccccc
Q 030241 20 SAGDTVCSECGLVLESHSIDETSEWRTF 47 (181)
Q Consensus 20 ~~G~~vC~~CG~Vl~e~~id~~~Ewr~F 47 (181)
+--.+.|..||.- +-+.-|+|-||.-.
T Consensus 14 epravtckrcgkt-glrweddggewvlm 40 (62)
T PHA00689 14 EPRAVTCKRCGKT-GLRWEDDGGEWVLM 40 (62)
T ss_pred Ccceeehhhcccc-CceeecCCCcEEEE
Confidence 4445678888865 44566777788643
No 276
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=33.97 E-value=22 Score=36.91 Aligned_cols=31 Identities=39% Similarity=0.813 Sum_probs=23.3
Q ss_pred CCCCCCCCCCCceeEeCCCC------ceEeCCCccccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAG------DTVCSECGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G------~~vC~~CG~Vl~ 34 (181)
...||+|+- .+++.|.+-| +-.|..||.-+.
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 467999995 7877775444 467999999875
No 277
>PRK05638 threonine synthase; Validated
Probab=33.86 E-value=22 Score=31.87 Aligned_cols=25 Identities=28% Similarity=0.735 Sum_probs=17.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.+|+.||. . ++.. -...| +||-.++
T Consensus 2 l~C~~Cg~-~---~~~~-~~~~C-~c~~~l~ 26 (442)
T PRK05638 2 MKCPKCGR-E---YNSY-IPPFC-ICGELLE 26 (442)
T ss_pred eEeCCCCC-C---CCCC-Cceec-CCCCcEE
Confidence 57999997 2 2322 23889 8997775
No 278
>PRK04023 DNA polymerase II large subunit; Validated
Probab=33.72 E-value=26 Score=35.10 Aligned_cols=8 Identities=38% Similarity=0.920 Sum_probs=4.8
Q ss_pred CCCCCCCC
Q 030241 4 AFCSDCKK 11 (181)
Q Consensus 4 ~~Cp~Cg~ 11 (181)
.+||.||.
T Consensus 627 RfCpsCG~ 634 (1121)
T PRK04023 627 RKCPSCGK 634 (1121)
T ss_pred ccCCCCCC
Confidence 45666664
No 279
>PF05460 ORC6: Origin recognition complex subunit 6 (ORC6); InterPro: IPR008721 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. This entry represents subunit 6, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; interacts with Spp1 and with trimethylated histone H3; phosphorylated by Cdc28 [, ]. In Saccharomyces cerevisiae (Baker's yeast), both ends of the Orc6 interact with Cdt1 [] and the N terminus mediates an interaction with the S-phase cyclin Clb5 []. ; GO: 0003677 DNA binding, 0006260 DNA replication, 0005664 nuclear origin of replication recognition complex; PDB: 3M03_B.
Probab=33.70 E-value=14 Score=32.47 Aligned_cols=46 Identities=11% Similarity=0.146 Sum_probs=0.0
Q ss_pred HHHHHhCC--chHHHHH--HHHHHHHhh---h---CHHHHHHHHHHHHHHhCCCCc
Q 030241 114 TMSDRIGQ--MRYIRRW--KIKSLVEAE---I---KTHYWLLACTLLVDKKTSHAL 159 (181)
Q Consensus 114 ~ia~~L~L--p~~v~e~--~i~k~a~~~---l---~~~~v~AAclYiACR~~~~p~ 159 (181)
+|+..+++ |..++.. ++|++.... + .--+=+.+|+|+||.+.+.++
T Consensus 3 ~l~p~~~~~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~ 58 (353)
T PF05460_consen 3 DLIPKLGGGLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKL 58 (353)
T ss_dssp --------------------------------------------------------
T ss_pred hhhhccCCCCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCcc
Confidence 34444544 5667777 788887632 3 223556789999999988776
No 280
>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=33.65 E-value=33 Score=21.17 Aligned_cols=30 Identities=27% Similarity=0.628 Sum_probs=22.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccCC
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~ 37 (181)
..|+.|+.. ++.-....-|..||.|+=..-
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 569999862 445677889999999975443
No 281
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=33.50 E-value=36 Score=20.68 Aligned_cols=35 Identities=26% Similarity=0.601 Sum_probs=22.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccccCCccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDE 40 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~ 40 (181)
+.+|-.|+. .| .-...--+.|..|++++-++=++.
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 467999986 23 223445689999999987665543
No 282
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=33.27 E-value=24 Score=22.17 Aligned_cols=31 Identities=23% Similarity=0.579 Sum_probs=18.3
Q ss_pred CCCCCCCCCC--CceeEeC--CCCceEeCCCcccc
Q 030241 3 DAFCSDCKKH--TEVVFDH--SAGDTVCSECGLVL 33 (181)
Q Consensus 3 ~~~Cp~Cg~~--~~iv~D~--~~G~~vC~~CG~Vl 33 (181)
...|..|+-. +..+.+- ..+-+.|.+||.+|
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcCCCeEECcCCCccC
Confidence 3568888741 1111121 34578999999875
No 283
>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=33.20 E-value=62 Score=26.56 Aligned_cols=29 Identities=7% Similarity=-0.036 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhCCchHHHHH--HHHHHHHhh
Q 030241 109 FKTIATMSDRIGQMRYIRRW--KIKSLVEAE 137 (181)
Q Consensus 109 ~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~ 137 (181)
-+.++++++.||||..-+++ .+|+.-.++
T Consensus 165 ~~~l~~l~~~L~ls~~kv~KDL~lYrsnLeK 195 (214)
T TIGR03060 165 NEILKELSEALGLSYDRVEKDLDLYKSNLEK 195 (214)
T ss_pred HHHHHHHHHHcCCCHHHHHhhHHHHHhHHHH
Confidence 45889999999999999888 899987665
No 284
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=32.98 E-value=86 Score=25.05 Aligned_cols=56 Identities=13% Similarity=0.137 Sum_probs=32.5
Q ss_pred CCchHHHHHHH---HHHHHHHHHhCCchHHHHH---HHHHHHHhhhCHHHHHHHHHHHHHHhC
Q 030241 99 SNPDRGLILAF---KTIATMSDRIGQMRYIRRW---KIKSLVEAEIKTHYWLLACTLLVDKKT 155 (181)
Q Consensus 99 ~~~er~l~~a~---~~I~~ia~~L~Lp~~v~e~---~i~k~a~~~l~~~~v~AAclYiACR~~ 155 (181)
+.+|+.+.+.+ ..-++||++|+++...++. .+|+|.--+ +...++.-.+-++|+.+
T Consensus 136 T~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv~-n~~eLv~~a~~~~~~~~ 197 (207)
T PRK11475 136 SPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVS-SDAGLLDAADILLCLRH 197 (207)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHhCcc
Confidence 44565543333 2357899999999987777 677665222 33333333444455544
No 285
>PRK00279 adk adenylate kinase; Reviewed
Probab=32.62 E-value=36 Score=27.04 Aligned_cols=33 Identities=24% Similarity=0.559 Sum_probs=20.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccC
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (181)
..||.||...++.+++......|..||.-+..+
T Consensus 128 ~~~~~~g~~~~~~~~~p~~~~~~~~~~~~l~~r 160 (215)
T PRK00279 128 RICPACGRTYHVKFNPPKVEGKCDVCGEELIQR 160 (215)
T ss_pred cccCccCCcccccCCCCCCcCcCcCCCCcccCC
Confidence 457777765556666655566677777544433
No 286
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=32.56 E-value=23 Score=33.31 Aligned_cols=33 Identities=24% Similarity=0.634 Sum_probs=22.4
Q ss_pred CCCCCCCCCCceeEeC------------CCCceEeCCCccccccC
Q 030241 4 AFCSDCKKHTEVVFDH------------SAGDTVCSECGLVLESH 36 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~------------~~G~~vC~~CG~Vl~e~ 36 (181)
.-||+||....+.++. +.-.+.|..|+.+|.+.
T Consensus 228 vpCPHCGe~q~l~~~e~~~~~g~~~~~~~~~~~~c~h~~~~i~~~ 272 (611)
T COG5525 228 VPCPHCGEEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVIRPK 272 (611)
T ss_pred eeCCCCCchhhccccccCCCcCcccchhhhhhhhccccCceeeee
Confidence 3599999744444422 22346899999999884
No 287
>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=32.53 E-value=16 Score=36.32 Aligned_cols=23 Identities=26% Similarity=0.473 Sum_probs=17.0
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
..+||.||.. +=...|..||.-.
T Consensus 625 ~RKCPkCG~y--------Tlk~rCP~CG~~T 647 (1095)
T TIGR00354 625 IRKCPQCGKE--------SFWLKCPVCGELT 647 (1095)
T ss_pred EEECCCCCcc--------cccccCCCCCCcc
Confidence 3689999973 2257899999763
No 288
>smart00400 ZnF_CHCC zinc finger.
Probab=32.46 E-value=60 Score=20.14 Aligned_cols=26 Identities=15% Similarity=0.310 Sum_probs=20.8
Q ss_pred CCCCCCCC-CceeEeCCCCceEeCCCc
Q 030241 5 FCSDCKKH-TEVVFDHSAGDTVCSECG 30 (181)
Q Consensus 5 ~Cp~Cg~~-~~iv~D~~~G~~vC~~CG 30 (181)
.||-+... +++.++...+..-|-.||
T Consensus 4 ~cPfh~d~~pSf~v~~~kn~~~Cf~cg 30 (55)
T smart00400 4 LCPFHGEKTPSFSVSPDKQFFHCFGCG 30 (55)
T ss_pred cCcCCCCCCCCEEEECCCCEEEEeCCC
Confidence 59988753 457788888889999997
No 289
>PRK09462 fur ferric uptake regulator; Provisional
Probab=32.01 E-value=23 Score=26.72 Aligned_cols=12 Identities=42% Similarity=1.113 Sum_probs=10.8
Q ss_pred ceEeCCCccccc
Q 030241 23 DTVCSECGLVLE 34 (181)
Q Consensus 23 ~~vC~~CG~Vl~ 34 (181)
-.+|..||.|++
T Consensus 90 H~iC~~Cg~i~~ 101 (148)
T PRK09462 90 HLICLDCGKVIE 101 (148)
T ss_pred ceEECCCCCEEE
Confidence 499999999986
No 290
>PRK13266 Thf1-like protein; Reviewed
Probab=31.88 E-value=66 Score=26.58 Aligned_cols=29 Identities=7% Similarity=0.023 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhCCchHHHHH--HHHHHHHhh
Q 030241 109 FKTIATMSDRIGQMRYIRRW--KIKSLVEAE 137 (181)
Q Consensus 109 ~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~ 137 (181)
.+.++++++.||||..-++. .+|+.-.++
T Consensus 167 ~~~l~~l~~~L~ls~~kv~KDL~lYrsnLeK 197 (225)
T PRK13266 167 NEALKDISEGLGLSKEKVEKDLDLYRSNLEK 197 (225)
T ss_pred HHHHHHHHHHcCCCHHHHHhhHHHHHhHHHH
Confidence 35889999999999998888 899987665
No 291
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=31.66 E-value=22 Score=23.49 Aligned_cols=13 Identities=31% Similarity=0.759 Sum_probs=10.7
Q ss_pred eEeCCCccccccC
Q 030241 24 TVCSECGLVLESH 36 (181)
Q Consensus 24 ~vC~~CG~Vl~e~ 36 (181)
+.|..||.|+.+.
