Query 030755
Match_columns 172
No_of_seqs 157 out of 1009
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 04:05:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030755.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030755hhsearch_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 2.6E-48 5.6E-53 317.8 14.8 167 4-172 12-189 (310)
2 KOG1597 Transcription initiati 100.0 2E-45 4.3E-50 290.1 13.4 168 4-172 1-171 (308)
3 COG1405 SUA7 Transcription ini 100.0 2E-42 4.3E-47 278.2 11.8 160 4-172 2-164 (285)
4 KOG1598 Transcription initiati 99.9 1.1E-24 2.5E-29 184.3 11.1 133 4-172 1-133 (521)
5 PF00382 TFIIB: Transcription 99.8 4.1E-20 8.9E-25 120.3 6.8 61 112-172 1-61 (71)
6 PF08271 TF_Zn_Ribbon: TFIIB z 99.7 5.9E-18 1.3E-22 99.6 3.5 43 4-47 1-43 (43)
7 PRK00423 tfb transcription ini 99.5 1.4E-13 3.1E-18 112.9 7.3 66 107-172 218-283 (310)
8 COG1405 SUA7 Transcription ini 99.3 2.3E-12 4.9E-17 104.3 6.1 67 106-172 192-258 (285)
9 KOG1597 Transcription initiati 99.2 6.9E-11 1.5E-15 94.4 6.8 66 107-172 202-267 (308)
10 cd00043 CYCLIN Cyclin box fold 99.1 5.1E-10 1.1E-14 73.7 7.6 65 107-171 4-68 (88)
11 smart00385 CYCLIN domain prese 98.9 3.1E-09 6.8E-14 69.2 6.5 60 111-171 2-62 (83)
12 TIGR00569 ccl1 cyclin ccl1. Un 98.3 2.8E-06 6E-11 69.7 6.9 70 102-171 52-124 (305)
13 KOG1598 Transcription initiati 98.2 2.9E-07 6.3E-12 79.1 1.0 70 103-172 161-233 (521)
14 KOG0834 CDK9 kinase-activating 98.2 3.1E-06 6.7E-11 69.7 5.3 66 106-171 40-105 (323)
15 PF01857 RB_B: Retinoblastoma- 98.0 1.8E-05 3.9E-10 57.5 6.8 68 104-171 10-79 (135)
16 COG5333 CCL1 Cdk activating ki 97.9 1.3E-05 2.9E-10 64.8 4.5 61 106-166 46-106 (297)
17 PF00134 Cyclin_N: Cyclin, N-t 97.9 5.8E-05 1.3E-09 53.3 6.9 67 104-170 30-97 (127)
18 KOG0794 CDK8 kinase-activating 97.6 0.00011 2.3E-09 57.5 5.0 60 106-165 42-101 (264)
19 KOG0835 Cyclin L [General func 97.6 0.00027 5.9E-09 57.9 7.4 70 102-171 20-89 (367)
20 PF11781 RRN7: RNA polymerase 97.5 6.7E-05 1.4E-09 42.0 2.3 27 5-34 10-36 (36)
21 PF08792 A2L_zn_ribbon: A2L zi 97.4 0.00019 4.1E-09 39.4 2.8 31 1-33 1-31 (33)
22 PRK00420 hypothetical protein; 97.1 0.00049 1.1E-08 48.3 2.8 31 1-34 21-51 (112)
23 KOG0835 Cyclin L [General func 96.9 0.0014 3.1E-08 53.7 4.5 63 106-168 139-203 (367)
24 COG2051 RPS27A Ribosomal prote 96.9 0.00081 1.8E-08 42.4 2.3 31 4-35 20-50 (67)
25 PF01667 Ribosomal_S27e: Ribos 96.8 0.00066 1.4E-08 41.5 1.7 30 4-34 8-37 (55)
26 PRK00415 rps27e 30S ribosomal 96.8 0.00083 1.8E-08 41.6 2.1 30 4-34 12-41 (59)
27 PHA00626 hypothetical protein 96.8 0.0013 2.9E-08 40.0 2.7 30 4-34 1-34 (59)
28 PRK00398 rpoP DNA-directed RNA 96.7 0.0014 3.1E-08 38.6 2.2 31 1-33 1-31 (46)
29 COG1645 Uncharacterized Zn-fin 96.6 0.001 2.2E-08 47.8 1.6 25 2-30 27-51 (131)
30 PF14803 Nudix_N_2: Nudix N-te 96.5 0.00083 1.8E-08 37.1 0.5 27 5-33 2-32 (34)
31 PF13240 zinc_ribbon_2: zinc-r 96.5 0.0012 2.6E-08 33.2 1.0 22 5-32 1-22 (23)
32 KOG2496 Cdk activating kinase 96.5 0.0036 7.7E-08 50.9 4.0 61 111-171 62-124 (325)
33 PF13248 zf-ribbon_3: zinc-rib 96.4 0.0017 3.7E-08 33.6 1.3 22 4-31 3-24 (26)
34 PLN00209 ribosomal protein S27 96.4 0.0026 5.5E-08 42.2 2.2 30 4-34 37-66 (86)
35 PTZ00083 40S ribosomal protein 96.3 0.003 6.4E-08 41.9 2.3 30 4-34 36-65 (85)
36 smart00778 Prim_Zn_Ribbon Zinc 96.3 0.0043 9.2E-08 34.9 2.4 28 4-31 4-33 (37)
37 PF02150 RNA_POL_M_15KD: RNA p 96.2 0.0051 1.1E-07 34.1 2.6 31 3-34 1-31 (35)
38 PF08274 PhnA_Zn_Ribbon: PhnA 96.2 0.0053 1.1E-07 32.9 2.5 28 3-33 2-29 (30)
39 PF09538 FYDLN_acid: Protein o 96.2 0.0031 6.8E-08 44.1 2.0 31 3-36 9-39 (108)
40 PF14354 Lar_restr_allev: Rest 96.2 0.0067 1.4E-07 37.7 3.2 29 2-31 2-37 (61)
41 PRK11827 hypothetical protein; 95.9 0.0051 1.1E-07 38.3 1.9 29 3-33 8-36 (60)
42 COG1997 RPL43A Ribosomal prote 95.9 0.0087 1.9E-07 39.8 2.8 30 3-34 35-64 (89)
43 TIGR01206 lysW lysine biosynth 95.8 0.0053 1.1E-07 37.5 1.6 31 3-34 2-33 (54)
44 PF06677 Auto_anti-p27: Sjogre 95.7 0.011 2.3E-07 34.1 2.5 27 1-30 15-41 (41)
45 PRK00432 30S ribosomal protein 95.7 0.0097 2.1E-07 35.7 2.2 27 4-33 21-47 (50)
46 COG2835 Uncharacterized conser 95.6 0.0093 2E-07 37.0 2.2 30 2-33 7-36 (60)
47 PRK10220 hypothetical protein; 95.6 0.036 7.9E-07 38.4 5.2 31 1-34 1-31 (111)
48 TIGR02098 MJ0042_CXXC MJ0042 f 95.5 0.0044 9.6E-08 34.8 0.4 29 4-34 3-36 (38)
49 TIGR02300 FYDLN_acid conserved 95.5 0.0092 2E-07 42.6 2.0 31 3-36 9-39 (129)
50 PF03966 Trm112p: Trm112p-like 95.5 0.016 3.6E-07 36.9 3.0 17 17-33 47-63 (68)
51 PF10571 UPF0547: Uncharacteri 95.3 0.0097 2.1E-07 30.8 1.2 25 4-34 1-25 (26)
52 smart00661 RPOL9 RNA polymeras 95.1 0.019 4.1E-07 34.3 2.2 28 5-34 2-31 (52)
53 TIGR03655 anti_R_Lar restricti 95.0 0.018 4E-07 34.9 2.0 31 4-34 2-37 (53)
54 PF08273 Prim_Zn_Ribbon: Zinc- 94.9 0.026 5.6E-07 32.3 2.3 29 4-32 4-35 (40)
55 PF09297 zf-NADH-PPase: NADH p 94.9 0.036 7.9E-07 29.9 2.8 28 4-33 4-31 (32)
56 COG2824 PhnA Uncharacterized Z 94.7 0.09 2E-06 36.3 4.9 33 1-36 1-33 (112)
57 PF02984 Cyclin_C: Cyclin, C-t 94.6 0.094 2E-06 36.0 5.1 57 108-164 3-59 (118)
58 PRK00464 nrdR transcriptional 94.3 0.041 8.8E-07 40.9 2.8 30 4-33 1-38 (154)
59 PF13719 zinc_ribbon_5: zinc-r 94.2 0.02 4.4E-07 32.1 0.8 30 4-33 3-35 (37)
60 PRK12495 hypothetical protein; 94.1 0.032 6.9E-07 43.5 2.0 32 1-36 40-71 (226)
61 KOG0656 G1/S-specific cyclin D 94.0 0.34 7.3E-06 40.4 7.9 59 106-164 79-140 (335)
62 PF01780 Ribosomal_L37ae: Ribo 93.9 0.038 8.3E-07 37.2 1.8 31 4-36 36-66 (90)
63 COG1998 RPS31 Ribosomal protei 93.8 0.043 9.4E-07 32.6 1.7 27 4-32 20-46 (51)
64 PF07282 OrfB_Zn_ribbon: Putat 93.7 0.059 1.3E-06 34.1 2.4 30 3-34 28-57 (69)
65 TIGR00244 transcriptional regu 93.6 0.082 1.8E-06 38.8 3.2 30 4-33 1-38 (147)
66 PF09862 DUF2089: Protein of u 93.6 0.062 1.4E-06 37.8 2.4 35 106-140 64-102 (113)
67 TIGR01384 TFS_arch transcripti 93.4 0.053 1.1E-06 37.3 1.9 27 5-35 2-28 (104)
68 PF05191 ADK_lid: Adenylate ki 93.3 0.013 2.8E-07 32.7 -1.1 29 5-33 3-31 (36)
69 PF12760 Zn_Tnp_IS1595: Transp 93.2 0.11 2.3E-06 30.4 2.8 27 4-31 19-45 (46)
70 smart00440 ZnF_C2C2 C2C2 Zinc 93.0 0.1 2.3E-06 29.7 2.4 28 5-33 2-38 (40)
71 TIGR00686 phnA alkylphosphonat 92.8 0.087 1.9E-06 36.5 2.3 30 4-36 3-32 (109)
72 PRK09710 lar restriction allev 92.8 0.14 3E-06 32.2 3.0 30 3-33 6-37 (64)
73 PTZ00255 60S ribosomal protein 92.7 0.099 2.2E-06 35.2 2.3 32 3-36 36-67 (90)
74 PRK14892 putative transcriptio 92.6 0.083 1.8E-06 36.3 1.9 31 4-34 22-53 (99)
75 KOG1779 40s ribosomal protein 92.2 0.097 2.1E-06 34.1 1.7 30 4-34 35-64 (84)
76 COG1594 RPB9 DNA-directed RNA 92.1 0.12 2.7E-06 36.3 2.4 34 3-36 2-35 (113)
77 TIGR00280 L37a ribosomal prote 92.0 0.12 2.7E-06 34.8 2.1 32 3-36 35-66 (91)
78 KOG4164 Cyclin ik3-1/CABLES [C 92.0 0.27 5.9E-06 41.6 4.6 60 106-165 383-442 (497)
79 COG4888 Uncharacterized Zn rib 91.9 0.11 2.3E-06 35.6 1.7 30 4-34 23-57 (104)
80 PF03604 DNA_RNApol_7kD: DNA d 91.9 0.099 2.1E-06 28.4 1.3 25 5-32 2-26 (32)
81 smart00834 CxxC_CXXC_SSSS Puta 91.7 0.12 2.5E-06 29.1 1.6 30 4-33 6-36 (41)
82 COG2888 Predicted Zn-ribbon RN 91.5 0.13 2.9E-06 31.8 1.6 24 5-30 11-34 (61)
83 PRK03976 rpl37ae 50S ribosomal 91.3 0.16 3.5E-06 34.2 2.1 32 3-36 36-67 (90)
84 smart00659 RPOLCX RNA polymera 91.1 0.17 3.6E-06 29.5 1.8 27 4-33 3-29 (44)
85 COG3478 Predicted nucleic-acid 90.8 0.18 3.9E-06 31.7 1.8 14 4-18 5-18 (68)
86 PF14446 Prok-RING_1: Prokaryo 90.8 0.2 4.3E-06 30.5 1.9 26 4-33 6-31 (54)
87 COG4640 Predicted membrane pro 90.6 0.14 3.1E-06 43.3 1.6 28 3-36 1-28 (465)
88 cd00350 rubredoxin_like Rubred 90.6 0.21 4.5E-06 27.1 1.8 24 4-31 2-25 (33)
89 PF05129 Elf1: Transcription e 90.6 0.17 3.6E-06 33.5 1.6 33 4-36 23-59 (81)
90 PF14255 Cys_rich_CPXG: Cystei 90.5 0.2 4.3E-06 30.3 1.8 19 5-23 2-20 (52)
91 PF01096 TFIIS_C: Transcriptio 90.4 0.21 4.5E-06 28.2 1.7 27 5-32 2-37 (39)
92 PF12773 DZR: Double zinc ribb 90.1 0.18 3.9E-06 29.8 1.4 27 4-33 13-39 (50)
93 PF13717 zinc_ribbon_4: zinc-r 90.1 0.12 2.7E-06 28.7 0.6 29 4-33 3-35 (36)
94 PF14122 YokU: YokU-like prote 89.5 0.27 5.9E-06 32.7 2.0 23 21-43 33-55 (87)
95 PF15616 TerY-C: TerY-C metal 89.5 0.23 5E-06 35.8 1.8 21 4-33 78-98 (131)
96 PF03119 DNA_ligase_ZBD: NAD-d 89.4 0.41 8.8E-06 25.1 2.2 22 5-28 1-22 (28)
97 PF09855 DUF2082: Nucleic-acid 89.3 0.37 8E-06 30.4 2.4 7 5-11 2-8 (64)
98 COG1996 RPC10 DNA-directed RNA 89.1 0.13 2.9E-06 30.6 0.2 29 3-33 6-34 (49)
99 TIGR02443 conserved hypothetic 89.1 0.47 1E-05 29.4 2.6 30 4-33 10-41 (59)
100 COG1327 Predicted transcriptio 89.0 0.3 6.5E-06 36.0 2.1 30 4-33 1-38 (156)
101 PRK12286 rpmF 50S ribosomal pr 88.9 0.3 6.4E-06 30.1 1.7 27 4-37 28-54 (57)
102 PRK06266 transcription initiat 88.6 0.1 2.3E-06 39.6 -0.6 30 4-35 118-148 (178)
103 PF14952 zf-tcix: Putative tre 88.3 0.28 6E-06 28.4 1.2 25 4-34 12-38 (44)
104 PRK05978 hypothetical protein; 88.1 0.37 8E-06 35.6 2.1 32 4-36 34-65 (148)
105 PHA02942 putative transposase; 88.0 0.38 8.3E-06 40.9 2.4 30 3-35 325-354 (383)
106 TIGR00569 ccl1 cyclin ccl1. Un 87.7 3.3 7.2E-05 34.2 7.7 45 122-166 180-224 (305)
107 KOG1010 Rb (Retinoblastoma tum 87.5 0.78 1.7E-05 42.4 4.2 65 107-171 679-745 (920)
108 PRK12336 translation initiatio 86.8 0.44 9.4E-06 36.9 1.9 29 5-33 100-129 (201)
109 PF05876 Terminase_GpA: Phage 86.5 0.37 8.1E-06 42.9 1.6 43 4-46 201-255 (557)
110 cd00730 rubredoxin Rubredoxin; 86.3 0.65 1.4E-05 27.8 2.1 13 24-36 2-14 (50)
111 COG0675 Transposase and inacti 86.2 0.54 1.2E-05 38.2 2.3 25 3-34 309-333 (364)
112 PRK09678 DNA-binding transcrip 86.1 1 2.2E-05 29.1 3.0 31 3-34 1-40 (72)
113 PRK13130 H/ACA RNA-protein com 85.9 0.39 8.4E-06 29.5 1.0 25 2-34 4-28 (56)
114 COG5349 Uncharacterized protei 85.8 0.38 8.3E-06 34.1 1.0 38 4-42 22-59 (126)
115 PF01783 Ribosomal_L32p: Ribos 85.7 0.5 1.1E-05 28.9 1.4 24 4-34 27-50 (56)
116 PF10122 Mu-like_Com: Mu-like 85.7 0.2 4.4E-06 30.0 -0.3 33 1-33 2-34 (51)
117 KOG1088 Uncharacterized conser 85.7 0.34 7.4E-06 34.1 0.7 18 17-34 92-109 (124)
118 TIGR01031 rpmF_bact ribosomal 85.7 0.6 1.3E-05 28.5 1.7 26 4-36 27-52 (55)
119 PRK05508 methionine sulfoxide 85.3 0.76 1.6E-05 32.6 2.3 32 18-49 28-61 (119)
120 PF00301 Rubredoxin: Rubredoxi 85.3 0.49 1.1E-05 28.0 1.1 14 24-37 2-15 (47)
121 PF11672 DUF3268: Protein of u 85.2 0.86 1.9E-05 31.5 2.5 30 4-34 3-42 (102)
122 PF09723 Zn-ribbon_8: Zinc rib 85.0 0.59 1.3E-05 26.8 1.4 28 4-31 6-34 (42)
123 KOG2906 RNA polymerase III sub 84.5 0.88 1.9E-05 31.1 2.3 31 3-34 1-32 (105)
124 PF09526 DUF2387: Probable met 84.4 1.1 2.4E-05 28.9 2.6 31 4-34 9-41 (71)
125 PRK08351 DNA-directed RNA poly 84.3 0.6 1.3E-05 29.2 1.3 23 1-31 1-23 (61)
126 PRK02935 hypothetical protein; 84.0 0.7 1.5E-05 32.0 1.6 27 4-34 71-97 (110)
127 TIGR02605 CxxC_CxxC_SSSS putat 83.6 0.73 1.6E-05 27.3 1.5 28 4-31 6-34 (52)
128 COG1773 Rubredoxin [Energy pro 83.6 0.78 1.7E-05 28.0 1.5 26 1-30 1-26 (55)
129 smart00401 ZnF_GATA zinc finge 83.3 1.2 2.5E-05 26.8 2.2 32 3-34 3-36 (52)
130 PRK08402 replication factor A; 83.2 1 2.2E-05 38.0 2.6 27 4-32 213-239 (355)
131 PRK00222 methionine sulfoxide 83.1 0.97 2.1E-05 33.1 2.2 32 18-49 38-71 (142)
132 PF04161 Arv1: Arv1-like famil 83.1 0.59 1.3E-05 36.3 1.1 34 4-37 1-38 (208)
133 KOG0653 Cyclin B and related k 82.6 6.4 0.00014 33.5 7.3 62 103-164 156-218 (391)
134 CHL00174 accD acetyl-CoA carbo 82.6 0.23 5.1E-06 40.7 -1.3 30 4-34 39-68 (296)
135 TIGR03826 YvyF flagellar opero 82.5 0.26 5.6E-06 35.9 -1.0 30 1-35 1-30 (137)
136 PRK14559 putative protein seri 82.5 0.78 1.7E-05 41.7 1.8 8 4-11 2-9 (645)
137 TIGR00515 accD acetyl-CoA carb 82.4 0.25 5.4E-06 40.4 -1.2 30 4-34 27-56 (285)
138 KOG0834 CDK9 kinase-activating 82.3 0.55 1.2E-05 39.0 0.7 64 105-168 148-215 (323)
139 PRK00241 nudC NADH pyrophospha 82.1 1.1 2.4E-05 36.0 2.4 30 3-34 99-128 (256)
140 COG1326 Uncharacterized archae 82.0 0.59 1.3E-05 35.9 0.7 31 4-35 7-42 (201)
141 PF06397 Desulfoferrod_N: Desu 81.6 0.59 1.3E-05 26.0 0.5 22 4-26 7-28 (36)
142 KOG0402 60S ribosomal protein 81.5 0.51 1.1E-05 31.2 0.2 29 4-34 37-65 (92)
143 COG4068 Uncharacterized protei 81.4 0.19 4E-06 31.0 -1.7 25 4-34 9-34 (64)
144 KOG2593 Transcription initiati 81.4 0.79 1.7E-05 39.3 1.4 31 4-34 129-164 (436)
145 PF14353 CpXC: CpXC protein 81.2 1.2 2.6E-05 31.7 2.0 12 23-34 38-49 (128)
146 COG4530 Uncharacterized protei 81.0 0.86 1.9E-05 31.8 1.2 32 3-37 9-40 (129)
147 cd00202 ZnF_GATA Zinc finger D 80.8 0.55 1.2E-05 28.5 0.2 30 5-34 1-32 (54)
148 COG3877 Uncharacterized protei 80.4 1.6 3.4E-05 30.4 2.3 28 4-37 7-34 (122)
149 TIGR03830 CxxCG_CxxCG_HTH puta 80.4 1.5 3.3E-05 30.7 2.4 13 22-34 30-42 (127)
150 PF08006 DUF1700: Protein of u 80.4 4.5 9.8E-05 30.4 5.1 39 111-149 6-45 (181)
151 PF08646 Rep_fac-A_C: Replicat 80.4 1.8 3.9E-05 31.4 2.8 27 5-34 20-48 (146)
152 PF10058 DUF2296: Predicted in 80.2 1.1 2.3E-05 27.3 1.3 29 4-32 23-53 (54)
153 PRK05654 acetyl-CoA carboxylas 79.9 0.34 7.4E-06 39.7 -1.3 30 4-34 28-57 (292)
154 COG5333 CCL1 Cdk activating ki 79.7 4.8 0.00011 33.0 5.3 45 123-167 167-211 (297)
155 cd00729 rubredoxin_SM Rubredox 79.5 1.8 3.8E-05 23.6 1.9 24 4-31 3-26 (34)
156 PRK12380 hydrogenase nickel in 79.3 1.2 2.6E-05 31.2 1.5 7 5-11 72-78 (113)
157 TIGR01384 TFS_arch transcripti 79.3 2.1 4.6E-05 29.2 2.8 29 4-33 63-100 (104)
158 COG1656 Uncharacterized conser 79.1 0.87 1.9E-05 34.1 0.8 29 3-33 97-140 (165)
159 PF12677 DUF3797: Domain of un 78.9 1.9 4.2E-05 25.5 2.1 17 5-24 15-31 (49)
160 PF13453 zf-TFIIB: Transcripti 78.8 1.8 3.9E-05 24.5 1.9 28 5-33 1-29 (41)
161 TIGR00100 hypA hydrogenase nic 78.5 1.4 3E-05 31.0 1.6 18 15-32 62-79 (115)
162 TIGR00357 methionine-R-sulfoxi 78.4 1.5 3.4E-05 31.7 1.9 32 18-49 35-68 (134)
163 cd00974 DSRD Desulforedoxin (D 78.2 1.8 3.8E-05 23.5 1.7 25 3-28 4-28 (34)
164 PF10080 DUF2318: Predicted me 77.9 2.4 5.1E-05 29.3 2.6 27 5-34 37-63 (102)
165 TIGR03831 YgiT_finger YgiT-typ 77.8 1.9 4.2E-05 24.4 1.9 9 25-33 34-42 (46)
166 TIGR00155 pqiA_fam integral me 77.3 1.6 3.4E-05 37.5 1.9 30 5-34 15-44 (403)
167 PRK12366 replication factor A; 77.2 1.5 3.2E-05 39.8 1.8 25 4-32 533-557 (637)
168 PF01641 SelR: SelR domain; I 77.1 1.7 3.7E-05 31.1 1.8 31 19-49 33-65 (124)
169 PF04606 Ogr_Delta: Ogr/Delta- 77.1 2 4.4E-05 25.1 1.8 29 5-34 1-38 (47)
170 PRK03824 hypA hydrogenase nick 76.8 1.6 3.5E-05 31.6 1.6 21 14-34 61-81 (135)
171 PRK14890 putative Zn-ribbon RN 76.8 2.3 5E-05 26.3 2.1 28 3-32 7-34 (59)
172 COG0777 AccD Acetyl-CoA carbox 76.6 0.66 1.4E-05 37.6 -0.5 43 4-48 29-78 (294)
173 PF08063 PADR1: PADR1 (NUC008) 75.9 1.8 3.8E-05 26.4 1.4 22 4-28 15-36 (55)
174 PF06827 zf-FPG_IleRS: Zinc fi 75.5 1.8 4E-05 22.6 1.2 28 4-31 2-29 (30)
175 PF07754 DUF1610: Domain of un 75.1 2.4 5.1E-05 21.4 1.5 23 6-31 1-24 (24)
176 PF11023 DUF2614: Protein of u 75.0 1 2.2E-05 31.6 0.1 38 4-48 70-107 (114)
177 KOG3134 Predicted membrane pro 74.9 0.76 1.6E-05 35.9 -0.5 33 5-37 2-38 (225)
178 TIGR00319 desulf_FeS4 desulfof 74.9 2.1 4.5E-05 23.1 1.4 23 4-27 8-30 (34)
179 PF12651 RHH_3: Ribbon-helix-h 74.7 9.2 0.0002 22.0 4.2 30 106-135 11-41 (44)
180 PRK14559 putative protein seri 74.7 1.7 3.7E-05 39.5 1.5 25 4-34 28-52 (645)
181 PF01155 HypA: Hydrogenase exp 74.5 0.82 1.8E-05 32.0 -0.4 24 5-32 72-95 (113)
182 PF13790 DUF4182: Domain of un 74.4 1.8 3.9E-05 24.3 1.0 14 21-34 1-14 (38)
183 PF05460 ORC6: Origin recognit 74.1 1 2.2E-05 37.9 0.0 49 120-168 11-60 (353)
184 cd04476 RPA1_DBD_C RPA1_DBD_C: 73.8 2.7 5.9E-05 31.1 2.2 26 5-33 36-61 (166)
185 PRK15103 paraquat-inducible me 73.1 2.1 4.5E-05 36.9 1.6 33 4-36 11-43 (419)
186 PF12172 DUF35_N: Rubredoxin-l 73.0 2 4.3E-05 23.7 1.0 21 4-30 12-32 (37)
187 PF07191 zinc-ribbons_6: zinc- 72.4 2.5 5.3E-05 27.2 1.4 27 4-34 2-28 (70)
188 KOG4557 Origin recognition com 72.2 7.1 0.00015 30.7 4.2 54 111-165 95-153 (262)
189 PHA03074 late transcription fa 72.0 2.1 4.6E-05 33.1 1.3 30 2-34 3-32 (225)
190 COG5024 Cyclin [Cell division 72.0 5.4 0.00012 34.6 3.9 59 107-165 215-273 (440)
191 PF06044 DRP: Dam-replacing fa 71.5 2 4.3E-05 34.2 1.1 29 4-33 32-63 (254)
192 PRK03681 hypA hydrogenase nick 70.9 2.6 5.7E-05 29.6 1.5 16 16-31 63-78 (114)
193 COG0229 Conserved domain frequ 70.7 3.4 7.3E-05 30.0 2.0 31 19-49 38-70 (140)
194 PF05066 HARE-HTH: HB1, ASXL, 70.7 5.3 0.00012 25.2 2.8 32 129-160 20-53 (72)
195 PF14768 RPA_interact_C: Repli 70.6 4 8.6E-05 26.9 2.2 26 5-34 1-26 (82)
196 COG2093 DNA-directed RNA polym 70.6 2.6 5.7E-05 26.3 1.2 26 1-32 2-27 (64)
197 PF01485 IBR: IBR domain; Int 70.5 3 6.6E-05 25.2 1.6 28 4-33 19-50 (64)
198 COG0333 RpmF Ribosomal protein 70.4 3.4 7.4E-05 25.4 1.7 26 4-36 28-53 (57)
199 PRK00085 recO DNA repair prote 70.2 3.2 6.8E-05 32.7 2.0 27 4-30 150-177 (247)
200 PF00320 GATA: GATA zinc finge 70.0 1.4 2.9E-05 24.4 -0.1 27 6-32 1-29 (36)
201 PF04216 FdhE: Protein involve 69.6 3.1 6.7E-05 33.9 1.8 30 4-33 173-207 (290)
202 TIGR01562 FdhE formate dehydro 69.6 4.3 9.4E-05 33.5 2.7 9 25-33 254-262 (305)
203 COG4643 Uncharacterized protei 68.7 2.9 6.3E-05 34.9 1.5 26 5-30 34-61 (366)
204 PF14206 Cys_rich_CPCC: Cystei 68.6 5.6 0.00012 26.1 2.6 27 4-33 2-30 (78)
205 PF13824 zf-Mss51: Zinc-finger 68.5 3.9 8.5E-05 24.9 1.7 24 5-33 1-24 (55)
206 PRK03564 formate dehydrogenase 68.3 5.2 0.00011 33.1 2.9 9 4-12 188-196 (309)
207 COG4391 Uncharacterized protei 67.7 3.5 7.7E-05 25.7 1.4 22 13-34 37-59 (62)
208 PRK04023 DNA polymerase II lar 67.7 4 8.8E-05 38.8 2.3 11 24-34 664-674 (1121)
209 PRK06260 threonine synthase; V 67.6 2.6 5.6E-05 35.9 1.0 30 1-34 1-30 (397)
210 TIGR03829 YokU_near_AblA uncha 67.5 2.7 6E-05 28.2 0.9 38 5-42 1-54 (89)
211 PF00488 MutS_V: MutS domain V 67.4 7.3 0.00016 30.7 3.5 26 113-138 209-234 (235)
212 TIGR00595 priA primosomal prot 67.4 4.9 0.00011 35.4 2.7 29 4-34 223-251 (505)
213 PF01599 Ribosomal_S27: Riboso 67.1 7.9 0.00017 22.8 2.7 26 4-31 19-46 (47)
214 KOG1010 Rb (Retinoblastoma tum 67.1 15 0.00033 34.4 5.8 57 109-166 35-91 (920)
215 KOG0856 Predicted pilin-like t 66.8 3.7 8E-05 29.9 1.5 31 19-49 50-82 (146)
216 TIGR00310 ZPR1_znf ZPR1 zinc f 66.7 4.6 9.9E-05 31.1 2.1 37 102-138 99-135 (192)
217 TIGR00613 reco DNA repair prot 66.5 4.4 9.6E-05 31.7 2.1 28 4-31 148-176 (241)
218 PRK05580 primosome assembly pr 66.4 5.2 0.00011 36.6 2.8 28 4-33 391-418 (679)
219 PRK06393 rpoE DNA-directed RNA 66.3 2.4 5.2E-05 26.7 0.4 21 3-31 5-25 (64)
220 PF14471 DUF4428: Domain of un 66.2 1.8 3.8E-05 26.0 -0.2 28 5-33 1-30 (51)
221 PRK06450 threonine synthase; V 65.3 3.2 6.9E-05 34.6 1.1 29 1-34 1-29 (338)
222 PRK07218 replication factor A; 65.1 3 6.4E-05 36.0 0.9 21 4-32 298-318 (423)
223 smart00647 IBR In Between Ring 63.9 7.2 0.00016 23.5 2.3 28 4-33 19-50 (64)
224 KOG3507 DNA-directed RNA polym 63.7 4 8.6E-05 25.2 1.0 27 4-33 21-47 (62)
225 PF01363 FYVE: FYVE zinc finge 63.7 5 0.00011 25.1 1.6 30 4-37 10-39 (69)
226 COG3809 Uncharacterized protei 63.7 6.8 0.00015 25.7 2.2 28 4-33 2-31 (88)
227 PRK06386 replication factor A; 63.7 3.9 8.5E-05 34.5 1.4 21 4-32 237-257 (358)
228 PF06689 zf-C4_ClpX: ClpX C4-t 63.4 2.6 5.6E-05 24.0 0.2 27 4-30 2-31 (41)
229 PRK14873 primosome assembly pr 63.3 5.8 0.00013 36.3 2.5 28 4-33 393-420 (665)
230 PRK14714 DNA polymerase II lar 63.2 4.5 9.8E-05 39.3 1.8 6 5-10 669-674 (1337)
231 PF01807 zf-CHC2: CHC2 zinc fi 63.0 7.4 0.00016 26.3 2.4 27 5-31 35-62 (97)
232 PRK00564 hypA hydrogenase nick 63.0 3.1 6.8E-05 29.3 0.6 18 14-31 62-79 (117)
233 PF04502 DUF572: Family of unk 62.9 3.7 8E-05 34.1 1.1 25 4-28 78-102 (324)
234 COG2816 NPY1 NTP pyrophosphohy 62.4 5.2 0.00011 32.6 1.8 29 4-34 112-140 (279)
235 TIGR00340 zpr1_rel ZPR1-relate 62.0 7.2 0.00016 29.2 2.4 36 102-138 97-132 (163)
236 PRK04194 hypothetical protein; 62.0 24 0.00052 30.3 5.8 48 110-157 76-138 (392)
237 PF04810 zf-Sec23_Sec24: Sec23 61.4 11 0.00023 21.2 2.5 29 4-32 3-33 (40)
238 PF03833 PolC_DP2: DNA polymer 61.3 2.7 5.8E-05 39.2 0.0 11 23-33 680-690 (900)
239 PF03685 UPF0147: Uncharacteri 61.3 46 0.00099 22.2 6.4 53 101-157 4-56 (85)
240 KOG0794 CDK8 kinase-activating 60.7 14 0.00031 29.4 3.8 55 112-166 157-212 (264)
241 PRK08197 threonine synthase; V 60.6 4.1 8.9E-05 34.6 1.0 26 4-34 8-33 (394)
242 PF09889 DUF2116: Uncharacteri 60.6 1.8 4E-05 26.8 -0.8 25 4-34 4-29 (59)
243 PF04216 FdhE: Protein involve 59.9 6.2 0.00013 32.1 1.9 31 4-34 212-249 (290)
244 COG1779 C4-type Zn-finger prot 59.3 6.6 0.00014 30.3 1.8 34 4-37 15-57 (201)
245 PF09082 DUF1922: Domain of un 58.9 8.1 0.00017 24.6 1.8 27 4-34 4-30 (68)
246 PF07295 DUF1451: Protein of u 58.8 5.1 0.00011 29.5 1.1 15 20-34 109-123 (146)
247 PF14951 DUF4503: Domain of un 58.6 6.6 0.00014 33.1 1.8 34 5-39 276-310 (389)
248 PF10005 DUF2248: Uncharacteri 58.5 6 0.00013 33.1 1.6 24 5-34 1-24 (343)
249 PRK01110 rpmF 50S ribosomal pr 58.2 6.8 0.00015 24.3 1.4 28 4-39 28-55 (60)
250 smart00290 ZnF_UBP Ubiquitin C 58.1 8.9 0.00019 22.2 1.9 22 5-34 1-22 (50)
251 PF14319 Zn_Tnp_IS91: Transpos 58.1 3.6 7.7E-05 28.7 0.2 34 4-39 43-76 (111)
252 PF01412 ArfGap: Putative GTPa 58.0 3.7 8.1E-05 28.7 0.3 32 3-34 13-44 (116)
253 smart00064 FYVE Protein presen 58.0 7.8 0.00017 24.1 1.7 30 4-37 11-40 (68)
254 PF14833 NAD_binding_11: NAD-b 57.7 38 0.00082 23.4 5.4 39 103-141 72-110 (122)
255 PRK05550 bifunctional methioni 57.4 6.9 0.00015 32.0 1.7 32 18-49 31-64 (283)
256 COG4311 SoxD Sarcosine oxidase 57.1 5.3 0.00011 27.1 0.8 11 1-11 1-11 (97)
257 TIGR01562 FdhE formate dehydro 57.1 7.3 0.00016 32.2 1.8 28 4-31 185-218 (305)
258 PF01396 zf-C4_Topoisom: Topoi 57.1 15 0.00032 20.6 2.6 29 4-33 2-34 (39)
259 PF13878 zf-C2H2_3: zinc-finge 56.5 5.4 0.00012 22.6 0.7 15 22-36 12-26 (41)
260 smart00709 Zpr1 Duplicated dom 56.1 10 0.00022 28.2 2.4 38 101-138 98-137 (160)
261 PF13913 zf-C2HC_2: zinc-finge 55.8 7.6 0.00016 19.5 1.1 9 3-11 2-10 (25)
262 TIGR00299 conserved hypothetic 55.0 35 0.00076 29.1 5.6 49 109-157 74-137 (382)
263 PRK08329 threonine synthase; V 55.0 9 0.0002 32.0 2.1 25 4-34 2-26 (347)