T Consensus 5 vRCFTCGkvi~~~ 17 (62)
T PRK04016 5 VRCFTCGKVIAEK 17 (62)
T ss_pred eEecCCCCChHHH
Confidence 6799999999643
No 292
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=31.47 E-value=30 Score=18.24 Aligned_cols=9 Identities=22% Similarity=0.501 Sum_probs=6.7
Q ss_pred CCCCCCCCC
Q 030241 3 DAFCSDCKK 11 (181)
Q Consensus 3 ~~~Cp~Cg~ 11 (181)
...||.||.
T Consensus 2 l~~C~~CgR 10 (25)
T PF13913_consen 2 LVPCPICGR 10 (25)
T ss_pred CCcCCCCCC
Confidence 456888886
No 293
>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=31.43 E-value=29 Score=32.08 Aligned_cols=33 Identities=27% Similarity=0.584 Sum_probs=20.8
Q ss_pred CCCCCCCCCCceeEeCC---CCceEeCCCccccccCC
Q 030241 4 AFCSDCKKHTEVVFDHS---AGDTVCSECGLVLESHS 37 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~---~G~~vC~~CG~Vl~e~~ 37 (181)
-.||+||.....+++.. +=.+.| +||.-.+-.+
T Consensus 169 pic~~cGrv~~~~~~~~~~~~v~Y~c-~cG~~g~~~~ 204 (515)
T TIGR00467 169 VFCENCGRDTTTVNNYDNEYSIEYSC-ECGNQESVDI 204 (515)
T ss_pred eecCCcCccCceEEEecCCceEEEEc-CCCCEEEEee
Confidence 36999998543444443 345678 5998865544
No 294
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.41 E-value=40 Score=23.42 Aligned_cols=28 Identities=29% Similarity=0.609 Sum_probs=18.4
Q ss_pred CCCCCCCCCCceeEeCCCCc--eEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGD--TVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~--~vC~~CG~Vl 33 (181)
..||.|+- +++--...|- --|..|+-|-
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 56999995 3444333343 3599999885
No 295
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=31.35 E-value=26 Score=25.08 Aligned_cols=12 Identities=25% Similarity=0.437 Sum_probs=9.4
Q ss_pred CCCCCCCCCCCC
Q 030241 1 MTDAFCSDCKKH 12 (181)
Q Consensus 1 m~~~~Cp~Cg~~ 12 (181)
|....||.||..
T Consensus 1 mlLI~CP~Cg~R 12 (97)
T COG4311 1 MLLIPCPYCGER 12 (97)
T ss_pred CceecCCCCCCC
Confidence 666789999973
No 296
>PRK08173 DNA topoisomerase III; Validated
Probab=31.18 E-value=31 Score=33.98 Aligned_cols=27 Identities=19% Similarity=0.533 Sum_probs=18.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
..||.||+ . ++. ..+...|++|+..+-
T Consensus 625 ~~CP~Cg~-~-~~~--~~~~~~Cs~C~f~~~ 651 (862)
T PRK08173 625 TPCPNCGG-V-VKE--NYRRFACTKCDFSIS 651 (862)
T ss_pred ccCCcccc-c-ccc--cCceeEcCCCCcccc
Confidence 46999997 2 322 234499999998773
No 297
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=30.99 E-value=18 Score=31.87 Aligned_cols=12 Identities=17% Similarity=0.697 Sum_probs=8.9
Q ss_pred CCCCCCCCCCCC
Q 030241 1 MTDAFCSDCKKH 12 (181)
Q Consensus 1 m~~~~Cp~Cg~~ 12 (181)
|..+.|+.||..
T Consensus 4 ~~~~~C~~CGr~ 15 (355)
T COG1499 4 ASTILCVRCGRS 15 (355)
T ss_pred CcccEeccCCCc
Confidence 345789999974
No 298
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=30.85 E-value=37 Score=32.46 Aligned_cols=34 Identities=24% Similarity=0.453 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCC---CccccccCCc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSE---CGLVLESHSI 38 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~---CG~Vl~e~~i 38 (181)
+..||.||+ .++.+...-.+.|.+ |-.-+..+++
T Consensus 404 P~~CP~Cgs--~l~~~~~~~~~~C~n~~~C~aq~~~~l~ 440 (665)
T PRK07956 404 PTHCPVCGS--ELVRVEGEAVLRCTNGLSCPAQLKERLI 440 (665)
T ss_pred CCCCCCCCC--EeEecCCCeEEECCCCCCCHHHHHHHHH
Confidence 468999997 455554445788973 8666655554
No 299
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=30.72 E-value=27 Score=25.90 Aligned_cols=19 Identities=16% Similarity=0.580 Sum_probs=10.4
Q ss_pred eeEeCCCCceEeCCCcccc
Q 030241 15 VVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 15 iv~D~~~G~~vC~~CG~Vl 33 (181)
+......++.-|.+||.++
T Consensus 62 l~Ie~~p~~~~C~~C~~~~ 80 (115)
T COG0375 62 LHIEEEPAECWCLDCGQEV 80 (115)
T ss_pred EEEEEeccEEEeccCCCee
Confidence 4444455666666665544
No 300
>PHA02540 61 DNA primase; Provisional
Probab=30.69 E-value=48 Score=29.05 Aligned_cols=28 Identities=18% Similarity=0.366 Sum_probs=22.2
Q ss_pred CCCCCCCC------CceeEeCCCC--ceEeCCCccc
Q 030241 5 FCSDCKKH------TEVVFDHSAG--DTVCSECGLV 32 (181)
Q Consensus 5 ~Cp~Cg~~------~~iv~D~~~G--~~vC~~CG~V 32 (181)
.||-|+.. +...+.++.| ..-|-+||.=
T Consensus 29 ~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa~ 64 (337)
T PHA02540 29 RCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGYH 64 (337)
T ss_pred cCCCCCCccccCcCCcEEEeccCCceEEEecCCCCC
Confidence 59999962 2477888888 8999999963
No 301
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=30.59 E-value=22 Score=26.35 Aligned_cols=18 Identities=22% Similarity=0.663 Sum_probs=11.1
Q ss_pred ceeEeCCCCceEeCCCccc
Q 030241 14 EVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 14 ~iv~D~~~G~~vC~~CG~V 32 (181)
.+......+..-| +||..
T Consensus 61 ~L~I~~vp~~~~C-~Cg~~ 78 (124)
T PRK00762 61 DLIVEMIPVEIEC-ECGYE 78 (124)
T ss_pred EEEEEecCeeEEe-eCcCc
Confidence 4555666666677 77743
No 302
>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=30.57 E-value=27 Score=20.31 Aligned_cols=10 Identities=40% Similarity=1.026 Sum_probs=8.1
Q ss_pred CCCCCCCCCCc
Q 030241 4 AFCSDCKKHTE 14 (181)
Q Consensus 4 ~~Cp~Cg~~~~ 14 (181)
..||.|++ +.
T Consensus 6 v~CP~C~s-~~ 15 (36)
T PF03811_consen 6 VHCPRCQS-TE 15 (36)
T ss_pred eeCCCCCC-CC
Confidence 57999998 55
No 303
>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=30.56 E-value=25 Score=24.95 Aligned_cols=13 Identities=31% Similarity=1.022 Sum_probs=11.4
Q ss_pred CceEeCCCccccc
Q 030241 22 GDTVCSECGLVLE 34 (181)
Q Consensus 22 G~~vC~~CG~Vl~ 34 (181)
.-.+|.+||.|.+
T Consensus 72 ~H~~C~~Cg~i~~ 84 (116)
T cd07153 72 HHLICTKCGKVID 84 (116)
T ss_pred CceEeCCCCCEEE
Confidence 3699999999986
No 304
>PF11264 ThylakoidFormat: Thylakoid formation protein; InterPro: IPR017499 Psp29, originally designated sll1414 (P73956 from SWISSPROT) in Synechocystis sp. (strain PCC 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.; GO: 0010027 thylakoid membrane organization, 0015979 photosynthesis, 0009523 photosystem II
Probab=30.53 E-value=78 Score=25.99 Aligned_cols=30 Identities=7% Similarity=0.021 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHhCCchHHHHH--HHHHHHHhh
Q 030241 108 AFKTIATMSDRIGQMRYIRRW--KIKSLVEAE 137 (181)
Q Consensus 108 a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~ 137 (181)
--..|+++++.||||..-+++ .+|+...++
T Consensus 161 ~~~~l~~l~~~l~ls~~kv~kDL~lYrsnLeK 192 (216)
T PF11264_consen 161 RPEALEKLSEALGLSKEKVEKDLDLYRSNLEK 192 (216)
T ss_pred HHHHHHHHHHHcCCCHHHHHhhHHHHHhHHHH
Confidence 345788899999999998888 899987766
No 305
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=30.26 E-value=25 Score=26.70 Aligned_cols=13 Identities=38% Similarity=0.991 Sum_probs=11.0
Q ss_pred CceEeCCCccccc
Q 030241 22 GDTVCSECGLVLE 34 (181)
Q Consensus 22 G~~vC~~CG~Vl~ 34 (181)
.-+||.+||.|++
T Consensus 92 ~HliC~~CG~v~e 104 (145)
T COG0735 92 HHLICLDCGKVIE 104 (145)
T ss_pred cEEEecCCCCEEE
Confidence 3589999999986
No 306
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=30.24 E-value=51 Score=29.44 Aligned_cols=34 Identities=15% Similarity=0.259 Sum_probs=26.0
Q ss_pred CCCCCCCC-CceeEeCCCCceEeCCCccccccCCccc
Q 030241 5 FCSDCKKH-TEVVFDHSAGDTVCSECGLVLESHSIDE 40 (181)
Q Consensus 5 ~Cp~Cg~~-~~iv~D~~~G~~vC~~CG~Vl~e~~id~ 40 (181)
.||.|+.. +++.+++..|..-|-.||. .-++|+.
T Consensus 36 ~CPfh~ek~pSf~v~~~k~~~~Cf~Cg~--~Gd~i~f 70 (415)
T TIGR01391 36 LCPFHHEKTPSFSVSPEKQFYHCFGCGA--GGDAIKF 70 (415)
T ss_pred eCCCCCCCCCeEEEEcCCCcEEECCCCC--CCCHHHH
Confidence 59999764 4688899999999999996 3345543
No 307
>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=29.89 E-value=17 Score=22.75 Aligned_cols=29 Identities=24% Similarity=0.361 Sum_probs=21.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccccCCccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDE 40 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~ 40 (181)
..||-|+. ++.| .|...||.|++...|..
T Consensus 2 ~~Cpi~~~---~~~~-----Pv~~~~G~v~~~~~i~~ 30 (63)
T smart00504 2 FLCPISLE---VMKD-----PVILPSGQTYERRAIEK 30 (63)
T ss_pred cCCcCCCC---cCCC-----CEECCCCCEEeHHHHHH
Confidence 46999996 3444 37789999998777753
No 308
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=29.70 E-value=29 Score=22.26 Aligned_cols=36 Identities=28% Similarity=0.592 Sum_probs=24.8
Q ss_pred CCCCCCCCC--CceeEeCCCCceEeCC-CccccccCCccc
Q 030241 4 AFCSDCKKH--TEVVFDHSAGDTVCSE-CGLVLESHSIDE 40 (181)
Q Consensus 4 ~~Cp~Cg~~--~~iv~D~~~G~~vC~~-CG~Vl~e~~id~ 40 (181)
.+|..|+.+ ...+++...| .||.. |-.-++|..+.+
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G-~VH~g~C~~y~~e~~~SE 40 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESG-PVHPGVCAQYLEELPVSE 40 (54)
T ss_pred CeeeeeCCccCcceEEEcCCC-ccCcHHHHHHHHhccccc
Confidence 579999974 2356666677 67764 877777776543
No 309
>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=29.54 E-value=30 Score=35.42 Aligned_cols=31 Identities=39% Similarity=0.865 Sum_probs=22.5
Q ss_pred CCCCCCCCCCCceeEeCCCC------ceEeCCCccccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAG------DTVCSECGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G------~~vC~~CG~Vl~ 34 (181)
...||+|+- .+++.|..-| +-.|..||.-+.
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 457999995 6777764333 457999998774
No 310
>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=29.39 E-value=35 Score=27.40 Aligned_cols=38 Identities=21% Similarity=0.373 Sum_probs=23.3
Q ss_pred CCCCCCCCCCCceeEeC------CCCceEeCCCccccccCCcccc
Q 030241 3 DAFCSDCKKHTEVVFDH------SAGDTVCSECGLVLESHSIDET 41 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~------~~G~~vC~~CG~Vl~e~~id~~ 41 (181)
...|..|+.... ..+. ......|..||-++..+++-.|
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 467999985211 1111 1123569999999888877654
No 311
>PF00488 MutS_V: MutS domain V C-terminus.; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....
Probab=29.27 E-value=62 Score=26.49 Aligned_cols=23 Identities=17% Similarity=0.128 Sum_probs=17.3
Q ss_pred HHHHHhCCchHHHHH--HHHHHHHh
Q 030241 114 TMSDRIGQMRYIRRW--KIKSLVEA 136 (181)
Q Consensus 114 ~ia~~L~Lp~~v~e~--~i~k~a~~ 136 (181)
++|..+|+|+.|+++ ++++++++
T Consensus 210 ~iA~~~g~p~~II~rA~~i~~~l~~ 234 (235)
T PF00488_consen 210 EIAKLAGLPEEIIERAKEILKQLEE 234 (235)
T ss_dssp HHHHHTT--HHHHHHHHHHHHHHHT
T ss_pred HHHHHhCcCHHHHHHHHHHHHHHhc
Confidence 567889999999999 78888764
No 312
>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=29.24 E-value=27 Score=25.09 Aligned_cols=13 Identities=31% Similarity=1.012 Sum_probs=10.1
Q ss_pred CceEeCCCccccc
Q 030241 22 GDTVCSECGLVLE 34 (181)
Q Consensus 22 G~~vC~~CG~Vl~ 34 (181)
.-.+|..||.|.+
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 4589999999985
No 313
>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=29.07 E-value=13 Score=32.84 Aligned_cols=34 Identities=26% Similarity=0.523 Sum_probs=17.1
Q ss_pred CCCCCCC-CCce--eEe--CCCCceEeCCCccccccCCc
Q 030241 5 FCSDCKK-HTEV--VFD--HSAGDTVCSECGLVLESHSI 38 (181)
Q Consensus 5 ~Cp~Cg~-~~~i--v~D--~~~G~~vC~~CG~Vl~e~~i 38 (181)
.|++||. .+.. .+| ..+=.+.|.+||..-+-.+-
T Consensus 176 iC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~i~ 214 (360)
T PF01921_consen 176 ICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVDIT 214 (360)
T ss_dssp EETTTEE--EEEEEEE--SSSEEEEE--TTS---EEETT
T ss_pred eccccCCcccceeeEeecCCCEEEEEecCCCCEEEEecC
Confidence 5999997 2333 334 23345789999998765553
No 314
>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=29.05 E-value=47 Score=18.52 Aligned_cols=26 Identities=15% Similarity=0.557 Sum_probs=13.9
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECG 30 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG 30 (181)
.|+.++...-.++=.+.+..+|..|-
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C~ 27 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDCD 27 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhcC
Confidence 58888752222333345556666663
No 315
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.95 E-value=42 Score=24.53 Aligned_cols=8 Identities=25% Similarity=0.908 Sum_probs=4.1
Q ss_pred CCCCCCCC
Q 030241 4 AFCSDCKK 11 (181)
Q Consensus 4 ~~Cp~Cg~ 11 (181)
..||.||.
T Consensus 50 t~CP~Cg~ 57 (115)
T COG1885 50 TSCPKCGE 57 (115)
T ss_pred ccCCCCCC
Confidence 34555554
No 316
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=28.83 E-value=40 Score=31.95 Aligned_cols=28 Identities=21% Similarity=0.535 Sum_probs=15.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
.+||.|++..-++.- ..--.+|..-|.+
T Consensus 3 ~~C~~C~g~G~i~v~-~e~c~vc~gtG~~ 30 (715)
T COG1107 3 KKCPECGGKGKIVVG-EEECPVCHGTGFS 30 (715)
T ss_pred ccccccCCCceEeee-eeecccccccccc
Confidence 679999985555442 2223444444555
No 317
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=28.75 E-value=46 Score=24.27 Aligned_cols=31 Identities=23% Similarity=0.574 Sum_probs=19.6
Q ss_pred CCCCCCCCC----CceeEeCCCC--ceEeCCCccccc
Q 030241 4 AFCSDCKKH----TEVVFDHSAG--DTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~----~~iv~D~~~G--~~vC~~CG~Vl~ 34 (181)
.+|+.|.+. .+...-...| .+.|.+||.+..
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 579999862 1222223334 567999999864
No 318
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.73 E-value=24 Score=30.20 Aligned_cols=28 Identities=36% Similarity=0.940 Sum_probs=21.4
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
|..-.||+||. .+-+| ...|..||.-|.
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 56678999997 35554 468999998876
No 319
>COG2979 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.61 E-value=66 Score=26.46 Aligned_cols=20 Identities=5% Similarity=0.071 Sum_probs=17.9
Q ss_pred HHHHHHHHHHhCCchHHHHH
Q 030241 109 FKTIATMSDRIGQMRYIRRW 128 (181)
Q Consensus 109 ~~~I~~ia~~L~Lp~~v~e~ 128 (181)
+.+++.++.+|+||+.++|.
T Consensus 194 r~YL~~La~~L~L~dalvd~ 213 (225)
T COG2979 194 RSYLNALAGALGLPDALVDH 213 (225)
T ss_pred HHHHHHHHHHhCCCHHHHHH
Confidence 45789999999999999887
No 320
>PF03685 UPF0147: Uncharacterised protein family (UPF0147); InterPro: IPR005354 The proteins in this entry are functionally uncharacterised.; PDB: 2QZG_C 2QSB_A.