264 PRK14067 exodeoxyribonuclease 54.7 23 0.00049 23.3 3.5 38 101-138 5-42 (80)
265 cd07973 Spt4 Transcription elo 54.6 8.9 0.00019 26.3 1.7 28 3-33 3-30 (98)
266 PRK04330 hypothetical protein; 54.0 64 0.0014 21.6 6.5 53 101-157 7-59 (88)
267 COG1198 PriA Primosomal protei 53.9 12 0.00025 34.7 2.8 27 4-32 445-471 (730)
268 cd00065 FYVE FYVE domain; Zinc 53.5 11 0.00023 22.4 1.7 31 3-37 2-32 (57)
269 PRK14018 trifunctional thiored 53.5 10 0.00022 33.7 2.3 31 19-49 414-446 (521)
270 PRK00750 lysK lysyl-tRNA synth 53.4 11 0.00024 33.3 2.5 32 5-37 177-213 (510)
271 COG4709 Predicted membrane pro 53.1 43 0.00094 25.7 5.3 42 111-152 6-48 (195)
272 PF08772 NOB1_Zn_bind: Nin one 53.1 7.4 0.00016 25.2 1.0 11 1-11 22-32 (73)
273 PRK00109 Holliday junction res 52.6 40 0.00086 24.3 4.9 52 106-157 75-132 (138)
274 TIGR02642 phage_xxxx uncharact 51.9 9.8 0.00021 29.1 1.7 24 3-30 99-122 (186)
275 smart00105 ArfGap Putative GTP 51.7 6.9 0.00015 27.2 0.8 32 3-34 3-34 (112)
276 PF09334 tRNA-synt_1g: tRNA sy 51.7 8.7 0.00019 32.7 1.5 24 4-34 137-160 (391)
277 PRK14714 DNA polymerase II lar 51.6 7.1 0.00015 38.1 1.1 8 5-12 681-688 (1337)
278 smart00342 HTH_ARAC helix_turn 51.3 16 0.00034 22.6 2.4 15 112-126 4-18 (84)
279 PF01402 RHH_1: Ribbon-helix-h 51.2 39 0.00084 18.2 4.2 27 107-133 9-36 (39)
280 PF14369 zf-RING_3: zinc-finge 50.6 11 0.00025 20.6 1.4 27 3-31 2-29 (35)
281 PF14205 Cys_rich_KTR: Cystein 50.2 15 0.00032 22.3 1.9 27 5-31 6-36 (55)
282 PRK11032 hypothetical protein; 49.4 9.3 0.0002 28.6 1.2 15 20-34 121-135 (160)
283 PRK09462 fur ferric uptake reg 49.4 9.5 0.00021 27.7 1.2 13 22-34 89-101 (148)
284 COG1571 Predicted DNA-binding 49.3 10 0.00023 32.6 1.6 33 4-39 351-383 (421)
285 COG4307 Uncharacterized protei 49.2 6.6 0.00014 31.9 0.4 28 1-34 1-28 (349)
286 PF14149 YhfH: YhfH-like prote 48.8 2.5 5.5E-05 23.6 -1.4 16 21-36 11-26 (37)
287 cd07153 Fur_like Ferric uptake 48.8 9.9 0.00022 26.0 1.2 13 22-34 72-84 (116)
288 PF04981 NMD3: NMD3 family ; 48.7 15 0.00033 28.9 2.4 31 5-35 15-47 (236)
289 PF03367 zf-ZPR1: ZPR1 zinc-fi 48.7 8.2 0.00018 28.8 0.8 31 4-34 2-41 (161)
290 PF13408 Zn_ribbon_recom: Reco 48.6 9.3 0.0002 22.6 0.9 14 21-34 3-16 (58)
291 PF01475 FUR: Ferric uptake re 48.3 10 0.00023 26.2 1.3 14 21-34 78-91 (120)
292 PRK14526 adenylate kinase; Pro 48.1 11 0.00025 29.1 1.6 27 5-31 124-150 (211)
293 smart00400 ZnF_CHCC zinc finge 48.0 27 0.00059 20.7 2.9 34 4-39 3-37 (55)
294 COG0735 Fur Fe2+/Zn2+ uptake r 47.7 10 0.00022 27.6 1.2 14 21-34 91-104 (145)
295 COG5525 Bacteriophage tail ass 47.2 11 0.00023 33.9 1.4 32 5-36 229-272 (611)
296 PRK14064 exodeoxyribonuclease 47.2 34 0.00074 22.1 3.5 37 102-138 5-41 (75)
297 PRK05638 threonine synthase; V 47.0 11 0.00023 32.6 1.4 25 4-34 2-26 (442)
298 KOG2907 RNA polymerase I trans 46.7 7.9 0.00017 27.1 0.4 28 4-34 8-36 (116)
299 TIGR00250 RNAse_H_YqgF RNAse H 46.4 55 0.0012 23.3 4.8 52 105-156 68-125 (130)
300 PF08421 Methyltransf_13: Puta 46.4 13 0.00029 22.9 1.4 17 23-39 40-56 (62)
301 KOG0655 G1/S-specific cyclin E 46.3 59 0.0013 27.4 5.4 67 106-172 146-214 (408)
302 PLN02569 threonine synthase 46.2 13 0.00027 32.8 1.7 26 4-34 50-75 (484)
303 PRK07591 threonine synthase; V 46.0 8.7 0.00019 33.0 0.7 26 4-34 19-44 (421)
304 cd00674 LysRS_core_class_I cat 45.9 17 0.00037 30.6 2.4 32 5-37 171-206 (353)
305 PRK03564 formate dehydrogenase 45.9 15 0.00033 30.4 2.0 9 25-33 254-262 (309)
306 PF00628 PHD: PHD-finger; Int 45.7 14 0.00031 21.3 1.4 25 5-34 1-25 (51)
307 PF07240 Turandot: Stress-indu 45.6 41 0.00089 22.4 3.7 43 101-143 8-51 (85)
308 PF02591 DUF164: Putative zinc 45.3 12 0.00027 22.4 1.1 31 3-33 22-56 (56)
309 PRK00481 NAD-dependent deacety 45.3 13 0.00027 29.4 1.4 37 4-41 123-160 (242)
310 smart00534 MUTSac ATPase domai 45.0 18 0.00039 27.1 2.2 23 111-133 163-185 (185)
311 PF09779 Ima1_N: Ima1 N-termin 44.9 16 0.00034 26.2 1.8 28 5-32 2-29 (131)
312 smart00504 Ubox Modified RING 43.9 13 0.00027 22.4 1.0 28 4-39 2-29 (63)
313 COG1545 Predicted nucleic-acid 43.9 12 0.00026 27.2 1.1 24 4-33 30-53 (140)
314 PRK08173 DNA topoisomerase III 43.9 15 0.00033 34.7 1.9 27 4-34 625-651 (862)
315 cd01411 SIR2H SIR2H: Uncharact 43.6 13 0.00029 29.0 1.3 36 4-41 119-154 (225)
316 PRK00448 polC DNA polymerase I 43.6 12 0.00026 37.3 1.3 32 4-36 909-946 (1437)
317 PHA01623 hypothetical protein 43.5 71 0.0015 19.3 4.3 30 106-135 22-52 (56)
318 PRK04023 DNA polymerase II lar 43.2 16 0.00034 35.1 1.9 12 23-34 651-662 (1121)
319 PRK11639 zinc uptake transcrip 43.1 13 0.00028 27.7 1.2 12 23-34 100-111 (169)
320 PF09845 DUF2072: Zn-ribbon co 43.0 11 0.00023 27.2 0.6 13 25-37 3-15 (131)
321 COG2260 Predicted Zn-ribbon RN 42.6 13 0.00029 22.9 0.9 8 26-33 20-27 (59)
322 PF10886 DUF2685: Protein of u 42.5 11 0.00024 22.9 0.5 36 3-39 1-39 (54)
323 cd01410 SIRT7 SIRT7: Eukaryoti 42.4 14 0.0003 28.6 1.2 38 3-41 95-138 (206)
324 TIGR01391 dnaG DNA primase, ca 42.0 27 0.00059 29.9 3.1 34 5-40 36-70 (415)
325 TIGR02384 RelB_DinJ addiction 41.8 99 0.0021 20.2 5.4 16 108-123 13-28 (83)
326 PF10083 DUF2321: Uncharacteri 41.0 16 0.00035 27.1 1.3 7 5-11 41-47 (158)
327 COG3024 Uncharacterized protei 40.9 14 0.0003 23.2 0.8 29 3-32 7-36 (65)
328 COG1885 Uncharacterized protei 40.8 29 0.00062 24.1 2.4 20 18-37 44-63 (115)
329 COG2995 PqiA Uncharacterized p 40.7 15 0.00032 31.5 1.2 31 4-34 19-49 (418)
330 cd03285 ABC_MSH2_euk MutS2 hom 40.7 31 0.00067 26.8 3.0 24 113-136 198-221 (222)
331 TIGR00320 dfx_rbo desulfoferro 40.7 18 0.00039 25.8 1.5 26 4-32 8-33 (125)
332 PF09339 HTH_IclR: IclR helix- 40.4 50 0.0011 19.2 3.2 29 111-142 20-48 (52)
333 PF00130 C1_1: Phorbol esters/ 40.2 28 0.00061 20.2 2.1 34 4-40 12-45 (53)
334 PRK09263 anaerobic ribonucleos 40.1 15 0.00033 33.9 1.4 26 4-31 642-667 (711)
335 TIGR01405 polC_Gram_pos DNA po 39.7 15 0.00033 36.0 1.3 32 4-36 684-721 (1213)
336 COG3654 Doc Prophage maintenan 39.5 1.5E+02 0.0032 21.5 6.2 39 120-158 49-87 (132)
337 PRK00977 exodeoxyribonuclease 39.4 47 0.001 21.7 3.2 38 101-138 8-45 (80)
338 COG1675 TFA1 Transcription ini 39.4 6.1 0.00013 30.0 -1.1 31 4-36 114-145 (176)
339 PTZ00408 NAD-dependent deacety 39.3 12 0.00026 29.8 0.5 38 4-41 118-157 (242)
340 PRK00762 hypA hydrogenase nick 39.0 14 0.00029 26.3 0.7 18 14-32 61-78 (124)
341 PHA02325 hypothetical protein 39.0 17 0.00037 22.9 1.0 11 1-11 1-11 (72)
342 COG0375 HybF Zn finger protein 38.9 17 0.00036 25.7 1.1 20 15-34 62-81 (115)
343 PF06676 DUF1178: Protein of u 38.7 17 0.00038 26.8 1.2 41 104-146 82-122 (148)
344 COG3364 Zn-ribbon containing p 38.2 13 0.00029 25.6 0.5 11 25-35 4-14 (112)
345 COG5134 Uncharacterized conser 37.9 29 0.00062 27.3 2.3 24 5-28 81-104 (272)
346 COG5347 GTPase-activating prot 37.9 28 0.0006 29.0 2.4 31 3-34 20-51 (319)
347 COG0846 SIR2 NAD-dependent pro 37.9 15 0.00033 29.4 0.9 38 4-41 123-165 (250)
348 COG3677 Transposase and inacti 37.6 30 0.00064 24.8 2.3 31 3-34 30-64 (129)
349 PHA00689 hypothetical protein 37.6 24 0.00053 21.0 1.5 27 20-47 14-40 (62)
350 KOG0706 Predicted GTPase-activ 37.4 21 0.00045 31.0 1.6 32 2-34 22-54 (454)
351 PRK04179 rpl37e 50S ribosomal 37.1 16 0.00034 22.8 0.6 23 4-31 18-40 (62)
352 PF02082 Rrf2: Transcriptional 37.0 42 0.0009 21.6 2.7 29 111-142 27-55 (83)
353 PRK09582 chaB cation transport 36.9 39 0.00085 22.0 2.5 22 119-140 7-32 (76)
354 COG5082 AIR1 Arginine methyltr 36.7 14 0.00031 28.3 0.5 26 2-29 59-84 (190)
355 PF14690 zf-ISL3: zinc-finger 36.6 23 0.0005 20.1 1.3 8 4-11 3-10 (47)
356 PF05605 zf-Di19: Drought indu 36.4 21 0.00045 21.2 1.1 9 3-11 2-10 (54)
357 PF06906 DUF1272: Protein of u 36.3 19 0.00042 22.0 0.9 8 4-11 42-49 (57)
358 PF01907 Ribosomal_L37e: Ribos 36.2 27 0.00059 21.3 1.6 23 5-32 17-39 (55)
359 COG4481 Uncharacterized protei 36.1 37 0.0008 20.7 2.1 28 7-34 17-45 (60)
360 COG0498 ThrC Threonine synthas 35.9 12 0.00025 32.3 -0.1 30 3-36 5-34 (411)
361 PF04221 RelB: RelB antitoxin; 35.7 81 0.0018 20.5 4.0 30 107-139 11-41 (83)
362 TIGR00354 polC DNA polymerase, 35.7 17 0.00037 34.6 0.9 22 4-33 626-647 (1095)
363 PRK14068 exodeoxyribonuclease 35.3 63 0.0014 20.9 3.3 36 103-138 6-41 (76)
364 TIGR00570 cdk7 CDK-activating 35.1 26 0.00057 29.0 1.8 11 1-11 1-11 (309)
365 PF03811 Zn_Tnp_IS1: InsA N-te 35.0 21 0.00045 19.7 0.9 13 4-17 6-19 (36)
366 PHA02540 61 DNA primase; Provi 35.0 39 0.00085 28.3 2.9 29 4-32 28-64 (337)
367 COG2176 PolC DNA polymerase II 34.9 21 0.00046 34.9 1.4 30 4-34 915-950 (1444)
368 COG2023 RPR2 RNase P subunit R 34.9 35 0.00077 23.6 2.2 31 4-34 57-93 (105)
369 PF06150 ChaB: ChaB; InterPro 34.9 43 0.00093 20.4 2.3 15 127-141 11-25 (57)
370 PF05864 Chordopox_RPO7: Chord 34.9 16 0.00034 22.5 0.4 13 23-35 4-16 (63)
371 PRK15103 paraquat-inducible me 34.8 25 0.00054 30.4 1.7 24 5-34 223-246 (419)
372 PF01397 Terpene_synth: Terpen 34.8 2E+02 0.0044 21.8 6.8 62 107-169 48-110 (183)
373 PRK14063 exodeoxyribonuclease 34.8 59 0.0013 21.0 3.1 36 103-138 5-40 (76)
374 PF02609 Exonuc_VII_S: Exonucl 34.7 67 0.0015 19.0 3.2 32 107-138 3-34 (53)
375 COG4393 Predicted membrane pro 34.7 23 0.00049 29.8 1.4 26 5-33 336-361 (405)
376 PLN03165 chaperone protein dna 34.7 16 0.00035 25.5 0.5 8 5-12 54-61 (111)
377 PRK05667 dnaG DNA primase; Val 34.6 41 0.0009 30.3 3.1 27 5-31 38-65 (580)
378 PF05819 NolX: NolX protein; 34.6 70 0.0015 28.4 4.3 54 101-159 362-415 (624)
379 PF10276 zf-CHCC: Zinc-finger 34.5 34 0.00073 19.4 1.7 20 14-33 18-39 (40)
380 PHA03082 DNA-dependent RNA pol 34.4 15 0.00033 22.5 0.3 13 23-35 4-16 (63)
381 PRK00133 metG methionyl-tRNA s 34.4 20 0.00044 32.7 1.2 24 4-34 140-163 (673)
382 COG1107 Archaea-specific RecJ- 34.3 31 0.00068 31.2 2.3 29 3-32 2-30 (715)
383 COG5257 GCD11 Translation init 33.9 20 0.00044 30.2 1.0 25 4-33 58-82 (415)
384 TIGR00617 rpa1 replication fac 33.8 29 0.00064 31.4 2.1 28 4-34 475-504 (608)
385 cd00021 BBOX B-Box-type zinc f 33.7 37 0.00081 18.1 1.8 25 5-29 2-26 (39)
386 PRK14066 exodeoxyribonuclease 33.4 64 0.0014 20.8 3.1 35 104-138 5-39 (75)
387 PF08996 zf-DNA_Pol: DNA Polym 33.3 21 0.00045 27.2 0.9 34 4-39 19-61 (188)
388 PRK14704 anaerobic ribonucleos 33.2 23 0.00051 32.2 1.4 21 4-31 560-580 (618)
389 PRK04016 DNA-directed RNA poly 33.1 19 0.00042 22.5 0.6 12 24-35 5-16 (62)
390 PF01399 PCI: PCI domain; Int 32.7 59 0.0013 21.2 3.1 31 112-145 63-93 (105)
391 PF13412 HTH_24: Winged helix- 32.7 80 0.0017 17.7 3.2 29 111-142 19-47 (48)
392 PF09567 RE_MamI: MamI restric 32.5 18 0.0004 29.1 0.5 23 3-31 82-104 (314)
393 cd01412 SIRT5_Af1_CobB SIRT5_A 32.5 33 0.00072 26.6 2.0 36 4-41 110-148 (224)
394 COG1499 NMD3 NMD protein affec 32.3 16 0.00035 30.8 0.2 11 2-12 5-15 (355)
395 PF02146 SIR2: Sir2 family; I 32.3 22 0.00048 26.5 0.9 37 4-41 106-147 (178)
396 PF00643 zf-B_box: B-box zinc 32.2 31 0.00067 19.0 1.3 24 2-33 2-25 (42)
397 cd01407 SIR2-fam SIR2 family o 32.2 26 0.00056 27.1 1.3 38 4-41 110-151 (218)
398 COG2126 RPL37A Ribosomal prote 32.1 27 0.00058 21.6 1.1 24 4-32 17-40 (61)
399 TIGR00382 clpX endopeptidase C 31.9 25 0.00055 30.3 1.3 29 5-33 9-39 (413)
400 TIGR00987 himA integration hos 31.8 77 0.0017 21.1 3.5 35 110-144 6-40 (96)
401 PRK10753 transcriptional regul 31.6 81 0.0018 20.8 3.5 35 110-144 5-39 (90)
402 KOG0704 ADP-ribosylation facto 31.6 34 0.00073 28.9 1.9 29 3-32 19-48 (386)
403 cd03284 ABC_MutS1 MutS1 homolo 31.4 46 0.00099 25.7 2.6 20 113-132 196-215 (216)
404 TIGR01446 DnaD_dom DnaD and ph 31.3 1.1E+02 0.0025 18.9 4.0 27 108-134 17-43 (73)
405 PF08613 Cyclin: Cyclin; Inte 31.1 2E+02 0.0044 20.7 7.5 55 107-161 53-112 (149)
406 PF01978 TrmB: Sugar-specific 31.0 82 0.0018 19.2 3.3 31 110-143 23-53 (68)
407 PF00096 zf-C2H2: Zinc finger, 30.8 39 0.00085 15.7 1.4 10 25-34 2-11 (23)
408 PF12156 ATPase-cat_bd: Putati 30.6 22 0.00047 23.7 0.5 39 4-43 1-45 (88)
409 KOG1247 Methionyl-tRNA synthet 30.5 17 0.00037 31.6 0.0 11 149-159 490-500 (567)
410 TIGR00467 lysS_arch lysyl-tRNA 30.4 33 0.00072 30.5 1.8 32 5-37 170-204 (515)
411 PRK00279 adk adenylate kinase; 30.4 38 0.00083 25.8 2.0 29 5-33 129-157 (215)
412 PRK07217 replication factor A; 30.1 27 0.00058 29.0 1.1 22 4-33 189-212 (311)
413 KOG1252 Cystathionine beta-syn 30.1 85 0.0018 26.5 4.0 42 122-166 290-331 (362)
414 PF06221 zf-C2HC5: Putative zi 30.0 26 0.00055 21.5 0.7 23 5-31 20-43 (57)
415 PRK14715 DNA polymerase II lar 29.5 27 0.00059 34.6 1.2 23 4-34 675-697 (1627)
416 KOG3002 Zn finger protein [Gen 29.4 32 0.00069 28.4 1.4 28 3-30 48-76 (299)
417 cd01413 SIR2_Af2 SIR2_Af2: Arc 29.3 33 0.00072 26.7 1.5 38 4-41 114-154 (222)
418 smart00109 C1 Protein kinase C 29.2 34 0.00075 19.1 1.2 30 3-36 11-40 (49)
419 PF06107 DUF951: Bacterial pro 29.2 52 0.0011 20.2 2.0 27 8-34 15-42 (57)
420 TIGR01505 tartro_sem_red 2-hyd 29.0 1.3E+02 0.0029 23.9 5.1 37 105-141 235-271 (291)
421 KOG4537 Zn-ribbon-containing p 28.9 11 0.00023 28.1 -1.2 29 2-33 39-67 (178)
422 PF14502 HTH_41: Helix-turn-he 28.8 1.1E+02 0.0023 18.1 3.2 26 111-136 8-33 (48)
423 COG1959 Predicted transcriptio 28.8 80 0.0017 23.1 3.4 46 111-159 27-83 (150)
424 KOG0818 GTPase-activating prot 28.5 23 0.0005 31.4 0.5 29 4-33 9-38 (669)
425 PRK15461 NADH-dependent gamma- 28.5 1.4E+02 0.0029 24.2 5.0 38 104-141 237-274 (296)
426 PF12013 DUF3505: Protein of u 28.5 38 0.00082 23.1 1.5 20 15-34 3-22 (109)
427 PF01726 LexA_DNA_bind: LexA D 28.4 1.2E+02 0.0025 18.9 3.6 23 107-129 10-32 (65)
428 cd00029 C1 Protein kinase C co 28.2 30 0.00066 19.5 0.9 30 4-36 12-41 (50)
429 PF14311 DUF4379: Domain of un 28.1 22 0.00047 21.2 0.2 10 25-34 30-39 (55)
430 PF13335 Mg_chelatase_2: Magne 27.9 1.9E+02 0.0041 19.3 6.5 51 106-156 45-95 (96)
431 PF01921 tRNA-synt_1f: tRNA sy 27.8 16 0.00035 30.9 -0.5 33 5-37 176-213 (360)
432 PRK10664 transcriptional regul 27.7 1E+02 0.0022 20.4 3.5 30 110-139 5-34 (90)
433 PRK10857 DNA-binding transcrip 27.6 87 0.0019 23.3 3.4 46 111-159 27-83 (164)
434 PRK03922 hypothetical protein; 27.6 59 0.0013 22.7 2.3 20 18-37 44-63 (113)
435 PF00216 Bac_DNA_binding: Bact 27.6 76 0.0017 20.4 2.8 35 110-144 5-39 (90)
436 PF08882 Acetone_carb_G: Aceto 27.5 31 0.00068 24.1 0.9 12 23-34 74-85 (112)
437 PF08784 RPA_C: Replication pr 27.4 92 0.002 20.8 3.3 22 112-133 68-89 (102)
438 PRK08116 hypothetical protein; 27.2 49 0.0011 26.5 2.2 28 4-32 17-48 (268)
439 TIGR01280 xseB exodeoxyribonuc 27.1 94 0.002 19.5 3.0 34 105-138 3-36 (67)
440 KOG0656 G1/S-specific cyclin D 27.1 2.5E+02 0.0053 23.7 6.3 54 106-159 180-237 (335)
441 PRK07111 anaerobic ribonucleos 27.1 33 0.00071 31.9 1.3 21 4-31 681-701 (735)
442 TIGR01692 HIBADH 3-hydroxyisob 27.0 1.4E+02 0.0031 23.8 4.9 38 104-141 238-275 (288)
443 TIGR01053 LSD1 zinc finger dom 26.9 95 0.0021 16.4 2.6 27 4-32 2-28 (31)
444 COG1066 Sms Predicted ATP-depe 26.8 32 0.00069 29.9 1.0 15 109-123 132-146 (456)
445 KOG3430 Dynein light chain typ 26.8 1.7E+02 0.0036 19.7 4.2 27 102-128 15-42 (90)
446 PRK09709 exonuclease VIII; Rev 26.7 33 0.00071 32.3 1.2 27 4-39 526-552 (877)
447 KOG2767 Translation initiation 26.6 25 0.00055 29.6 0.4 29 5-33 98-128 (400)
448 smart00132 LIM Zinc-binding do 26.5 56 0.0012 17.0 1.7 10 24-33 28-37 (39)
449 PHA01748 hypothetical protein 26.5 1.6E+02 0.0035 18.0 4.3 28 107-134 12-40 (60)
450 PF00325 Crp: Bacterial regula 26.4 1.1E+02 0.0025 16.3 3.3 26 113-141 6-31 (32)
451 PF06573 Churchill: Churchill 26.3 31 0.00067 24.0 0.7 32 5-37 29-72 (112)
452 KOG1129 TPR repeat-containing 26.1 75 0.0016 27.1 3.0 30 127-156 341-370 (478)
453 smart00411 BHL bacterial (prok 25.9 1.2E+02 0.0025 19.6 3.5 35 110-144 5-39 (90)
454 COG1110 Reverse gyrase [DNA re 25.9 21 0.00046 34.4 -0.2 24 4-30 9-33 (1187)
455 PRK07956 ligA NAD-dependent DN 25.7 50 0.0011 30.4 2.1 32 4-37 405-439 (665)
456 smart00345 HTH_GNTR helix_turn 25.6 1.3E+02 0.0029 17.1 3.5 29 111-142 22-50 (60)
457 TIGR03060 PS_II_psb29 photosys 25.5 1E+02 0.0022 24.2 3.5 32 108-139 164-195 (214)
458 PHA02956 hypothetical protein; 25.4 45 0.00098 24.4 1.5 20 13-32 107-126 (189)
459 PRK09568 DNA primase large sub 25.3 4E+02 0.0086 22.1 7.2 39 104-142 10-54 (306)
460 KOG4557 Origin recognition com 25.3 2.8E+02 0.0062 22.0 5.9 55 111-165 2-60 (262)
461 PF04032 Rpr2: RNAse P Rpr2/Rp 25.3 35 0.00076 21.9 0.9 22 15-36 38-59 (85)
462 TIGR03844 cysteate_syn cysteat 25.2 30 0.00066 29.6 0.6 25 4-33 3-27 (398)
463 PF00392 GntR: Bacterial regul 25.2 1.3E+02 0.0028 18.1 3.4 24 112-135 27-50 (64)
464 cd08313 Death_TNFR1 Death doma 25.2 1.2E+02 0.0026 19.8 3.4 23 109-131 11-33 (80)
465 PF03107 C1_2: C1 domain; Int 24.9 72 0.0016 16.5 1.9 25 5-34 2-26 (30)
466 COG0143 MetG Methionyl-tRNA sy 24.8 40 0.00087 30.3 1.3 17 119-135 211-227 (558)
467 PF08238 Sel1: Sel1 repeat; I 24.8 1.1E+02 0.0025 15.7 2.9 20 120-140 19-38 (39)
468 PF04475 DUF555: Protein of un 24.8 42 0.00091 23.0 1.1 21 17-37 41-61 (102)
469 PF04391 DUF533: Protein of un 24.8 79 0.0017 24.2 2.8 20 109-128 163-182 (188)
470 PRK13266 Thf1-like protein; Re 24.6 1.1E+02 0.0023 24.3 3.5 32 108-139 166-197 (225)
471 TIGR02010 IscR iron-sulfur clu 24.6 87 0.0019 22.2 2.9 47 111-160 27-84 (135)
472 PF11264 ThylakoidFormat: Thyl 24.6 1.1E+02 0.0025 23.9 3.7 32 108-139 161-192 (216)
473 TIGR02944 suf_reg_Xantho FeS a 24.6 1.1E+02 0.0023 21.4 3.3 29 111-142 27-55 (130)
474 PRK04338 N(2),N(2)-dimethylgua 24.6 45 0.00098 28.3 1.6 34 4-44 245-278 (382)
475 KOG1842 FYVE finger-containing 24.6 15 0.00034 31.8 -1.2 27 3-33 180-206 (505)
476 PRK11559 garR tartronate semia 24.4 1.9E+02 0.004 23.1 5.1 37 105-141 238-274 (296)
477 TIGR00575 dnlj DNA ligase, NAD 24.4 54 0.0012 30.1 2.1 32 4-37 393-426 (652)
478 TIGR00201 comF comF family pro 24.4 33 0.00071 25.9 0.7 23 6-34 1-23 (190)
479 COG3357 Predicted transcriptio 24.4 33 0.00072 23.2 0.6 13 24-36 59-71 (97)
480 TIGR01070 mutS1 DNA mismatch r 24.3 94 0.002 29.4 3.7 28 113-140 758-785 (840)
481 PTZ00073 60S ribosomal protein 24.3 36 0.00078 22.9 0.7 23 4-31 17-39 (91)
482 PRK15059 tartronate semialdehy 24.1 1.9E+02 0.0041 23.4 5.1 38 104-141 234-271 (292)
483 cd00591 HU_IHF Integration hos 24.0 1.4E+02 0.0031 19.0 3.6 35 110-144 4-38 (87)
484 PRK14069 exodeoxyribonuclease 23.9 1.1E+02 0.0023 20.9 3.0 37 102-138 7-43 (95)
485 KOG1814 Predicted E3 ubiquitin 23.8 57 0.0012 28.2 2.0 28 4-33 369-396 (445)
486 cd08768 Cdc6_C Winged-helix do 23.8 1.8E+02 0.0039 18.4 4.1 42 102-143 22-63 (87)
487 TIGR01069 mutS2 MutS2 family p 23.8 78 0.0017 29.6 3.0 26 111-136 484-509 (771)
488 PLN03131 hypothetical protein; 23.7 56 0.0012 29.8 2.0 31 4-34 24-54 (705)
489 PF12668 DUF3791: Protein of u 23.3 1.5E+02 0.0032 18.1 3.4 24 109-135 5-28 (62)
490 TIGR01795 CM_mono_cladeE monof 23.3 2.4E+02 0.0052 18.9 4.7 31 105-138 50-80 (94)
491 COG2979 Uncharacterized protei 23.3 91 0.002 24.5 2.9 22 109-130 194-215 (225)
492 smart00351 PAX Paired Box doma 23.3 1.9E+02 0.0042 20.2 4.4 58 111-171 35-99 (125)
493 COG1813 Predicted transcriptio 23.3 37 0.00081 25.5 0.7 33 1-34 1-36 (165)
494 KOG3084 NADH pyrophosphatase I 23.2 52 0.0011 27.4 1.6 25 4-30 151-177 (345)
495 PF05402 PqqD: Coenzyme PQQ sy 23.2 1.8E+02 0.0039 17.5 4.8 35 108-142 32-67 (68)
496 COG1644 RPB10 DNA-directed RNA 23.1 27 0.00058 21.8 -0.0 13 24-36 5-17 (63)
497 PRK07220 DNA topoisomerase I; 23.0 80 0.0017 29.4 3.0 26 4-31 636-665 (740)
498 PRK09401 reverse gyrase; Revie 22.9 27 0.00058 34.3 -0.1 25 4-31 8-33 (1176)
499 TIGR02487 NrdD anaerobic ribon 22.9 48 0.001 29.9 1.4 22 4-31 525-546 (579)
500 PF13451 zf-trcl: Probable zin 22.9 39 0.00086 20.0 0.6 11 23-33 4-14 (49)
No 1
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=2.6e-48 Score=317.82 Aligned_cols=167 Identities=35% Similarity=0.691 Sum_probs=151.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccccccCcccccccCCCCCCCCcccCCCCCccccCCCceeEEecCC-CC
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPN-GA 82 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~~~~ewr~f~~~~~~~~~~r~g~~~~~~~~~~~~~t~i~~~~-~~ 82 (172)
..||+||+ +++++|+++|++||.+||+||+|++||+|||||+|++++ ..+++|||+|.++++||.|++|.|+++. +.
T Consensus 12 ~~Cp~Cg~-~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~-~~~~~RvG~~~~~~~~~~gl~T~I~~~~~~~ 89 (310)
T PRK00423 12 LVCPECGS-DKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQ-REKRSRVGAPMTYTIHDKGLSTDIDWRNKDS 89 (310)
T ss_pred CcCcCCCC-CCeeEECCCCeEeecccCCcccccccccCCCccCCCccc-cCCccccCCCCCccccCCCCceEeecCCccc
Confidence 57999998 689999999999999999999999999999999999654 4699999999999999999999999654 33
Q ss_pred Ccccccc-------cccccccCC---CCchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHH
Q 030755 83 SGEFLSS-------SLGRWQNRG---SNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLA 152 (172)
Q Consensus 83 ~~~~l~~-------~l~~~~~~~---~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aA 152 (172)
.|..++. +|++||++. ++.|+.|..++..|+++|+.|+||+.++++|..||++++++++++||+++.++|
T Consensus 90 ~g~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~A 169 (310)
T PRK00423 90 YGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVA 169 (310)
T ss_pred ccccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHH
Confidence 4444442 478888764 668999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhCCCCCCccccC
Q 030755 153 ACLYIACRQEDKPRTVKGTA 172 (172)
Q Consensus 153 AclYiacR~~~~~~tl~eia 172 (172)
||||+|||++++|+||+||+
T Consensus 170 AclYiACR~~~~prtl~eI~ 189 (310)
T PRK00423 170 AALYAACRRCKVPRTLDEIA 189 (310)
T ss_pred HHHHHHHHHcCCCcCHHHHH
Confidence 99999999999999999985
No 2
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=2e-45 Score=290.09 Aligned_cols=168 Identities=65% Similarity=0.978 Sum_probs=156.1
Q ss_pred CCCCCCCCCCc-eeEeCCCCceEeCCCcceecccccccCcccccccCCCCCCCCcccCCCCCccccCCCceeEEecCCCC
Q 030755 4 AFCSDCKKHTE-VVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGA 82 (172)
Q Consensus 4 ~~C~~Cg~~~~-i~~D~~~G~~vC~~CG~V~~e~~i~~~~ewr~f~~~~~~~~~~r~g~~~~~~~~~~~~~t~i~~~~~~ 82 (172)
.+|++|+..+. +|+|+..|+.+|..||+|+++++||.++|||+|++++++.||+|||++.+|++.++++.|+|+++.+.