Probab=28.61 E-value=1.9e+02 Score=20.21 Aligned_cols=50 Identities=14% Similarity=0.159 Sum_probs=30.9
Q ss_pred chHHHHHHHHHHHHHHHHhCCchHHHHH--HHHHHHHhh-hCHHHHHHHHHHH
Q 030241 101 PDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-IKTHYWLLACTLL 150 (181)
Q Consensus 101 ~er~l~~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~-l~~~~v~AAclYi 150 (181)
.|..++++...+++|.+--.+|.+|... +......+. .....=+|.++++
T Consensus 4 ~e~~i~~~~~~L~~I~~D~sVPRNIRr~a~ea~~~L~~e~~~~~vRaataIs~ 56 (85)
T PF03685_consen 4 NEEKIKQAIQMLERIINDTSVPRNIRRAAEEAKEILNNEEESPGVRAATAISI 56 (85)
T ss_dssp HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHCT-TTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHhCCCcchhHhHHHHHHH
Confidence 3667889999999999999999999877 444433332 2333334444444
No 321
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=28.33 E-value=99 Score=20.11 Aligned_cols=27 Identities=15% Similarity=0.107 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCchHHHHHHHHHHHHhh
Q 030241 111 TIATMSDRIGQMRYIRRWKIKSLVEAE 137 (181)
Q Consensus 111 ~I~~ia~~L~Lp~~v~e~~i~k~a~~~ 137 (181)
...+||..|||+...+.+.+|++..++
T Consensus 24 ta~eLa~~lgl~~~~v~r~L~~L~~~G 50 (68)
T smart00550 24 TALQLAKNLGLPKKEVNRVLYSLEKKG 50 (68)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 367899999999997777778777665
No 322
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=28.24 E-value=1.4e+02 Score=17.86 Aligned_cols=22 Identities=14% Similarity=0.249 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHhCCchH-HHHH
Q 030241 107 LAFKTIATMSDRIGQMRY-IRRW 128 (181)
Q Consensus 107 ~a~~~I~~ia~~L~Lp~~-v~e~ 128 (181)
+-+..++.++...|+|.+ ++++
T Consensus 12 el~~~L~~ls~~t~i~~S~Ll~e 34 (44)
T PF12651_consen 12 ELYEKLKELSEETGIPKSKLLRE 34 (44)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHH
Confidence 356799999999999986 4444
No 323
>PRK11032 hypothetical protein; Provisional
Probab=28.19 E-value=27 Score=27.29 Aligned_cols=14 Identities=36% Similarity=0.790 Sum_probs=12.3
Q ss_pred CCCceEeCCCcccc
Q 030241 20 SAGDTVCSECGLVL 33 (181)
Q Consensus 20 ~~G~~vC~~CG~Vl 33 (181)
.-|.+||.+||.-+
T Consensus 121 g~G~LvC~~Cg~~~ 134 (160)
T PRK11032 121 GLGNLVCEKCHHHL 134 (160)
T ss_pred ecceEEecCCCCEE
Confidence 47999999999987
No 324
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=28.09 E-value=27 Score=29.27 Aligned_cols=39 Identities=26% Similarity=0.371 Sum_probs=24.2
Q ss_pred CCCCCCCCCCCc---eeEeCCCC-ceEeCCCcc-ccccCCcccc
Q 030241 3 DAFCSDCKKHTE---VVFDHSAG-DTVCSECGL-VLESHSIDET 41 (181)
Q Consensus 3 ~~~Cp~Cg~~~~---iv~D~~~G-~~vC~~CG~-Vl~e~~id~~ 41 (181)
..+|..||.... +......+ -..|..||- +|..+++-.|
T Consensus 122 ~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~~lrP~VV~fG 165 (250)
T COG0846 122 RVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGPVLRPDVVWFG 165 (250)
T ss_pred eeEeCCCcCccchhhhhhhcccCCCCcCccCCCccccCCEEEeC
Confidence 357999986221 11112233 467999999 9988876443
No 325
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=28.00 E-value=38 Score=20.39 Aligned_cols=26 Identities=19% Similarity=0.567 Sum_probs=19.7
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcccccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e 35 (181)
+|+.|++ .+.....+.|..|+..+=.
T Consensus 1 ~C~vC~~-----~~~~~~~i~C~~C~~~~H~ 26 (51)
T PF00628_consen 1 YCPVCGQ-----SDDDGDMIQCDSCNRWYHQ 26 (51)
T ss_dssp EBTTTTS-----SCTTSSEEEBSTTSCEEET
T ss_pred eCcCCCC-----cCCCCCeEEcCCCChhhCc
Confidence 4888986 2556778999999987643
No 326
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=28.00 E-value=43 Score=25.05 Aligned_cols=28 Identities=21% Similarity=0.571 Sum_probs=21.0
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
.|-.||..+.+-.+...-...|..|+.+
T Consensus 2 ~C~fC~~~s~~~~~~~~~~w~C~~C~q~ 29 (131)
T PF09779_consen 2 NCWFCGQNSKVPYDNRNSNWTCPHCEQY 29 (131)
T ss_pred eeccCCCCCCCCCCCCCCeeECCCCCCc
Confidence 5999998555555544555999999987
No 327
>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=27.91 E-value=35 Score=26.33 Aligned_cols=8 Identities=25% Similarity=0.700 Sum_probs=4.7
Q ss_pred CCCCCCCC
Q 030241 4 AFCSDCKK 11 (181)
Q Consensus 4 ~~Cp~Cg~ 11 (181)
..||.||+
T Consensus 33 v~CP~Cgs 40 (148)
T PF06676_consen 33 VSCPVCGS 40 (148)
T ss_pred ccCCCCCC
Confidence 44666665
No 328
>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=27.85 E-value=44 Score=31.83 Aligned_cols=34 Identities=15% Similarity=0.283 Sum_probs=22.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeC--CCccccccCCc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCS--ECGLVLESHSI 38 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~--~CG~Vl~e~~i 38 (181)
+..||.||+ .++.+...-.+.|. .|-.-+..+++
T Consensus 392 P~~CP~C~s--~l~~~~~~~~~~C~n~~C~aq~~~~l~ 427 (652)
T TIGR00575 392 PTHCPSCGS--PLVKIEEEAVIRCPNLNCPAQRVERIK 427 (652)
T ss_pred CCCCCCCCC--EeEecCCcEEEEECCCCCHHHHHHHhH
Confidence 467999997 45555444567896 47666655554
No 329
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=27.38 E-value=24 Score=29.17 Aligned_cols=39 Identities=21% Similarity=0.282 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCc--cccccCCcccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECG--LVLESHSIDET 41 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG--~Vl~e~~id~~ 41 (181)
.+.|..|+..-+...+...+...|..|| -++..+++-.|
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 3679999962221112223457799998 56777776543
No 330
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=27.23 E-value=39 Score=27.71 Aligned_cols=38 Identities=18% Similarity=0.420 Sum_probs=22.6
Q ss_pred CCCCCCCCCCCceeEeC-CCCceEeCCCccccccCCcccc
Q 030241 3 DAFCSDCKKHTEVVFDH-SAGDTVCSECGLVLESHSIDET 41 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~-~~G~~vC~~CG~Vl~e~~id~~ 41 (181)
...|..|+..-. ..+. ......|..||-++..+++-.+
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 356999985211 1111 1223349999999988876443
No 331
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.22 E-value=34 Score=32.96 Aligned_cols=26 Identities=27% Similarity=0.606 Sum_probs=14.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (181)
.+|++||-...+..+ ..| ..|..||-
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 568888852222121 223 57888884
No 332
>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=27.18 E-value=44 Score=19.45 Aligned_cols=14 Identities=29% Similarity=0.672 Sum_probs=9.3
Q ss_pred CCCceEeCCCcccc
Q 030241 20 SAGDTVCSECGLVL 33 (181)
Q Consensus 20 ~~G~~vC~~CG~Vl 33 (181)
.---.+|..||..+
T Consensus 29 ~vp~~~C~~CGE~~ 42 (46)
T TIGR03831 29 NVPALVCPQCGEEY 42 (46)
T ss_pred CCCccccccCCCEe
Confidence 34457788888765
No 333
>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=27.06 E-value=40 Score=25.17 Aligned_cols=26 Identities=27% Similarity=0.592 Sum_probs=17.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
.+|+.||. --.+.+...|+++| ||.-
T Consensus 8 YkC~~CGn-iv~v~~~g~~~l~C--Cge~ 33 (125)
T TIGR00320 8 YKCEVCGN-IVEVLNAGIGQLVC--CNQP 33 (125)
T ss_pred EECCCCCc-EEEEEECCCcceee--CCcc
Confidence 57999996 33346667778877 4643
No 334
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=27.04 E-value=49 Score=25.39 Aligned_cols=33 Identities=27% Similarity=0.593 Sum_probs=27.0
Q ss_pred eCCCCceEeCCCccccc--cCCccccccccccccC
Q 030241 18 DHSAGDTVCSECGLVLE--SHSIDETSEWRTFANE 50 (181)
Q Consensus 18 D~~~G~~vC~~CG~Vl~--e~~id~~~Ewr~F~~~ 50 (181)
..+.|-++|..||.-|= +.-+|.|--|.+|.+.
T Consensus 49 ~~e~GvY~C~~C~~pLykS~tKfdsgcGWPAF~e~ 83 (146)
T KOG0856|consen 49 HFEEGVYVCAGCGTPLYKSTTKFDSGCGWPAFFEA 83 (146)
T ss_pred ccCCceEEEeecCCccccccccccCCCCCchhhhc
Confidence 34899999999998874 4457889999999865
No 335
>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=26.77 E-value=34 Score=27.81 Aligned_cols=37 Identities=19% Similarity=0.420 Sum_probs=23.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccccCCcccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDET 41 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~ 41 (181)
...|..|+.. ...+.......|..||-++..+++-.|
T Consensus 118 ~~~C~~C~~~--~~~~~~~~~p~C~~Cgg~lrP~vv~fg 154 (225)
T cd01411 118 RIYCTVCGKT--VDWEEYLKSPYHAKCGGVIRPDIVLYE 154 (225)
T ss_pred eeEeCCCCCc--cchhhcCCCCCCCCCCCEeCCCEEEcC
Confidence 3569999752 111222224679999999988877544
No 336
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=26.67 E-value=29 Score=26.30 Aligned_cols=13 Identities=46% Similarity=0.997 Sum_probs=10.4
Q ss_pred EeCCCccccccCC
Q 030241 25 VCSECGLVLESHS 37 (181)
Q Consensus 25 vC~~CG~Vl~e~~ 37 (181)
-|++||.|+++..
T Consensus 3 ~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 3 QCTKCGRVFEDGS 15 (131)
T ss_pred ccCcCCCCcCCCc
Confidence 4999999987654
No 337
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=26.47 E-value=31 Score=26.78 Aligned_cols=12 Identities=42% Similarity=0.891 Sum_probs=10.8
Q ss_pred ceEeCCCccccc
Q 030241 23 DTVCSECGLVLE 34 (181)
Q Consensus 23 ~~vC~~CG~Vl~ 34 (181)
-.+|.+||.|++
T Consensus 100 H~iC~~CGki~~ 111 (169)
T PRK11639 100 MFICDRCGAVKE 111 (169)
T ss_pred eEEeCCCCCEEE
Confidence 489999999986
No 338
>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=26.41 E-value=38 Score=26.41 Aligned_cols=27 Identities=30% Similarity=0.716 Sum_probs=15.2
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccccccCCccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDE 40 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~ 40 (181)
+|..||. ..| ..|.+|+.=|.-....+
T Consensus 30 fC~kCG~-~tI--------~~Cp~C~~~IrG~y~v~ 56 (158)
T PF10083_consen 30 FCSKCGA-KTI--------TSCPNCSTPIRGDYHVE 56 (158)
T ss_pred HHHHhhH-HHH--------HHCcCCCCCCCCceecC
Confidence 4666765 222 35777776666554443
No 339
>PRK07217 replication factor A; Reviewed
Probab=26.05 E-value=33 Score=29.70 Aligned_cols=21 Identities=33% Similarity=0.748 Sum_probs=14.9
Q ss_pred CCCCC--CCCCCceeEeCCCCceEeCCCccc
Q 030241 4 AFCSD--CKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~--Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
.+||+ |+.. + ....|.+||.|
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 9862 2 22589999977
No 340
>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=25.94 E-value=84 Score=17.62 Aligned_cols=27 Identities=22% Similarity=0.694 Sum_probs=18.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
..|..|+. .+.+-+.....-|+-|..|
T Consensus 2 ~~C~~C~t--~L~yP~gA~~vrCs~C~~v 28 (31)
T TIGR01053 2 VVCGGCRT--LLMYPRGASSVRCALCQTV 28 (31)
T ss_pred cCcCCCCc--EeecCCCCCeEECCCCCeE
Confidence 46888874 4555556667778888766
No 341
>KOG3251 consensus Golgi SNAP receptor complex member [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.72 E-value=3.3e+02 Score=22.36 Aligned_cols=27 Identities=19% Similarity=0.081 Sum_probs=22.8
Q ss_pred hHHHHHHHHHHHHHHHHhCCchHHHHH
Q 030241 102 DRGLILAFKTIATMSDRIGQMRYIRRW 128 (181)
Q Consensus 102 er~l~~a~~~I~~ia~~L~Lp~~v~e~ 128 (181)
..+|..+-++|..+++.|||+.+++.-
T Consensus 156 ~~~L~~~~~ki~~~~ntLGlSn~ti~l 182 (213)
T KOG3251|consen 156 RLTLKGTQKKILDILNTLGLSNQTIRL 182 (213)
T ss_pred HHHHHHHHHHHHHHHHhcCCcHHHHHH
Confidence 457788999999999999999987554
No 342
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=25.58 E-value=20 Score=30.31 Aligned_cols=24 Identities=25% Similarity=0.598 Sum_probs=18.9
Q ss_pred CCceEeCCCccccccCCccc-cccc
Q 030241 21 AGDTVCSECGLVLESHSIDE-TSEW 44 (181)
Q Consensus 21 ~G~~vC~~CG~Vl~e~~id~-~~Ew 44 (181)
-|-.||..|-.+|+|++|.. |--|
T Consensus 193 mgipiCgaC~rpIeervi~amgKhW 217 (332)
T KOG2272|consen 193 MGIPICGACRRPIEERVIFAMGKHW 217 (332)
T ss_pred cCCcccccccCchHHHHHHHhcccc
Confidence 57788899999999998854 5555
No 343
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=25.54 E-value=90 Score=25.47 Aligned_cols=27 Identities=4% Similarity=0.038 Sum_probs=24.1
Q ss_pred HHHHHHHHhCCchHHHHH--HHHHHHHhh
Q 030241 111 TIATMSDRIGQMRYIRRW--KIKSLVEAE 137 (181)
Q Consensus 111 ~I~~ia~~L~Lp~~v~e~--~i~k~a~~~ 137 (181)
.++++++.||||..-+++ .+|+.-.++
T Consensus 159 ~l~~l~~~L~ls~~kv~kDL~lYrsnLeK 187 (206)
T PLN03060 159 VLEKLSKALNVSKRSVDRDLDVYRNLLSK 187 (206)
T ss_pred HHHHHHHHcCCCHHHHHhhHHHHHhHHHH
Confidence 889999999999998888 899987666
No 344
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=25.35 E-value=39 Score=29.58 Aligned_cols=32 Identities=19% Similarity=0.599 Sum_probs=24.9
Q ss_pred CCCCCCCC--CCCCCceeEeCCCCceEeCC-Cccccc
Q 030241 1 MTDAFCSD--CKKHTEVVFDHSAGDTVCSE-CGLVLE 34 (181)
Q Consensus 1 m~~~~Cp~--Cg~~~~iv~D~~~G~~vC~~-CG~Vl~ 34 (181)
|....||. ||. .+...++.+..-|.+ ||.+.=
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 44567875 885 467788999999998 999874
No 345
>PRK00039 ruvC Holliday junction resolvase; Reviewed
Probab=25.09 E-value=82 Score=24.45 Aligned_cols=63 Identities=8% Similarity=0.019 Sum_probs=39.6
Q ss_pred hHHHHHHHHHHHHHHHHhCCchHHHHHHHHHH-HHhhhCHHHHHHHHHHHHHHhCCCCccccChh
Q 030241 102 DRGLILAFKTIATMSDRIGQMRYIRRWKIKSL-VEAEIKTHYWLLACTLLVDKKTSHALLRVQPK 165 (181)
Q Consensus 102 er~l~~a~~~I~~ia~~L~Lp~~v~e~~i~k~-a~~~l~~~~v~AAclYiACR~~~~p~t~~~~~ 165 (181)
.++|...++.|.++-+..+...-++|..+|.+ ....++. ..+...++.+|.+++.|+..++|.
T Consensus 43 ~~Rl~~I~~~l~~~i~~~~Pd~vaiE~~f~~~n~~sa~~l-~~arGvi~la~~~~~ipv~ey~P~ 106 (164)
T PRK00039 43 PERLKQIYDGLSELIDEYQPDEVAIEEVFFNKNPQSALKL-GQARGVAILAAAQRGLPVAEYTPL 106 (164)
T ss_pred HHHHHHHHHHHHHHHHHhCCCEEEEehhhhccChHHHHHH-HHHHHHHHHHHHHcCCCEEEECHH
Confidence 45677888888888887765545567633332 2222222 225567788999999998755543
No 346
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=25.04 E-value=25 Score=23.17 Aligned_cols=13 Identities=31% Similarity=0.736 Sum_probs=10.5
Q ss_pred eEeCCCccccccC
Q 030241 24 TVCSECGLVLESH 36 (181)
Q Consensus 24 ~vC~~CG~Vl~e~ 36 (181)
+-|-.||.|+.+.
T Consensus 5 iRCFsCGkvi~~~ 17 (63)
T COG1644 5 VRCFSCGKVIGHK 17 (63)
T ss_pred eEeecCCCCHHHH
Confidence 5699999999744
No 347
>COG4393 Predicted membrane protein [Function unknown]
Probab=25.03 E-value=32 Score=30.25 Aligned_cols=27 Identities=19% Similarity=0.559 Sum_probs=19.9
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.|--||-..-+. +.+++||-.|+.++-
T Consensus 336 AC~iCGd~GYv~---e~dqvICv~C~Vrmf 362 (405)
T COG4393 336 ACDICGDQGYVM---EGDQVICVRCDVRMF 362 (405)
T ss_pred HHHhccccceEe---ECCEEEEEEccEEEE
Confidence 488899633333 468999999999873
No 348
>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=25.02 E-value=50 Score=19.20 Aligned_cols=30 Identities=23% Similarity=0.544 Sum_probs=19.4
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccccC
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (181)
+.+|..|+.. + .....| +.|..|++++-.+
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 4679999862 2 222134 7799999987433
No 349
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=24.99 E-value=42 Score=29.71 Aligned_cols=34 Identities=24% Similarity=0.451 Sum_probs=21.7
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccccccCCcccccccc
Q 030241 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWR 45 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~Ewr 45 (181)
.|+.|+. ...+.. .....|..||- +....||=|-
T Consensus 246 ~C~~c~~-~~~~~~--~~~~~C~~c~~----~~~~~GPlW~ 279 (382)
T PRK04338 246 YCPKCLY-REEVEG--LPPEECPVCGG----KFGTAGPLWL 279 (382)
T ss_pred ECCCCCc-EEEecC--CCCCCCCCCCC----cceecccccc
Confidence 5999997 333322 33457999976 4456778773
No 350
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=24.60 E-value=51 Score=29.62 Aligned_cols=10 Identities=30% Similarity=0.617 Sum_probs=5.8
Q ss_pred eEeCCCcccc
Q 030241 24 TVCSECGLVL 33 (181)
Q Consensus 24 ~vC~~CG~Vl 33 (181)
..|..||.++
T Consensus 236 a~CpRC~~~L 245 (419)
T PRK15103 236 PVCPRCHTKG 245 (419)
T ss_pred CCCCCCCCcC
Confidence 3566666665
No 351
>PRK05667 dnaG DNA primase; Validated
Probab=24.59 E-value=73 Score=29.88 Aligned_cols=27 Identities=15% Similarity=0.320 Sum_probs=23.1
Q ss_pred CCCCCCCC-CceeEeCCCCceEeCCCcc
Q 030241 5 FCSDCKKH-TEVVFDHSAGDTVCSECGL 31 (181)
Q Consensus 5 ~Cp~Cg~~-~~iv~D~~~G~~vC~~CG~ 31 (181)
.||.|+.. +++.+++..|..-|-.||.
T Consensus 38 ~CPfH~ektpSf~V~~~k~~~~CF~Cg~ 65 (580)
T PRK05667 38 LCPFHDEKTPSFTVSPDKQFYHCFGCGA 65 (580)
T ss_pred cCCCCCCCCCceEEECCCCeEEECCCCC
Confidence 49999864 3688899999999999996
No 352
>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=24.45 E-value=52 Score=18.95 Aligned_cols=9 Identities=11% Similarity=0.505 Sum_probs=6.2
Q ss_pred CCCCCCCCC
Q 030241 3 DAFCSDCKK 11 (181)
Q Consensus 3 ~~~Cp~Cg~ 11 (181)
...|+.|+.