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 36999998765 99999999999999999999999999999999998888999999999999999999999999998766
Q ss_pred CcccccccccccccC--CCCchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHH
Q 030755 83 SGEFLSSSLGRWQNR--GSNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACR 160 (172)
Q Consensus 83 ~~~~l~~~l~~~~~~--~~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR 160 (172)
.+.+++. |.+||++ +++.++.+..++..|..+++.|+||..+.++|.+||+++.+.+.++||+.++++|||||+|||
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 SSSFASS-LGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACR 159 (308)
T ss_pred CHHHHHH-HHHHhcccccCCccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHH
Confidence 6555543 8888874 477899999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCCCCccccC
Q 030755 161 QEDKPRTVKGTA 172 (172)
Q Consensus 161 ~~~~~~tl~eia 172 (172)
+++.|||++||+
T Consensus 160 q~~~pRT~kEI~ 171 (308)
T KOG1597|consen 160 QEDVPRTFKEIS 171 (308)
T ss_pred hcCCCchHHHHH
Confidence 999999999985
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=2e-42 Score=278.19 Aligned_cols=160 Identities=38% Similarity=0.719 Sum_probs=144.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccccccCcccccccCCCCCCCCcccCCCCCccccCCCceeEEecCCCCC
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGAS 83 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~~~~ewr~f~~~~~~~~~~r~g~~~~~~~~~~~~~t~i~~~~~~~ 83 (172)
..||+||+ +++++|+++|++||.+||+|++|+.||.|||||.|.+ . ..+ |+|+|.++.+||.+++|.|+++...
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-TNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAFDE--R-HER-RVGAPLTPSIHDKGLSTIIGWGDKD- 75 (285)
T ss_pred CCCCCCCC-ccceeeccCCeEEeccCCEEeccccccCCCCcccccc--c-ccc-cccCCCccccCccchhhhcccchhH-
Confidence 57999999 6999999999999999999999999999999999932 2 233 9999999999999999999986532
Q ss_pred cccccccccccccCC---CCchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHH
Q 030755 84 GEFLSSSLGRWQNRG---SNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACR 160 (172)
Q Consensus 84 ~~~l~~~l~~~~~~~---~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR 160 (172)
...+|++||.+. +.+|+.+..++..|.++++.|+||.++.++|..||++++++++++||+.++++|||||+|||
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 123578888643 56899999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCCCCccccC
Q 030755 161 QEDKPRTVKGTA 172 (172)
Q Consensus 161 ~~~~~~tl~eia 172 (172)
+++.|+||.|||
T Consensus 153 ~~~~prtl~eIa 164 (285)
T COG1405 153 INGVPRTLDEIA 164 (285)
T ss_pred HcCCCccHHHHH
Confidence 999999999985
No 4
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=99.92 E-value=1.1e-24 Score=184.28 Aligned_cols=133 Identities=24% Similarity=0.470 Sum_probs=112.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccccccCcccccccCCCCCCCCcccCCCCCccccCCCceeEEecCCCCC
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGAS 83 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~~~~ewr~f~~~~~~~~~~r~g~~~~~~~~~~~~~t~i~~~~~~~ 83 (172)
++|++||+ +++..|+.+|.++|+.||+|+++++|+.+ .+|.+. + -|+.|+....+.
T Consensus 1 ~~C~~C~~-s~fe~d~a~g~~~C~~CG~v~E~~~ivse---v~F~e~-----------~---------~G~~v~~~~~g~ 56 (521)
T KOG1598|consen 1 MVCKNCGG-SNFERDEATGNLYCTACGTVLEYNNIVAE---VTFVEG-----------A---------QGQFVRVGQSGA 56 (521)
T ss_pred CcCCCCCC-CCcccccccCCceeccccceeeccceeEE---eeeecc-----------c---------ceeEEeccccCC
Confidence 46999999 79999999999999999999999999965 588742 1 123344332222
Q ss_pred cccccccccccccCCCCchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCC
Q 030755 84 GEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQED 163 (172)
Q Consensus 84 ~~~l~~~l~~~~~~~~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~ 163 (172)
+. ...+++++++++.+.|..++.+|+|++ +++.|+.+|+++.+.+|++||+...++|||+|++||+++
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 11 015689999999999999999999999 999999999999999999999999999999999999999
Q ss_pred CCCCccccC
Q 030755 164 KPRTVKGTA 172 (172)
Q Consensus 164 ~~~tl~eia 172 (172)
+++.|.|++
T Consensus 125 t~hlliDfS 133 (521)
T KOG1598|consen 125 TDHLLIDFS 133 (521)
T ss_pred CceEEEEec
Confidence 999999875
No 5
>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=99.81 E-value=4.1e-20 Score=120.30 Aligned_cols=61 Identities=41% Similarity=0.811 Sum_probs=56.5
Q ss_pred HHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCCCccccC
Q 030755 112 IATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGTA 172 (172)
Q Consensus 112 I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~tl~eia 172 (172)
|++||+.|+||+.+.++|.+||+++.+.++++||+|.+++|||||+|||+++.|+|++||+
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa 61 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIA 61 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHH
Confidence 6899999999999999999999999999999999999999999999999999999999985
No 6
>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=99.71 E-value=5.9e-18 Score=99.58 Aligned_cols=43 Identities=51% Similarity=1.076 Sum_probs=38.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccccccCcccccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTF 47 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~~~~ewr~f 47 (172)
++||+||+ +.+++|+.+|++||++||.||+|+.+++++|||+|
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 36999999 57999999999999999999999999999999987
No 7
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.46 E-value=1.4e-13 Score=112.93 Aligned_cols=66 Identities=26% Similarity=0.400 Sum_probs=63.5
Q ss_pred HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCCCccccC
Q 030755 107 LAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGTA 172 (172)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~tl~eia 172 (172)
++.++|.++|+.|+||..+.+.|.+|++++.+.+++.||+|.++||||||+||+++|.|+|++|||
T Consensus 218 ~p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa 283 (310)
T PRK00423 218 DPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVA 283 (310)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence 367999999999999999999999999999999999999999999999999999999999999985
No 8
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.32 E-value=2.3e-12 Score=104.25 Aligned_cols=67 Identities=28% Similarity=0.380 Sum_probs=64.6
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCCCccccC
Q 030755 106 ILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGTA 172 (172)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~tl~eia 172 (172)
.++.++|.+||+.|+||+.+...|.+|.+++.+.+++-||+|.++||||||+|+++++.++|++|||
T Consensus 192 ~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva 258 (285)
T COG1405 192 VDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVA 258 (285)
T ss_pred CCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHH
Confidence 4678999999999999999999999999999999999999999999999999999999999999985
No 9
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.17 E-value=6.9e-11 Score=94.43 Aligned_cols=66 Identities=24% Similarity=0.352 Sum_probs=63.3
Q ss_pred HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCCCccccC
Q 030755 107 LAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGTA 172 (172)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~tl~eia 172 (172)
...++|.+||+.|+||.++++.|.++.+++.+..+..||+|.+||||.||+++++...++|++||.
T Consensus 202 ~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~ 267 (308)
T KOG1597|consen 202 STGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIG 267 (308)
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHH
Confidence 367899999999999999999999999999999999999999999999999999999999999983
No 10
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=99.09 E-value=5.1e-10 Score=73.67 Aligned_cols=65 Identities=23% Similarity=0.300 Sum_probs=61.5
Q ss_pred HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCCCcccc
Q 030755 107 LAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGT 171 (172)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~tl~ei 171 (172)
.+.++|.+++..+++|+.+...|..+++++...+...++++..+++||||+||+.++.|.+++|+
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~ 68 (88)
T cd00043 4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDL 68 (88)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHH
Confidence 57889999999999999999999999999999888889999999999999999999999998876
No 11
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.94 E-value=3.1e-09 Score=69.18 Aligned_cols=60 Identities=20% Similarity=0.216 Sum_probs=54.1
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHHhh-CcCCCCCCHHHHHHHHHHHHHHhCCCCCCcccc
Q 030755 111 TIATMSDRLGLVATIKDRANEIYKKVED-QKSSRGRNQDALLAACLYIACRQEDKPRTVKGT 171 (172)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~~~a~~-~~~~~Gr~~~~~aAAclYiacR~~~~~~tl~ei 171 (172)
+|.++++.+++|+.+...|..+++++.. ..+. .+++..+||||+|+||+.++.+++..++
T Consensus 2 ~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~-~~~~~~ia~a~l~lA~k~~~~~~~~~~~ 62 (83)
T smart00385 2 FLRRVCKALNLDPETLNLAVNLLDRFLSDYKFL-KYSPSLIAAAALYLAAKTEEIPPWTKEL 62 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcc-cCCHHHHHHHHHHHHHHHhcCCCCchhH
Confidence 6889999999999999999999999988 4544 4999999999999999999998887765
No 12
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=98.26 E-value=2.8e-06 Score=69.72 Aligned_cols=70 Identities=13% Similarity=0.247 Sum_probs=62.3
Q ss_pred hhhH-HHHHHHHHHHHHhcC--CcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCCCcccc
Q 030755 102 DRGL-ILAFKTIATMSDRLG--LVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGT 171 (172)
Q Consensus 102 e~~l-~~~~~~I~~~~~~L~--Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~tl~ei 171 (172)
|..+ ......|.++|..|+ ||..++-+|.-+|++.+-.+.+.-..+..++++|||+||+.+..|+++.++
T Consensus 52 E~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~f 124 (305)
T TIGR00569 52 ELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQF 124 (305)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHH
Confidence 3444 457889999999999 999999999999999988877777889999999999999999999988775
No 13
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.24 E-value=2.9e-07 Score=79.10 Aligned_cols=70 Identities=24% Similarity=0.248 Sum_probs=57.2
Q ss_pred hhHHHHHHHHHHHHHhcCCc-H--HHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCCCccccC
Q 030755 103 RGLILAFKTIATMSDRLGLV-A--TIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGTA 172 (172)
Q Consensus 103 ~~l~~~~~~I~~~~~~L~Lp-~--~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~tl~eia 172 (172)
-.+.+..-+|.+++..|-.- + .|+.+|.+|...+..-.+..||+|.++++||||+|||.+|+++|..||+
T Consensus 161 ~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv 233 (521)
T KOG1598|consen 161 SPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIA 233 (521)
T ss_pred ccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHH
Confidence 34456667788887776444 2 4788888888888777778999999999999999999999999999985
No 14
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=98.16 E-value=3.1e-06 Score=69.69 Aligned_cols=66 Identities=21% Similarity=0.276 Sum_probs=61.5
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCCCcccc
Q 030755 106 ILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGT 171 (172)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~tl~ei 171 (172)
..+.++|.+++.+|++|...+.+|+-||.+.+-.-.++.-.+..+|++|||+|++.+..|+.++||
T Consensus 40 ~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dI 105 (323)
T KOG0834|consen 40 QEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDI 105 (323)
T ss_pred HHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHH
Confidence 678999999999999999999999999999988777777778899999999999999999999987
No 15
>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=98.05 E-value=1.8e-05 Score=57.51 Aligned_cols=68 Identities=15% Similarity=0.314 Sum_probs=56.9
Q ss_pred hHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhC--cCCCCCCHHHHHHHHHHHHHHhCCCCCCcccc
Q 030755 104 GLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQ--KSSRGRNQDALLAACLYIACRQEDKPRTVKGT 171 (172)
Q Consensus 104 ~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~--~~~~Gr~~~~~aAAclYiacR~~~~~~tl~ei 171 (172)
.+.-|...|+.+|+.|+|++.+.+..-.+|+.+... .++++|-.+.++-+|+|+.||..+.++|++||
T Consensus 10 vy~la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~I 79 (135)
T PF01857_consen 10 VYKLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDI 79 (135)
T ss_dssp HHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHH
T ss_pred HHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHH
Confidence 345588999999999999999999999999887754 56899999999999999999999999999987
No 16
>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=97.91 E-value=1.3e-05 Score=64.84 Aligned_cols=61 Identities=28% Similarity=0.481 Sum_probs=57.0
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCC
Q 030755 106 ILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPR 166 (172)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~ 166 (172)
...+..|..+|.+|+||..+..+|+-+|++.+-+....+.++..++++|||+||+.+..|+
T Consensus 46 i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~ 106 (297)
T COG5333 46 IYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPR 106 (297)
T ss_pred HHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccc
Confidence 5678999999999999999999999999999999989999999999999999999998654
No 17
>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=97.88 E-value=5.8e-05 Score=53.35 Aligned_cols=67 Identities=16% Similarity=0.308 Sum_probs=55.5
Q ss_pred hHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCC-CCCccc
Q 030755 104 GLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDK-PRTVKG 170 (172)
Q Consensus 104 ~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~-~~tl~e 170 (172)
......++|..++..++++..+...|..++.+..........++..+++||+|+||+.+.. +.++.+
T Consensus 30 ~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~ 97 (127)
T PF00134_consen 30 MRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISD 97 (127)
T ss_dssp HHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHH
T ss_pred HHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHH
Confidence 3467889999999999999999999999999998888777788999999999999998876 554444
No 18
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=97.61 E-value=0.00011 Score=57.53 Aligned_cols=60 Identities=25% Similarity=0.433 Sum_probs=56.1
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCC
Q 030755 106 ILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKP 165 (172)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~ 165 (172)
......|..++..|+|.+.|+-+|.-++++.+-++..++-.|..+|+.|||+||+.+..|
T Consensus 42 i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~ 101 (264)
T KOG0794|consen 42 IFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECP 101 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcc
Confidence 346789999999999999999999999999999888999999999999999999999887
No 19
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=97.60 E-value=0.00027 Score=57.86 Aligned_cols=70 Identities=19% Similarity=0.302 Sum_probs=63.5
Q ss_pred hhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCCCcccc
Q 030755 102 DRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGT 171 (172)
Q Consensus 102 e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~tl~ei 171 (172)
+....=+..+|+.-|-.|+||....-++.-+|+...-..-+.+...+.++.|||.+|.+.+..|++++||
T Consensus 20 ~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdV 89 (367)
T KOG0835|consen 20 EELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDV 89 (367)
T ss_pred HHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHH
Confidence 3344557899999999999999999999999999988877888999999999999999999999999987
No 20
>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=97.55 E-value=6.7e-05 Score=42.05 Aligned_cols=27 Identities=30% Similarity=0.554 Sum_probs=23.3
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.|+.|++ . .+...+|..+|..||.|++
T Consensus 10 ~C~~C~~-~--~~~~~dG~~yC~~cG~~~E 36 (36)
T PF11781_consen 10 PCPVCGS-R--WFYSDDGFYYCDRCGHQSE 36 (36)
T ss_pred cCCCCCC-e--EeEccCCEEEhhhCceEcC
Confidence 4999998 3 6777899999999999974
No 21
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=97.38 E-value=0.00019 Score=39.38 Aligned_cols=31 Identities=23% Similarity=0.454 Sum_probs=25.6
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
|....|+.|+++ .++....+..+|.+||.+.
T Consensus 1 ~~~~~C~~C~~~--~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 1 SNLKKCSKCGGN--GIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred CCceEcCCCCCC--eEEEecCCeEEcccCCcEe
Confidence 567889999983 4555779999999999985
No 22
>PRK00420 hypothetical protein; Validated
Probab=97.06 E-value=0.00049 Score=48.30 Aligned_cols=31 Identities=29% Similarity=0.594 Sum_probs=24.4
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
|-...||.||.+ .+-..+|..+|..||.++.
T Consensus 21 ml~~~CP~Cg~p---Lf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 21 MLSKHCPVCGLP---LFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred HccCCCCCCCCc---ceecCCCceECCCCCCeee
Confidence 445689999973 3444799999999999874
No 23
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=96.90 E-value=0.0014 Score=53.70 Aligned_cols=63 Identities=17% Similarity=0.217 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHHhcCCcHHH--HHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCCCc
Q 030755 106 ILAFKTIATMSDRLGLVATI--KDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTV 168 (172)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~~v--~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~tl 168 (172)
..+.+.|-.+-..|+||++. ...+-.+....+.-.+..--+|+.||+||||+|.|..++|.+.
T Consensus 139 ~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~ 203 (367)
T KOG0835|consen 139 EHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPF 203 (367)
T ss_pred eccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCC
Confidence 34667888889999999866 5555555555555555555689999999999999999988764
No 24
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=96.87 E-value=0.00081 Score=42.40 Aligned_cols=31 Identities=35% Similarity=0.778 Sum_probs=28.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e 35 (172)
.+||.|+. ..++|+..+-.+.|..||.+|-+
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 47999998 68999999999999999999953
No 25
>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=96.84 E-value=0.00066 Score=41.52 Aligned_cols=30 Identities=33% Similarity=0.722 Sum_probs=22.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+||.|+. ..+||+.++-.+.|..||.+|-
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 57999998 6899999999999999999995
No 26
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=96.83 E-value=0.00083 Score=41.58 Aligned_cols=30 Identities=37% Similarity=0.780 Sum_probs=27.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+||.|+. ..++|+.++-.+.|..||.+|-
T Consensus 12 VkCp~C~n-~q~vFsha~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 12 VKCPDCGN-EQVVFSHASTVVRCLVCGKTLA 41 (59)
T ss_pred EECCCCCC-eEEEEecCCcEEECcccCCCcc
Confidence 57999998 6899999999999999999995
No 27
>PHA00626 hypothetical protein
Probab=96.79 E-value=0.0013 Score=40.01 Aligned_cols=30 Identities=23% Similarity=0.588 Sum_probs=23.1
Q ss_pred CCCCCCCCCCceeEeC----CCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDH----SAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~----~~G~~vC~~CG~V~~ 34 (172)
+.||.||+ .+++... ....++|.+||.-..
T Consensus 1 m~CP~CGS-~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 1 MSCPKCGS-GNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCC-ceeeeeceecccCcceEcCCCCCeec
Confidence 36999998 5666532 268999999999874
No 28
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=96.67 E-value=0.0014 Score=38.57 Aligned_cols=31 Identities=29% Similarity=0.682 Sum_probs=25.2
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
|....|++||. .+.+|+..+.+.|..||.-+
T Consensus 1 ~~~y~C~~CG~--~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 1 MAEYKCARCGR--EVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred CCEEECCCCCC--EEEECCCCCceECCCCCCeE
Confidence 56789999997 46777777799999999744
No 29
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=96.62 E-value=0.001 Score=47.77 Aligned_cols=25 Identities=28% Similarity=0.873 Sum_probs=20.4
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCc
Q 030755 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECG 30 (172)
Q Consensus 2 ~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG 30 (172)
-...||.||.+ + |- .+|.++|..||
T Consensus 27 L~~hCp~Cg~P--L-F~-KdG~v~CPvC~ 51 (131)
T COG1645 27 LAKHCPKCGTP--L-FR-KDGEVFCPVCG 51 (131)
T ss_pred HHhhCcccCCc--c-ee-eCCeEECCCCC
Confidence 34589999984 3 33 89999999999
No 30
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=96.52 E-value=0.00083 Score=37.08 Aligned_cols=27 Identities=26% Similarity=0.727 Sum_probs=16.0
Q ss_pred CCCCCCCCCceeEe----CCCCceEeCCCccee
Q 030755 5 FCSDCKKHTEVVFD----HSAGDTVCSECGLVL 33 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D----~~~G~~vC~~CG~V~ 33 (172)
.||.||.. +... ...--.||+.||.|-
T Consensus 2 fC~~CG~~--l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 2 FCPQCGGP--LERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp B-TTT--B---EEE--TT-SS-EEEETTTTEEE
T ss_pred ccccccCh--hhhhcCCCCCccceECCCCCCEE
Confidence 69999984 3332 356678999999984
No 31
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=96.51 E-value=0.0012 Score=33.16 Aligned_cols=22 Identities=23% Similarity=0.915 Sum_probs=17.1
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
+||+||.. + ..+..+|..||.-
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 59999983 2 2478899999974
No 32
>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=96.47 E-value=0.0036 Score=50.92 Aligned_cols=61 Identities=16% Similarity=0.374 Sum_probs=50.2
Q ss_pred HHHHHHHhc--CCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCCCcccc
Q 030755 111 TIATMSDRL--GLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGT 171 (172)
Q Consensus 111 ~I~~~~~~L--~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~tl~ei 171 (172)
.+-.+++++ +||.+|+-+|..+|++++=.+...--.|..|.++|+|+||+.+..-+|..+|
T Consensus 62 ~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqF 124 (325)
T KOG2496|consen 62 SLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQF 124 (325)
T ss_pred HHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHH
Confidence 344444444 7899999999999999988887777889999999999999988877776655
No 33
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=96.44 E-value=0.0017 Score=33.58 Aligned_cols=22 Identities=27% Similarity=0.975 Sum_probs=17.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
..||+||.. + ..+..+|..||.
T Consensus 3 ~~Cp~Cg~~--~----~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAE--I----DPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCc--C----CcccccChhhCC
Confidence 679999972 2 357999999996
No 34
>PLN00209 ribosomal protein S27; Provisional
Probab=96.38 E-value=0.0026 Score=42.24 Aligned_cols=30 Identities=37% Similarity=0.677 Sum_probs=27.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+||.|+. ..+||+.++-.+.|..||.+|-
T Consensus 37 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~ 66 (86)
T PLN00209 37 VKCQGCFN-ITTVFSHSQTVVVCGSCQTVLC 66 (86)
T ss_pred EECCCCCC-eeEEEecCceEEEccccCCEee
Confidence 57999998 6899999999999999999995
No 35
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=96.34 E-value=0.003 Score=41.85 Aligned_cols=30 Identities=27% Similarity=0.636 Sum_probs=27.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+||.|+. ..+||+.++-.+.|..||.+|-
T Consensus 36 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~ 65 (85)
T PTZ00083 36 VKCPGCSQ-ITTVFSHAQTVVLCGGCSSQLC 65 (85)
T ss_pred EECCCCCC-eeEEEecCceEEEccccCCEee
Confidence 57999998 6899999999999999999995
No 36
>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=96.27 E-value=0.0043 Score=34.88 Aligned_cols=28 Identities=32% Similarity=0.741 Sum_probs=21.6
Q ss_pred CCCCCCCCCCceeEeC--CCCceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFDH--SAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~--~~G~~vC~~CG~ 31 (172)
..||.||+...+-+|. ..|..+|..||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 5799999865555555 459999999984
No 37
>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=96.23 E-value=0.0051 Score=34.14 Aligned_cols=31 Identities=19% Similarity=0.484 Sum_probs=19.3
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
+..||+||+ --+......+...|..||++.+
T Consensus 1 m~FCp~C~n-lL~p~~~~~~~~~C~~C~Y~~~ 31 (35)
T PF02150_consen 1 MRFCPECGN-LLYPKEDKEKRVACRTCGYEEP 31 (35)
T ss_dssp --BETTTTS-BEEEEEETTTTEEESSSS-EEE
T ss_pred CeeCCCCCc-cceEcCCCccCcCCCCCCCccC
Confidence 357999997 3333333455558999999864
No 38
>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=96.20 E-value=0.0053 Score=32.85 Aligned_cols=28 Identities=29% Similarity=0.426 Sum_probs=15.3
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
.-+||.|++. ....| ...+||..||.-+
T Consensus 2 ~p~Cp~C~se-~~y~D--~~~~vCp~C~~ew 29 (30)
T PF08274_consen 2 LPKCPLCGSE-YTYED--GELLVCPECGHEW 29 (30)
T ss_dssp S---TTT------EE---SSSEEETTTTEEE
T ss_pred CCCCCCCCCc-ceecc--CCEEeCCcccccC
Confidence 3579999994 33444 7899999999754
No 39
>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=96.18 E-value=0.0031 Score=44.06 Aligned_cols=31 Identities=23% Similarity=0.664 Sum_probs=26.3
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
++.||+||.. .+|--..-+||..||.++...
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 5789999983 688888899999999998644
No 40
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=96.16 E-value=0.0067 Score=37.67 Aligned_cols=29 Identities=24% Similarity=0.633 Sum_probs=20.9
Q ss_pred CCCCCCCCCCCCceeEeCCCC-------ceEeCCCcc
Q 030755 2 TDAFCSDCKKHTEVVFDHSAG-------DTVCSECGL 31 (172)
Q Consensus 2 ~~~~C~~Cg~~~~i~~D~~~G-------~~vC~~CG~ 31 (172)
+...||.||+ ..+..+...+ .+.|.+||.
T Consensus 2 ~LkPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence 3568999997 4565555444 366999999
No 41
>PRK11827 hypothetical protein; Provisional
Probab=95.95 E-value=0.0051 Score=38.33 Aligned_cols=29 Identities=14% Similarity=0.433 Sum_probs=24.7
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
...||.|++ .+.+|....+++|..||.+.
T Consensus 8 ILaCP~ckg--~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 8 IIACPVCNG--KLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred heECCCCCC--cCeEcCCCCeEECCccCeec
Confidence 357999997 47888888899999999886
No 42
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=95.87 E-value=0.0087 Score=39.85 Aligned_cols=30 Identities=27% Similarity=0.550 Sum_probs=25.7
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.-.||.||. + .+.-...|-..|..||.++.
T Consensus 35 ~~~Cp~C~~-~-~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 35 KHVCPFCGR-T-TVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred CCcCCCCCC-c-ceeeeccCeEEcCCCCCeec
Confidence 357999998 4 67788999999999999875
No 43
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=95.83 E-value=0.0053 Score=37.47 Aligned_cols=31 Identities=35% Similarity=0.788 Sum_probs=21.1
Q ss_pred CCCCCCCCCCCceeEeCCCCc-eEeCCCcceec
Q 030755 3 DAFCSDCKKHTEVVFDHSAGD-TVCSECGLVLE 34 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~-~vC~~CG~V~~ 34 (172)
+..||.||..-. +.|...|+ +.|..||.-++
T Consensus 2 ~~~CP~CG~~ie-v~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 2 QFECPDCGAEIE-LENPELGELVICDECGAELE 33 (54)
T ss_pred ccCCCCCCCEEe-cCCCccCCEEeCCCCCCEEE
Confidence 368999998422 23334454 56999999885
No 44
>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=95.74 E-value=0.011 Score=34.08 Aligned_cols=27 Identities=33% Similarity=0.842 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCc
Q 030755 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECG 30 (172)
Q Consensus 1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG 30 (172)
|-...||.||.+ +.. ..+|.++|..|+
T Consensus 15 ML~~~Cp~C~~P--L~~-~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 15 MLDEHCPDCGTP--LMR-DKDGKIYCVSCG 41 (41)
T ss_pred HhcCccCCCCCe--eEE-ecCCCEECCCCC
Confidence 345689999863 444 579999999996
No 45
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=95.65 E-value=0.0097 Score=35.74 Aligned_cols=27 Identities=22% Similarity=0.630 Sum_probs=21.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
..||.||+ . +..+ ..+...|..||...
T Consensus 21 ~fCP~Cg~-~-~m~~-~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 21 KFCPRCGS-G-FMAE-HLDRWHCGKCGYTE 47 (50)
T ss_pred CcCcCCCc-c-hhec-cCCcEECCCcCCEE
Confidence 57999998 4 4444 45899999999864
No 46
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=95.64 E-value=0.0093 Score=36.97 Aligned_cols=30 Identities=27% Similarity=0.662 Sum_probs=26.5
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 2 ~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
+...||.|+.+ +.+|.+.++++|..|+...
T Consensus 7 eiLaCP~~kg~--L~~~~~~~~L~c~~~~~aY 36 (60)
T COG2835 7 EILACPVCKGP--LVYDEEKQELICPRCKLAY 36 (60)
T ss_pred eeeeccCcCCc--ceEeccCCEEEecccCcee
Confidence 45689999983 8999999999999999986
No 47
>PRK10220 hypothetical protein; Provisional
Probab=95.61 E-value=0.036 Score=38.45 Aligned_cols=31 Identities=26% Similarity=0.561 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
|+.-.||.|++ .....| ...+||.+||.--.
T Consensus 1 m~lP~CP~C~s-eytY~d--~~~~vCpeC~hEW~ 31 (111)
T PRK10220 1 MSLPHCPKCNS-EYTYED--NGMYICPECAHEWN 31 (111)
T ss_pred CCCCcCCCCCC-cceEcC--CCeEECCcccCcCC
Confidence 77789999998 344444 56799999997553
No 48
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=95.53 E-value=0.0044 Score=34.77 Aligned_cols=29 Identities=28% Similarity=0.653 Sum_probs=20.8
Q ss_pred CCCCCCCCCCceeEeC-----CCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDH-----SAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~-----~~G~~vC~~CG~V~~ 34 (172)
..||+|+.. +..+. ..+.+.|..||.++.
T Consensus 3 ~~CP~C~~~--~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTS--FRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCE--EEeCHHHcCCCCCEEECCCCCCEEE
Confidence 579999973 22332 345799999999874
No 49
>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=95.50 E-value=0.0092 Score=42.57 Aligned_cols=31 Identities=13% Similarity=0.288 Sum_probs=26.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
++.||+||.. .+|.-.--+||..||.++...
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 5789999983 688888999999999998644
No 50
>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=95.48 E-value=0.016 Score=36.88 Aligned_cols=17 Identities=29% Similarity=0.788 Sum_probs=15.6
Q ss_pred EeCCCCceEeCCCccee
Q 030755 17 FDHSAGDTVCSECGLVL 33 (172)
Q Consensus 17 ~D~~~G~~vC~~CG~V~ 33 (172)
++..+|.++|.+||.+.
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 51
>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=95.30 E-value=0.0097 Score=30.76 Aligned_cols=25 Identities=28% Similarity=0.794 Sum_probs=19.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..||+|+.. + ......|..||.++.
T Consensus 1 K~CP~C~~~--V----~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 1 KTCPECGAE--V----PESAKFCPHCGYDFE 25 (26)
T ss_pred CcCCCCcCC--c----hhhcCcCCCCCCCCc
Confidence 369999983 2 356889999999864
No 52
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=95.07 E-value=0.019 Score=34.31 Aligned_cols=28 Identities=25% Similarity=0.679 Sum_probs=19.5
Q ss_pred CCCCCCCCCceeEeCC-C-CceEeCCCcceec
Q 030755 5 FCSDCKKHTEVVFDHS-A-GDTVCSECGLVLE 34 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~-~-G~~vC~~CG~V~~ 34 (172)
.||.||+- +..... . ..++|..||.+..
T Consensus 2 FCp~Cg~~--l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNM--LIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCc--cccccCCCCCEEECCcCCCeEE
Confidence 69999972 333322 2 3899999998864
No 53
>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=95.00 E-value=0.018 Score=34.85 Aligned_cols=31 Identities=23% Similarity=0.283 Sum_probs=20.7
Q ss_pred CCCCCCCCCCceeE---eC--CCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVF---DH--SAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~---D~--~~G~~vC~~CG~V~~ 34 (172)
..||.||+....+. +. ..|...|..||....
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~ 37 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP 37 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence 57999999533132 32 344557999999864
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=94.89 E-value=0.026 Score=32.27 Aligned_cols=29 Identities=28% Similarity=0.634 Sum_probs=16.2
Q ss_pred CCCCCCCCCCcee-EeC--CCCceEeCCCcce
Q 030755 4 AFCSDCKKHTEVV-FDH--SAGDTVCSECGLV 32 (172)
Q Consensus 4 ~~C~~Cg~~~~i~-~D~--~~G~~vC~~CG~V 32 (172)
..||.||+...+- ++. .+|..+|..|+-+
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 3699999854443 443 4699999999434
No 55
>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=94.87 E-value=0.036 Score=29.90 Aligned_cols=28 Identities=21% Similarity=0.464 Sum_probs=16.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
..|+.||++ .+.....-..+|.+||...
T Consensus 4 rfC~~CG~~--t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 4 RFCGRCGAP--TKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp SB-TTT--B--EEE-SSSS-EEESSSS-EE
T ss_pred cccCcCCcc--ccCCCCcCEeECCCCcCEe
Confidence 679999984 4555667889999999763
No 56
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=94.65 E-value=0.09 Score=36.33 Aligned_cols=33 Identities=24% Similarity=0.696 Sum_probs=24.5
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
|+...||+|.+ +.+++. .+.++|.+|+.--.+.
T Consensus 1 ~~lp~cp~c~s--EytYed-~~~~~cpec~~ew~~~ 33 (112)
T COG2824 1 MSLPPCPKCNS--EYTYED-GGQLICPECAHEWNEN 33 (112)
T ss_pred CCCCCCCccCC--ceEEec-CceEeCchhccccccc
Confidence 56778999997 355553 5599999999866543
No 57
>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=94.61 E-value=0.094 Score=36.01 Aligned_cols=57 Identities=9% Similarity=0.013 Sum_probs=43.7
Q ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCC
Q 030755 108 AFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDK 164 (172)
Q Consensus 108 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~ 164 (172)
++.+|+.+....+....+...|.-+.....-....-.-+|..+||||+|+|.+..+.
T Consensus 3 p~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~ 59 (118)
T PF02984_consen 3 PYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGK 59 (118)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCc
Confidence 567888886666666788888888888865554455688999999999999998553
No 58
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=94.27 E-value=0.041 Score=40.88 Aligned_cols=30 Identities=27% Similarity=0.585 Sum_probs=19.9
Q ss_pred CCCCCCCCCCceeEeCC---CCce-----EeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHS---AGDT-----VCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~---~G~~-----vC~~CG~V~ 33 (172)
++||+||++...+.|.. .|.. -|.+||.-.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 47999998432455543 5544 499999765
No 59
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.18 E-value=0.02 Score=32.06 Aligned_cols=30 Identities=27% Similarity=0.635 Sum_probs=21.1
Q ss_pred CCCCCCCCCCceeEe---CCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFD---HSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D---~~~G~~vC~~CG~V~ 33 (172)
..||+|+..-++-.| ...+.+-|..||.+.
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 579999973222211 247789999999986
No 60
>PRK12495 hypothetical protein; Provisional
Probab=94.12 E-value=0.032 Score=43.48 Aligned_cols=32 Identities=28% Similarity=0.778 Sum_probs=25.6
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
|....|+.||.+ |+ ...|.++|..|+.++.+.
T Consensus 40 msa~hC~~CG~P---Ip-a~pG~~~Cp~CQ~~~~~~ 71 (226)
T PRK12495 40 MTNAHCDECGDP---IF-RHDGQEFCPTCQQPVTED 71 (226)
T ss_pred cchhhcccccCc---cc-CCCCeeECCCCCCccccc
Confidence 556789999984 34 458999999999998653
No 61
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=94.01 E-value=0.34 Score=40.40 Aligned_cols=59 Identities=15% Similarity=0.190 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCC-CCC--CHHHHHHHHHHHHHHhCCC
Q 030755 106 ILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSS-RGR--NQDALLAACLYIACRQEDK 164 (172)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~-~Gr--~~~~~aAAclYiacR~~~~ 164 (172)
..|.++|-++|+..+..+.+.=.|+.++.+.+...-+ +++ -...+|+||+.+|++.+.+
T Consensus 79 ~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~ 140 (335)
T KOG0656|consen 79 KQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEET 140 (335)
T ss_pred HHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCc
Confidence 5799999999999999999999999999997765433 333 2689999999999998877
No 62
>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=93.90 E-value=0.038 Score=37.19 Aligned_cols=31 Identities=29% Similarity=0.479 Sum_probs=25.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
..||.||. .. +.-...|-..|..||.++...