T Consensus 3 ~~~C~~H~~ 11 (42)
T PF00643_consen 3 EPKCPEHPE 11 (42)
T ss_dssp SSB-SSTTT
T ss_pred CccCccCCc
Confidence 567999986
No 353
>PHA02956 hypothetical protein; Provisional
Probab=24.42 E-value=49 Score=25.52 Aligned_cols=20 Identities=25% Similarity=0.793 Sum_probs=18.1
Q ss_pred CceeEeCCCCceEeCCCccc
Q 030241 13 TEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 13 ~~iv~D~~~G~~vC~~CG~V 32 (181)
++++.|..+|.++|..=|.+
T Consensus 107 nsiiidsssgkiicegigii 126 (189)
T PHA02956 107 NSIIIDSSSGKIICEGIGII 126 (189)
T ss_pred ceEEEecCCCcEEeecchHH
Confidence 56999999999999998876
No 354
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=24.35 E-value=64 Score=28.03 Aligned_cols=30 Identities=23% Similarity=0.452 Sum_probs=21.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
.+|=+||.+.+.-.--.-|-.+|.+|--|-
T Consensus 21 k~CaDCga~~P~W~S~nlGvfiCi~CagvH 50 (319)
T COG5347 21 KKCADCGAPNPTWASVNLGVFLCIDCAGVH 50 (319)
T ss_pred CccccCCCCCCceEecccCeEEEeecchhh
Confidence 568899984333334467889999998774
No 355
>PRK14067 exodeoxyribonuclease VII small subunit; Provisional
Probab=24.22 E-value=1.3e+02 Score=20.63 Aligned_cols=37 Identities=3% Similarity=-0.112 Sum_probs=27.6
Q ss_pred CchHHHHHHHHHHHHHHHHhCCchHHHHH--HHHHHHHh
Q 030241 100 NPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEA 136 (181)
Q Consensus 100 ~~er~l~~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~ 136 (181)
+.+.+...++.+|++|..+|.=++.-.|. .+|+.+..
T Consensus 4 ~k~~sfEeal~~LEeIV~~LE~~~l~Lees~~lyeeG~~ 42 (80)
T PRK14067 4 KKTADFEQQLARLQEIVDALEGGDLPLEESVALYKEGLG 42 (80)
T ss_pred cccCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence 34567788999999999999777655555 67776544
No 356
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=24.20 E-value=50 Score=31.59 Aligned_cols=36 Identities=22% Similarity=0.419 Sum_probs=27.2
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCC---CccccccCCccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSE---CGLVLESHSIDE 40 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~---CG~Vl~e~~id~ 40 (181)
+..||.||+ .++.-.+.-.+-|.+ |-...-|+++-.
T Consensus 404 P~~CP~C~s--~l~r~~~e~~~rC~n~~~C~aq~~e~l~hf 442 (667)
T COG0272 404 PTHCPVCGS--ELVREEGEVVIRCTNGLNCPAQLKERLIHF 442 (667)
T ss_pred CCCCCCCCC--eeEeccCceeEecCCCCCChHHHhhheeeE
Confidence 467999997 465544566788987 988888888653
No 357
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=24.08 E-value=45 Score=19.85 Aligned_cols=8 Identities=38% Similarity=0.958 Sum_probs=4.4
Q ss_pred CCCCCCCC
Q 030241 4 AFCSDCKK 11 (181)
Q Consensus 4 ~~Cp~Cg~ 11 (181)
..||.||+
T Consensus 3 ~~C~~Cg~ 10 (47)
T PF13005_consen 3 RACPDCGG 10 (47)
T ss_pred CcCCCCCc
Confidence 44666654
No 358
>PRK04330 hypothetical protein; Provisional
Probab=24.00 E-value=2.7e+02 Score=19.66 Aligned_cols=51 Identities=14% Similarity=0.147 Sum_probs=36.0
Q ss_pred CchHHHHHHHHHHHHHHHHhCCchHHHHH--HHHHHHHhh-hCHHHHHHHHHHH
Q 030241 100 NPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-IKTHYWLLACTLL 150 (181)
Q Consensus 100 ~~er~l~~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~-l~~~~v~AAclYi 150 (181)
..|..++++...+++|.+--.+|.+|+.. +......+. .....=+|.++++
T Consensus 6 ~~e~~ik~~~~~L~~I~~D~sVPRNIRraa~ea~~~L~~e~~~~~vRaA~AIs~ 59 (88)
T PRK04330 6 DNEEKIKQAIQMLEEIINDTSVPRNIRRAATEAKEILLNEEESPGVRAATAISI 59 (88)
T ss_pred chHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHhCcCcchhHHHHHHHHH
Confidence 45778899999999999999999999877 555554443 3344444445544
No 359
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=23.92 E-value=56 Score=27.95 Aligned_cols=33 Identities=24% Similarity=0.614 Sum_probs=27.1
Q ss_pred eCCCCceEeCCCccccc--cCCccccccccccccC
Q 030241 18 DHSAGDTVCSECGLVLE--SHSIDETSEWRTFANE 50 (181)
Q Consensus 18 D~~~G~~vC~~CG~Vl~--e~~id~~~Ewr~F~~~ 50 (181)
..+.|.++|..||.-|= +.-+|+|.-|.+|.+.
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 45899999999999884 4457889999999753
No 360
>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=23.91 E-value=55 Score=30.88 Aligned_cols=27 Identities=30% Similarity=0.744 Sum_probs=20.5
Q ss_pred CCCCC--CCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSD--CKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~--Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
..||. |++. +.+...|.+.|..|+...
T Consensus 475 ~ACp~~~CnKK---V~~~~~g~~~CekC~~~~ 503 (608)
T TIGR00617 475 RACPSEDCNKK---VVDQGDGTYRCEKCNKNF 503 (608)
T ss_pred ccCChhhCCCc---cccCCCCCEECCCCCCCC
Confidence 35987 9873 345667999999999765
No 361
>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=23.90 E-value=32 Score=28.19 Aligned_cols=31 Identities=23% Similarity=0.574 Sum_probs=18.8
Q ss_pred CCCCCCCC-CceeE-eCCCCceEeCCCcccccc
Q 030241 5 FCSDCKKH-TEVVF-DHSAGDTVCSECGLVLES 35 (181)
Q Consensus 5 ~Cp~Cg~~-~~iv~-D~~~G~~vC~~CG~Vl~e 35 (181)
.|+.|=-. .+++. +..---.+|..||.....
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 46666321 22322 223477899999999865
No 362
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=23.89 E-value=47 Score=21.47 Aligned_cols=7 Identities=57% Similarity=1.421 Sum_probs=3.3
Q ss_pred EeCCCcc
Q 030241 25 VCSECGL 31 (181)
Q Consensus 25 vC~~CG~ 31 (181)
+|.+||-
T Consensus 43 ~CPNCgG 49 (57)
T PF06906_consen 43 VCPNCGG 49 (57)
T ss_pred cCcCCCC
Confidence 4555543
No 363
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=23.69 E-value=17 Score=28.86 Aligned_cols=31 Identities=29% Similarity=0.605 Sum_probs=20.4
Q ss_pred CCCCCCCCCCceeEeC-CCCceEeCCCccccccC
Q 030241 4 AFCSDCKKHTEVVFDH-SAGDTVCSECGLVLESH 36 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~-~~G~~vC~~CG~Vl~e~ 36 (181)
-.||.|... .-+|. -.-.-.|+.||-+|++.
T Consensus 114 y~C~~~~~r--~sfdeA~~~~F~Cp~Cg~~L~~~ 145 (176)
T COG1675 114 YVCPNCHVK--YSFDEAMELGFTCPKCGEDLEEY 145 (176)
T ss_pred eeCCCCCCc--ccHHHHHHhCCCCCCCCchhhhc
Confidence 359988853 44554 22337899999998643
No 364
>PF11020 DUF2610: Domain of unknown function (DUF2610); InterPro: IPR021277 This family is conserved in Proteobacteria. One member is annotated as being elongation factor P but this could not be confirmed.
Probab=23.55 E-value=2e+02 Score=19.94 Aligned_cols=25 Identities=8% Similarity=-0.031 Sum_probs=14.1
Q ss_pred CCchHHHHH--HHHHHHHhh-hCHHHHH
Q 030241 120 GQMRYIRRW--KIKSLVEAE-IKTHYWL 144 (181)
Q Consensus 120 ~Lp~~v~e~--~i~k~a~~~-l~~~~v~ 144 (181)
.+|+.|.|. .+|++|.+. +..+.++
T Consensus 45 ~IP~~V~~sl~kL~~La~~N~v~feeLc 72 (82)
T PF11020_consen 45 QIPEKVMDSLSKLYKLAKENNVSFEELC 72 (82)
T ss_pred CCCHHHHHHHHHHHHHHHHcCCCHHHHH
Confidence 356666666 566666555 4444443
No 365
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=22.90 E-value=42 Score=34.74 Aligned_cols=23 Identities=35% Similarity=0.605 Sum_probs=17.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
.+||.||.. . =...|..||.-.+
T Consensus 675 ~~Cp~Cg~~-~-------~~~~Cp~CG~~~~ 697 (1627)
T PRK14715 675 FKCPKCGKV-G-------LYHVCPFCGTRVE 697 (1627)
T ss_pred eeCCCCCCc-c-------ccccCcccCCccc
Confidence 579999962 2 2579999998754
No 366
>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=22.84 E-value=54 Score=29.32 Aligned_cols=37 Identities=19% Similarity=0.390 Sum_probs=24.3
Q ss_pred EeCCCCceEeCCCccccccCCccccccccccccCCCCCCCccccCCC
Q 030241 17 FDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPT 63 (181)
Q Consensus 17 ~D~~~G~~vC~~CG~Vl~e~~id~~~Ewr~F~~~~~~~d~sr~G~p~ 63 (181)
.|...+-..|.+||.|++...+..+. ...=.|+|...
T Consensus 7 ~~~~~~~~~C~~Cd~l~~~~~l~~g~----------~a~CpRCg~~L 43 (403)
T TIGR00155 7 HHPAAKHILCSQCDMLVALPRIESGQ----------KAACPRCGTTL 43 (403)
T ss_pred cCCCCCeeeCCCCCCcccccCCCCCC----------eeECCCCCCCC
Confidence 35566777899999998766554332 12356787654
No 367
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.74 E-value=33 Score=25.97 Aligned_cols=11 Identities=36% Similarity=0.866 Sum_probs=5.3
Q ss_pred CceEeCCCccc
Q 030241 22 GDTVCSECGLV 32 (181)
Q Consensus 22 G~~vC~~CG~V 32 (181)
|.+.|..||..
T Consensus 31 gLv~CPvCgs~ 41 (142)
T COG5319 31 GLVTCPVCGST 41 (142)
T ss_pred CceeCCCCCcH
Confidence 34445555544
No 368
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=22.44 E-value=49 Score=19.49 Aligned_cols=31 Identities=23% Similarity=0.541 Sum_probs=19.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccccccC
Q 030241 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~ 36 (181)
+.+|..|++. + .....--+.|..|++++-.+
T Consensus 11 ~~~C~~C~~~--i-~~~~~~~~~C~~C~~~~H~~ 41 (50)
T cd00029 11 PTFCDVCRKS--I-WGLFKQGLRCSWCKVKCHKK 41 (50)
T ss_pred CCChhhcchh--h-hccccceeEcCCCCCchhhh
Confidence 4578899862 2 22223446799999987543
No 369
>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=22.38 E-value=59 Score=28.19 Aligned_cols=11 Identities=45% Similarity=0.908 Sum_probs=9.8
Q ss_pred CCCCCCCCCCC
Q 030241 1 MTDAFCSDCKK 11 (181)
Q Consensus 1 m~~~~Cp~Cg~ 11 (181)
|....||.|++
T Consensus 1 md~~~CP~Ck~ 11 (309)
T TIGR00570 1 MDDQGCPRCKT 11 (309)
T ss_pred CCCCCCCcCCC
Confidence 78889999997
No 370
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=22.33 E-value=68 Score=29.81 Aligned_cols=33 Identities=21% Similarity=0.233 Sum_probs=26.9
Q ss_pred eCCCCceEeCCCccccc--cCCccccccccccccC
Q 030241 18 DHSAGDTVCSECGLVLE--SHSIDETSEWRTFANE 50 (181)
Q Consensus 18 D~~~G~~vC~~CG~Vl~--e~~id~~~Ewr~F~~~ 50 (181)
..+.|.++|..||.-|= +.-+|+|.-|.+|.+.
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 35899999999999874 4457889999999853
No 371
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=22.23 E-value=1.1e+02 Score=26.26 Aligned_cols=28 Identities=0% Similarity=-0.020 Sum_probs=24.0
Q ss_pred HHHHHHHHHhCCchHHHHH--HHHHHHHhh
Q 030241 110 KTIATMSDRIGQMRYIRRW--KIKSLVEAE 137 (181)
Q Consensus 110 ~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~ 137 (181)
+.++++++.|||+..-+++ .+|+.-.++
T Consensus 211 ~~l~~l~e~Lgls~~kv~KDLdlYrsnLeK 240 (283)
T PLN00047 211 TALEKLCAALNINKRSVDRDLDVYRGLLSK 240 (283)
T ss_pred HHHHHHHHHcCCCHHHHHhhHHHHHhHHHH
Confidence 3889999999999998888 899876665
No 372
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=22.21 E-value=52 Score=33.77 Aligned_cols=31 Identities=39% Similarity=0.845 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCceeEeCCCC------ceEeCCCccccc
Q 030241 3 DAFCSDCKKHTEVVFDHSAG------DTVCSECGLVLE 34 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~D~~~G------~~vC~~CG~Vl~ 34 (181)
...||+|+- .+++.|...| +--|..||.=+.
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 457999985 6777766444 346888887653
No 373
>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=22.16 E-value=51 Score=26.68 Aligned_cols=38 Identities=16% Similarity=0.407 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCceeE--eC-CCCceEeCCCccccccCCccc
Q 030241 3 DAFCSDCKKHTEVVF--DH-SAGDTVCSECGLVLESHSIDE 40 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~--D~-~~G~~vC~~CG~Vl~e~~id~ 40 (181)
...|..|+...+... .. ......|..||-++..+++-.
T Consensus 113 ~~~C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg~lrP~Vv~f 153 (222)
T cd01413 113 TAYCVNCGSKYDLEEVKYAKKHEVPRCPKCGGIIRPDVVLF 153 (222)
T ss_pred cceECCCCCCcchhHHHHhccCCCCcCCCCCCccCCCEEEC
Confidence 356888886211100 01 122457888988887776643
No 374
>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=21.82 E-value=64 Score=25.51 Aligned_cols=34 Identities=26% Similarity=0.529 Sum_probs=16.0
Q ss_pred CCCCCCCCCCceeEeC---------CCCceEeCCCccccccCCcc
Q 030241 4 AFCSDCKKHTEVVFDH---------SAGDTVCSECGLVLESHSID 39 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~---------~~G~~vC~~CG~Vl~e~~id 39 (181)
..||.||. ...++. ...-..|.+|+..+....|.
T Consensus 19 ~~C~~C~~--~~~f~g~~~~~~~~~~~~~~~C~~C~~~~~~~~l~ 61 (188)
T PF08996_consen 19 LTCPSCGT--EFEFPGVFEEDGDDVSPSGLQCPNCSTPLSPASLV 61 (188)
T ss_dssp EE-TTT----EEEE-SSS--SSEEEETTEEEETTT--B--HHHHH
T ss_pred eECCCCCC--CccccccccCCccccccCcCcCCCCCCcCCHHHHH
Confidence 46999996 233332 23468999999977654443
No 375
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.81 E-value=15 Score=25.25 Aligned_cols=29 Identities=34% Similarity=0.667 Sum_probs=12.9
Q ss_pred CCCCCCCCCceeEeC-CCCceEeCCCcccc
Q 030241 5 FCSDCKKHTEVVFDH-SAGDTVCSECGLVL 33 (181)
Q Consensus 5 ~Cp~Cg~~~~iv~D~-~~G~~vC~~CG~Vl 33 (181)
.|.+||...+++.-. +.-.+.|.+||--+
T Consensus 14 ~c~~cg~~~dvvq~~~ddplt~ce~c~a~~ 43 (82)
T COG2331 14 ECTECGNRFDVVQAMTDDPLTTCEECGARL 43 (82)
T ss_pred eecccchHHHHHHhcccCccccChhhChHH
Confidence 366666422222111 33455666666533
No 376
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=21.62 E-value=1.4e+02 Score=18.33 Aligned_cols=24 Identities=8% Similarity=0.158 Sum_probs=16.3
Q ss_pred HHHHHHHHhCCchHHHHH---HHHHHH
Q 030241 111 TIATMSDRIGQMRYIRRW---KIKSLV 134 (181)
Q Consensus 111 ~I~~ia~~L~Lp~~v~e~---~i~k~a 134 (181)
...+||..|+++..-+.. .++++.
T Consensus 20 ~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 20 SNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp -HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred CcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 467888889888765555 566654
No 377
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=21.61 E-value=89 Score=26.38 Aligned_cols=18 Identities=6% Similarity=0.146 Sum_probs=15.9
Q ss_pred HHHHHHHHhCCchHHHHH
Q 030241 111 TIATMSDRIGQMRYIRRW 128 (181)
Q Consensus 111 ~I~~ia~~L~Lp~~v~e~ 128 (181)
.++++|..||||+++...
T Consensus 39 NvneiAe~lgLpqst~s~ 56 (308)
T COG4189 39 NVNEIAEALGLPQSTMSA 56 (308)
T ss_pred CHHHHHHHhCCchhhhhh
Confidence 588999999999988776
No 378
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=21.61 E-value=49 Score=31.35 Aligned_cols=21 Identities=29% Similarity=0.692 Sum_probs=13.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (181)
.+|++||- .- +. ...|..||-
T Consensus 560 ~~C~~CGy-~g-~~-----~~~CP~CG~ 580 (618)
T PRK14704 560 DRCKCCSY-HG-VI-----GNECPSCGN 580 (618)
T ss_pred eecCCCCC-CC-Cc-----CccCcCCCC
Confidence 56888884 21 11 168888885
No 379
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=21.34 E-value=80 Score=20.36 Aligned_cols=17 Identities=18% Similarity=0.380 Sum_probs=14.1
Q ss_pred HHHHHHHHHhCCchHHH
Q 030241 110 KTIATMSDRIGQMRYIR 126 (181)
Q Consensus 110 ~~I~~ia~~L~Lp~~v~ 126 (181)
..++++|..|||+..++
T Consensus 33 ~~r~~la~~lgl~~~vv 49 (58)
T TIGR01565 33 EEVREFCEEIGVTRKVF 49 (58)
T ss_pred HHHHHHHHHhCCCHHHe
Confidence 37889999999998764
No 380
>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=21.30 E-value=46 Score=23.12 Aligned_cols=42 Identities=19% Similarity=0.329 Sum_probs=26.6
Q ss_pred CCCCCCCCCCc------eeEeCCCCceEeCCCccccccCCccccccccccc
Q 030241 4 AFCSDCKKHTE------VVFDHSAGDTVCSECGLVLESHSIDETSEWRTFA 48 (181)
Q Consensus 4 ~~Cp~Cg~~~~------iv~D~~~G~~vC~~CG~Vl~e~~id~~~Ewr~F~ 48 (181)
|.|-+||.+-+ +..|..+-.-.|..|-.|. +-+.+.|.+ .|-
T Consensus 1 ~~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~-~~i~~~gL~--~yY 48 (88)
T PF12156_consen 1 MKCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVY-QLIHENGLE--SYY 48 (88)
T ss_pred CCCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHH-HHHHHcchH--HHH
Confidence 46999997421 2233344589999999996 344455554 454
No 381
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=21.16 E-value=1.2e+02 Score=20.76 Aligned_cols=20 Identities=10% Similarity=-0.001 Sum_probs=16.8
Q ss_pred HHHHHHHHHHhCCchHHHHH
Q 030241 109 FKTIATMSDRIGQMRYIRRW 128 (181)
Q Consensus 109 ~~~I~~ia~~L~Lp~~v~e~ 128 (181)
++.-.+++.+|||+++.+|.