T Consensus 36 y~Cp~Cgk-~~-vkR~a~GIW~C~~C~~~~AGG 66 (90)
T PF01780_consen 36 YTCPFCGK-TS-VKRVATGIWKCKKCGKKFAGG 66 (90)
T ss_dssp BEESSSSS-SE-EEEEETTEEEETTTTEEEE-B
T ss_pred CcCCCCCC-ce-eEEeeeEEeecCCCCCEEeCC
Confidence 47999998 44 667789999999999998533
No 63
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=93.83 E-value=0.043 Score=32.61 Aligned_cols=27 Identities=30% Similarity=0.768 Sum_probs=21.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
..||.||. ..+..|... -+.|..||..
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 47999996 556666654 8999999986
No 64
>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=93.74 E-value=0.059 Score=34.14 Aligned_cols=30 Identities=20% Similarity=0.563 Sum_probs=22.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+.||.||.. . .........+|..||.+.+
T Consensus 28 Sq~C~~CG~~-~-~~~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 28 SQTCPRCGHR-N-KKRRSGRVFTCPNCGFEMD 57 (69)
T ss_pred ccCccCcccc-c-ccccccceEEcCCCCCEEC
Confidence 3679999973 2 2246778999999999975
No 65
>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=93.58 E-value=0.082 Score=38.81 Aligned_cols=30 Identities=30% Similarity=0.742 Sum_probs=23.1
Q ss_pred CCCCCCCCCCceeEeC---CCCceE-----eCCCccee
Q 030755 4 AFCSDCKKHTEVVFDH---SAGDTV-----CSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~---~~G~~v-----C~~CG~V~ 33 (172)
+.||.||.+..-|.|. ..|..| |..||.=.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence 4699999866667786 577766 99999654
No 66
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=93.56 E-value=0.062 Score=37.78 Aligned_cols=35 Identities=20% Similarity=0.307 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHhcCC----cHHHHHHHHHHHHHHhhCc
Q 030755 106 ILAFKTIATMSDRLGL----VATIKDRANEIYKKVEDQK 140 (172)
Q Consensus 106 ~~~~~~I~~~~~~L~L----p~~v~~~A~~i~~~a~~~~ 140 (172)
..++.+++++..+|++ +........+|+.++.+..
T Consensus 64 PTvR~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~Ge 102 (113)
T PF09862_consen 64 PTVRNRLDKIIEKLGYEEDEEEEEEDERKEILDKLEKGE 102 (113)
T ss_pred HHHHHHHHHHHHHhCCCCCcccccchhHHHHHHHHHcCC
Confidence 4678899999999999 2344566677777765433
No 67
>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=93.38 E-value=0.053 Score=37.32 Aligned_cols=27 Identities=33% Similarity=0.783 Sum_probs=21.4
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcceecc
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e 35 (172)
.||.||+. +.+..+.++|..||.+.+.
T Consensus 2 fC~~Cg~~----l~~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSL----MTPKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcc----cccCCCeEECcCCCCcccc
Confidence 69999972 3456789999999998653
No 68
>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=93.28 E-value=0.013 Score=32.71 Aligned_cols=29 Identities=28% Similarity=0.718 Sum_probs=21.8
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
.||.||..-++.+++..-+-+|..||.-|
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred CcCCCCCccccccCCCCCCCccCCCCCee
Confidence 58999985577888888888999999754
No 69
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=93.21 E-value=0.11 Score=30.44 Aligned_cols=27 Identities=22% Similarity=0.469 Sum_probs=20.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
..||.||+ .....-...+..-|.+|+.
T Consensus 19 ~~CP~Cg~-~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGS-TKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCC-eeeEEeCCCCeEECCCCCC
Confidence 46999998 4555555579999999974
No 70
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=92.98 E-value=0.1 Score=29.68 Aligned_cols=28 Identities=29% Similarity=0.540 Sum_probs=19.3
Q ss_pred CCCCCCCCCceeEe---------CCCCceEeCCCccee
Q 030755 5 FCSDCKKHTEVVFD---------HSAGDTVCSECGLVL 33 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D---------~~~G~~vC~~CG~V~ 33 (172)
.||.||. .+.++- +.+-.++|.+||..-
T Consensus 2 ~Cp~C~~-~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w 38 (40)
T smart00440 2 PCPKCGN-REATFFQLQTRSADEPMTVFYVCTKCGHRW 38 (40)
T ss_pred cCCCCCC-CeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence 6999997 455432 224478999999653
No 71
>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=92.85 E-value=0.087 Score=36.55 Aligned_cols=30 Identities=17% Similarity=0.479 Sum_probs=21.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
-.||.|++ .....| ...+||.+||.--...
T Consensus 3 p~CP~C~s-eytY~d--g~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 3 PPCPKCNS-EYTYHD--GTQLICPSCLYEWNEN 32 (109)
T ss_pred CcCCcCCC-cceEec--CCeeECcccccccccc
Confidence 47999998 344444 5579999999876433
No 72
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=92.84 E-value=0.14 Score=32.20 Aligned_cols=30 Identities=20% Similarity=0.308 Sum_probs=20.0
Q ss_pred CCCCCCCCCCCceeEeCCCC--ceEeCCCccee
Q 030755 3 DAFCSDCKKHTEVVFDHSAG--DTVCSECGLVL 33 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G--~~vC~~CG~V~ 33 (172)
...||.||.....+.. ..| ..+|..||...
T Consensus 6 lKPCPFCG~~~~~v~~-~~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 6 VKPCPFCGCPSVTVKA-ISGYYRAKCNGCESRT 37 (64)
T ss_pred ccCCCCCCCceeEEEe-cCceEEEEcCCCCcCc
Confidence 4689999985333333 333 36899999953
No 73
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=92.72 E-value=0.099 Score=35.21 Aligned_cols=32 Identities=25% Similarity=0.474 Sum_probs=25.4
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
...||.||. .. +.-...|-..|..||.++.-.
T Consensus 36 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 36 KYFCPFCGK-HA-VKRQAVGIWRCKGCKKTVAGG 67 (90)
T ss_pred CccCCCCCC-Cc-eeeeeeEEEEcCCCCCEEeCC
Confidence 357999997 44 455678999999999998643
No 74
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=92.65 E-value=0.083 Score=36.31 Aligned_cols=31 Identities=29% Similarity=0.590 Sum_probs=22.7
Q ss_pred CCCCCCCCCC-ceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHT-EVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~-~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..||+||... .+-.|.-.+.++|..||+.-+
T Consensus 22 f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 22 FECPRCGKVSISVKIKKNIAIITCGNCGLYTE 53 (99)
T ss_pred eECCCCCCeEeeeecCCCcceEECCCCCCccC
Confidence 4699999621 223455678999999999874
No 75
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=92.17 E-value=0.097 Score=34.14 Aligned_cols=30 Identities=33% Similarity=0.692 Sum_probs=26.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+||.|-. ...++..++..++|.+|++|+=
T Consensus 35 VkC~gc~~-iT~vfSHaqtvVvc~~c~~il~ 64 (84)
T KOG1779|consen 35 VKCPGCFK-ITTVFSHAQTVVVCEGCSTILC 64 (84)
T ss_pred EEcCCceE-EEEEeecCceEEEcCCCceEEE
Confidence 57999997 5678999999999999999983
No 76
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=92.14 E-value=0.12 Score=36.33 Aligned_cols=34 Identities=29% Similarity=0.579 Sum_probs=24.1
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
+..||.||+---.-.|...+.++|..||...+-.
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 5789999973111223367799999999987644
No 77
>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=92.04 E-value=0.12 Score=34.82 Aligned_cols=32 Identities=28% Similarity=0.507 Sum_probs=25.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
...||.||. .. +.-...|-..|..||.++.-.
T Consensus 35 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 35 KYVCPFCGK-KT-VKRGSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred CccCCCCCC-Cc-eEEEeeEEEEcCCCCCEEeCC
Confidence 357999997 44 556789999999999998533
No 78
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=92.02 E-value=0.27 Score=41.65 Aligned_cols=60 Identities=15% Similarity=0.180 Sum_probs=50.4
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCC
Q 030755 106 ILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKP 165 (172)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~ 165 (172)
....+.+.+++..-+|....+.+|.-+|.++.-+|++.-.+....|+|||.+|.+.+...
T Consensus 383 rSlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~K 442 (497)
T KOG4164|consen 383 RSLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLK 442 (497)
T ss_pred HHHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhh
Confidence 335567788888888888899999999999988888877788899999999999987543
No 79
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=91.93 E-value=0.11 Score=35.62 Aligned_cols=30 Identities=33% Similarity=0.816 Sum_probs=22.7
Q ss_pred CCCCCCCCCCcee---EeC--CCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVV---FDH--SAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~---~D~--~~G~~vC~~CG~V~~ 34 (172)
..||.||.. .++ +|- ..|.++|..||.-.+
T Consensus 23 FtCp~Cghe-~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 23 FTCPRCGHE-KVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred EecCccCCe-eeeEEEEEecCceeEEEcccCcceEE
Confidence 369999984 444 443 578999999998764
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=91.90 E-value=0.099 Score=28.35 Aligned_cols=25 Identities=28% Similarity=0.660 Sum_probs=17.5
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
.|.+||.. +.+.....+-|..||.=
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 58899974 23556778899999963
No 81
>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=91.74 E-value=0.12 Score=29.12 Aligned_cols=30 Identities=33% Similarity=0.545 Sum_probs=19.8
Q ss_pred CCCCCCCCCCceeEeCC-CCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHS-AGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~-~G~~vC~~CG~V~ 33 (172)
.+|++||..-++..... ...+.|..||.-+
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 47999997323333322 5677899999844
No 82
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.47 E-value=0.13 Score=31.78 Aligned_cols=24 Identities=29% Similarity=0.808 Sum_probs=10.7
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCc
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECG 30 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG 30 (172)
.|..||. .|-.+..--...|.+||
T Consensus 11 ~CtSCg~--~i~p~e~~v~F~CPnCG 34 (61)
T COG2888 11 VCTSCGR--EIAPGETAVKFPCPNCG 34 (61)
T ss_pred eeccCCC--EeccCCceeEeeCCCCC
Confidence 4555554 12223223334566666
No 83
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=91.28 E-value=0.16 Score=34.18 Aligned_cols=32 Identities=22% Similarity=0.502 Sum_probs=25.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
...||.||. .. +.-...|-.-|..||.++.-.
T Consensus 36 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 36 KHVCPVCGR-PK-VKRVGTGIWECRKCGAKFAGG 67 (90)
T ss_pred CccCCCCCC-Cc-eEEEEEEEEEcCCCCCEEeCC
Confidence 357999997 33 556789999999999998644
No 84
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=91.13 E-value=0.17 Score=29.53 Aligned_cols=27 Identities=26% Similarity=0.680 Sum_probs=20.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
..|..||.. +..+ ..+.+-|.+||.=|
T Consensus 3 Y~C~~Cg~~--~~~~-~~~~irC~~CG~rI 29 (44)
T smart00659 3 YICGECGRE--NEIK-SKDVVRCRECGYRI 29 (44)
T ss_pred EECCCCCCE--eecC-CCCceECCCCCceE
Confidence 579999983 2233 57889999999754
No 85
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=90.84 E-value=0.18 Score=31.69 Aligned_cols=14 Identities=21% Similarity=0.358 Sum_probs=9.8
Q ss_pred CCCCCCCCCCceeEe
Q 030755 4 AFCSDCKKHTEVVFD 18 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D 18 (172)
..||.||+ ++..++
T Consensus 5 ~kCpKCgn-~~~~ek 18 (68)
T COG3478 5 FKCPKCGN-TNYEEK 18 (68)
T ss_pred ccCCCcCC-cchhhc
Confidence 35999998 555544
No 86
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=90.75 E-value=0.2 Score=30.52 Aligned_cols=26 Identities=31% Similarity=0.664 Sum_probs=20.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
.+|+.||.. + -+...-+||..||.+.
T Consensus 6 ~~C~~Cg~~---~-~~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 6 CKCPVCGKK---F-KDGDDIVVCPECGAPY 31 (54)
T ss_pred ccChhhCCc---c-cCCCCEEECCCCCCcc
Confidence 589999973 2 2356789999999987
No 87
>COG4640 Predicted membrane protein [Function unknown]
Probab=90.63 E-value=0.14 Score=43.28 Aligned_cols=28 Identities=29% Similarity=0.800 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
|..||.||+. . .+++.-|+.||.-+...
T Consensus 1 M~fC~kcG~q-k-----~Ed~~qC~qCG~~~t~~ 28 (465)
T COG4640 1 MKFCPKCGSQ-K-----AEDDVQCTQCGHKFTSR 28 (465)
T ss_pred CCcccccccc-c-----ccccccccccCCcCCch
Confidence 4689999973 2 35667799999988644
No 88
>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=90.62 E-value=0.21 Score=27.13 Aligned_cols=24 Identities=29% Similarity=0.743 Sum_probs=17.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
..|+.||- ++|.......|..||.
T Consensus 2 ~~C~~CGy----~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGY----IYDGEEAPWVCPVCGA 25 (33)
T ss_pred EECCCCCC----EECCCcCCCcCcCCCC
Confidence 35888885 4566667778888886
No 89
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=90.61 E-value=0.17 Score=33.52 Aligned_cols=33 Identities=24% Similarity=0.524 Sum_probs=17.8
Q ss_pred CCCCCCCCCCce--eEeC--CCCceEeCCCcceeccc
Q 030755 4 AFCSDCKKHTEV--VFDH--SAGDTVCSECGLVLESH 36 (172)
Q Consensus 4 ~~C~~Cg~~~~i--~~D~--~~G~~vC~~CG~V~~e~ 36 (172)
..||.|+....+ ..|. ..|.+.|..||...+-.
T Consensus 23 F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 23 FDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp ---TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred EcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 469999953333 4444 47899999999987533
No 90
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=90.49 E-value=0.2 Score=30.29 Aligned_cols=19 Identities=42% Similarity=0.796 Sum_probs=16.1
Q ss_pred CCCCCCCCCceeEeCCCCc
Q 030755 5 FCSDCKKHTEVVFDHSAGD 23 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~ 23 (172)
.||+||....+..|.+.|.
T Consensus 2 ~CPyCge~~~~~iD~s~~~ 20 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGD 20 (52)
T ss_pred CCCCCCCeeEEEEecCCCC
Confidence 5999998778889988774
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=90.41 E-value=0.21 Score=28.24 Aligned_cols=27 Identities=33% Similarity=0.583 Sum_probs=15.3
Q ss_pred CCCCCCCCCceeEe-C--------CCCceEeCCCcce
Q 030755 5 FCSDCKKHTEVVFD-H--------SAGDTVCSECGLV 32 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D-~--------~~G~~vC~~CG~V 32 (172)
.||.||.. +.++- . .+-.++|.+||..
T Consensus 2 ~Cp~Cg~~-~a~~~~~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 2 KCPKCGHN-EAVFFQIQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp --SSS-SS-EEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred CCcCCCCC-eEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence 69999984 44332 1 2335789999964
No 92
>PF12773 DZR: Double zinc ribbon
Probab=90.13 E-value=0.18 Score=29.78 Aligned_cols=27 Identities=22% Similarity=0.688 Sum_probs=12.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
..||+||.. +. .......+|..||..+
T Consensus 13 ~fC~~CG~~--l~-~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 13 KFCPHCGTP--LP-PPDQSKKICPNCGAEN 39 (50)
T ss_pred cCChhhcCC--hh-hccCCCCCCcCCcCCC
Confidence 345555542 11 2223345555665554
No 93
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=90.05 E-value=0.12 Score=28.67 Aligned_cols=29 Identities=31% Similarity=0.722 Sum_probs=19.8
Q ss_pred CCCCCCCCCCceeEe----CCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFD----HSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D----~~~G~~vC~~CG~V~ 33 (172)
..||+|+..-+ +-| +....+-|+.||.+.
T Consensus 3 i~Cp~C~~~y~-i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYE-IDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEe-CCHHHCCCCCcEEECCCCCCEe
Confidence 57999997322 222 245678899999875
No 94
>PF14122 YokU: YokU-like protein
Probab=89.52 E-value=0.27 Score=32.66 Aligned_cols=23 Identities=26% Similarity=0.654 Sum_probs=17.6
Q ss_pred CCceEeCCCcceecccccccCcc
Q 030755 21 AGDTVCSECGLVLESHSIDETSE 43 (172)
Q Consensus 21 ~G~~vC~~CG~V~~e~~i~~~~e 43 (172)
+=.++|.+||.|..+..+..+.|
T Consensus 33 tP~i~C~~CgmvYq~d~vi~EIE 55 (87)
T PF14122_consen 33 TPAIICSNCGMVYQDDEVIKEIE 55 (87)
T ss_pred CceeeecCCCcEEehhHHHHHHh
Confidence 34589999999998776665555
No 95
>PF15616 TerY-C: TerY-C metal binding domain
Probab=89.48 E-value=0.23 Score=35.83 Aligned_cols=21 Identities=29% Similarity=0.763 Sum_probs=13.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
--||+||+. .+..+| +||.|.
T Consensus 78 PgCP~CGn~--------~~fa~C-~CGkl~ 98 (131)
T PF15616_consen 78 PGCPHCGNQ--------YAFAVC-GCGKLF 98 (131)
T ss_pred CCCCCCcCh--------hcEEEe-cCCCEE
Confidence 359999973 245555 466554
No 96
>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=89.37 E-value=0.41 Score=25.05 Aligned_cols=22 Identities=23% Similarity=0.540 Sum_probs=11.9
Q ss_pred CCCCCCCCCceeEeCCCCceEeCC
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSE 28 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~ 28 (172)
.||.||+ .++.++.+=.+.|.+
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 467666666788864
No 97
>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=89.27 E-value=0.37 Score=30.41 Aligned_cols=7 Identities=29% Similarity=0.966 Sum_probs=6.3
Q ss_pred CCCCCCC
Q 030755 5 FCSDCKK 11 (172)
Q Consensus 5 ~C~~Cg~ 11 (172)
.||.||+
T Consensus 2 ~C~KCg~ 8 (64)
T PF09855_consen 2 KCPKCGN 8 (64)
T ss_pred CCCCCCC
Confidence 6999997
No 98
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=89.09 E-value=0.13 Score=30.62 Aligned_cols=29 Identities=24% Similarity=0.641 Sum_probs=22.1
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
...|-.||.. +..|.....+-|..||.=|
T Consensus 6 ~Y~C~~Cg~~--~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 6 EYKCARCGRE--VELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEEhhhcCCe--eehhhccCceeCCCCCcEE
Confidence 3579999973 4446788899999999744
No 99
>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=89.05 E-value=0.47 Score=29.36 Aligned_cols=30 Identities=23% Similarity=0.516 Sum_probs=19.8
Q ss_pred CCCCCCCCCCceeEeCCC--CceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSA--GDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~--G~~vC~~CG~V~ 33 (172)
.+||.|+.-..+..=.++ -.+-|..||+--
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 479999984344332233 347899999864
No 100
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=89.04 E-value=0.3 Score=35.99 Aligned_cols=30 Identities=30% Similarity=0.644 Sum_probs=21.2
Q ss_pred CCCCCCCCCCceeEeC---CCCce-----EeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDH---SAGDT-----VCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~---~~G~~-----vC~~CG~V~ 33 (172)
++||.|+++..-|.|. +.|.. .|.+||.=+
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RF 38 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERF 38 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhccccccccc
Confidence 4799999865556775 45544 499998654
No 101
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=88.86 E-value=0.3 Score=30.10 Aligned_cols=27 Identities=22% Similarity=0.582 Sum_probs=19.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~ 37 (172)
..||+||.. ..--.+|..||+--+..+
T Consensus 28 ~~C~~CG~~-------~~~H~vC~~CG~Y~gr~v 54 (57)
T PRK12286 28 VECPNCGEP-------KLPHRVCPSCGYYKGREV 54 (57)
T ss_pred eECCCCCCc-------cCCeEECCCCCcCCCEEe
Confidence 479999973 234789999997665443
No 102
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=88.56 E-value=0.1 Score=39.60 Aligned_cols=30 Identities=30% Similarity=0.747 Sum_probs=21.6
Q ss_pred CCCCCCCCCCceeE-eCCCCceEeCCCcceecc
Q 030755 4 AFCSDCKKHTEVVF-DHSAGDTVCSECGLVLES 35 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~-D~~~G~~vC~~CG~V~~e 35 (172)
..||.|+.. .-+ |.-+....|..||.++.+
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 469999962 333 334678999999999864
No 103
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=88.28 E-value=0.28 Score=28.41 Aligned_cols=25 Identities=24% Similarity=0.763 Sum_probs=18.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCC--Ccceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSE--CGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~--CG~V~~ 34 (172)
.+||+||. ++-.+| +.|.+ |+.|+.
T Consensus 12 rkCp~CGt-----~NG~R~-~~CKN~~C~~~~~ 38 (44)
T PF14952_consen 12 RKCPKCGT-----YNGTRG-LSCKNKSCPQVFN 38 (44)
T ss_pred ccCCcCcC-----ccCccc-ccccCCccchhhh
Confidence 58999997 233455 77985 999875
No 104
>PRK05978 hypothetical protein; Provisional
Probab=88.12 E-value=0.37 Score=35.56 Aligned_cols=32 Identities=19% Similarity=0.445 Sum_probs=22.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
.+||.||. ..+..-+-.=..-|..||.-++-.
T Consensus 34 grCP~CG~-G~LF~g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 34 GRCPACGE-GKLFRAFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred CcCCCCCC-CcccccccccCCCccccCCccccC
Confidence 47999998 566443344456799999988633
No 105
>PHA02942 putative transposase; Provisional
Probab=87.99 E-value=0.38 Score=40.86 Aligned_cols=30 Identities=17% Similarity=0.451 Sum_probs=22.2
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceecc
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e 35 (172)
.+.||.||.. . .+.......|..||.+.+-
T Consensus 325 Sq~Cs~CG~~-~--~~l~~r~f~C~~CG~~~dr 354 (383)
T PHA02942 325 SVSCPKCGHK-M--VEIAHRYFHCPSCGYENDR 354 (383)
T ss_pred CccCCCCCCc-c--CcCCCCEEECCCCCCEeCc
Confidence 3679999973 2 2445568999999999853
No 106
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=87.74 E-value=3.3 Score=34.15 Aligned_cols=45 Identities=4% Similarity=0.003 Sum_probs=33.6
Q ss_pred cHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCC
Q 030755 122 VATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPR 166 (172)
Q Consensus 122 p~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~ 166 (172)
++.+...|-.+...++-....==..|..||+||||+|++..++..
T Consensus 180 ~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAAI~lA~~~~~~~l 224 (305)
T TIGR00569 180 PEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAGLNM 224 (305)
T ss_pred hHHHHHHHHHHHHHHHcCCceecCCHHHHHHHHHHHHHHHhCCCC
Confidence 345677777777776654443337899999999999999988754
No 107
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=87.55 E-value=0.78 Score=42.43 Aligned_cols=65 Identities=17% Similarity=0.309 Sum_probs=57.2
Q ss_pred HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhC--cCCCCCCHHHHHHHHHHHHHHhCCCCCCcccc
Q 030755 107 LAFKTIATMSDRLGLVATIKDRANEIYKKVEDQ--KSSRGRNQDALLAACLYIACRQEDKPRTVKGT 171 (172)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~--~~~~Gr~~~~~aAAclYiacR~~~~~~tl~ei 171 (172)
-|..+|+.+|++|.|.+...+.--.+|...... .+.+.|-.+.+.-.|+|+.+|..+...|++||
T Consensus 679 LAavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eI 745 (920)
T KOG1010|consen 679 LAAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEI 745 (920)
T ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHH
Confidence 378899999999999998888888888876655 46688999999999999999999999999887
No 108
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=86.82 E-value=0.44 Score=36.93 Aligned_cols=29 Identities=28% Similarity=0.534 Sum_probs=21.6
Q ss_pred CCCCCCCC-CceeEeCCCCceEeCCCccee
Q 030755 5 FCSDCKKH-TEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 5 ~C~~Cg~~-~~i~~D~~~G~~vC~~CG~V~ 33 (172)
.||.|+++ +.++.+...=.+.|..||..-
T Consensus 100 ~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~ 129 (201)
T PRK12336 100 ICSECGLPDTRLVKEDRVLMLRCDACGAHR 129 (201)
T ss_pred ECCCCCCCCcEEEEcCCeEEEEcccCCCCc
Confidence 59999995 466665444467899999874
No 109
>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=86.47 E-value=0.37 Score=42.93 Aligned_cols=43 Identities=23% Similarity=0.636 Sum_probs=28.7
Q ss_pred CCCCCCCCCCce-----eEe----CCCCceEeCCCcceecccc---cccCccccc
Q 030755 4 AFCSDCKKHTEV-----VFD----HSAGDTVCSECGLVLESHS---IDETSEWRT 46 (172)
Q Consensus 4 ~~C~~Cg~~~~i-----~~D----~~~G~~vC~~CG~V~~e~~---i~~~~ewr~ 46 (172)
..||+||.-..+ .+| +..--++|..||..++|+- ....-+|+.
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 479999974333 222 4567899999999998753 222346765
No 110
>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=86.32 E-value=0.65 Score=27.81 Aligned_cols=13 Identities=23% Similarity=0.726 Sum_probs=7.5
Q ss_pred eEeCCCcceeccc
Q 030755 24 TVCSECGLVLESH 36 (172)
Q Consensus 24 ~vC~~CG~V~~e~ 36 (172)
.+|..||.|.++.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 3566666666543
No 111
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=86.19 E-value=0.54 Score=38.19 Aligned_cols=25 Identities=28% Similarity=0.615 Sum_probs=20.8
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
...||.||. ...+...|..||.+.+
T Consensus 309 S~~C~~cg~-------~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 309 SKTCPCCGH-------LSGRLFKCPRCGFVHD 333 (364)
T ss_pred cccccccCC-------ccceeEECCCCCCeeh
Confidence 368999996 4478899999999985
No 112
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=86.06 E-value=1 Score=29.15 Aligned_cols=31 Identities=13% Similarity=0.305 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCceeEeCC-------CCceEeC--CCcceec
Q 030755 3 DAFCSDCKKHTEVVFDHS-------AGDTVCS--ECGLVLE 34 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~-------~G~~vC~--~CG~V~~ 34 (172)
++.||.||. .+.+.+.. +=...|+ +||...-
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 468999998 45666642 3345688 8998774
No 113
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=85.90 E-value=0.39 Score=29.50 Aligned_cols=25 Identities=20% Similarity=0.517 Sum_probs=18.9
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 2 ~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+.+|+.||. ..+ ..+|..||....
T Consensus 4 ~mr~C~~Cgv-YTL-------k~~CP~CG~~t~ 28 (56)
T PRK13130 4 KIRKCPKCGV-YTL-------KEICPVCGGKTK 28 (56)
T ss_pred cceECCCCCC-EEc-------cccCcCCCCCCC
Confidence 4578999996 322 678999997764
No 114
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=85.82 E-value=0.38 Score=34.11 Aligned_cols=38 Identities=18% Similarity=0.378 Sum_probs=24.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccccccCc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETS 42 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~~~~ 42 (172)
-.||+||. ..+..-.-.=.-.|..||.=+..+--+.+|
T Consensus 22 grCP~CGe-GrLF~gFLK~~p~C~aCG~dyg~~~a~DgP 59 (126)
T COG5349 22 GRCPRCGE-GRLFRGFLKVVPACEACGLDYGFADADDGP 59 (126)
T ss_pred CCCCCCCC-chhhhhhcccCchhhhccccccCCcccCCC
Confidence 36999997 555322334456899999877655444444
No 115
>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=85.73 E-value=0.5 Score=28.88 Aligned_cols=24 Identities=25% Similarity=0.674 Sum_probs=17.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..||+||.. ..--.+|.+||+.=.
T Consensus 27 ~~c~~cg~~-------~~~H~vc~~cG~y~~ 50 (56)
T PF01783_consen 27 VKCPNCGEP-------KLPHRVCPSCGYYKG 50 (56)
T ss_dssp EESSSSSSE-------ESTTSBCTTTBBSSS
T ss_pred eeeccCCCE-------ecccEeeCCCCeECC
Confidence 469999962 245789999996544
No 116
>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=85.72 E-value=0.2 Score=30.01 Aligned_cols=33 Identities=15% Similarity=0.363 Sum_probs=23.1
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
++...|++|+.--.-.-+..+.++-|..||++-
T Consensus 2 ~~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 2 LKEIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred CcceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 355789999962111124557899999999995
No 117
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=85.70 E-value=0.34 Score=34.10 Aligned_cols=18 Identities=39% Similarity=0.696 Sum_probs=15.3
Q ss_pred EeCCCCceEeCCCcceec
Q 030755 17 FDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 17 ~D~~~G~~vC~~CG~V~~ 34 (172)
.|-.+|+++|.+||.|..
T Consensus 92 ~~v~EG~l~CpetG~vfp 109 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVFP 109 (124)
T ss_pred hhhccceEecCCCCcEee
Confidence 455789999999999973
No 118
>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=85.69 E-value=0.6 Score=28.50 Aligned_cols=26 Identities=23% Similarity=0.691 Sum_probs=17.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
..||+||.. ..---||..||+--+..
T Consensus 27 ~~C~~cG~~-------~~~H~vc~~cG~Y~gr~ 52 (55)
T TIGR01031 27 VVCPNCGEF-------KLPHRVCPSCGYYKGRQ 52 (55)
T ss_pred eECCCCCCc-------ccCeeECCccCeECCEE
Confidence 469999972 23467899999765433
No 119
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=85.29 E-value=0.76 Score=32.59 Aligned_cols=32 Identities=25% Similarity=0.628 Sum_probs=27.7
Q ss_pred eCCCCceEeCCCccee--cccccccCcccccccC
Q 030755 18 DHSAGDTVCSECGLVL--ESHSIDETSEWRTFAN 49 (172)
Q Consensus 18 D~~~G~~vC~~CG~V~--~e~~i~~~~ewr~f~~ 49 (172)
..+.|.++|..||.-| .+.-+|++.-|.+|.+
T Consensus 28 ~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~ 61 (119)
T PRK05508 28 FFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDD 61 (119)
T ss_pred cCCCeEEEecCCCCccccccccccCCCCCcccCc
Confidence 3579999999999998 5667899999999985
No 120
>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=85.27 E-value=0.49 Score=27.97 Aligned_cols=14 Identities=29% Similarity=0.755 Sum_probs=8.7
Q ss_pred eEeCCCcceecccc
Q 030755 24 TVCSECGLVLESHS 37 (172)
Q Consensus 24 ~vC~~CG~V~~e~~ 37 (172)
..|..||.|.++..
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 45777777765554
No 121
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=85.22 E-value=0.86 Score=31.49 Aligned_cols=30 Identities=20% Similarity=0.455 Sum_probs=20.3
Q ss_pred CCCCCCCCCCceeEeC--------CC-Cc-eEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDH--------SA-GD-TVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~--------~~-G~-~vC~~CG~V~~ 34 (172)
..||+||.+ ....+. .. .. .+|+.|+.-|.
T Consensus 3 ~~CpYCg~~-~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG 42 (102)
T PF11672_consen 3 IICPYCGGP-AELVDGSEIYGHRYDDGPYLYVCTPCDAYVG 42 (102)
T ss_pred cccCCCCCe-eEEcccchhcCccCCCCceeEECCCCCceee
Confidence 579999984 333331 12 32 79999998886
No 122
>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=84.99 E-value=0.59 Score=26.75 Aligned_cols=28 Identities=32% Similarity=0.640 Sum_probs=16.3
Q ss_pred CCCCCCCCCCceeEeCC-CCceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFDHS-AGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~-~G~~vC~~CG~ 31 (172)
.+|+.||..-++..-.+ .....|..||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 36888885322222222 36777888887
No 123
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=84.53 E-value=0.88 Score=31.08 Aligned_cols=31 Identities=23% Similarity=0.515 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCceeEeCC-CCceEeCCCcceec
Q 030755 3 DAFCSDCKKHTEVVFDHS-AGDTVCSECGLVLE 34 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~-~G~~vC~~CG~V~~ 34 (172)
+..||.||+ .=+|.... -....|..|++|..
T Consensus 1 m~FCP~Cgn-~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 1 MLFCPTCGN-MLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred CcccCCCCC-EEEEecCCeEeeEEcCCCCceee
Confidence 357999997 32332222 25678999999973
No 124
>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=84.38 E-value=1.1 Score=28.89 Aligned_cols=31 Identities=23% Similarity=0.606 Sum_probs=22.0
Q ss_pred CCCCCCCCCCcee--EeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVV--FDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~--~D~~~G~~vC~~CG~V~~ 34 (172)
..||.|++-..|. .+...-..-|..||+.-.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYTER 41 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCeec
Confidence 4799999843343 344566678999999853
No 125
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=84.35 E-value=0.6 Score=29.17 Aligned_cols=23 Identities=30% Similarity=0.735 Sum_probs=16.4
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030755 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
|....|.+|+.. + +. -.|..||.
T Consensus 1 M~~kAC~~C~~i---~-~~----~~CP~Cgs 23 (61)
T PRK08351 1 MTEKACRHCHYI---T-TE----DRCPVCGS 23 (61)
T ss_pred CchhhhhhCCcc---c-CC----CcCCCCcC
Confidence 666789999972 2 32 16999997
No 126
>PRK02935 hypothetical protein; Provisional
Probab=83.99 E-value=0.7 Score=31.97 Aligned_cols=27 Identities=26% Similarity=0.679 Sum_probs=19.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..||+|+.++... --...|..|+.-+-
T Consensus 71 V~CP~C~K~TKmL----GrvD~CM~C~~PLT 97 (110)
T PRK02935 71 VICPSCEKPTKML----GRVDACMHCNQPLT 97 (110)
T ss_pred eECCCCCchhhhc----cceeecCcCCCcCC
Confidence 4799999864332 22458999998874
No 127
>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=83.63 E-value=0.73 Score=27.35 Aligned_cols=28 Identities=29% Similarity=0.567 Sum_probs=17.0
Q ss_pred CCCCCCCCCCceeEe-CCCCceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFD-HSAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D-~~~G~~vC~~CG~ 31 (172)
.+|++||..-++..- .+...+.|..||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 478999863222221 1245677999997
No 128
>COG1773 Rubredoxin [Energy production and conversion]
Probab=83.58 E-value=0.78 Score=28.02 Aligned_cols=26 Identities=35% Similarity=0.588 Sum_probs=14.2
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCc
Q 030755 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECG 30 (172)
Q Consensus 1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG 30 (172)
|....|..||- |+|++.|+-.|.-|+
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 33445666663 466666665555443
No 129
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=83.26 E-value=1.2 Score=26.81 Aligned_cols=32 Identities=28% Similarity=0.768 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCceeEe-CCCCc-eEeCCCcceec
Q 030755 3 DAFCSDCKKHTEVVFD-HSAGD-TVCSECGLVLE 34 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D-~~~G~-~vC~~CG~V~~ 34 (172)
...|.+|+.....++- ...|. ++|..||+-..