T Consensus 11 ~~~wk~~~R~LGlse~~Id~ 30 (80)
T cd08313 11 PRRWKEFVRRLGLSDNEIER 30 (80)
T ss_pred HHHHHHHHHHcCCCHHHHHH
Confidence 34677899999999998887
No 382
>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=21.12 E-value=38 Score=22.02 Aligned_cols=13 Identities=46% Similarity=0.871 Sum_probs=10.0
Q ss_pred ceEeCCCcccccc
Q 030241 23 DTVCSECGLVLES 35 (181)
Q Consensus 23 ~~vC~~CG~Vl~e 35 (181)
.+||+.||.=+.|
T Consensus 4 ~lvCSTCGrDlSe 16 (63)
T PF05864_consen 4 QLVCSTCGRDLSE 16 (63)
T ss_pred eeeecccCCcchH
Confidence 4799999987643
No 383
>PF04031 Las1: Las1-like ; InterPro: IPR007174 Las1 is an essential nuclear protein involved in cell morphogenesis and cell surface growth [].
Probab=21.08 E-value=81 Score=24.27 Aligned_cols=19 Identities=21% Similarity=0.478 Sum_probs=17.1
Q ss_pred HHHHHHHHHhCCchHHHHH
Q 030241 110 KTIATMSDRIGQMRYIRRW 128 (181)
Q Consensus 110 ~~I~~ia~~L~Lp~~v~e~ 128 (181)
.-|..+|..+|||..++|-
T Consensus 102 ~si~~~A~~iglP~~lVdl 120 (154)
T PF04031_consen 102 RSIASLAKEIGLPSWLVDL 120 (154)
T ss_pred hhHHHHHHHcCCCHHHHHH
Confidence 5889999999999998875
No 384
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=21.02 E-value=38 Score=22.06 Aligned_cols=13 Identities=46% Similarity=0.871 Sum_probs=10.1
Q ss_pred ceEeCCCcccccc
Q 030241 23 DTVCSECGLVLES 35 (181)
Q Consensus 23 ~~vC~~CG~Vl~e 35 (181)
.+||+.||.=+.|
T Consensus 4 ~lVCsTCGrDlSe 16 (63)
T PHA03082 4 QLVCSTCGRDLSE 16 (63)
T ss_pred eeeecccCcchhH
Confidence 4799999987653
No 385
>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=20.96 E-value=1.8e+02 Score=18.95 Aligned_cols=18 Identities=11% Similarity=0.274 Sum_probs=14.8
Q ss_pred HHHHHHHHhCCchHHHHH
Q 030241 111 TIATMSDRIGQMRYIRRW 128 (181)
Q Consensus 111 ~I~~ia~~L~Lp~~v~e~ 128 (181)
.+.+||+.||++...+..
T Consensus 24 ~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRK 41 (60)
T ss_pred cHHHHHHHHCCCHHHHHH
Confidence 688999999999876544
No 386
>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=20.95 E-value=42 Score=26.32 Aligned_cols=23 Identities=26% Similarity=0.644 Sum_probs=16.3
Q ss_pred CCCCCCCCceeEeCCCCceEeCCCccccc
Q 030241 6 CSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 6 Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~ 34 (181)
|+.||. .+. .++.+|.+|+.-+.
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 23579999987664
No 387
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=20.77 E-value=44 Score=24.35 Aligned_cols=11 Identities=36% Similarity=1.084 Sum_probs=8.0
Q ss_pred EeCCCcccccc
Q 030241 25 VCSECGLVLES 35 (181)
Q Consensus 25 vC~~CG~Vl~e 35 (181)
.|+.||.|.++
T Consensus 4 ~CtrCG~vf~~ 14 (112)
T COG3364 4 QCTRCGEVFDD 14 (112)
T ss_pred eeccccccccc
Confidence 57888888764
No 388
>PHA02325 hypothetical protein
Probab=20.74 E-value=51 Score=21.95 Aligned_cols=11 Identities=27% Similarity=0.827 Sum_probs=7.3
Q ss_pred CCCCCCCCCCC
Q 030241 1 MTDAFCSDCKK 11 (181)
Q Consensus 1 m~~~~Cp~Cg~ 11 (181)
|....||.|+.
T Consensus 1 m~~k~CPkC~A 11 (72)
T PHA02325 1 MDTKICPKCGA 11 (72)
T ss_pred CCccccCccCC
Confidence 55666777774
No 389
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=20.52 E-value=47 Score=23.54 Aligned_cols=23 Identities=26% Similarity=0.816 Sum_probs=15.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~ 31 (181)
..|..||. ... . --.-.|..||+
T Consensus 17 tlCrRCG~-~sy--H--~qK~~CasCGy 39 (91)
T PTZ00073 17 TLCRRCGK-RSF--H--VQKKRCASCGY 39 (91)
T ss_pred chhcccCc-ccc--c--cccccchhcCC
Confidence 56999997 332 2 12456999998
No 390
>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=20.50 E-value=55 Score=26.30 Aligned_cols=39 Identities=21% Similarity=0.331 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCceeE---e-CCCCceEeCCCccccccCCcccc
Q 030241 3 DAFCSDCKKHTEVVF---D-HSAGDTVCSECGLVLESHSIDET 41 (181)
Q Consensus 3 ~~~Cp~Cg~~~~iv~---D-~~~G~~vC~~CG~Vl~e~~id~~ 41 (181)
...|..|+....... . .......|..||-.+..+++-.+
T Consensus 109 ~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~lrP~Vv~fg 151 (218)
T cd01407 109 RVRCTKCGKEYPRDELQADIDREEVPRCPKCGGLLRPDVVFFG 151 (218)
T ss_pred cceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCccCCCeEECC
Confidence 367999986311100 0 12234679999999888876443
No 391
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=20.45 E-value=92 Score=19.89 Aligned_cols=18 Identities=17% Similarity=0.229 Sum_probs=14.0
Q ss_pred HHHHHHHHhCCchHHHHH
Q 030241 111 TIATMSDRIGQMRYIRRW 128 (181)
Q Consensus 111 ~I~~ia~~L~Lp~~v~e~ 128 (181)
.+.+||+.||+|...+-.
T Consensus 15 ~~~eIA~~Lg~~~~TV~~ 32 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYS 32 (58)
T ss_pred CHHHHHHHHCCChHHHHH
Confidence 578999999999665443
No 392
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=20.43 E-value=58 Score=23.90 Aligned_cols=7 Identities=29% Similarity=0.743 Sum_probs=4.3
Q ss_pred CCCCCCC
Q 030241 5 FCSDCKK 11 (181)
Q Consensus 5 ~Cp~Cg~ 11 (181)
.|+.|+.
T Consensus 54 ~C~~C~G 60 (111)
T PLN03165 54 VCRFCVG 60 (111)
T ss_pred CCCCCcC
Confidence 4666665
No 393
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=20.37 E-value=4.5e+02 Score=23.24 Aligned_cols=65 Identities=12% Similarity=0.127 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHhCCchHHHHH--HHHHHHHhh--h---CHHHHHHHHHH-HHHHhCCCCccccChhhheec
Q 030241 106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTL-LVDKKTSHALLRVQPKILLTS 170 (181)
Q Consensus 106 ~~a~~~I~~ia~~L~Lp~~v~e~--~i~k~a~~~--l---~~~~v~AAclY-iACR~~~~p~t~~~~~~~~~~ 170 (181)
..-.+.+-++-.+++|.....=- .|+...... + +...+.++||+ |||+.+...+..++=-++.+.
T Consensus 159 ~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd 231 (391)
T KOG0653|consen 159 AILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITD 231 (391)
T ss_pred HHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeC
Confidence 34555666777777776432111 233222211 1 55666677755 999976554444433333333
No 394
>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=20.18 E-value=52 Score=22.01 Aligned_cols=20 Identities=25% Similarity=0.614 Sum_probs=10.0
Q ss_pred eeEeCCCCceEeCCCccccc
Q 030241 15 VVFDHSAGDTVCSECGLVLE 34 (181)
Q Consensus 15 iv~D~~~G~~vC~~CG~Vl~ 34 (181)
+-.+++--..+|..||.++-
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 34566677889999999984
No 395
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=20.09 E-value=88 Score=23.64 Aligned_cols=24 Identities=29% Similarity=0.758 Sum_probs=16.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl 33 (181)
.+|+.||+ +.+- -...|..||.-.
T Consensus 30 ~kC~~CG~---v~~P---Pr~~Cp~C~~~~ 53 (140)
T COG1545 30 TKCKKCGR---VYFP---PRAYCPKCGSET 53 (140)
T ss_pred EEcCCCCe---EEcC---CcccCCCCCCCC
Confidence 57999996 2332 247899998764
No 396
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=20.07 E-value=49 Score=17.08 Aligned_cols=11 Identities=36% Similarity=0.969 Sum_probs=7.7
Q ss_pred CceEeCCCccc
Q 030241 22 GDTVCSECGLV 32 (181)
Q Consensus 22 G~~vC~~CG~V 32 (181)
|+..|..|+.+
T Consensus 1 g~W~C~~C~~~ 11 (26)
T smart00547 1 GDWECPACTFL 11 (26)
T ss_pred CcccCCCCCCc
Confidence 56678888765
No 397
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=20.06 E-value=52 Score=30.62 Aligned_cols=29 Identities=28% Similarity=0.596 Sum_probs=20.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccc
Q 030241 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (181)
Q Consensus 4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V 32 (181)
..|-+||.+..--..-.+|..+|.+|=.|
T Consensus 9 evC~DC~~~dp~WASvnrGt~lC~eCcsv 37 (669)
T KOG0818|consen 9 EVCADCSGPDPSWASVNRGTFLCDECCSV 37 (669)
T ss_pred hhhcccCCCCCcceeecCceEehHhhhHH
Confidence 45899987422223347899999999776
No 398
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=20.02 E-value=1.9e+02 Score=18.21 Aligned_cols=18 Identities=11% Similarity=0.224 Sum_probs=14.0
Q ss_pred HHHHHHHHhCCchHHHHH
Q 030241 111 TIATMSDRIGQMRYIRRW 128 (181)
Q Consensus 111 ~I~~ia~~L~Lp~~v~e~ 128 (181)
.+.++|+.||++++....
T Consensus 25 tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 25 TLEELAEELGISKSTVSE 42 (53)
T ss_pred CHHHHHHHhCCCHHHHHH
Confidence 578899999999875444
Done!