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~ 36 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYK 36 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHH
Confidence 4679999975344442 34555 99999998764
No 130
>PRK08402 replication factor A; Reviewed
Probab=83.16 E-value=1 Score=38.02 Aligned_cols=27 Identities=30% Similarity=0.759 Sum_probs=22.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
..||.|... ++.|...|...|..||.|
T Consensus 213 ~aCp~CnKk--v~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 213 DACPECRRK--VDYDPATDTWICPEHGEV 239 (355)
T ss_pred ecCCCCCeE--EEEecCCCCEeCCCCCCc
Confidence 479999973 555888899999999975
No 131
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=83.15 E-value=0.97 Score=33.07 Aligned_cols=32 Identities=28% Similarity=0.625 Sum_probs=27.6
Q ss_pred eCCCCceEeCCCccee--cccccccCcccccccC
Q 030755 18 DHSAGDTVCSECGLVL--ESHSIDETSEWRTFAN 49 (172)
Q Consensus 18 D~~~G~~vC~~CG~V~--~e~~i~~~~ewr~f~~ 49 (172)
....|.++|..||.-| .+.-+++|.-|.+|.+
T Consensus 38 ~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~ 71 (142)
T PRK00222 38 NKEKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTK 71 (142)
T ss_pred CCCCeEEEecCCCchhcCCcccccCCCCCcCcCc
Confidence 3579999999999998 5567899999999985
No 132
>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=83.08 E-value=0.59 Score=36.32 Aligned_cols=34 Identities=26% Similarity=0.599 Sum_probs=24.8
Q ss_pred CCCCCCCCC-CceeEeCCCCc---eEeCCCcceecccc
Q 030755 4 AFCSDCKKH-TEVVFDHSAGD---TVCSECGLVLESHS 37 (172)
Q Consensus 4 ~~C~~Cg~~-~~i~~D~~~G~---~vC~~CG~V~~e~~ 37 (172)
+.|-+||.+ ..+..+++.|. ..|.+||.|.|..+
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 369999985 24556666553 68999999997554
No 133
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=82.60 E-value=6.4 Score=33.55 Aligned_cols=62 Identities=13% Similarity=0.186 Sum_probs=50.9
Q ss_pred hhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHH-HHHHhCCC
Q 030755 103 RGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLY-IACRQEDK 164 (172)
Q Consensus 103 ~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclY-iacR~~~~ 164 (172)
+......+++-.+..+++|..+..-.|+.|+.+.+....+..++...+..+|++ |||+.+..
T Consensus 156 ~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~ 218 (391)
T KOG0653|consen 156 KMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEI 218 (391)
T ss_pred HHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhc
Confidence 344556889999999999999999999999999988866777777777777755 99996443
No 134
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=82.57 E-value=0.23 Score=40.67 Aligned_cols=30 Identities=20% Similarity=0.470 Sum_probs=22.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+||+|+. .-...|-.....||..||.-..
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 47999997 3334445677899999999763
No 135
>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=82.54 E-value=0.26 Score=35.88 Aligned_cols=30 Identities=33% Similarity=0.596 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcceecc
Q 030755 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (172)
Q Consensus 1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e 35 (172)
|....||.||.. |.. .|..+|.+|....++
T Consensus 1 m~l~nC~~Cgkl----F~~-~~~~iCp~C~~~~e~ 30 (137)
T TIGR03826 1 MELANCPKCGRL----FVK-TGRDVCPSCYEEEER 30 (137)
T ss_pred CCCccccccchh----hhh-cCCccCHHHhHHHHH
Confidence 778899999982 444 488999999988653
No 136
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=82.53 E-value=0.78 Score=41.65 Aligned_cols=8 Identities=25% Similarity=0.928 Sum_probs=3.9
Q ss_pred CCCCCCCC
Q 030755 4 AFCSDCKK 11 (172)
Q Consensus 4 ~~C~~Cg~ 11 (172)
..||+||.
T Consensus 2 ~~Cp~Cg~ 9 (645)
T PRK14559 2 LICPQCQF 9 (645)
T ss_pred CcCCCCCC
Confidence 34555554
No 137
>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=82.42 E-value=0.25 Score=40.36 Aligned_cols=30 Identities=17% Similarity=0.429 Sum_probs=21.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+||+|+. .-...|-.....||..||.-..
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 47999997 3233344567899999999763
No 138
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=82.30 E-value=0.55 Score=39.04 Aligned_cols=64 Identities=9% Similarity=0.084 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHhcCCcHH----HHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCCCc
Q 030755 105 LILAFKTIATMSDRLGLVAT----IKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTV 168 (172)
Q Consensus 105 l~~~~~~I~~~~~~L~Lp~~----v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~tl 168 (172)
+..+..++-+++..|+-... +...|-.+......-.+.---.|..||+||||+|+...|.+...
T Consensus 148 v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA~~~~~~~~~~ 215 (323)
T KOG0834|consen 148 VEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAVACIHLAAKLLGVELPS 215 (323)
T ss_pred ccCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEEeehhhHHHHHcCCCCCC
Confidence 34455666666666655543 44555544444443332222467899999999999999886543
No 139
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=82.08 E-value=1.1 Score=35.96 Aligned_cols=30 Identities=17% Similarity=0.406 Sum_probs=21.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+.||.||+. +......-..+|..||.+.=
T Consensus 99 ~~fC~~CG~~--~~~~~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 99 HRFCGYCGHP--MHPSKTEWAMLCPHCRERYY 128 (256)
T ss_pred CccccccCCC--CeecCCceeEECCCCCCEEC
Confidence 3689999984 33344566789999997653
No 140
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=82.01 E-value=0.59 Score=35.87 Aligned_cols=31 Identities=32% Similarity=0.587 Sum_probs=19.6
Q ss_pred CCCCCCCCCCce--eEeCCCC---ceEeCCCcceecc
Q 030755 4 AFCSDCKKHTEV--VFDHSAG---DTVCSECGLVLES 35 (172)
Q Consensus 4 ~~C~~Cg~~~~i--~~D~~~G---~~vC~~CG~V~~e 35 (172)
..||.||. -+. ..=-..| .+-|.+||+|-.+
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 47999994 222 0111223 4789999999854
No 141
>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=81.64 E-value=0.59 Score=26.01 Aligned_cols=22 Identities=27% Similarity=0.578 Sum_probs=10.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEe
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVC 26 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC 26 (172)
.+|..||. ---+.+...|.++|
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 47888886 33345667788888
No 142
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=81.45 E-value=0.51 Score=31.24 Aligned_cols=29 Identities=31% Similarity=0.504 Sum_probs=24.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..|+.||.. -+-...-|...|.+|..|+.
T Consensus 37 y~CsfCGK~--~vKR~AvGiW~C~~C~kv~a 65 (92)
T KOG0402|consen 37 YTCSFCGKK--TVKRKAVGIWKCGSCKKVVA 65 (92)
T ss_pred hhhhhcchh--hhhhhceeEEecCCccceec
Confidence 479999983 35667899999999999985
No 143
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=81.43 E-value=0.19 Score=31.00 Aligned_cols=25 Identities=40% Similarity=0.907 Sum_probs=19.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCC-Ccceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSE-CGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~-CG~V~~ 34 (172)
..|+.||.. |- .|+.+|++ ||.+++
T Consensus 9 ~HC~VCg~a--Ip----~de~~CSe~C~eil~ 34 (64)
T COG4068 9 RHCVVCGKA--IP----PDEQVCSEECGEILN 34 (64)
T ss_pred ccccccCCc--CC----CccchHHHHHHHHHH
Confidence 579999973 33 56899986 998874
No 144
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=81.39 E-value=0.79 Score=39.25 Aligned_cols=31 Identities=32% Similarity=0.775 Sum_probs=23.8
Q ss_pred CCCCCCCCC-Cc----eeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKH-TE----VVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~-~~----i~~D~~~G~~vC~~CG~V~~ 34 (172)
..||.|++. +. -.+|..+|...|..||.=|.
T Consensus 129 Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelv 164 (436)
T KOG2593|consen 129 YVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELV 164 (436)
T ss_pred ccCCccccchhhhHHHHhhcccCceEEEecCCCchh
Confidence 579999984 11 24577899999999997663
No 145
>PF14353 CpXC: CpXC protein
Probab=81.18 E-value=1.2 Score=31.66 Aligned_cols=12 Identities=25% Similarity=0.758 Sum_probs=10.1
Q ss_pred ceEeCCCcceec
Q 030755 23 DTVCSECGLVLE 34 (172)
Q Consensus 23 ~~vC~~CG~V~~ 34 (172)
..+|..||....
T Consensus 38 ~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 38 SFTCPSCGHKFR 49 (128)
T ss_pred EEECCCCCCcee
Confidence 679999998873
No 146
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.95 E-value=0.86 Score=31.81 Aligned_cols=32 Identities=13% Similarity=0.122 Sum_probs=25.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceecccc
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~ 37 (172)
++.||+||+. .+|--+.-+||..||.-.....
T Consensus 9 KridPetg~K---FYDLNrdPiVsPytG~s~P~s~ 40 (129)
T COG4530 9 KRIDPETGKK---FYDLNRDPIVSPYTGKSYPRSY 40 (129)
T ss_pred cccCccccch---hhccCCCccccCcccccchHHH
Confidence 4689999984 6788889999999998764333
No 147
>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=80.85 E-value=0.55 Score=28.55 Aligned_cols=30 Identities=37% Similarity=0.849 Sum_probs=19.7
Q ss_pred CCCCCCCCCceeEe--CCCCceEeCCCcceec
Q 030755 5 FCSDCKKHTEVVFD--HSAGDTVCSECGLVLE 34 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D--~~~G~~vC~~CG~V~~ 34 (172)
.|.+|+......+- +..+...|..||+-..
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~ 32 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWK 32 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHH
Confidence 48888874333333 2377788888888764
No 148
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.43 E-value=1.6 Score=30.35 Aligned_cols=28 Identities=21% Similarity=0.535 Sum_probs=22.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~ 37 (172)
..||.||. .-||+ ++-|..|++-+..+.
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 57999998 45665 799999999997443
No 149
>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=80.42 E-value=1.5 Score=30.67 Aligned_cols=13 Identities=31% Similarity=0.524 Sum_probs=9.3
Q ss_pred CceEeCCCcceec
Q 030755 22 GDTVCSECGLVLE 34 (172)
Q Consensus 22 G~~vC~~CG~V~~ 34 (172)
...+|..||.++-
T Consensus 30 ~~~~C~~CGe~~~ 42 (127)
T TIGR03830 30 PGWYCPACGEELL 42 (127)
T ss_pred eeeECCCCCCEEE
Confidence 3457999988764
No 150
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=80.40 E-value=4.5 Score=30.43 Aligned_cols=39 Identities=15% Similarity=0.302 Sum_probs=25.6
Q ss_pred HHHHHHHhc-CCcHHHHHHHHHHHHHHhhCcCCCCCCHHH
Q 030755 111 TIATMSDRL-GLVATIKDRANEIYKKVEDQKSSRGRNQDA 149 (172)
Q Consensus 111 ~I~~~~~~L-~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~ 149 (172)
+++.+-..| +||++-.+++.+.|+...+.+.-.|++-+.
T Consensus 6 fL~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEee 45 (181)
T PF08006_consen 6 FLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEE 45 (181)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHH
Confidence 444444444 378777888888888877776666765443
No 151
>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=80.37 E-value=1.8 Score=31.37 Aligned_cols=27 Identities=30% Similarity=0.732 Sum_probs=19.5
Q ss_pred CCC--CCCCCCceeEeCCCCceEeCCCcceec
Q 030755 5 FCS--DCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 5 ~C~--~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.|| .|+.. +..+ ..|.+.|..||..++
T Consensus 20 aC~~~~C~kK--v~~~-~~~~y~C~~C~~~~~ 48 (146)
T PF08646_consen 20 ACPNEKCNKK--VTEN-GDGSYRCEKCNKTVE 48 (146)
T ss_dssp E-TSTTTS-B---EEE-TTTEEEETTTTEEES
T ss_pred CCCCccCCCE--eecC-CCcEEECCCCCCcCC
Confidence 599 99973 4555 679999999998874
No 152
>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=80.16 E-value=1.1 Score=27.29 Aligned_cols=29 Identities=24% Similarity=0.566 Sum_probs=21.2
Q ss_pred CCCCCCCCCCcee--EeCCCCceEeCCCcce
Q 030755 4 AFCSDCKKHTEVV--FDHSAGDTVCSECGLV 32 (172)
Q Consensus 4 ~~C~~Cg~~~~i~--~D~~~G~~vC~~CG~V 32 (172)
..|++|..++-.. .+.+.=..+|..||..
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred EECcccchhhcccccccCCceEEEcCCCCCc
Confidence 4699999764333 6667778999999863
No 153
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=79.94 E-value=0.34 Score=39.70 Aligned_cols=30 Identities=23% Similarity=0.519 Sum_probs=21.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+||+|+. .-...|-.....||..||.-..
T Consensus 28 ~~c~~c~~-~~~~~~l~~~~~vc~~c~~h~r 57 (292)
T PRK05654 28 TKCPSCGQ-VLYRKELEANLNVCPKCGHHMR 57 (292)
T ss_pred eECCCccc-hhhHHHHHhcCCCCCCCCCCee
Confidence 47999997 3333444566789999999773
No 154
>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=79.66 E-value=4.8 Score=33.02 Aligned_cols=45 Identities=18% Similarity=0.090 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCCC
Q 030755 123 ATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRT 167 (172)
Q Consensus 123 ~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~t 167 (172)
....+.|-.+...++...+.-=-.|..+|.||+++||+..+.|.-
T Consensus 167 ~~~~~~aw~~inDa~~t~~~llypphiIA~a~l~ia~~~~~~~~~ 211 (297)
T COG5333 167 YKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPII 211 (297)
T ss_pred HHHHHHHHHHHHhhhhceeeeecChHHHHHHHHHHHHHhcCCccc
Confidence 347777777777777666544467889999999999999988754
No 155
>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=79.54 E-value=1.8 Score=23.64 Aligned_cols=24 Identities=21% Similarity=0.589 Sum_probs=13.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
..|+.||- +.+...-..+|.-||.
T Consensus 3 ~~C~~CG~----i~~g~~~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGY----IHEGEEAPEKCPICGA 26 (34)
T ss_pred EECCCCCC----EeECCcCCCcCcCCCC
Confidence 45777774 2332233347777775
No 156
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=79.33 E-value=1.2 Score=31.23 Aligned_cols=7 Identities=43% Similarity=1.407 Sum_probs=3.9
Q ss_pred CCCCCCC
Q 030755 5 FCSDCKK 11 (172)
Q Consensus 5 ~C~~Cg~ 11 (172)
+|+.||.
T Consensus 72 ~C~~Cg~ 78 (113)
T PRK12380 72 WCWDCSQ 78 (113)
T ss_pred EcccCCC
Confidence 4566654
No 157
>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=79.31 E-value=2.1 Score=29.19 Aligned_cols=29 Identities=24% Similarity=0.550 Sum_probs=20.0
Q ss_pred CCCCCCCCCCceeEe---------CCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFD---------HSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D---------~~~G~~vC~~CG~V~ 33 (172)
..||.||+ ...++- +.+=.++|.+||..-
T Consensus 63 ~~Cp~Cg~-~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w 100 (104)
T TIGR01384 63 VECPKCGH-KEAYYWLLQTRRADEPETRFYKCTKCGYVW 100 (104)
T ss_pred CCCCCCCC-CeeEEEEeccCCCCCCcEEEEEeCCCCCee
Confidence 57999998 454442 234478899999743
No 158
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=79.11 E-value=0.87 Score=34.10 Aligned_cols=29 Identities=17% Similarity=0.410 Sum_probs=19.0
Q ss_pred CCCCCCCCCCCceeEe---------------CCCCceEeCCCccee
Q 030755 3 DAFCSDCKKHTEVVFD---------------HSAGDTVCSECGLVL 33 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D---------------~~~G~~vC~~CG~V~ 33 (172)
...||+|+.. ++.- ..+-...|..||.+.
T Consensus 97 ~~RCp~CN~~--L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 97 FSRCPECNGE--LEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred cccCcccCCE--eccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 3579999963 2211 123356799999886
No 159
>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=78.88 E-value=1.9 Score=25.51 Aligned_cols=17 Identities=24% Similarity=0.538 Sum_probs=10.5
Q ss_pred CCCCCCCCCceeEeCCCCce
Q 030755 5 FCSDCKKHTEVVFDHSAGDT 24 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~ 24 (172)
.||.||+ +.+-+ .+|.+
T Consensus 15 ~Cp~CGN--~~vGn-gEG~l 31 (49)
T PF12677_consen 15 KCPKCGN--DKVGN-GEGTL 31 (49)
T ss_pred cCcccCC--cEeec-CcceE
Confidence 6999997 34443 34544
No 160
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=78.80 E-value=1.8 Score=24.45 Aligned_cols=28 Identities=21% Similarity=0.456 Sum_probs=15.9
Q ss_pred CCCCCCCCCceeEeC-CCCceEeCCCccee
Q 030755 5 FCSDCKKHTEVVFDH-SAGDTVCSECGLVL 33 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~-~~G~~vC~~CG~V~ 33 (172)
+||.|+.. -..... .--..+|..||=+-
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 59999973 111111 12234699998765
No 161
>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=78.46 E-value=1.4 Score=31.02 Aligned_cols=18 Identities=11% Similarity=0.423 Sum_probs=8.4
Q ss_pred eeEeCCCCceEeCCCcce
Q 030755 15 VVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 15 i~~D~~~G~~vC~~CG~V 32 (172)
+..+..-+...|.+||..
T Consensus 62 L~I~~~p~~~~C~~Cg~~ 79 (115)
T TIGR00100 62 LNIEDEPVECECEDCSEE 79 (115)
T ss_pred EEEEeeCcEEEcccCCCE
Confidence 344444445555555533
No 162
>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=78.42 E-value=1.5 Score=31.71 Aligned_cols=32 Identities=25% Similarity=0.471 Sum_probs=27.4
Q ss_pred eCCCCceEeCCCccee--cccccccCcccccccC
Q 030755 18 DHSAGDTVCSECGLVL--ESHSIDETSEWRTFAN 49 (172)
Q Consensus 18 D~~~G~~vC~~CG~V~--~e~~i~~~~ewr~f~~ 49 (172)
....|.++|..||.-| .+.-+|+|.-|.+|.+
T Consensus 35 ~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~ 68 (134)
T TIGR00357 35 NKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYK 68 (134)
T ss_pred CCCCeEEEccCCCCccccccchhcCCCCCcCcCc
Confidence 3579999999999998 5567899999999974
No 163
>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=78.24 E-value=1.8 Score=23.46 Aligned_cols=25 Identities=24% Similarity=0.432 Sum_probs=14.3
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCC
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSE 28 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~ 28 (172)
..+|..||. --.+.+...|.++|-.
T Consensus 4 ~ykC~~CGn-iv~v~~~~~~~l~Ccg 28 (34)
T cd00974 4 VYKCEICGN-IVEVLNVGGGTLVCCG 28 (34)
T ss_pred EEEcCCCCc-EEEEEECCCcceeecC
Confidence 346777775 2334455566666653
No 164
>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=77.89 E-value=2.4 Score=29.29 Aligned_cols=27 Identities=22% Similarity=0.628 Sum_probs=21.3
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.|--|+. .-.. ...+++||..||.++.
T Consensus 37 aCeiC~~-~GY~--q~g~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 37 ACEICGP-KGYY--QEGDQLVCKNCGVRFN 63 (102)
T ss_pred eccccCC-CceE--EECCEEEEecCCCEEe
Confidence 5899986 3333 4678999999999985
No 165
>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=77.80 E-value=1.9 Score=24.44 Aligned_cols=9 Identities=44% Similarity=1.125 Sum_probs=7.0
Q ss_pred EeCCCccee
Q 030755 25 VCSECGLVL 33 (172)
Q Consensus 25 vC~~CG~V~ 33 (172)
+|..||..+
T Consensus 34 ~C~~CGE~~ 42 (46)
T TIGR03831 34 VCPQCGEEY 42 (46)
T ss_pred ccccCCCEe
Confidence 588888765
No 166
>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=77.35 E-value=1.6 Score=37.47 Aligned_cols=30 Identities=27% Similarity=0.607 Sum_probs=18.9
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.||+|+...+...-.......|..||.++.
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 588898632222122445678888998885
No 167
>PRK12366 replication factor A; Reviewed
Probab=77.24 E-value=1.5 Score=39.84 Aligned_cols=25 Identities=36% Similarity=0.930 Sum_probs=20.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
..||.|+.. + .+ ..|...|..||.+
T Consensus 533 ~aCp~CnkK--v-~~-~~g~~~C~~c~~~ 557 (637)
T PRK12366 533 YLCPNCRKR--V-EE-VDGEYICEFCGEV 557 (637)
T ss_pred ecccccCeE--e-Ec-CCCcEECCCCCCC
Confidence 479999873 3 33 5799999999988
No 168
>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=77.14 E-value=1.7 Score=31.06 Aligned_cols=31 Identities=29% Similarity=0.627 Sum_probs=25.8
Q ss_pred CCCCceEeCCCccee--cccccccCcccccccC
Q 030755 19 HSAGDTVCSECGLVL--ESHSIDETSEWRTFAN 49 (172)
Q Consensus 19 ~~~G~~vC~~CG~V~--~e~~i~~~~ewr~f~~ 49 (172)
...|.++|..||.-| .+.-++++.-|.+|.+
T Consensus 33 ~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~ 65 (124)
T PF01641_consen 33 KEEGIYVCAVCGTPLFSSDTKFDSGCGWPSFWQ 65 (124)
T ss_dssp TSSEEEEETTTS-EEEEGGGEETSSSSSSEESS
T ss_pred CCCEEEEcCCCCCccccCcccccCCcCCccccC
Confidence 479999999999998 5566899999999985
No 169
>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=77.11 E-value=2 Score=25.12 Aligned_cols=29 Identities=17% Similarity=0.446 Sum_probs=18.3
Q ss_pred CCCCCCCCCceeEeC-------CCCceEeCC--Ccceec
Q 030755 5 FCSDCKKHTEVVFDH-------SAGDTVCSE--CGLVLE 34 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~-------~~G~~vC~~--CG~V~~ 34 (172)
+||+||+. ..+.-. .+-...|++ ||.-..
T Consensus 1 ~CP~Cg~~-a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 1 RCPHCGSK-ARIRTSRQLSPLTRELYCQCTNPECGHTFV 38 (47)
T ss_pred CcCCCCCe-eEEEEchhhCcceEEEEEEECCCcCCCEEE
Confidence 59999983 443322 234567887 997653
No 170
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=76.82 E-value=1.6 Score=31.58 Aligned_cols=21 Identities=24% Similarity=0.629 Sum_probs=13.8
Q ss_pred ceeEeCCCCceEeCCCcceec
Q 030755 14 EVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 14 ~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+..+.......|.+||.+..
T Consensus 61 ~L~i~~~p~~~~C~~CG~~~~ 81 (135)
T PRK03824 61 EIIFEEEEAVLKCRNCGNEWS 81 (135)
T ss_pred EEEEEecceEEECCCCCCEEe
Confidence 455555667778888886653
No 171
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=76.82 E-value=2.3 Score=26.29 Aligned_cols=28 Identities=25% Similarity=0.581 Sum_probs=16.3
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
..+|..||.. |..-..--...|.+||.+
T Consensus 7 ~~~CtSCg~~--i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 7 PPKCTSCGIE--IAPREKAVKFLCPNCGEV 34 (59)
T ss_pred CccccCCCCc--ccCCCccCEeeCCCCCCe
Confidence 3468888862 321111345678888877
No 172
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=76.59 E-value=0.66 Score=37.59 Aligned_cols=43 Identities=21% Similarity=0.459 Sum_probs=28.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec-------ccccccCccccccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE-------SHSIDETSEWRTFA 48 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~-------e~~i~~~~ewr~f~ 48 (172)
.+||.|+. .-...|-.....||..||.-.. +..+|.|+ |+.+.
T Consensus 29 ~KCp~c~~-~~y~~eL~~n~~vcp~c~~h~ri~A~~Ri~~llD~gs-f~el~ 78 (294)
T COG0777 29 TKCPSCGE-MLYRKELESNLKVCPKCGHHMRISARERLEALLDEGS-FEELD 78 (294)
T ss_pred eECCCccc-eeeHHHHHhhhhcccccCcccccCHHHHHHHhhCCCc-ceecc
Confidence 47999997 3334455678999999998762 23456553 45554
No 173
>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=75.89 E-value=1.8 Score=26.42 Aligned_cols=22 Identities=32% Similarity=0.677 Sum_probs=14.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCC
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSE 28 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~ 28 (172)
..||.|+. ..+++|.. .++|+.
T Consensus 15 ~~Cp~C~~-~~l~~~~~--~Y~C~G 36 (55)
T PF08063_consen 15 EPCPKCKG-GQLYFDGS--GYKCTG 36 (55)
T ss_dssp ---SSSSE--EEEEETT--EEEEES
T ss_pred CCCCCCCC-CeEEecCC--ccEeCc
Confidence 47999998 68888854 788873
No 174
>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=75.48 E-value=1.8 Score=22.62 Aligned_cols=28 Identities=18% Similarity=0.372 Sum_probs=15.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
.+||-|+....-+........+|..|-.
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 4799999743333344677788988853
No 175
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=75.10 E-value=2.4 Score=21.39 Aligned_cols=23 Identities=26% Similarity=0.778 Sum_probs=12.7
Q ss_pred CCCCCCCCceeEeCC-CCceEeCCCcc
Q 030755 6 CSDCKKHTEVVFDHS-AGDTVCSECGL 31 (172)
Q Consensus 6 C~~Cg~~~~i~~D~~-~G~~vC~~CG~ 31 (172)
|..||.. +.... --...|.+||.
T Consensus 1 C~sC~~~---i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRP---IAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCc---ccCcccCceEeCCCCCC
Confidence 5667652 22222 34567888873
No 176
>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=74.98 E-value=1 Score=31.57 Aligned_cols=38 Identities=26% Similarity=0.522 Sum_probs=23.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccccccCccccccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFA 48 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~~~~ewr~f~ 48 (172)
..||+|+..+...=. ..-|..|+.-+- +|.+.|-.+|+
T Consensus 70 V~CP~C~K~TKmLGr----~D~CM~C~~pLT---Ld~~legkef~ 107 (114)
T PF11023_consen 70 VECPNCGKQTKMLGR----VDACMHCKEPLT---LDPSLEGKEFD 107 (114)
T ss_pred eECCCCCChHhhhch----hhccCcCCCcCc---cCchhhcchhh
Confidence 469999985322211 248999998874 34333333454
No 177
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=74.94 E-value=0.76 Score=35.90 Aligned_cols=33 Identities=24% Similarity=0.494 Sum_probs=26.7
Q ss_pred CCCCCCCC-CceeEeCCCC---ceEeCCCcceecccc
Q 030755 5 FCSDCKKH-TEVVFDHSAG---DTVCSECGLVLESHS 37 (172)
Q Consensus 5 ~C~~Cg~~-~~i~~D~~~G---~~vC~~CG~V~~e~~ 37 (172)
+|-+||.. ..+..+++.| -.-|.+|+.|+|+.+
T Consensus 2 ~CVeCg~~vksLy~~Ys~g~irlt~C~nC~e~vDkYi 38 (225)
T KOG3134|consen 2 RCVECGSEVKSLYTQYSPGNIRLTKCPNCQEVVDKYI 38 (225)
T ss_pred cccccCchHHHHHHhcCCCcEEEeeCCchhhHHHhHe
Confidence 69999975 4678888888 467999999997554
No 178
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=74.87 E-value=2.1 Score=23.14 Aligned_cols=23 Identities=26% Similarity=0.540 Sum_probs=12.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeC
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCS 27 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~ 27 (172)
.+|..||. --.+.+...|.++|-
T Consensus 8 ykC~~Cgn-iv~v~~~~~~~l~Cc 30 (34)
T TIGR00319 8 YKCEVCGN-IVEVLHAGGGQLVCC 30 (34)
T ss_pred EEcCCCCc-EEEEEECCCcceecc
Confidence 35666665 233344455566664
No 179
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=74.67 E-value=9.2 Score=22.00 Aligned_cols=30 Identities=17% Similarity=0.264 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHhcCCcH-HHHHHHHHHHHH
Q 030755 106 ILAFKTIATMSDRLGLVA-TIKDRANEIYKK 135 (172)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~-~v~~~A~~i~~~ 135 (172)
.+....++.++...++|. .+++.|++.|=+
T Consensus 11 ~el~~~L~~ls~~t~i~~S~Ll~eAle~~l~ 41 (44)
T PF12651_consen 11 KELYEKLKELSEETGIPKSKLLREALEDYLE 41 (44)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 356779999999999995 789999987743
No 180
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=74.65 E-value=1.7 Score=39.54 Aligned_cols=25 Identities=20% Similarity=0.602 Sum_probs=16.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..||+||.. ...|.-+|.+||.-+.
T Consensus 28 ~~Cp~CG~~------~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 28 KPCPQCGTE------VPVDEAHCPNCGAETG 52 (645)
T ss_pred CcCCCCCCC------CCcccccccccCCccc
Confidence 356677652 2357778888887664
No 181
>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=74.50 E-value=0.82 Score=32.02 Aligned_cols=24 Identities=33% Similarity=0.747 Sum_probs=11.5
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
+|+.||. .++...-...|..||.-
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 4666665 13333344556666654
No 182
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=74.44 E-value=1.8 Score=24.33 Aligned_cols=14 Identities=29% Similarity=0.843 Sum_probs=12.4
Q ss_pred CCceEeCCCcceec
Q 030755 21 AGDTVCSECGLVLE 34 (172)
Q Consensus 21 ~G~~vC~~CG~V~~ 34 (172)
.|.+||..|..+|+
T Consensus 1 MGtIvCq~C~~~Id 14 (38)
T PF13790_consen 1 MGTIVCQHCNETID 14 (38)
T ss_pred CCEEEeccccceee
Confidence 38899999999995
No 183
>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=74.10 E-value=1 Score=37.90 Aligned_cols=49 Identities=20% Similarity=0.373 Sum_probs=0.0
Q ss_pred CCcHHHHHHHHHHHHHHh-hCcCCCCCCHHHHHHHHHHHHHHhCCCCCCc
Q 030755 120 GLVATIKDRANEIYKKVE-DQKSSRGRNQDALLAACLYIACRQEDKPRTV 168 (172)
Q Consensus 120 ~Lp~~v~~~A~~i~~~a~-~~~~~~Gr~~~~~aAAclYiacR~~~~~~tl 168 (172)
.+|+.++..|.+||+... ....+++..--+=+.+|+||||...+.++-+
T Consensus 11 ~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl 60 (353)
T PF05460_consen 11 GLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDL 60 (353)
T ss_dssp --------------------------------------------------
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCc
Confidence 456899999999999988 3445566665677889999999998887654
No 184
>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=73.77 E-value=2.7 Score=31.12 Aligned_cols=26 Identities=27% Similarity=0.753 Sum_probs=20.2
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
.||.|++. + .+...|...|..|+..+
T Consensus 36 aC~~C~kk--v-~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 36 ACPGCNKK--V-VEEGNGTYRCEKCNKSV 61 (166)
T ss_pred cccccCcc--c-EeCCCCcEECCCCCCcC
Confidence 69999983 3 33334999999999887
No 185
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=73.10 E-value=2.1 Score=36.90 Aligned_cols=33 Identities=18% Similarity=0.496 Sum_probs=20.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
..||+|+.......-...+...|..||.++..+
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~~ 43 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTLTVR 43 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCCcCC
Confidence 459999973211111234457799999999533
No 186
>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=72.98 E-value=2 Score=23.65 Aligned_cols=21 Identities=43% Similarity=1.053 Sum_probs=10.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECG 30 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG 30 (172)
++|+.||. +.+-+ ..+|..||
T Consensus 12 ~rC~~Cg~---~~~pP---r~~Cp~C~ 32 (37)
T PF12172_consen 12 QRCRDCGR---VQFPP---RPVCPHCG 32 (37)
T ss_dssp EE-TTT-----EEES-----SEETTTT
T ss_pred EEcCCCCC---EecCC---CcCCCCcC
Confidence 46888886 33433 27888887
No 187
>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=72.44 E-value=2.5 Score=27.15 Aligned_cols=27 Identities=19% Similarity=0.624 Sum_probs=16.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..||.|+.+ +.. ..|.+.|..|+.-+.
T Consensus 2 ~~CP~C~~~--L~~--~~~~~~C~~C~~~~~ 28 (70)
T PF07191_consen 2 NTCPKCQQE--LEW--QGGHYHCEACQKDYK 28 (70)
T ss_dssp -B-SSS-SB--EEE--ETTEEEETTT--EEE
T ss_pred CcCCCCCCc--cEE--eCCEEECccccccce
Confidence 469999972 444 459999999988653
No 188
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=72.20 E-value=7.1 Score=30.68 Aligned_cols=54 Identities=15% Similarity=0.375 Sum_probs=33.4
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHHhhC-cCC----CCCCHHHHHHHHHHHHHHhCCCC
Q 030755 111 TIATMSDRLGLVATIKDRANEIYKKVEDQ-KSS----RGRNQDALLAACLYIACRQEDKP 165 (172)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~-~~~----~Gr~~~~~aAAclYiacR~~~~~ 165 (172)
-|+++|-+|++- +++..|.++.....+. --+ ..-+...+++|++|.||+..+..
T Consensus 95 ~VrdlaVQfgc~-evi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlK 153 (262)
T KOG4557|consen 95 NVRDLAVQFGCV-EVIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLK 153 (262)
T ss_pred CHHHHHHHHhHH-HHHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHh
Confidence 355566666665 4667777776665442 001 11234588999999999976643
No 189
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=72.00 E-value=2.1 Score=33.11 Aligned_cols=30 Identities=23% Similarity=0.569 Sum_probs=25.0
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 2 ~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
....|..|++ ..++.+ .|-..|..|+.|..
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 3468999998 577764 79999999999985
No 190
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=71.97 E-value=5.4 Score=34.59 Aligned_cols=59 Identities=14% Similarity=0.170 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCC
Q 030755 107 LAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKP 165 (172)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~ 165 (172)
...++|.++-..++|-+.....|..|..+.+..+.+.=.+...++++|++|||+.+.+-
T Consensus 215 ~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~ 273 (440)
T COG5024 215 ILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVN 273 (440)
T ss_pred HHHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhc
Confidence 35678888999999999999999999999998887776778899999999999977643
No 191
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=71.51 E-value=2 Score=34.21 Aligned_cols=29 Identities=17% Similarity=0.598 Sum_probs=10.5
Q ss_pred CCCCCCCCCCcee---EeCCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVV---FDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~---~D~~~G~~vC~~CG~V~ 33 (172)
..||+||+. .+- -+.--.+..|.+|+.-.
T Consensus 32 ~yCP~Cg~~-~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 32 MYCPNCGSK-PLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp ---TTT--S-S-EE--------EEE-TTT--EE
T ss_pred CcCCCCCCh-hHhhccCCCccceeECCCCchHH
Confidence 479999984 221 12245678999998755
No 192
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=70.91 E-value=2.6 Score=29.56 Aligned_cols=16 Identities=13% Similarity=0.499 Sum_probs=7.0
Q ss_pred eEeCCCCceEeCCCcc
Q 030755 16 VFDHSAGDTVCSECGL 31 (172)
Q Consensus 16 ~~D~~~G~~vC~~CG~ 31 (172)
..+..-+...|.+||.
T Consensus 63 ~i~~~p~~~~C~~Cg~ 78 (114)
T PRK03681 63 HLEEQEAECWCETCQQ 78 (114)
T ss_pred EEEeeCcEEEcccCCC
Confidence 3333444444444443
No 193
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=70.71 E-value=3.4 Score=30.01 Aligned_cols=31 Identities=29% Similarity=0.626 Sum_probs=26.9
Q ss_pred CCCCceEeCCCccee--cccccccCcccccccC
Q 030755 19 HSAGDTVCSECGLVL--ESHSIDETSEWRTFAN 49 (172)
Q Consensus 19 ~~~G~~vC~~CG~V~--~e~~i~~~~ewr~f~~ 49 (172)
.+.|.++|.-||.-| .+.-+|+|--|.+|.+
T Consensus 38 ~~~GiY~c~~cg~pLF~S~~KfdSgcGWPSF~~ 70 (140)
T COG0229 38 KEKGIYVCIVCGEPLFSSEDKFDSGCGWPSFTK 70 (140)
T ss_pred cCCceEEeecCCCccccccccccCCCCCccccc
Confidence 479999999999988 5567899999999975
No 194
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 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. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=70.67 E-value=5.3 Score=25.23 Aligned_cols=32 Identities=25% Similarity=0.525 Sum_probs=24.7
Q ss_pred HHHHHHHHhhCcCCC--CCCHHHHHHHHHHHHHH
Q 030755 129 ANEIYKKVEDQKSSR--GRNQDALLAACLYIACR 160 (172)
Q Consensus 129 A~~i~~~a~~~~~~~--Gr~~~~~aAAclYiacR 160 (172)
..+|++++.+.++.. |+.|...++|.||--.+
T Consensus 20 ~~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~ 53 (72)
T PF05066_consen 20 FKEIWEEIQERGLYKKSGKTPEATIAAQLYTDIK 53 (72)
T ss_dssp HHHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH
T ss_pred HHHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcc
Confidence 345777777777776 89999999999998887
No 195
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=70.64 E-value=4 Score=26.86 Aligned_cols=26 Identities=31% Similarity=0.724 Sum_probs=19.7
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.||.|.. .++.. ..+.+.| .||.-|.
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 5999998 56665 5788888 6786664
No 196
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=70.57 E-value=2.6 Score=26.34 Aligned_cols=26 Identities=27% Similarity=0.768 Sum_probs=17.7
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
|....|.+|+.- + .+..-+|..||.-
T Consensus 2 ~~~kAC~~Ck~l---~---~~d~e~CP~Cgs~ 27 (64)
T COG2093 2 STEKACKNCKRL---T---PEDTEICPVCGST 27 (64)
T ss_pred chhHHHhhcccc---C---CCCCccCCCCCCc
Confidence 445679999872 2 2456789999853
No 197
>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=70.53 E-value=3 Score=25.24 Aligned_cols=28 Identities=21% Similarity=0.706 Sum_probs=15.7
Q ss_pred CCCCC--CCCCCceeEeCCCCc--eEeCCCccee
Q 030755 4 AFCSD--CKKHTEVVFDHSAGD--TVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~--Cg~~~~i~~D~~~G~--~vC~~CG~V~ 33 (172)
..||. |+.. +..+..... +.|..||..+
T Consensus 19 ~~Cp~~~C~~~--~~~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 19 RWCPNPDCEYI--IEKDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp C--TTSST-----ECS-SSTTS--CCTTSCCSEE
T ss_pred cCCCCCCCccc--EEecCCCCCCeeECCCCCCcC
Confidence 58987 9872 455555555 8999999875
No 198
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=70.42 E-value=3.4 Score=25.42 Aligned_cols=26 Identities=23% Similarity=0.676 Sum_probs=17.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
..||+||. .- .---||.+||+--+..
T Consensus 28 ~~c~~cG~-~~------l~Hrvc~~cg~Y~g~~ 53 (57)
T COG0333 28 SVCPNCGE-YK------LPHRVCLKCGYYKGRQ 53 (57)
T ss_pred eeccCCCC-cc------cCceEcCCCCCccCeE
Confidence 57888886 21 2367899999765433
No 199
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=70.16 E-value=3.2 Score=32.65 Aligned_cols=27 Identities=37% Similarity=0.827 Sum_probs=22.0
Q ss_pred CCCCCCCCCC-ceeEeCCCCceEeCCCc
Q 030755 4 AFCSDCKKHT-EVVFDHSAGDTVCSECG 30 (172)
Q Consensus 4 ~~C~~Cg~~~-~i~~D~~~G~~vC~~CG 30 (172)
..|-.||... ...+++.+|..+|..|+
T Consensus 150 ~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 150 DHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hhHhcCCCCCCceEEecccCCccccccc
Confidence 4699999742 35688899999999998
No 200
>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=69.97 E-value=1.4 Score=24.36 Aligned_cols=27 Identities=30% Similarity=0.844 Sum_probs=14.3
Q ss_pred CCCCCCCCceeE-eCCCCce-EeCCCcce
Q 030755 6 CSDCKKHTEVVF-DHSAGDT-VCSECGLV 32 (172)
Q Consensus 6 C~~Cg~~~~i~~-D~~~G~~-vC~~CG~V 32 (172)
|.+|+....... ....|.. +|..||+-
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 778886422322 2346777 89988864
No 201
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=69.59 E-value=3.1 Score=33.87 Aligned_cols=30 Identities=27% Similarity=0.597 Sum_probs=12.9
Q ss_pred CCCCCCCCCCce-eEeCCC--C--ceEeCCCccee
Q 030755 4 AFCSDCKKHTEV-VFDHSA--G--DTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i-~~D~~~--G--~~vC~~CG~V~ 33 (172)
..||.||+.+.+ +..... | .+.|.-||+-=
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W 207 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEW 207 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EE
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCee
Confidence 589999985322 223222 4 58899998753
No 202
>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=69.57 E-value=4.3 Score=33.51 Aligned_cols=9 Identities=33% Similarity=0.785 Sum_probs=5.8
Q ss_pred EeCCCccee
Q 030755 25 VCSECGLVL 33 (172)
Q Consensus 25 vC~~CG~V~ 33 (172)
+|.+|+.-+
T Consensus 254 ~C~~C~~Yl 262 (305)
T TIGR01562 254 TCDSCQGYL 262 (305)
T ss_pred eccccccch
Confidence 666666665
No 203
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.73 E-value=2.9 Score=34.87 Aligned_cols=26 Identities=31% Similarity=0.717 Sum_probs=22.1
Q ss_pred CCCCCCCCCceeEeCC--CCceEeCCCc
Q 030755 5 FCSDCKKHTEVVFDHS--AGDTVCSECG 30 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~--~G~~vC~~CG 30 (172)
.||.||....+-+|.. .|..+|..||
T Consensus 34 ~cpvcg~k~RFr~dD~kGrGtw~c~y~~ 61 (366)
T COG4643 34 PCPVCGGKDRFRFDDRKGRGTWFCNYCG 61 (366)
T ss_pred CCCccCCccccccCCccCCccEEEEeec
Confidence 7999998767777753 7999999999
No 204
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=68.60 E-value=5.6 Score=26.07 Aligned_cols=27 Identities=15% Similarity=0.290 Sum_probs=19.5
Q ss_pred CCCCCCCCCCceeEeCCCC--ceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAG--DTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G--~~vC~~CG~V~ 33 (172)
..||-||.. +++...+ .-||.-|+.--
T Consensus 2 ~~CPCCg~~---Tl~~~~~~~ydIC~VC~WEd 30 (78)
T PF14206_consen 2 YPCPCCGYY---TLEERGEGTYDICPVCFWED 30 (78)
T ss_pred ccCCCCCcE---EeccCCCcCceECCCCCccc
Confidence 579999972 3444344 88999999863
No 205
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=68.50 E-value=3.9 Score=24.94 Aligned_cols=24 Identities=29% Similarity=0.798 Sum_probs=18.7
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
.||.|+.. . +..=...|.+||...
T Consensus 1 ~Cpv~~~~--~---~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKD--L---PAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCccc--c---ccccCCcCCCCCCcC
Confidence 49999973 1 456678999999987
No 206
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=68.27 E-value=5.2 Score=33.10 Aligned_cols=9 Identities=33% Similarity=0.925 Sum_probs=5.3
Q ss_pred CCCCCCCCC
Q 030755 4 AFCSDCKKH 12 (172)
Q Consensus 4 ~~C~~Cg~~ 12 (172)
..||.||+.
T Consensus 188 ~~CPvCGs~ 196 (309)
T PRK03564 188 QFCPVCGSM 196 (309)
T ss_pred CCCCCCCCc
Confidence 456666654
No 207
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.74 E-value=3.5 Score=25.66 Aligned_cols=22 Identities=27% Similarity=0.619 Sum_probs=16.9
Q ss_pred CceeEeC-CCCceEeCCCcceec
Q 030755 13 TEVVFDH-SAGDTVCSECGLVLE 34 (172)
Q Consensus 13 ~~i~~D~-~~G~~vC~~CG~V~~ 34 (172)
..+..|. .+|+++|.-||++..
T Consensus 37 PrV~L~mg~~gev~CPYC~t~y~ 59 (62)
T COG4391 37 PRVFLDMGDEGEVVCPYCSTRYR 59 (62)
T ss_pred CEEEEEcCCCCcEecCccccEEE
Confidence 3455554 799999999999863
No 208
>PRK04023 DNA polymerase II large subunit; Validated
Probab=67.73 E-value=4 Score=38.79 Aligned_cols=11 Identities=27% Similarity=0.685 Sum_probs=6.6
Q ss_pred eEeCCCcceec
Q 030755 24 TVCSECGLVLE 34 (172)
Q Consensus 24 ~vC~~CG~V~~ 34 (172)
..|..||..+.
T Consensus 664 y~CPKCG~El~ 674 (1121)
T PRK04023 664 DECEKCGREPT 674 (1121)
T ss_pred CcCCCCCCCCC
Confidence 45666666664
No 209
>PRK06260 threonine synthase; Validated
Probab=67.60 E-value=2.6 Score=35.87 Aligned_cols=30 Identities=37% Similarity=0.630 Sum_probs=22.6
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
|-..+|+.||.. ++...-...|..||-.++
T Consensus 1 ~~~~~C~~cg~~----~~~~~~~~~Cp~cg~~l~ 30 (397)
T PRK06260 1 MYWLKCIECGKE----YDPDEIIYTCPECGGLLE 30 (397)
T ss_pred CCEEEECCCCCC----CCCCCccccCCCCCCeEE
Confidence 566789999973 444455678999998774
No 210
>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=67.52 E-value=2.7 Score=28.24 Aligned_cols=38 Identities=24% Similarity=0.569 Sum_probs=23.6
Q ss_pred CCCCCCCC------CceeEeCCCC----------ceEeCCCcceecccccccCc
Q 030755 5 FCSDCKKH------TEVVFDHSAG----------DTVCSECGLVLESHSIDETS 42 (172)
Q Consensus 5 ~C~~Cg~~------~~i~~D~~~G----------~~vC~~CG~V~~e~~i~~~~ 42 (172)
.|+-|+.. +...+|...| -++|.+||.+.-+.-+....
T Consensus 1 ~C~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~dev~~eI 54 (89)
T TIGR03829 1 KCRWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQDDTTVKEI 54 (89)
T ss_pred CCcccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEeecHHHHHHH
Confidence 48899541 2345555444 46899999988655444333
No 211
>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=67.44 E-value=7.3 Score=30.72 Aligned_cols=26 Identities=35% Similarity=0.532 Sum_probs=20.5
Q ss_pred HHHHHhcCCcHHHHHHHHHHHHHHhh
Q 030755 113 ATMSDRLGLVATIKDRANEIYKKVED 138 (172)
Q Consensus 113 ~~~~~~L~Lp~~v~~~A~~i~~~a~~ 138 (172)
-+++..+|+|+.++++|.++++++.+
T Consensus 209 i~iA~~~g~p~~II~rA~~i~~~l~~ 234 (235)
T PF00488_consen 209 IEIAKLAGLPEEIIERAKEILKQLEE 234 (235)
T ss_dssp HHHHHHTT--HHHHHHHHHHHHHHHT
T ss_pred HHHHHHhCcCHHHHHHHHHHHHHHhc
Confidence 35778899999999999999998754
No 212
>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=67.36 E-value=4.9 Score=35.44 Aligned_cols=29 Identities=21% Similarity=0.647 Sum_probs=22.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..||+|+. .+.+-..++.+.|..||....
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 46999986 366767788999999988753
No 213
>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=67.11 E-value=7.9 Score=22.82 Aligned_cols=26 Identities=23% Similarity=0.662 Sum_probs=17.7
Q ss_pred CCCC--CCCCCCceeEeCCCCceEeCCCcc
Q 030755 4 AFCS--DCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~--~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
..|| .||. .-+.-+. ..-..|..||+
T Consensus 19 k~CP~~~CG~-GvFMA~H-~dR~~CGKCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGA-GVFMAEH-KDRHYCGKCGY 46 (47)
T ss_dssp EE-TSTTTTS-SSEEEE--SSEEEETTTSS
T ss_pred hcCCCcccCC-ceEeeec-CCCccCCCccc
Confidence 4699 9997 4445554 45899999986
No 214
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=67.09 E-value=15 Score=34.36 Aligned_cols=57 Identities=26% Similarity=0.402 Sum_probs=46.9
Q ss_pred HHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCC
Q 030755 109 FKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPR 166 (172)
Q Consensus 109 ~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~ 166 (172)
.......|..|+|+......|-+.|..+.+.-.+-|- -.+..|.+||.+||...+|.
T Consensus 35 ~q~~~~~c~~lnld~~~~~ea~d~yta~~q~~slegs-~~hW~~cAlY~~~r~S~~~~ 91 (920)
T KOG1010|consen 35 EQDSDELCRPLNLDEQTETEAWDTYTAVSQRLSLEGS-ESHWLACALYTACRRSSVPT 91 (920)
T ss_pred hhhhhhhhhhhcccchhhhhhHHHHHHHHhHhCCCcc-HHHHHHHHHHHHHHhccCCc
Confidence 3456678999999999999999999998776544443 56899999999999998874
No 215
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=66.77 E-value=3.7 Score=29.90 Aligned_cols=31 Identities=29% Similarity=0.658 Sum_probs=26.9
Q ss_pred CCCCceEeCCCccee--cccccccCcccccccC
Q 030755 19 HSAGDTVCSECGLVL--ESHSIDETSEWRTFAN 49 (172)
Q Consensus 19 ~~~G~~vC~~CG~V~--~e~~i~~~~ewr~f~~ 49 (172)
.+.|.++|..||.-| .+.-+|+|--|.+|.+
T Consensus 50 ~e~GvY~C~~C~~pLykS~tKfdsgcGWPAF~e 82 (146)
T KOG0856|consen 50 FEEGVYVCAGCGTPLYKSTTKFDSGCGWPAFFE 82 (146)
T ss_pred cCCceEEEeecCCccccccccccCCCCCchhhh
Confidence 479999999999988 4557899999999985
No 216
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=66.72 E-value=4.6 Score=31.10 Aligned_cols=37 Identities=19% Similarity=0.158 Sum_probs=20.4
Q ss_pred hhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhh
Q 030755 102 DRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVED 138 (172)
Q Consensus 102 e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~ 138 (172)
|=.|.++.+.++.........+...+.+.++.+++.+
T Consensus 99 EGlL~~~~~~L~~~~~~d~~~~e~~~k~~~~i~kL~~ 135 (192)
T TIGR00310 99 EGVLRRVEEELETAIRWQSEDEETKKRAEEILERLKE 135 (192)
T ss_pred HhHHHHHHHHHHhhhhccccCHHHHHHHHHHHHHHHH
Confidence 4455555555555432213345566677777777644
No 217
>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=66.46 E-value=4.4 Score=31.68 Aligned_cols=28 Identities=25% Similarity=0.705 Sum_probs=21.1
Q ss_pred CCCCCCCCCC-ceeEeCCCCceEeCCCcc
Q 030755 4 AFCSDCKKHT-EVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~-~i~~D~~~G~~vC~~CG~ 31 (172)
..|..||... ...+++..|..+|..|+.
T Consensus 148 ~~C~~cg~~~~~~~fs~~~gg~~C~~c~~ 176 (241)
T TIGR00613 148 DKCAVCGSKEDLIYFSMTYGGALCRQCGE 176 (241)
T ss_pred CccCCCCCcCCCceEchhcCeEEChhhCc
Confidence 4788998621 256788899999999865
No 218
>PRK05580 primosome assembly protein PriA; Validated
Probab=66.39 E-value=5.2 Score=36.62 Aligned_cols=28 Identities=21% Similarity=0.540 Sum_probs=22.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
..||+|+. .+.+....+.+.|..||...
T Consensus 391 ~~C~~C~~--~l~~h~~~~~l~Ch~Cg~~~ 418 (679)
T PRK05580 391 AECPHCDA--SLTLHRFQRRLRCHHCGYQE 418 (679)
T ss_pred cCCCCCCC--ceeEECCCCeEECCCCcCCC
Confidence 46999986 47777778899999999875
No 219
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=66.26 E-value=2.4 Score=26.72 Aligned_cols=21 Identities=24% Similarity=0.561 Sum_probs=14.3
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
...|.+|+.- + + ..+|..||.
T Consensus 5 ~~AC~~C~~i---~-~----~~~Cp~Cgs 25 (64)
T PRK06393 5 YRACKKCKRL---T-P----EKTCPVHGD 25 (64)
T ss_pred hhhHhhCCcc---c-C----CCcCCCCCC
Confidence 3578899872 2 2 228999987
No 220
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=66.15 E-value=1.8 Score=25.99 Aligned_cols=28 Identities=29% Similarity=0.652 Sum_probs=18.5
Q ss_pred CCCCCCCCCcee--EeCCCCceEeCCCccee
Q 030755 5 FCSDCKKHTEVV--FDHSAGDTVCSECGLVL 33 (172)
Q Consensus 5 ~C~~Cg~~~~i~--~D~~~G~~vC~~CG~V~ 33 (172)
.|+-||..--+. +..+.| +||.+|--=+
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 499999742111 235677 7999997544
No 221
>PRK06450 threonine synthase; Validated
Probab=65.32 E-value=3.2 Score=34.65 Aligned_cols=29 Identities=28% Similarity=0.626 Sum_probs=21.2
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
|+..+|+.||.. ++. .-...|..||-.++
T Consensus 1 ~~~~~C~~Cg~~----~~~-~~~~~C~~cg~~l~ 29 (338)
T PRK06450 1 MVKEVCMKCGKE----RES-IYEIRCKKCGGPFE 29 (338)
T ss_pred CceeEECCcCCc----CCC-cccccCCcCCCEeE
Confidence 677899999983 233 33578999998764
No 222
>PRK07218 replication factor A; Provisional
Probab=65.10 E-value=3 Score=36.04 Aligned_cols=21 Identities=24% Similarity=0.689 Sum_probs=16.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
..||+|+.. + + ...|..||.|
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 479999983 2 2 2699999988
No 223
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=63.92 E-value=7.2 Score=23.55 Aligned_cols=28 Identities=21% Similarity=0.858 Sum_probs=19.9
Q ss_pred CCCC--CCCCCCceeEe--CCCCceEeCCCccee
Q 030755 4 AFCS--DCKKHTEVVFD--HSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~--~Cg~~~~i~~D--~~~G~~vC~~CG~V~ 33 (172)
.+|| .|+.. +..+ .....+.|..||...
T Consensus 19 ~~CP~~~C~~~--~~~~~~~~~~~v~C~~C~~~f 50 (64)
T smart00647 19 KWCPAPDCSAA--IIVTEEEGCNRVTCPKCGFSF 50 (64)
T ss_pred cCCCCCCCcce--EEecCCCCCCeeECCCCCCeE
Confidence 5799 89862 3343 367789999998766
No 224
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=63.75 E-value=4 Score=25.22 Aligned_cols=27 Identities=26% Similarity=0.689 Sum_probs=16.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
..|-+||.. +.+- ....+-|.+||.=|
T Consensus 21 YiCgdC~~e-n~lk--~~D~irCReCG~RI 47 (62)
T KOG3507|consen 21 YICGDCGQE-NTLK--RGDVIRCRECGYRI 47 (62)
T ss_pred EEecccccc-cccc--CCCcEehhhcchHH
Confidence 358888874 3321 24456688888644
No 225
>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=63.69 E-value=5 Score=25.05 Aligned_cols=30 Identities=30% Similarity=0.551 Sum_probs=16.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~ 37 (172)
..|..|+.. |..-.-.-.|..||.|+=..-
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 579999973 455688899999999985443
No 226
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.66 E-value=6.8 Score=25.71 Aligned_cols=28 Identities=29% Similarity=0.598 Sum_probs=18.3
Q ss_pred CCCCCCCCCCceeEeCCCC--ceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAG--DTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G--~~vC~~CG~V~ 33 (172)
..||.|+- +++.-...| .-.|..|+-|-
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 56999996 233332223 34699999885
No 227
>PRK06386 replication factor A; Reviewed
Probab=63.66 E-value=3.9 Score=34.52 Aligned_cols=21 Identities=33% Similarity=0.705 Sum_probs=15.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
..||+|+.. + + .| .|..||.|
T Consensus 237 ~rCP~C~R~---l-~--~g--~C~~HG~v 257 (358)
T PRK06386 237 TKCSVCNKI---I-E--DG--VCKDHPDA 257 (358)
T ss_pred ecCcCCCeE---c-c--CC--cCCCCCCC
Confidence 479999973 2 2 23 89999975
No 228
>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=63.37 E-value=2.6 Score=24.00 Aligned_cols=27 Identities=26% Similarity=0.593 Sum_probs=13.7
Q ss_pred CCCCCCCCCC---ceeEeCCCCceEeCCCc
Q 030755 4 AFCSDCKKHT---EVVFDHSAGDTVCSECG 30 (172)
Q Consensus 4 ~~C~~Cg~~~---~i~~D~~~G~~vC~~CG 30 (172)
.+|..||.+. .....-..|-.+|.+|=
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~Cv 31 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDECV 31 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHHH
Confidence 5799999741 12333344788998873
No 229
>PRK14873 primosome assembly protein PriA; Provisional
Probab=63.30 E-value=5.8 Score=36.29 Aligned_cols=28 Identities=25% Similarity=0.579 Sum_probs=20.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
..||+|+. .+.+-...+.+.|..||.-.
T Consensus 393 ~~C~~C~~--~L~~h~~~~~l~Ch~CG~~~ 420 (665)
T PRK14873 393 ARCRHCTG--PLGLPSAGGTPRCRWCGRAA 420 (665)
T ss_pred eECCCCCC--ceeEecCCCeeECCCCcCCC
Confidence 46888886 35665567889999999843
No 230
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=63.16 E-value=4.5 Score=39.34 Aligned_cols=6 Identities=33% Similarity=1.088 Sum_probs=2.6
Q ss_pred CCCCCC
Q 030755 5 FCSDCK 10 (172)
Q Consensus 5 ~C~~Cg 10 (172)
+||+||
T Consensus 669 kCPkCG 674 (1337)
T PRK14714 669 RCPSCG 674 (1337)
T ss_pred ECCCCC
Confidence 344444
No 231
>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=63.03 E-value=7.4 Score=26.32 Aligned_cols=27 Identities=15% Similarity=0.389 Sum_probs=17.2
Q ss_pred CCCCCCCC-CceeEeCCCCceEeCCCcc
Q 030755 5 FCSDCKKH-TEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 5 ~C~~Cg~~-~~i~~D~~~G~~vC~~CG~ 31 (172)
.||.|+.. +++..++..|...|-.||.
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 59999953 4788899999999999994
No 232
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=63.00 E-value=3.1 Score=29.30 Aligned_cols=18 Identities=11% Similarity=0.279 Sum_probs=9.6
Q ss_pred ceeEeCCCCceEeCCCcc
Q 030755 14 EVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 14 ~i~~D~~~G~~vC~~CG~ 31 (172)
.+..+..-+...|.+||.
T Consensus 62 ~L~Ie~vp~~~~C~~Cg~ 79 (117)
T PRK00564 62 ILDIVDEKVELECKDCSH 79 (117)
T ss_pred EEEEEecCCEEEhhhCCC
Confidence 344444555556666663
No 233
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=62.93 E-value=3.7 Score=34.11 Aligned_cols=25 Identities=24% Similarity=0.380 Sum_probs=18.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCC
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSE 28 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~ 28 (172)
.+|+.|++.-.|-+||.+++++|..
T Consensus 78 ~kC~~C~~~i~~kTDPkn~dY~~~~ 102 (324)
T PF04502_consen 78 IKCPRCSNEIEFKTDPKNTDYVVES 102 (324)
T ss_pred EEcCCCCCEEeeecCCCCCCeeeec
Confidence 3688888755677888887777765
No 234
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=62.37 E-value=5.2 Score=32.58 Aligned_cols=29 Identities=28% Similarity=0.536 Sum_probs=19.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..|+.||.++. .-...=..+|.+||...=
T Consensus 112 RFCg~CG~~~~--~~~~g~~~~C~~cg~~~f 140 (279)
T COG2816 112 RFCGRCGTKTY--PREGGWARVCPKCGHEHF 140 (279)
T ss_pred cCCCCCCCcCc--cccCceeeeCCCCCCccC
Confidence 57999998521 122344578999998763
No 235
>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=62.01 E-value=7.2 Score=29.21 Aligned_cols=36 Identities=19% Similarity=0.159 Sum_probs=18.9
Q ss_pred hhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhh
Q 030755 102 DRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVED 138 (172)
Q Consensus 102 e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~ 138 (172)
|=.|.+..+.++.... ..-.+...+.+.++.+++.+
T Consensus 97 EGlL~~i~~~L~~~~~-~~~~~e~~~k~~~~l~kL~~ 132 (163)
T TIGR00340 97 EGVLERIEEVLDTASD-DDEDDEAVKKCEEILKRIRE 132 (163)
T ss_pred HhHHHHHHHHHHHhhh-cccCHHHHHHHHHHHHHHHH
Confidence 4445555555554432 22344555666677666653
No 236
>PRK04194 hypothetical protein; Provisional
Probab=61.97 E-value=24 Score=30.27 Aligned_cols=48 Identities=19% Similarity=0.427 Sum_probs=34.7
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHhhCc-CCCCC--------------CHHHHHHHHHHH
Q 030755 110 KTIATMSDRLGLVATIKDRANEIYKKVEDQK-SSRGR--------------NQDALLAACLYI 157 (172)
Q Consensus 110 ~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~-~~~Gr--------------~~~~~aAAclYi 157 (172)
..|..+.+.++||+.+.+.|.++|+.+.+.. .++|. +...++++|+-+
T Consensus 76 ~~I~~ii~~s~l~~~vk~~a~~iF~~lA~AEa~VHG~~~e~VHFHEVGa~DsIvDIvG~~~~l 138 (392)
T PRK04194 76 SEIKALIENSDLPEKVKERALAVFERLAEAEAKVHGIDLEKVHFHEVGAIDAIVDIVGACLAL 138 (392)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHeeEeeccchhhHHHHHHHHHHH
Confidence 3455555788999999999999999876643 46676 345666666654
No 237
>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=61.38 E-value=11 Score=21.18 Aligned_cols=29 Identities=24% Similarity=0.567 Sum_probs=17.3
Q ss_pred CCCCCCCCC--CceeEeCCCCceEeCCCcce
Q 030755 4 AFCSDCKKH--TEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 4 ~~C~~Cg~~--~~i~~D~~~G~~vC~~CG~V 32 (172)
.+|..|++- .-..+|......+|.-|+..
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred cccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 479999962 34467777778999999985
No 238
>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=61.34 E-value=2.7 Score=39.16 Aligned_cols=11 Identities=36% Similarity=1.029 Sum_probs=0.0
Q ss_pred ceEeCCCccee
Q 030755 23 DTVCSECGLVL 33 (172)
Q Consensus 23 ~~vC~~CG~V~ 33 (172)
..+|..||..+
T Consensus 680 ~~~Cp~C~~~~ 690 (900)
T PF03833_consen 680 VYVCPDCGIEV 690 (900)
T ss_dssp -----------
T ss_pred ceecccccccc
Confidence 34566665555
No 239
>PF03685 UPF0147: Uncharacterised protein family (UPF0147); InterPro: IPR005354 The proteins in this entry are functionally uncharacterised.; PDB: 2QZG_C 2QSB_A.
Probab=61.34 E-value=46 Score=22.18 Aligned_cols=53 Identities=11% Similarity=0.201 Sum_probs=38.2
Q ss_pred chhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHH
Q 030755 101 PDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYI 157 (172)
Q Consensus 101 ~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYi 157 (172)
.+..+.++...++++.+.-.+|..+...|.+....+.+.+ .++..=||.++++
T Consensus 4 ~e~~i~~~~~~L~~I~~D~sVPRNIRr~a~ea~~~L~~e~----~~~~vRaataIs~ 56 (85)
T PF03685_consen 4 NEEKIKQAIQMLERIINDTSVPRNIRRAAEEAKEILNNEE----ESPGVRAATAISI 56 (85)
T ss_dssp HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHCT-TT----S-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHhCCC----cchhHhHHHHHHH
Confidence 4667889999999999999999999999888888765543 4555556666654
No 240
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=60.71 E-value=14 Score=29.41 Aligned_cols=55 Identities=20% Similarity=0.275 Sum_probs=36.8
Q ss_pred HHHHHHhcCCc-HHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCC
Q 030755 112 IATMSDRLGLV-ATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPR 166 (172)
Q Consensus 112 I~~~~~~L~Lp-~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~ 166 (172)
+.++-..+++. ....+-+-.|...-+...+.-=..|..+|-|||||||-..+.+.
T Consensus 157 L~q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia~~~~~k~~ 212 (264)
T KOG0794|consen 157 LLQFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIACVIDEKDI 212 (264)
T ss_pred HHHHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHHHhhcCCCh
Confidence 44444555553 34666666666665555544446789999999999998777654
No 241
>PRK08197 threonine synthase; Validated
Probab=60.64 E-value=4.1 Score=34.60 Aligned_cols=26 Identities=31% Similarity=0.733 Sum_probs=19.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+|+.||.. ++...-...| .||-.++
T Consensus 8 ~~C~~Cg~~----~~~~~~~~~C-~cg~~l~ 33 (394)
T PRK08197 8 LECSKCGET----YDADQVHNLC-KCGKPLL 33 (394)
T ss_pred EEECCCCCC----CCCCCcceec-CCCCeeE
Confidence 589999973 4444557889 8997764
No 242
>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=60.58 E-value=1.8 Score=26.79 Aligned_cols=25 Identities=24% Similarity=0.587 Sum_probs=18.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeC-CCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCS-ECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~-~CG~V~~ 34 (172)
..||+||.+ |-. ++..|. .|+....
T Consensus 4 kHC~~CG~~--Ip~----~~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 4 KHCPVCGKP--IPP----DESFCSPKCREEYR 29 (59)
T ss_pred CcCCcCCCc--CCc----chhhhCHHHHHHHH
Confidence 579999973 322 488995 7987764
No 243
>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=59.91 E-value=6.2 Score=32.09 Aligned_cols=31 Identities=23% Similarity=0.502 Sum_probs=16.3
Q ss_pred CCCCCCCCCCceeEe-------CCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFD-------HSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D-------~~~G~~vC~~CG~V~~ 34 (172)
..||+||+....-+. +..--.+|..||.-+.
T Consensus 212 ~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 212 IKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp TS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred CCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 479999974322111 1233468999999883
No 244
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=59.31 E-value=6.6 Score=30.33 Aligned_cols=34 Identities=24% Similarity=0.499 Sum_probs=21.0
Q ss_pred CCCCCCCCCC---ceeEe-CCCCc-----eEeCCCcceecccc
Q 030755 4 AFCSDCKKHT---EVVFD-HSAGD-----TVCSECGLVLESHS 37 (172)
Q Consensus 4 ~~C~~Cg~~~---~i~~D-~~~G~-----~vC~~CG~V~~e~~ 37 (172)
..||.||+.- ...+| |--|. .+|..||+=..|-.
T Consensus 15 ~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~ 57 (201)
T COG1779 15 IDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVK 57 (201)
T ss_pred ecCCcccceeeEEEeeecCCccceEEEEEEEccccCCccccee
Confidence 4799999731 11122 23454 58999999775443
No 245
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=58.86 E-value=8.1 Score=24.62 Aligned_cols=27 Identities=30% Similarity=0.634 Sum_probs=20.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..| .||. .++.|...-.--| .||..+.
T Consensus 4 frC-~Cgr--~lya~e~~kTkkC-~CG~~l~ 30 (68)
T PF09082_consen 4 FRC-DCGR--YLYAKEGAKTKKC-VCGKTLK 30 (68)
T ss_dssp EEE-TTS----EEEETT-SEEEE-TTTEEEE
T ss_pred EEe-cCCC--EEEecCCcceeEe-cCCCeee
Confidence 368 7997 4788888888999 9999984
No 246
>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=58.79 E-value=5.1 Score=29.49 Aligned_cols=15 Identities=40% Similarity=0.926 Sum_probs=13.3
Q ss_pred CCCceEeCCCcceec
Q 030755 20 SAGDTVCSECGLVLE 34 (172)
Q Consensus 20 ~~G~~vC~~CG~V~~ 34 (172)
..|.++|.+||..+.
T Consensus 109 g~G~l~C~~Cg~~~~ 123 (146)
T PF07295_consen 109 GPGTLVCENCGHEVE 123 (146)
T ss_pred cCceEecccCCCEEE
Confidence 579999999999874
No 247
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=58.57 E-value=6.6 Score=33.08 Aligned_cols=34 Identities=21% Similarity=0.530 Sum_probs=27.0
Q ss_pred CCCCCCCCCceeEeC-CCCceEeCCCcceecccccc
Q 030755 5 FCSDCKKHTEVVFDH-SAGDTVCSECGLVLESHSID 39 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~-~~G~~vC~~CG~V~~e~~i~ 39 (172)
.|..||+ .+++..+ .+|.+.|.+|-.|+.+..+-
T Consensus 276 vCd~CGn-~rLe~~pe~rg~~~C~~Cs~~V~sP~~r 310 (389)
T PF14951_consen 276 VCDRCGN-GRLEQSPEDRGAFSCGDCSRVVTSPVLR 310 (389)
T ss_pred cccccCC-ccceeCccCCCceeccchhhhccCccee
Confidence 6999998 6787665 47789999999999765543
No 248
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=58.51 E-value=6 Score=33.14 Aligned_cols=24 Identities=38% Similarity=0.937 Sum_probs=19.2
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.|++||. .+.|+ ...|..||.-|.
T Consensus 1 ~C~~Cg~--~v~Fe----Nt~C~~Cg~~LG 24 (343)
T PF10005_consen 1 SCPNCGQ--PVFFE----NTRCLSCGSALG 24 (343)
T ss_pred CCCCCCC--cceeC----CCccccCCcccc
Confidence 4999997 35564 689999999885
No 249
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=58.17 E-value=6.8 Score=24.27 Aligned_cols=28 Identities=7% Similarity=-0.031 Sum_probs=17.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~ 39 (172)
..||+||.. . .---+|. ||+--+..+++
T Consensus 28 ~~c~~cg~~---~----~pH~vc~-cG~Y~gr~v~~ 55 (60)
T PRK01110 28 SVDKTTGEY---H----LPHHVSP-KGYYKGRKVLK 55 (60)
T ss_pred eEcCCCCce---e----ccceecC-CcccCCeEeec
Confidence 468888862 1 2356788 88776655544
No 250
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=58.10 E-value=8.9 Score=22.20 Aligned_cols=22 Identities=36% Similarity=0.546 Sum_probs=17.0
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
+|..|+.. + ...+|..||.|.-
T Consensus 1 ~C~~C~~~-~-------~l~~CL~C~~~~c 22 (50)
T smart00290 1 RCSVCGTI-E-------NLWLCLTCGQVGC 22 (50)
T ss_pred CcccCCCc-C-------CeEEecCCCCccc
Confidence 58899973 1 2779999999975
No 251
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=58.05 E-value=3.6 Score=28.74 Aligned_cols=34 Identities=21% Similarity=0.566 Sum_probs=24.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~ 39 (172)
..|++||. ..++...-..- .|..||..-.+..++
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 47999997 56666554444 999999997655443
No 252
>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=58.02 E-value=3.7 Score=28.71 Aligned_cols=32 Identities=22% Similarity=0.471 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
...|-.||+...--.+..-|..+|..|.-|-.
T Consensus 13 N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR 44 (116)
T PF01412_consen 13 NKVCADCGAPNPTWASLNYGIFLCLECAGIHR 44 (116)
T ss_dssp CTB-TTT-SBS--EEETTTTEEE-HHHHHHHH
T ss_pred cCcCCCCCCCCCCEEEeecChhhhHHHHHHHH
Confidence 35799999843334455679999999997764
No 253
>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 PF14833 NAD_binding_11: NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase; PDB: 3OBB_A 3Q3C_A 2UYY_D 3G0O_A 1WP4_A 2CVZ_B 1YB4_A 3PDU_G 2I9P_D 2GF2_D ....
Probab=57.69 E-value=38 Score=23.42 Aligned_cols=39 Identities=10% Similarity=0.177 Sum_probs=30.9
Q ss_pred hhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcC
Q 030755 103 RGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKS 141 (172)
Q Consensus 103 ~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~ 141 (172)
....+-.+.+.+.+...++|-.+.+.+.++|+.+.+.+.
T Consensus 72 ~~~~KDl~l~~~~a~~~g~~~p~~~~~~~~~~~a~~~g~ 110 (122)
T PF14833_consen 72 DLARKDLRLALDLAKEAGVPLPLGSAARQLYQAAKAQGG 110 (122)
T ss_dssp HHHHHHHHHHHHHHHHTT---HHHHHHHHHHHHHHHTTT
T ss_pred HhhccHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhcCC
Confidence 344556788999999999999999999999999998874
No 255
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=57.41 E-value=6.9 Score=31.97 Aligned_cols=32 Identities=22% Similarity=0.638 Sum_probs=27.5
Q ss_pred eCCCCceEeCCCccee--cccccccCcccccccC
Q 030755 18 DHSAGDTVCSECGLVL--ESHSIDETSEWRTFAN 49 (172)
Q Consensus 18 D~~~G~~vC~~CG~V~--~e~~i~~~~ewr~f~~ 49 (172)
..+.|.++|..||.-| .+.-+|+|.-|.+|.+
T Consensus 31 ~~~~G~y~c~~c~~~LF~s~~Kf~sg~GWPsF~~ 64 (283)
T PRK05550 31 HDEKGVYLCRRCGAPLFRSEDKFNSGCGWPSFDD 64 (283)
T ss_pred CCCCcEEEcCCCCchhcCChhhccCCCCCcCcCc
Confidence 3579999999999998 5567899999999975
No 256
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=57.11 E-value=5.3 Score=27.10 Aligned_cols=11 Identities=27% Similarity=0.459 Sum_probs=9.5
Q ss_pred CCCCCCCCCCC
Q 030755 1 MTDAFCSDCKK 11 (172)
Q Consensus 1 ~~~~~C~~Cg~ 11 (172)
|....||+||.
T Consensus 1 mlLI~CP~Cg~ 11 (97)
T COG4311 1 MLLIPCPYCGE 11 (97)
T ss_pred CceecCCCCCC
Confidence 67789999996
No 257
>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=57.09 E-value=7.3 Score=32.19 Aligned_cols=28 Identities=25% Similarity=0.585 Sum_probs=17.4
Q ss_pred CCCCCCCCCC--ceeEeC--CCC--ceEeCCCcc
Q 030755 4 AFCSDCKKHT--EVVFDH--SAG--DTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~--~i~~D~--~~G--~~vC~~CG~ 31 (172)
..||.||+.+ ..+... .+| .+.|.-|++
T Consensus 185 ~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~t 218 (305)
T TIGR01562 185 TLCPACGSPPVASMVRQGGKETGLRYLSCSLCAT 218 (305)
T ss_pred CcCCCCCChhhhhhhcccCCCCCceEEEcCCCCC
Confidence 3899999853 223331 344 677887765
No 258
>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=57.07 E-value=15 Score=20.57 Aligned_cols=29 Identities=24% Similarity=0.408 Sum_probs=17.7
Q ss_pred CCCCCCCCCCceeEeCCCC-ceEeCC---Cccee
Q 030755 4 AFCSDCKKHTEVVFDHSAG-DTVCSE---CGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G-~~vC~~---CG~V~ 33 (172)
..||.||+ .-++.....| .+.|++ |....
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 57999997 4444444443 456775 66654
No 259
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=56.53 E-value=5.4 Score=22.63 Aligned_cols=15 Identities=33% Similarity=0.944 Sum_probs=12.4
Q ss_pred CceEeCCCcceeccc
Q 030755 22 GDTVCSECGLVLESH 36 (172)
Q Consensus 22 G~~vC~~CG~V~~e~ 36 (172)
|...|..||++....
T Consensus 12 ~~~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 12 GATTCPTCGMLYSPG 26 (41)
T ss_pred CCcCCCCCCCEECCC
Confidence 678999999998544
No 260
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=56.15 E-value=10 Score=28.25 Aligned_cols=38 Identities=11% Similarity=0.128 Sum_probs=20.0
Q ss_pred chhhHHHHHHHHHHHHHhc-C-CcHHHHHHHHHHHHHHhh
Q 030755 101 PDRGLILAFKTIATMSDRL-G-LVATIKDRANEIYKKVED 138 (172)
Q Consensus 101 ~e~~l~~~~~~I~~~~~~L-~-Lp~~v~~~A~~i~~~a~~ 138 (172)
-|-.|.++.+.+...+... + ..+...+.+.++.+++.+
T Consensus 98 VEGlL~~i~~~L~~~~~~~~~~~~~e~~~k~~~~~~~L~~ 137 (160)
T smart00709 98 VEGLLSRVREVLSQAIQETRDDSDPETKEKIDEFLEKLKE 137 (160)
T ss_pred hHHHHHHHHHHHHhhhhhhcccCCHHHHHHHHHHHHHHHH
Confidence 3445555555555543221 1 234566677777776643
No 261
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=55.84 E-value=7.6 Score=19.49 Aligned_cols=9 Identities=22% Similarity=0.501 Sum_probs=7.0
Q ss_pred CCCCCCCCC
Q 030755 3 DAFCSDCKK 11 (172)
Q Consensus 3 ~~~C~~Cg~ 11 (172)
+..||.||.
T Consensus 2 l~~C~~CgR 10 (25)
T PF13913_consen 2 LVPCPICGR 10 (25)
T ss_pred CCcCCCCCC
Confidence 467888886
No 262
>TIGR00299 conserved hypothetical protein TIGR00299. Members of this family are found in the Archaea and in several different bacteria lineages. The function in unknown and the genomic context is not well conserved.
Probab=54.96 E-value=35 Score=29.15 Aligned_cols=49 Identities=20% Similarity=0.272 Sum_probs=35.0
Q ss_pred HHHHHHHHHhcCCcHHHHHHHHHHHHHHhhC-cCCCCC--------------CHHHHHHHHHHH
Q 030755 109 FKTIATMSDRLGLVATIKDRANEIYKKVEDQ-KSSRGR--------------NQDALLAACLYI 157 (172)
Q Consensus 109 ~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~-~~~~Gr--------------~~~~~aAAclYi 157 (172)
+..|..+.+.+.||+.+.+.|.++|+.+.+. .-+.|. +...++++|+-+
T Consensus 74 ~~dI~~~i~~s~l~~~vk~~a~~iF~~la~AEa~VHG~~~e~VHFHEVGa~DsIvDIvG~~~~l 137 (382)
T TIGR00299 74 FKEILELIKSSNLPERVKRWALAIFHQLAIAEGKVHGVDPEEVHFHEVGATDAIADIVGAVLAL 137 (382)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHeeeeeccccccHHHHHHHHHHH
Confidence 3456666678899999999999999997664 235565 345666666644
No 263
>PRK08329 threonine synthase; Validated
Probab=54.96 E-value=9 Score=31.96 Aligned_cols=25 Identities=24% Similarity=0.701 Sum_probs=17.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+|+.||.. ++.... ..| .||-.++
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 689999973 333333 789 7997764
No 264
>PRK14067 exodeoxyribonuclease VII small subunit; Provisional
Probab=54.67 E-value=23 Score=23.31 Aligned_cols=38 Identities=11% Similarity=0.056 Sum_probs=30.8
Q ss_pred chhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhh
Q 030755 101 PDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVED 138 (172)
Q Consensus 101 ~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~ 138 (172)
++.+...++..+..|..+|.=++--.+.++.+|++...
T Consensus 5 k~~sfEeal~~LEeIV~~LE~~~l~Lees~~lyeeG~~ 42 (80)
T PRK14067 5 KTADFEQQLARLQEIVDALEGGDLPLEESVALYKEGLG 42 (80)
T ss_pred ccCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence 34567889999999999998887778888888887654
No 265
>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=54.61 E-value=8.9 Score=26.26 Aligned_cols=28 Identities=18% Similarity=0.309 Sum_probs=18.0
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
...|..|+- |..+..--...|.+||.++
T Consensus 3 lrAC~~C~~---I~~~~qf~~~gCpnC~~~l 30 (98)
T cd07973 3 LRACLLCSL---IKTEDQFERDGCPNCEGYL 30 (98)
T ss_pred CchhccCCc---ccccccccCCCCCCCcchh
Confidence 457889986 2333223356799998776
No 266
>PRK04330 hypothetical protein; Provisional
Probab=54.05 E-value=64 Score=21.62 Aligned_cols=53 Identities=11% Similarity=0.176 Sum_probs=41.9
Q ss_pred chhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHH
Q 030755 101 PDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYI 157 (172)
Q Consensus 101 ~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYi 157 (172)
.+..+.++...+++|.+--.+|..+...|.+....+.+.+ ..+..=||.+|++
T Consensus 7 ~e~~ik~~~~~L~~I~~D~sVPRNIRraa~ea~~~L~~e~----~~~~vRaA~AIs~ 59 (88)
T PRK04330 7 NEEKIKQAIQMLEEIINDTSVPRNIRRAATEAKEILLNEE----ESPGVRAATAISI 59 (88)
T ss_pred hHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHhCcC----cchhHHHHHHHHH
Confidence 5778899999999999999999999999988888876654 3444445666654
No 267
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=53.86 E-value=12 Score=34.72 Aligned_cols=27 Identities=26% Similarity=0.742 Sum_probs=21.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
..||+|.. .+.+-..+|.+.|-.||..
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 46888886 3667777899999999987
No 268
>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=53.53 E-value=11 Score=22.44 Aligned_cols=31 Identities=26% Similarity=0.605 Sum_probs=23.0
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceecccc
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~ 37 (172)
...|+.|+.. +.......-|..||.|+=..-
T Consensus 2 ~~~C~~C~~~----F~~~~rk~~Cr~Cg~~~C~~C 32 (57)
T cd00065 2 ASSCMGCGKP----FTLTRRRHHCRNCGRIFCSKC 32 (57)
T ss_pred cCcCcccCcc----ccCCccccccCcCcCCcChHH
Confidence 3579999973 445677889999999985443
No 269
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=53.47 E-value=10 Score=33.70 Aligned_cols=31 Identities=23% Similarity=0.340 Sum_probs=27.1
Q ss_pred CCCCceEeCCCccee--cccccccCcccccccC
Q 030755 19 HSAGDTVCSECGLVL--ESHSIDETSEWRTFAN 49 (172)
Q Consensus 19 ~~~G~~vC~~CG~V~--~e~~i~~~~ewr~f~~ 49 (172)
.+.|.++|..||.-| .+.-+|+|.-|.+|.+
T Consensus 414 ~~~G~y~c~~c~~pLf~s~~Kf~sg~GWPsF~~ 446 (521)
T PRK14018 414 FKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTR 446 (521)
T ss_pred CCCEEEEecCCCCccccCcccccCCCCCcccCc
Confidence 479999999999998 5567899999999984
No 270
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=53.35 E-value=11 Score=33.33 Aligned_cols=32 Identities=34% Similarity=0.641 Sum_probs=20.8
Q ss_pred CCCCCCCCCce---eEeCCCC--ceEeCCCcceecccc
Q 030755 5 FCSDCKKHTEV---VFDHSAG--DTVCSECGLVLESHS 37 (172)
Q Consensus 5 ~C~~Cg~~~~i---~~D~~~G--~~vC~~CG~V~~e~~ 37 (172)
.||+||..... -+|...| .+.| .||.-.+-.+
T Consensus 177 ic~~cg~~~~~~~~~~d~~~~~v~y~~-~cG~~~~~~~ 213 (510)
T PRK00750 177 ICPKCGKVLTTPVISYDAEAGTVTYDC-ECGHEGEVPV 213 (510)
T ss_pred eCCCCCccceEEEEEEeCCCCEEEEEc-CCCCEEEEec
Confidence 69999985332 3577777 3445 5998865443
No 271
>COG4709 Predicted membrane protein [Function unknown]
Probab=53.13 E-value=43 Score=25.74 Aligned_cols=42 Identities=12% Similarity=0.207 Sum_probs=30.2
Q ss_pred HHHHHHHhc-CCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHH
Q 030755 111 TIATMSDRL-GLVATIKDRANEIYKKVEDQKSSRGRNQDALLA 152 (172)
Q Consensus 111 ~I~~~~~~L-~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aA 152 (172)
+++++-..| +||++-.++++..|+...+..-..||+-+.+++
T Consensus 6 fL~eL~~yL~~Lp~~~r~e~m~dyeehF~~a~~~GksE~EI~~ 48 (195)
T COG4709 6 FLNELEQYLEGLPREERREIMYDYEEHFREAQEAGKSEEEIAK 48 (195)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHH
Confidence 344443333 678888999999998888887788877666654
No 272
>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=53.07 E-value=7.4 Score=25.17 Aligned_cols=11 Identities=45% Similarity=1.141 Sum_probs=3.7
Q ss_pred CCCCCCCCCCC
Q 030755 1 MTDAFCSDCKK 11 (172)
Q Consensus 1 ~~~~~C~~Cg~ 11 (172)
|....||.||.
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 44556777775
No 273
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=52.55 E-value=40 Score=24.33 Aligned_cols=52 Identities=23% Similarity=0.160 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHhcCCc------HHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHH
Q 030755 106 ILAFKTIATMSDRLGLV------ATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYI 157 (172)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp------~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYi 157 (172)
..+..+++.+...+++| .-....|.+++...-..+--+-+..+.+||++|.-
T Consensus 75 ~~v~~f~~~L~~~~~~~v~~~DEr~TT~~A~~~l~~~~~~~~~~k~~vD~~AA~iILq 132 (138)
T PRK00109 75 ERARKFANRLEGRFGLPVVLVDERLSTVEAERALADVGSRKKLRKGVIDSLAAVIILQ 132 (138)
T ss_pred HHHHHHHHHHHHHhCCCEEEEcCCcCHHHHHHHHHHcCCChhhcccchhHHHHHHHHH
Confidence 45677888888877888 23467777887654222211123467888877753
No 274
>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=51.93 E-value=9.8 Score=29.15 Aligned_cols=24 Identities=17% Similarity=0.542 Sum_probs=15.2
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCc
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECG 30 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG 30 (172)
...||.|+....++.+ .-.|..|+
T Consensus 99 ~~~C~~C~G~G~~i~~----~~~C~~C~ 122 (186)
T TIGR02642 99 SCKCPRCRGTGLIQRR----QRECDTCA 122 (186)
T ss_pred CCcCCCCCCeeEEecC----CCCCCCCC
Confidence 3679999984333321 25688885
No 275
>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=51.73 E-value=6.9 Score=27.20 Aligned_cols=32 Identities=22% Similarity=0.416 Sum_probs=22.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
...|-.||+..---....-|..+|..|.-|-.
T Consensus 3 N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR 34 (112)
T smart00105 3 NKKCFDCGAPNPTWASVNLGVFLCIECSGIHR 34 (112)
T ss_pred CCcccCCCCCCCCcEEeccceeEhHHhHHHHH
Confidence 35799999842123344679999999998875
No 276
>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=51.68 E-value=8.7 Score=32.73 Aligned_cols=24 Identities=33% Similarity=0.816 Sum_probs=15.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..||.|+.. ...| ..|..||..++
T Consensus 137 g~CP~C~~~------~a~g-~~Ce~cG~~~~ 160 (391)
T PF09334_consen 137 GTCPYCGSD------KARG-DQCENCGRPLE 160 (391)
T ss_dssp CEETTT--S------SCTT-TEETTTSSBEE
T ss_pred ccccCcCcc------ccCC-CcccCCCCCcc
Confidence 468888852 2233 56889999887
No 277
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=51.64 E-value=7.1 Score=38.06 Aligned_cols=8 Identities=50% Similarity=1.244 Sum_probs=4.7
Q ss_pred CCCCCCCC
Q 030755 5 FCSDCKKH 12 (172)
Q Consensus 5 ~C~~Cg~~ 12 (172)
.||+||+.
T Consensus 681 fCP~CGs~ 688 (1337)
T PRK14714 681 RCPDCGTH 688 (1337)
T ss_pred cCcccCCc
Confidence 56666653
No 278
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=51.34 E-value=16 Score=22.60 Aligned_cols=15 Identities=13% Similarity=0.379 Sum_probs=7.7
Q ss_pred HHHHHHhcCCcHHHH
Q 030755 112 IATMSDRLGLVATIK 126 (172)
Q Consensus 112 I~~~~~~L~Lp~~v~ 126 (172)
|..++..++++....
T Consensus 4 ~~~la~~~~~s~~~l 18 (84)
T smart00342 4 LEDLAEALGMSPRHL 18 (84)
T ss_pred HHHHHHHhCCCHHHH
Confidence 345555555554433
No 279
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=51.16 E-value=39 Score=18.22 Aligned_cols=27 Identities=15% Similarity=0.272 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHhcCCcH-HHHHHHHHHH
Q 030755 107 LAFKTIATMSDRLGLVA-TIKDRANEIY 133 (172)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~-~v~~~A~~i~ 133 (172)
+..+.|+.+|...|++. .++..|.+-|
T Consensus 9 ~~~~~l~~~a~~~g~s~s~~ir~ai~~~ 36 (39)
T PF01402_consen 9 ELYERLDELAKELGRSRSELIREAIREY 36 (39)
T ss_dssp HHHHHHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45778999999999994 6777776654
No 280
>PF14369 zf-RING_3: zinc-finger
Probab=50.55 E-value=11 Score=20.56 Aligned_cols=27 Identities=22% Similarity=0.660 Sum_probs=15.9
Q ss_pred CCCCCCCCCCCceeEe-CCCCceEeCCCcc
Q 030755 3 DAFCSDCKKHTEVVFD-HSAGDTVCSECGL 31 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D-~~~G~~vC~~CG~ 31 (172)
..+|-.|... +... .....+.|..|+-
T Consensus 2 ~ywCh~C~~~--V~~~~~~~~~~~CP~C~~ 29 (35)
T PF14369_consen 2 RYWCHQCNRF--VRIAPSPDSDVACPRCHG 29 (35)
T ss_pred CEeCccCCCE--eEeCcCCCCCcCCcCCCC
Confidence 3578899873 2222 2344445999974
No 281
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=50.24 E-value=15 Score=22.34 Aligned_cols=27 Identities=22% Similarity=0.476 Sum_probs=16.6
Q ss_pred CCCCCCCCCce--eEeC--CCCceEeCCCcc
Q 030755 5 FCSDCKKHTEV--VFDH--SAGDTVCSECGL 31 (172)
Q Consensus 5 ~C~~Cg~~~~i--~~D~--~~G~~vC~~CG~ 31 (172)
.||.||+.+.+ -.|. .+=-++|..|-.
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~ 36 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLYCPKCKQ 36 (55)
T ss_pred ECCCCCCccceeeecCceeccccccCCCCCc
Confidence 59999975422 2232 345678888863
No 282
>PRK11032 hypothetical protein; Provisional
Probab=49.43 E-value=9.3 Score=28.57 Aligned_cols=15 Identities=33% Similarity=0.738 Sum_probs=13.0
Q ss_pred CCCceEeCCCcceec
Q 030755 20 SAGDTVCSECGLVLE 34 (172)
Q Consensus 20 ~~G~~vC~~CG~V~~ 34 (172)
.-|.+||.+||.-+.
T Consensus 121 g~G~LvC~~Cg~~~~ 135 (160)
T PRK11032 121 GLGNLVCEKCHHHLA 135 (160)
T ss_pred ecceEEecCCCCEEE
Confidence 579999999999873
No 283
>PRK09462 fur ferric uptake regulator; Provisional
Probab=49.38 E-value=9.5 Score=27.67 Aligned_cols=13 Identities=38% Similarity=1.030 Sum_probs=11.3
Q ss_pred CceEeCCCcceec
Q 030755 22 GDTVCSECGLVLE 34 (172)
Q Consensus 22 G~~vC~~CG~V~~ 34 (172)
--++|..||.|++
T Consensus 89 ~H~iC~~Cg~i~~ 101 (148)
T PRK09462 89 DHLICLDCGKVIE 101 (148)
T ss_pred CceEECCCCCEEE
Confidence 3599999999986
No 284
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=49.30 E-value=10 Score=32.64 Aligned_cols=33 Identities=18% Similarity=0.434 Sum_probs=23.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~ 39 (172)
-.||.||... .-.-++..-|..||+-..+..+.
T Consensus 351 p~Cp~Cg~~m---~S~G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 351 PVCPRCGGRM---KSAGRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCCccCCch---hhcCCCCcccccccccCCccccc
Confidence 4799999831 22234479999999999766555
No 285
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.17 E-value=6.6 Score=31.89 Aligned_cols=28 Identities=36% Similarity=0.940 Sum_probs=21.9
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
|-...||+||. -+.+| ...|..||.-+.
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 55678999996 35565 678999998885
No 286
>PF14149 YhfH: YhfH-like protein
Probab=48.82 E-value=2.5 Score=23.60 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=12.3
Q ss_pred CCceEeCCCcceeccc
Q 030755 21 AGDTVCSECGLVLESH 36 (172)
Q Consensus 21 ~G~~vC~~CG~V~~e~ 36 (172)
-..-.|+.||..|+|.
T Consensus 11 Lp~K~C~~CG~~i~EQ 26 (37)
T PF14149_consen 11 LPPKKCTECGKEIEEQ 26 (37)
T ss_pred CCCcccHHHHHHHHHH
Confidence 4566899999998765
No 287
>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=48.76 E-value=9.9 Score=26.02 Aligned_cols=13 Identities=31% Similarity=1.022 Sum_probs=11.6
Q ss_pred CceEeCCCcceec
Q 030755 22 GDTVCSECGLVLE 34 (172)
Q Consensus 22 G~~vC~~CG~V~~ 34 (172)
.-++|.+||.|.+
T Consensus 72 ~H~~C~~Cg~i~~ 84 (116)
T cd07153 72 HHLICTKCGKVID 84 (116)
T ss_pred CceEeCCCCCEEE
Confidence 4799999999986
No 288
>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=48.69 E-value=15 Score=28.91 Aligned_cols=31 Identities=23% Similarity=0.595 Sum_probs=18.8
Q ss_pred CCCCCCCCC-ceeE-eCCCCceEeCCCcceecc
Q 030755 5 FCSDCKKHT-EVVF-DHSAGDTVCSECGLVLES 35 (172)
Q Consensus 5 ~C~~Cg~~~-~i~~-D~~~G~~vC~~CG~V~~e 35 (172)
.|+.|=-.. +++. +..---.+|..||.....
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 455555321 2222 223478899999999864
No 289
>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=48.69 E-value=8.2 Score=28.78 Aligned_cols=31 Identities=19% Similarity=0.557 Sum_probs=15.0
Q ss_pred CCCCCCCCCCce---eEe-CCCCc-----eEeCCCcceec
Q 030755 4 AFCSDCKKHTEV---VFD-HSAGD-----TVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i---~~D-~~~G~-----~vC~~CG~V~~ 34 (172)
..||+||..... .+| |--++ ..|..||+=-.
T Consensus 2 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ 41 (161)
T PF03367_consen 2 SLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNN 41 (161)
T ss_dssp EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEE
T ss_pred CcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEee
Confidence 469999985211 122 33444 37999998643
No 290
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=48.63 E-value=9.3 Score=22.63 Aligned_cols=14 Identities=29% Similarity=0.707 Sum_probs=12.1
Q ss_pred CCceEeCCCcceec
Q 030755 21 AGDTVCSECGLVLE 34 (172)
Q Consensus 21 ~G~~vC~~CG~V~~ 34 (172)
.|.++|..||.-+-
T Consensus 3 ~g~l~C~~CG~~m~ 16 (58)
T PF13408_consen 3 SGLLRCGHCGSKMT 16 (58)
T ss_pred CCcEEcccCCcEeE
Confidence 68999999998874
No 291
>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=48.29 E-value=10 Score=26.24 Aligned_cols=14 Identities=29% Similarity=0.921 Sum_probs=10.9
Q ss_pred CCceEeCCCcceec
Q 030755 21 AGDTVCSECGLVLE 34 (172)
Q Consensus 21 ~G~~vC~~CG~V~~ 34 (172)
-..++|..||.|++
T Consensus 78 h~h~iC~~Cg~v~~ 91 (120)
T PF01475_consen 78 HHHFICTQCGKVID 91 (120)
T ss_dssp CEEEEETTTS-EEE
T ss_pred ceEEEECCCCCEEE
Confidence 45699999999985
No 292
>PRK14526 adenylate kinase; Provisional
Probab=48.06 E-value=11 Score=29.13 Aligned_cols=27 Identities=15% Similarity=0.449 Sum_probs=13.6
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcc
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
.||.||..-++.+++..-..+|..||.
T Consensus 124 ~~~~~g~~y~~~~~pp~~~~~~~~~~~ 150 (211)
T PRK14526 124 ICKSCNNIFNIYTLPTKEKGICDVCKG 150 (211)
T ss_pred cccccCCccccccCCCCccCcCCCCCC
Confidence 355555543444554444445555553
No 293
>smart00400 ZnF_CHCC zinc finger.
Probab=48.04 E-value=27 Score=20.75 Aligned_cols=34 Identities=15% Similarity=0.273 Sum_probs=24.7
Q ss_pred CCCCCCCCC-CceeEeCCCCceEeCCCcceecccccc
Q 030755 4 AFCSDCKKH-TEVVFDHSAGDTVCSECGLVLESHSID 39 (172)
Q Consensus 4 ~~C~~Cg~~-~~i~~D~~~G~~vC~~CG~V~~e~~i~ 39 (172)
..||.+... +++..++..+...|-.||. .-++|+
T Consensus 3 ~~cPfh~d~~pSf~v~~~kn~~~Cf~cg~--gGd~i~ 37 (55)
T smart00400 3 GLCPFHGEKTPSFSVSPDKQFFHCFGCGA--GGNVIS 37 (55)
T ss_pred ccCcCCCCCCCCEEEECCCCEEEEeCCCC--CCCHHH
Confidence 359998853 4778888889999999983 334444
No 294
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=47.65 E-value=10 Score=27.61 Aligned_cols=14 Identities=36% Similarity=0.902 Sum_probs=11.9
Q ss_pred CCceEeCCCcceec
Q 030755 21 AGDTVCSECGLVLE 34 (172)
Q Consensus 21 ~G~~vC~~CG~V~~ 34 (172)
-.-++|.+||.|++
T Consensus 91 H~HliC~~CG~v~e 104 (145)
T COG0735 91 HHHLICLDCGKVIE 104 (145)
T ss_pred ccEEEecCCCCEEE
Confidence 34789999999986
No 295
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=47.20 E-value=11 Score=33.93 Aligned_cols=32 Identities=25% Similarity=0.651 Sum_probs=22.2
Q ss_pred CCCCCCCCCceeEeCC------------CCceEeCCCcceeccc
Q 030755 5 FCSDCKKHTEVVFDHS------------AGDTVCSECGLVLESH 36 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~------------~G~~vC~~CG~V~~e~ 36 (172)
.||+||...-+.++.. .-.+.|..|+.+|.+.
T Consensus 229 pCPHCGe~q~l~~~e~~~~~g~~~~~~~~~~~~c~h~~~~i~~~ 272 (611)
T COG5525 229 PCPHCGEEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVIRPK 272 (611)
T ss_pred eCCCCCchhhccccccCCCcCcccchhhhhhhhccccCceeeee
Confidence 6999997544444222 2346899999999873
No 296
>PRK14064 exodeoxyribonuclease VII small subunit; Provisional
Probab=47.18 E-value=34 Score=22.13 Aligned_cols=37 Identities=14% Similarity=0.182 Sum_probs=28.8
Q ss_pred hhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhh
Q 030755 102 DRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVED 138 (172)
Q Consensus 102 e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~ 138 (172)
..+...++..+..|.+.|.=++--.+.+..+|++...
T Consensus 5 ~~sfEe~l~~LE~IV~~LE~~~l~Leesl~~ye~G~~ 41 (75)
T PRK14064 5 KKTFEEAIAELETIVEALENGSASLEDSLDMYQKGIE 41 (75)
T ss_pred cCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence 3467788999999999997777667788888877654
No 297
>PRK05638 threonine synthase; Validated
Probab=46.99 E-value=11 Score=32.63 Aligned_cols=25 Identities=28% Similarity=0.741 Sum_probs=17.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+|+.||.. ++.. -...| .||-.++
T Consensus 2 l~C~~Cg~~----~~~~-~~~~C-~c~~~l~ 26 (442)
T PRK05638 2 MKCPKCGRE----YNSY-IPPFC-ICGELLE 26 (442)
T ss_pred eEeCCCCCC----CCCC-Cceec-CCCCcEE
Confidence 579999973 2322 23889 8997774
No 298
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=46.74 E-value=7.9 Score=27.15 Aligned_cols=28 Identities=25% Similarity=0.725 Sum_probs=20.4
Q ss_pred CCCCCCCCCCceeEeC-CCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDH-SAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~-~~G~~vC~~CG~V~~ 34 (172)
..|+.||+ |...+ ..+..+|..|+.+..
T Consensus 8 ~FC~~CG~---ll~~~~~~~~~~C~~Ck~~~~ 36 (116)
T KOG2907|consen 8 DFCSDCGS---LLEEPSAQSTVLCIRCKIEYP 36 (116)
T ss_pred chhhhhhh---hcccccccCceEeccccccCC
Confidence 47999997 33343 577777999998874
No 299
>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF. This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.
Probab=46.37 E-value=55 Score=23.30 Aligned_cols=52 Identities=15% Similarity=0.026 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHhcCCcH------HHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHH
Q 030755 105 LILAFKTIATMSDRLGLVA------TIKDRANEIYKKVEDQKSSRGRNQDALLAACLY 156 (172)
Q Consensus 105 l~~~~~~I~~~~~~L~Lp~------~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclY 156 (172)
-..+.++.+++...+++|= -....|.++|...--++..+-...+.+||++|.
T Consensus 68 a~~v~~f~~~L~~~~~~~v~~~DEr~TT~~A~~~l~~~g~~~~~~k~~vD~~AA~iIL 125 (130)
T TIGR00250 68 TERAQKFANRLEGRFGVPVVLWDERLSTVEAESGLFARGGFRALRKGKIDKAAAVIIL 125 (130)
T ss_pred HHHHHHHHHHHHHHhCCCEEEEcCCcCHHHHHHHHHHcCCChhhccccHhHHHHHHHH
Confidence 3567788888888888882 245677777776321111111235777777764
No 300
>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=46.35 E-value=13 Score=22.94 Aligned_cols=17 Identities=35% Similarity=0.687 Sum_probs=10.1
Q ss_pred ceEeCCCcceecccccc
Q 030755 23 DTVCSECGLVLESHSID 39 (172)
Q Consensus 23 ~~vC~~CG~V~~e~~i~ 39 (172)
..+|.+||+|.=++.++
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 46899999998777665
No 301
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=46.26 E-value=59 Score=27.41 Aligned_cols=67 Identities=13% Similarity=0.152 Sum_probs=50.4
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcC-CCCCCHHHHHHHHHHHHHHhCCC-CCCccccC
Q 030755 106 ILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKS-SRGRNQDALLAACLYIACRQEDK-PRTVKGTA 172 (172)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~-~~Gr~~~~~aAAclYiacR~~~~-~~tl~eia 172 (172)
.-.++++-++|+--.|..+..-.|..+|.+.+..-. ..--....|--+|||||++.+.+ |--+.|||
T Consensus 146 aILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFA 214 (408)
T KOG0655|consen 146 AILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFA 214 (408)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCcccccee
Confidence 446889999999999999999999999998765321 12233467778999999998775 55566654
No 302
>PLN02569 threonine synthase
Probab=46.18 E-value=13 Score=32.78 Aligned_cols=26 Identities=12% Similarity=0.120 Sum_probs=20.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..|+.||.. ++...-...| .||-.|+
T Consensus 50 l~C~~Cg~~----y~~~~~~~~C-~cgg~l~ 75 (484)
T PLN02569 50 LECPLTGEK----YSLDEVVYRS-KSGGLLD 75 (484)
T ss_pred cEeCCCCCc----CCCccccccC-CCCCeEE
Confidence 579999973 5556667899 7998885
No 303
>PRK07591 threonine synthase; Validated
Probab=46.01 E-value=8.7 Score=33.02 Aligned_cols=26 Identities=31% Similarity=0.574 Sum_probs=19.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+|..||.. ++...- ..|..||-.++
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 579999973 333333 88999998775
No 304
>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=45.94 E-value=17 Score=30.62 Aligned_cols=32 Identities=38% Similarity=0.788 Sum_probs=19.7
Q ss_pred CCCCCCCCCcee--EeCCCC--ceEeCCCcceecccc
Q 030755 5 FCSDCKKHTEVV--FDHSAG--DTVCSECGLVLESHS 37 (172)
Q Consensus 5 ~C~~Cg~~~~i~--~D~~~G--~~vC~~CG~V~~e~~ 37 (172)
.|++||.-+..+ +|.+.| .+.| .||...+-.+
T Consensus 171 ~c~~cg~~~~~v~~~d~~~~~v~y~c-~cG~~g~~~~ 206 (353)
T cd00674 171 YCEKCGKDTTTVEAYDAKAGTVTYKC-ECGHEETVDI 206 (353)
T ss_pred ecCCcCcceeEEEEEeCCCCeEEEEc-CCCCEEEEee
Confidence 699999533333 454444 5678 5998765333
No 305
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=45.86 E-value=15 Score=30.41 Aligned_cols=9 Identities=44% Similarity=1.232 Sum_probs=4.1
Q ss_pred EeCCCccee
Q 030755 25 VCSECGLVL 33 (172)
Q Consensus 25 vC~~CG~V~ 33 (172)
+|..|+.-+
T Consensus 254 ~C~~C~~Yl 262 (309)
T PRK03564 254 SCGDCGTYL 262 (309)
T ss_pred ecccccccc
Confidence 444444444
No 306
>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=45.68 E-value=14 Score=21.33 Aligned_cols=25 Identities=20% Similarity=0.587 Sum_probs=19.8
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
+|+.|+. .+.....+.|..|+..+=
T Consensus 1 ~C~vC~~-----~~~~~~~i~C~~C~~~~H 25 (51)
T PF00628_consen 1 YCPVCGQ-----SDDDGDMIQCDSCNRWYH 25 (51)
T ss_dssp EBTTTTS-----SCTTSSEEEBSTTSCEEE
T ss_pred eCcCCCC-----cCCCCCeEEcCCCChhhC
Confidence 4888997 255678999999998873
No 307
>PF07240 Turandot: Stress-inducible humoral factor Turandot; InterPro: IPR010825 This family consists of several Drosophila species specific Turandot proteins. The Turandot A (TotA) gene encodes a humoral factor, which is secreted from the fat body and accumulates in the body fluids. TotA is strongly induced upon bacterial challenge, as well as by other types of stress such as high temperature, mechanical pressure, dehydration, UV irradiation, and oxidative agents. It is also upregulated during metamorphosis and at high age. Flies that overexpress TotA show prolonged survival and retain normal activity at otherwise lethal temperatures. Although TotA is only induced by severe stress, it responds to a much wider range of stimuli than heat shock genes such as hsp70 or immune genes such as Cecropin A1 [].
Probab=45.63 E-value=41 Score=22.40 Aligned_cols=43 Identities=14% Similarity=0.173 Sum_probs=36.0
Q ss_pred chhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCc-CCC
Q 030755 101 PDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQK-SSR 143 (172)
Q Consensus 101 ~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~-~~~ 143 (172)
+.+++.+...+-+++...|.|++...+.+-++.++..+.+ ++.
T Consensus 8 K~rni~eLi~fY~ky~~~~~L~~~~r~~~d~~i~~y~~~~~lVD 51 (85)
T PF07240_consen 8 KIRNIQELIAFYEKYSPRLPLTPQDRQRIDRFIRRYKEENNLVD 51 (85)
T ss_pred HHhhHHHHHHHHHHcCccCCCCHHHHHHHHHHHHHHHHHhhccc
Confidence 4677889999999999999999998888888888877766 444
No 308
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=45.29 E-value=12 Score=22.44 Aligned_cols=31 Identities=23% Similarity=0.579 Sum_probs=18.8
Q ss_pred CCCCCCCCCC--CceeEeC--CCCceEeCCCccee
Q 030755 3 DAFCSDCKKH--TEVVFDH--SAGDTVCSECGLVL 33 (172)
Q Consensus 3 ~~~C~~Cg~~--~~i~~D~--~~G~~vC~~CG~V~ 33 (172)
...|..|+-. +..+.+- ..+.+.|.+||.+|
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcCCCeEECcCCCccC
Confidence 3578888842 1111111 24689999999875
No 309
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=45.26 E-value=13 Score=29.41 Aligned_cols=37 Identities=19% Similarity=0.415 Sum_probs=22.6
Q ss_pred CCCCCCCCCCceeEeCC-CCceEeCCCcceecccccccC
Q 030755 4 AFCSDCKKHTEVVFDHS-AGDTVCSECGLVLESHSIDET 41 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~-~G~~vC~~CG~V~~e~~i~~~ 41 (172)
..|..|+..-. ..+.. .....|..||-++..+++-.+
T Consensus 123 ~~C~~C~~~~~-~~~~~~~~~p~C~~Cgg~lrP~Vv~fg 160 (242)
T PRK00481 123 ARCTKCGQTYD-LDEYLKPEPPRCPKCGGILRPDVVLFG 160 (242)
T ss_pred eeeCCCCCCcC-hhhhccCCCCCCCCCCCccCCCeEECC
Confidence 46999986311 11111 223449999999988876544
No 310
>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family.
Probab=45.04 E-value=18 Score=27.09 Aligned_cols=23 Identities=26% Similarity=0.291 Sum_probs=18.9
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHH
Q 030755 111 TIATMSDRLGLVATIKDRANEIY 133 (172)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~ 133 (172)
+=-.++...++|+.++++|.++|
T Consensus 163 ~a~~~a~~~g~~~~i~~~a~~~~ 185 (185)
T smart00534 163 YGIEVAKLAGLPKEVIERAKEIL 185 (185)
T ss_pred HHHHHHHHhCCCHHHHHHHHHhC
Confidence 34456788899999999999875
No 311
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=44.92 E-value=16 Score=26.23 Aligned_cols=28 Identities=21% Similarity=0.571 Sum_probs=21.4
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
.|-.||..+.+-.+...-...|..|+.+
T Consensus 2 ~C~fC~~~s~~~~~~~~~~w~C~~C~q~ 29 (131)
T PF09779_consen 2 NCWFCGQNSKVPYDNRNSNWTCPHCEQY 29 (131)
T ss_pred eeccCCCCCCCCCCCCCCeeECCCCCCc
Confidence 5999998655555555556999999987
No 312
>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=43.94 E-value=13 Score=22.40 Aligned_cols=28 Identities=25% Similarity=0.345 Sum_probs=20.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~ 39 (172)
..||-|+. +..|+ |...||.|++...|.
T Consensus 2 ~~Cpi~~~---~~~~P-----v~~~~G~v~~~~~i~ 29 (63)
T smart00504 2 FLCPISLE---VMKDP-----VILPSGQTYERRAIE 29 (63)
T ss_pred cCCcCCCC---cCCCC-----EECCCCCEEeHHHHH
Confidence 46999997 24443 778999999877666
No 313
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=43.92 E-value=12 Score=27.16 Aligned_cols=24 Identities=25% Similarity=0.678 Sum_probs=16.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
.+|++||.. .+ + -...|..||.-.
T Consensus 30 ~kC~~CG~v---~~-P--Pr~~Cp~C~~~~ 53 (140)
T COG1545 30 TKCKKCGRV---YF-P--PRAYCPKCGSET 53 (140)
T ss_pred EEcCCCCeE---Ec-C--CcccCCCCCCCC
Confidence 479999972 22 2 367899998774
No 314
>PRK08173 DNA topoisomerase III; Validated
Probab=43.90 E-value=15 Score=34.69 Aligned_cols=27 Identities=19% Similarity=0.508 Sum_probs=18.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..||.||+. ++. ..+.+.|++|+..+-
T Consensus 625 ~~CP~Cg~~--~~~--~~~~~~Cs~C~f~~~ 651 (862)
T PRK08173 625 TPCPNCGGV--VKE--NYRRFACTKCDFSIS 651 (862)
T ss_pred ccCCccccc--ccc--cCceeEcCCCCcccc
Confidence 469999973 322 234499999998773
No 315
>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=43.60 E-value=13 Score=29.05 Aligned_cols=36 Identities=19% Similarity=0.434 Sum_probs=23.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccccccC
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDET 41 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~~~ 41 (172)
..|..|+.. ...+.......|..||-++..+++..|
T Consensus 119 ~~C~~C~~~--~~~~~~~~~p~C~~Cgg~lrP~vv~fg 154 (225)
T cd01411 119 IYCTVCGKT--VDWEEYLKSPYHAKCGGVIRPDIVLYE 154 (225)
T ss_pred eEeCCCCCc--cchhhcCCCCCCCCCCCEeCCCEEEcC
Confidence 469999762 212222234679999999998886544
No 316
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=43.59 E-value=12 Score=37.31 Aligned_cols=32 Identities=38% Similarity=0.788 Sum_probs=24.2
Q ss_pred CCCCCCCCCCceeEeCCCC------ceEeCCCcceeccc
Q 030755 4 AFCSDCKKHTEVVFDHSAG------DTVCSECGLVLESH 36 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G------~~vC~~CG~V~~e~ 36 (172)
..||+|+- .+++.|.+-| +-.|..||.-+.-.
T Consensus 909 y~C~~C~~-~ef~~~~~~~sG~Dlpdk~Cp~Cg~~~~kd 946 (1437)
T PRK00448 909 YVCPNCKY-SEFFTDGSVGSGFDLPDKDCPKCGTKLKKD 946 (1437)
T ss_pred ccCccccc-ccccccccccccccCccccCcccccccccc
Confidence 47999997 6888776544 35699999988433
No 317
>PHA01623 hypothetical protein
Probab=43.49 E-value=71 Score=19.32 Aligned_cols=30 Identities=10% Similarity=0.002 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHhcCCc-HHHHHHHHHHHHH
Q 030755 106 ILAFKTIATMSDRLGLV-ATIKDRANEIYKK 135 (172)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp-~~v~~~A~~i~~~ 135 (172)
.+..+.|..+|...|++ ..++..|++.|-.
T Consensus 22 eel~~~Ld~y~~~~g~~rSe~IreAI~~yL~ 52 (56)
T PHA01623 22 KDLKTRLKVYCAKNNLQLTQAIEEAIKEYLQ 52 (56)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 34677999999999999 4788888877754
No 318
>PRK04023 DNA polymerase II large subunit; Validated
Probab=43.25 E-value=16 Score=35.07 Aligned_cols=12 Identities=33% Similarity=0.830 Sum_probs=6.6
Q ss_pred ceEeCCCcceec
Q 030755 23 DTVCSECGLVLE 34 (172)
Q Consensus 23 ~~vC~~CG~V~~ 34 (172)
...|..||....
T Consensus 651 i~fCP~CG~~~~ 662 (1121)
T PRK04023 651 VYRCPRCGIEVE 662 (1121)
T ss_pred ceeCccccCcCC
Confidence 445666665543
No 319
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=43.05 E-value=13 Score=27.75 Aligned_cols=12 Identities=42% Similarity=0.891 Sum_probs=10.9
Q ss_pred ceEeCCCcceec
Q 030755 23 DTVCSECGLVLE 34 (172)
Q Consensus 23 ~~vC~~CG~V~~ 34 (172)
-++|.+||.|++
T Consensus 100 H~iC~~CGki~~ 111 (169)
T PRK11639 100 MFICDRCGAVKE 111 (169)
T ss_pred eEEeCCCCCEEE
Confidence 499999999996
No 320
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=42.96 E-value=11 Score=27.23 Aligned_cols=13 Identities=46% Similarity=0.997 Sum_probs=10.4
Q ss_pred EeCCCcceecccc
Q 030755 25 VCSECGLVLESHS 37 (172)
Q Consensus 25 vC~~CG~V~~e~~ 37 (172)
-|+.||.|+++.-
T Consensus 3 ~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 3 QCTKCGRVFEDGS 15 (131)
T ss_pred ccCcCCCCcCCCc
Confidence 4999999997653
No 321
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=42.56 E-value=13 Score=22.88 Aligned_cols=8 Identities=38% Similarity=0.812 Sum_probs=5.2
Q ss_pred eCCCccee
Q 030755 26 CSECGLVL 33 (172)
Q Consensus 26 C~~CG~V~ 33 (172)
|..||-+.
T Consensus 20 Cp~CG~~t 27 (59)
T COG2260 20 CPVCGGDT 27 (59)
T ss_pred CCCCCCcc
Confidence 66677654
No 322
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=42.48 E-value=11 Score=22.89 Aligned_cols=36 Identities=25% Similarity=0.531 Sum_probs=24.2
Q ss_pred CCCCCCCCCC--CceeEeCCCCceEeCC-Ccceecccccc
Q 030755 3 DAFCSDCKKH--TEVVFDHSAGDTVCSE-CGLVLESHSID 39 (172)
Q Consensus 3 ~~~C~~Cg~~--~~i~~D~~~G~~vC~~-CG~V~~e~~i~ 39 (172)
+.+|..|+.+ ....++...| .||.. |-.-++|..+.
T Consensus 1 m~~CvVCKqpi~~a~~v~T~~G-~VH~g~C~~y~~e~~~S 39 (54)
T PF10886_consen 1 MEICVVCKQPIDDALVVETESG-PVHPGVCAQYLEELPVS 39 (54)
T ss_pred CCeeeeeCCccCcceEEEcCCC-ccCcHHHHHHHHhcccc
Confidence 3579999975 3456666666 66664 77777766544
No 323
>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=42.40 E-value=14 Score=28.59 Aligned_cols=38 Identities=24% Similarity=0.413 Sum_probs=23.7
Q ss_pred CCCCCCCCCCCceeEeC------CCCceEeCCCcceecccccccC
Q 030755 3 DAFCSDCKKHTEVVFDH------SAGDTVCSECGLVLESHSIDET 41 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~------~~G~~vC~~CG~V~~e~~i~~~ 41 (172)
...|+.|+.. -...+. ..-...|..||-++..+++-.|
T Consensus 95 ~~~C~~C~~~-~~~~~~~~~~~~~~~~p~C~~Cgg~lrP~VV~Fg 138 (206)
T cd01410 95 IEVCKSCGPE-YVRDDVVETRGDKETGRRCHACGGILKDTIVDFG 138 (206)
T ss_pred cccCCCCCCc-cchHHHHHHhhcCCCCCcCCCCcCccCCcEEECC
Confidence 3579999963 111111 1123569999999988887655
No 324
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=42.03 E-value=27 Score=29.95 Aligned_cols=34 Identities=15% Similarity=0.259 Sum_probs=26.3
Q ss_pred CCCCCCCC-CceeEeCCCCceEeCCCcceeccccccc
Q 030755 5 FCSDCKKH-TEVVFDHSAGDTVCSECGLVLESHSIDE 40 (172)
Q Consensus 5 ~C~~Cg~~-~~i~~D~~~G~~vC~~CG~V~~e~~i~~ 40 (172)
.||.|+.. +++..++..|...|-.||. .-++|+.
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 59999864 4788889999999999996 3455553
No 325
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=41.77 E-value=99 Score=20.23 Aligned_cols=16 Identities=25% Similarity=0.272 Sum_probs=11.6
Q ss_pred HHHHHHHHHHhcCCcH
Q 030755 108 AFKTIATMSDRLGLVA 123 (172)
Q Consensus 108 ~~~~I~~~~~~L~Lp~ 123 (172)
.......+++.|||+.
T Consensus 13 lK~~a~~i~~~lGl~~ 28 (83)
T TIGR02384 13 LKKEAYAVFEELGLTP 28 (83)
T ss_pred HHHHHHHHHHHhCCCH
Confidence 4456677788888885
No 326
>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=41.00 E-value=16 Score=27.13 Aligned_cols=7 Identities=29% Similarity=1.094 Sum_probs=3.3
Q ss_pred CCCCCCC
Q 030755 5 FCSDCKK 11 (172)
Q Consensus 5 ~C~~Cg~ 11 (172)
.||+|+.
T Consensus 41 ~Cp~C~~ 47 (158)
T PF10083_consen 41 SCPNCST 47 (158)
T ss_pred HCcCCCC
Confidence 3555543
No 327
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.93 E-value=14 Score=23.24 Aligned_cols=29 Identities=31% Similarity=0.533 Sum_probs=15.9
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeC-CCcce
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCS-ECGLV 32 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~-~CG~V 32 (172)
...||.||.+ ..-.+.+.=.-+|. .|-.|
T Consensus 7 ~v~CP~Cgkp-v~w~~~s~frPFCSkRCklI 36 (65)
T COG3024 7 TVPCPTCGKP-VVWGEESPFRPFCSKRCKLI 36 (65)
T ss_pred cccCCCCCCc-ccccccCCcCcchhHhhhhc
Confidence 3689999984 22222333445555 47543
No 328
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=40.84 E-value=29 Score=24.07 Aligned_cols=20 Identities=35% Similarity=0.670 Sum_probs=13.6
Q ss_pred eCCCCceEeCCCcceecccc
Q 030755 18 DHSAGDTVCSECGLVLESHS 37 (172)
Q Consensus 18 D~~~G~~vC~~CG~V~~e~~ 37 (172)
+.+-|...|..||.-++.-.
T Consensus 44 ~ie~G~t~CP~Cg~~~e~~f 63 (115)
T COG1885 44 EIEVGSTSCPKCGEPFESAF 63 (115)
T ss_pred EEecccccCCCCCCccceeE
Confidence 44678888888887775333
No 329
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=40.71 E-value=15 Score=31.52 Aligned_cols=31 Identities=23% Similarity=0.560 Sum_probs=21.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..||+|+...++-.=...-.-.|..||..+-
T Consensus 19 ~~C~eCd~~~~~P~l~~~q~A~CPRC~~~l~ 49 (418)
T COG2995 19 ILCPECDMLVSLPRLDSGQSAYCPRCGHTLT 49 (418)
T ss_pred ecCCCCCceeccccCCCCCcccCCCCCCccc
Confidence 4699999743333323455678999999884
No 330
>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=40.70 E-value=31 Score=26.83 Aligned_cols=24 Identities=4% Similarity=0.065 Sum_probs=20.2
Q ss_pred HHHHHhcCCcHHHHHHHHHHHHHH
Q 030755 113 ATMSDRLGLVATIKDRANEIYKKV 136 (172)
Q Consensus 113 ~~~~~~L~Lp~~v~~~A~~i~~~a 136 (172)
-.++..+|+|+.++++|.++.+..
T Consensus 198 ~~~a~~~g~p~~vi~~A~~~~~~~ 221 (222)
T cd03285 198 IHVAELANFPKEVIEMAKQKALEL 221 (222)
T ss_pred HHHHHHhCcCHHHHHHHHHHHHhc
Confidence 356778899999999999998764
No 331
>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=40.66 E-value=18 Score=25.81 Aligned_cols=26 Identities=27% Similarity=0.592 Sum_probs=17.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
.+|+.||. --.+.+...|.++| ||.-
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 57999997 33335667778888 4643
No 332
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=40.40 E-value=50 Score=19.17 Aligned_cols=29 Identities=14% Similarity=0.336 Sum_probs=20.3
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCC
Q 030755 111 TIATMSDRLGLVATIKDRANEIYKKVEDQKSS 142 (172)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~ 142 (172)
.+.+++..+++|.. ++.++.+...+.|++
T Consensus 20 t~~eia~~~gl~~s---tv~r~L~tL~~~g~v 48 (52)
T PF09339_consen 20 TLSEIARALGLPKS---TVHRLLQTLVEEGYV 48 (52)
T ss_dssp EHHHHHHHHTS-HH---HHHHHHHHHHHTTSE
T ss_pred CHHHHHHHHCcCHH---HHHHHHHHHHHCcCe
Confidence 36678899999986 455577777777765
No 333
>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=40.18 E-value=28 Score=20.23 Aligned_cols=34 Identities=26% Similarity=0.662 Sum_probs=22.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceeccccccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDE 40 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~~ 40 (172)
..|-.|+.. +.-...-.+.|..|++++=..-++.
T Consensus 12 ~~C~~C~~~---i~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 12 TYCDVCGKF---IWGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp EB-TTSSSB---ECSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCCcccCcc---cCCCCCCeEEECCCCChHhhhhhhh
Confidence 579999972 3334556789999999997665443
No 334
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=40.10 E-value=15 Score=33.87 Aligned_cols=26 Identities=27% Similarity=0.606 Sum_probs=15.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
..|+.||-...+..+ ..| ..|..||-
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 479999963332121 223 67999984
No 335
>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=39.67 E-value=15 Score=36.01 Aligned_cols=32 Identities=38% Similarity=0.839 Sum_probs=23.4
Q ss_pred CCCCCCCCCCceeEeCCCC------ceEeCCCcceeccc
Q 030755 4 AFCSDCKKHTEVVFDHSAG------DTVCSECGLVLESH 36 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G------~~vC~~CG~V~~e~ 36 (172)
..||+|+- .+++.|.+-| +-.|..||.-+.-.
T Consensus 684 y~c~~c~~-~ef~~~~~~~sg~dlp~k~cp~c~~~~~~d 721 (1213)
T TIGR01405 684 YLCPNCKY-SEFITDGSVGSGFDLPDKDCPKCGAPLKKD 721 (1213)
T ss_pred ccCccccc-ccccccccccccccCccccCcccccccccc
Confidence 47999997 6777775433 45799999988433
No 336
>COG3654 Doc Prophage maintenance system killer protein [General function prediction only]
Probab=39.47 E-value=1.5e+02 Score=21.50 Aligned_cols=39 Identities=21% Similarity=0.280 Sum_probs=29.4
Q ss_pred CCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHH
Q 030755 120 GLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIA 158 (172)
Q Consensus 120 ~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYia 158 (172)
++|+-+.-.|.-++..+.++-|..|-++.+++|+.+|+.
T Consensus 49 ~~~dvfelAA~~~~~l~knH~F~dgNKRtal~a~~~FL~ 87 (132)
T COG3654 49 GYPDVFELAAAYFVALIKNHAFADGNKRTALAAALLFLL 87 (132)
T ss_pred CCCcHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHHH
Confidence 466555555556666677788889999899999999875
No 337
>PRK00977 exodeoxyribonuclease VII small subunit; Provisional
Probab=39.36 E-value=47 Score=21.73 Aligned_cols=38 Identities=8% Similarity=0.017 Sum_probs=30.2
Q ss_pred chhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhh
Q 030755 101 PDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVED 138 (172)
Q Consensus 101 ~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~ 138 (172)
.+.+...++..+..|.++|.=++--.+.+..+|+++..
T Consensus 8 ~~~sfEea~~~LEeIv~~LE~~~l~Lees~~lyeeg~~ 45 (80)
T PRK00977 8 KPLSFEEALAELEEIVTRLESGDLPLEESLAAFERGVA 45 (80)
T ss_pred CcCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence 34567889999999999998777777888888887654
No 338
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=39.36 E-value=6.1 Score=30.00 Aligned_cols=31 Identities=29% Similarity=0.632 Sum_probs=21.4
Q ss_pred CCCCCCCCCCceeEeCC-CCceEeCCCcceeccc
Q 030755 4 AFCSDCKKHTEVVFDHS-AGDTVCSECGLVLESH 36 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~-~G~~vC~~CG~V~~e~ 36 (172)
..||.|... .-+|.+ +-...|..||.++++.
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 479888853 445542 3448899999999643
No 339
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=39.32 E-value=12 Score=29.76 Aligned_cols=38 Identities=21% Similarity=0.285 Sum_probs=23.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCc--ceecccccccC
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECG--LVLESHSIDET 41 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG--~V~~e~~i~~~ 41 (172)
..|..|+..-....+...+...|..|| -++..+++-.|
T Consensus 118 ~~C~~C~~~~~~~~~~~~~~p~C~~Cg~~g~lrP~vV~FG 157 (242)
T PTZ00408 118 VRCTATGHVFDWTEDVVHGSSRCKCCGCVGTLRPHIVWFG 157 (242)
T ss_pred EEECCCCcccCchhhhhcCCCccccCCCCCCCCCCEEEcC
Confidence 579999963111112223446799998 57877776654
No 340
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.00 E-value=14 Score=26.33 Aligned_cols=18 Identities=22% Similarity=0.663 Sum_probs=9.8
Q ss_pred ceeEeCCCCceEeCCCcce
Q 030755 14 EVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 14 ~i~~D~~~G~~vC~~CG~V 32 (172)
.+......+...| +||..
T Consensus 61 ~L~I~~vp~~~~C-~Cg~~ 78 (124)
T PRK00762 61 DLIVEMIPVEIEC-ECGYE 78 (124)
T ss_pred EEEEEecCeeEEe-eCcCc
Confidence 3444555566666 66633
No 341
>PHA02325 hypothetical protein
Probab=38.97 E-value=17 Score=22.86 Aligned_cols=11 Identities=27% Similarity=0.827 Sum_probs=8.3
Q ss_pred CCCCCCCCCCC
Q 030755 1 MTDAFCSDCKK 11 (172)
Q Consensus 1 ~~~~~C~~Cg~ 11 (172)
|....||.|++
T Consensus 1 m~~k~CPkC~A 11 (72)
T PHA02325 1 MDTKICPKCGA 11 (72)
T ss_pred CCccccCccCC
Confidence 56677888886
No 342
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=38.89 E-value=17 Score=25.70 Aligned_cols=20 Identities=20% Similarity=0.611 Sum_probs=12.7
Q ss_pred eeEeCCCCceEeCCCcceec
Q 030755 15 VVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 15 i~~D~~~G~~vC~~CG~V~~ 34 (172)
+......+..-|.+|+.++.
T Consensus 62 l~Ie~~p~~~~C~~C~~~~~ 81 (115)
T COG0375 62 LHIEEEPAECWCLDCGQEVE 81 (115)
T ss_pred EEEEEeccEEEeccCCCeec
Confidence 44555667777777766654
No 343
>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=38.69 E-value=17 Score=26.76 Aligned_cols=41 Identities=12% Similarity=0.140 Sum_probs=25.3
Q ss_pred hHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCC
Q 030755 104 GLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRN 146 (172)
Q Consensus 104 ~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~ 146 (172)
.+.++.++|..=++ .+.+...++|.+|..--.+..-++|.-
T Consensus 82 ~l~~~~~~v~~n~e--~VG~~FAeEAR~iHyGea~~R~I~G~a 122 (148)
T PF06676_consen 82 ALRKLRRHVEKNSE--DVGDRFAEEARKIHYGEAEERGIYGEA 122 (148)
T ss_pred HHHHHHHHHHHhCc--chhHHHHHHHHHHHcCCCccccCcCcC
Confidence 33444444444444 455788899988876655656667763
No 344
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=38.20 E-value=13 Score=25.63 Aligned_cols=11 Identities=36% Similarity=1.084 Sum_probs=9.4
Q ss_pred EeCCCcceecc
Q 030755 25 VCSECGLVLES 35 (172)
Q Consensus 25 vC~~CG~V~~e 35 (172)
.|+.||.|.++
T Consensus 4 ~CtrCG~vf~~ 14 (112)
T COG3364 4 QCTRCGEVFDD 14 (112)
T ss_pred eeccccccccc
Confidence 59999999975
No 345
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=37.94 E-value=29 Score=27.31 Aligned_cols=24 Identities=21% Similarity=0.328 Sum_probs=18.6
Q ss_pred CCCCCCCCCceeEeCCCCceEeCC
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSE 28 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~ 28 (172)
.||-|+..-.+-+|+.+|++|=..
T Consensus 81 ~C~~C~n~i~~RTDPkN~~YV~Es 104 (272)
T COG5134 81 KCHLCSNPIDVRTDPKNTEYVVES 104 (272)
T ss_pred EccCCCCceeeecCCCCceEEEec
Confidence 588888755777888888887655
No 346
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=37.93 E-value=28 Score=29.01 Aligned_cols=31 Identities=23% Similarity=0.538 Sum_probs=24.1
Q ss_pred CCCCCCCCCCCceeEe-CCCCceEeCCCcceec
Q 030755 3 DAFCSDCKKHTEVVFD-HSAGDTVCSECGLVLE 34 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D-~~~G~~vC~~CG~V~~ 34 (172)
..+|=.||++ ++.+= ..-|..+|.+|--|..
T Consensus 20 Nk~CaDCga~-~P~W~S~nlGvfiCi~CagvHR 51 (319)
T COG5347 20 NKKCADCGAP-NPTWASVNLGVFLCIDCAGVHR 51 (319)
T ss_pred cCccccCCCC-CCceEecccCeEEEeecchhhh
Confidence 4689999984 55554 3579999999998874
No 347
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=37.90 E-value=15 Score=29.42 Aligned_cols=38 Identities=26% Similarity=0.383 Sum_probs=23.6
Q ss_pred CCCCCCCCCCc---eeEeCCCC-ceEeCCCcc-eecccccccC
Q 030755 4 AFCSDCKKHTE---VVFDHSAG-DTVCSECGL-VLESHSIDET 41 (172)
Q Consensus 4 ~~C~~Cg~~~~---i~~D~~~G-~~vC~~CG~-V~~e~~i~~~ 41 (172)
..|..|+.... .......+ ...|..||. +|..+++-.|
T Consensus 123 ~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~~lrP~VV~fG 165 (250)
T COG0846 123 VRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGPVLRPDVVWFG 165 (250)
T ss_pred eEeCCCcCccchhhhhhhcccCCCCcCccCCCccccCCEEEeC
Confidence 57999996311 01111222 467999999 9987775544
No 348
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=37.65 E-value=30 Score=24.81 Aligned_cols=31 Identities=26% Similarity=0.528 Sum_probs=20.0
Q ss_pred CCCCCCCCCCCceeEeC----CCCceEeCCCcceec
Q 030755 3 DAFCSDCKKHTEVVFDH----SAGDTVCSECGLVLE 34 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~----~~G~~vC~~CG~V~~ 34 (172)
+..||.|++ .+++.-. ..--..|.+||.-..
T Consensus 30 ~~~cP~C~s-~~~~k~g~~~~~~qRyrC~~C~~tf~ 64 (129)
T COG3677 30 KVNCPRCKS-SNVVKIGGIRRGHQRYKCKSCGSTFT 64 (129)
T ss_pred cCcCCCCCc-cceeeECCccccccccccCCcCccee
Confidence 368999998 4533221 133578999997663
No 349
>PHA00689 hypothetical protein
Probab=37.65 E-value=24 Score=21.00 Aligned_cols=27 Identities=22% Similarity=0.471 Sum_probs=15.6
Q ss_pred CCCceEeCCCcceecccccccCcccccc
Q 030755 20 SAGDTVCSECGLVLESHSIDETSEWRTF 47 (172)
Q Consensus 20 ~~G~~vC~~CG~V~~e~~i~~~~ewr~f 47 (172)
+--.+.|..||.-= =..-|.|-||.-.
T Consensus 14 epravtckrcgktg-lrweddggewvlm 40 (62)
T PHA00689 14 EPRAVTCKRCGKTG-LRWEDDGGEWVLM 40 (62)
T ss_pred CcceeehhhccccC-ceeecCCCcEEEE
Confidence 34456777777652 2444666677554
No 350
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=37.43 E-value=21 Score=30.96 Aligned_cols=32 Identities=22% Similarity=0.570 Sum_probs=24.4
Q ss_pred CCCCCCCCCCCCceeEeC-CCCceEeCCCcceec
Q 030755 2 TDAFCSDCKKHTEVVFDH-SAGDTVCSECGLVLE 34 (172)
Q Consensus 2 ~~~~C~~Cg~~~~i~~D~-~~G~~vC~~CG~V~~ 34 (172)
....|=.||.+ +..+-. .=|..+|.+|-.|-.
T Consensus 22 ~NKvCFDCgAk-nPtWaSVTYGIFLCiDCSAvHR 54 (454)
T KOG0706|consen 22 ENKVCFDCGAK-NPTWASVTYGIFLCIDCSAVHR 54 (454)
T ss_pred CCceecccCCC-CCCceeecceEEEEEecchhhh
Confidence 45689999984 454433 469999999999975
No 351
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=37.11 E-value=16 Score=22.83 Aligned_cols=23 Identities=26% Similarity=0.832 Sum_probs=14.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
..|.-||.. .. ---...|..||.
T Consensus 18 t~CrRCG~~-sy----h~qK~~CasCGy 40 (62)
T PRK04179 18 IRCRRCGRH-SY----NVRKKYCAACGF 40 (62)
T ss_pred chhcccCcc-cc----cccccchhhcCC
Confidence 457788863 22 123567888886
No 352
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=36.98 E-value=42 Score=21.63 Aligned_cols=29 Identities=17% Similarity=0.358 Sum_probs=20.4
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCC
Q 030755 111 TIATMSDRLGLVATIKDRANEIYKKVEDQKSS 142 (172)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~ 142 (172)
.++.+++.+++|+..++. +++.+.+.|++
T Consensus 27 s~~eiA~~~~i~~~~l~k---il~~L~~~Gli 55 (83)
T PF02082_consen 27 SSKEIAERLGISPSYLRK---ILQKLKKAGLI 55 (83)
T ss_dssp EHHHHHHHHTS-HHHHHH---HHHHHHHTTSE
T ss_pred CHHHHHHHHCcCHHHHHH---HHHHHhhCCee
Confidence 467789999999988877 55555555664
No 353
>PRK09582 chaB cation transport regulator; Reviewed
Probab=36.91 E-value=39 Score=22.02 Aligned_cols=22 Identities=27% Similarity=0.443 Sum_probs=15.4
Q ss_pred cCCcHHHHH----HHHHHHHHHhhCc
Q 030755 119 LGLVATIKD----RANEIYKKVEDQK 140 (172)
Q Consensus 119 L~Lp~~v~~----~A~~i~~~a~~~~ 140 (172)
-.||..|.+ .|.+||+++++.-
T Consensus 7 ~dLP~sv~~~LP~hAQ~iy~~afNsA 32 (76)
T PRK09582 7 SDLPESVKHVLPAHAQDIYKEAFNSA 32 (76)
T ss_pred hhCcHHHHHhCcHHHHHHHHHHHHHH
Confidence 356766653 7888888887753
No 354
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=36.67 E-value=14 Score=28.33 Aligned_cols=26 Identities=19% Similarity=0.682 Sum_probs=18.4
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCC
Q 030755 2 TDAFCSDCKKHTEVVFDHSAGDTVCSEC 29 (172)
Q Consensus 2 ~~~~C~~Cg~~~~i~~D~~~G~~vC~~C 29 (172)
....|.+||....+.+|=- ..+|..|
T Consensus 59 ~~~~C~nCg~~GH~~~DCP--~~iC~~C 84 (190)
T COG5082 59 ENPVCFNCGQNGHLRRDCP--HSICYNC 84 (190)
T ss_pred cccccchhcccCcccccCC--hhHhhhc
Confidence 3467999998777888854 3666666
No 355
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=36.55 E-value=23 Score=20.05 Aligned_cols=8 Identities=25% Similarity=0.829 Sum_probs=5.4
Q ss_pred CCCCCCCC
Q 030755 4 AFCSDCKK 11 (172)
Q Consensus 4 ~~C~~Cg~ 11 (172)
..||+||+
T Consensus 3 ~~Cp~Cg~ 10 (47)
T PF14690_consen 3 PRCPHCGS 10 (47)
T ss_pred ccCCCcCC
Confidence 35777776
No 356
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=36.40 E-value=21 Score=21.20 Aligned_cols=9 Identities=33% Similarity=0.693 Sum_probs=7.1
Q ss_pred CCCCCCCCC
Q 030755 3 DAFCSDCKK 11 (172)
Q Consensus 3 ~~~C~~Cg~ 11 (172)
...||+||.
T Consensus 2 ~f~CP~C~~ 10 (54)
T PF05605_consen 2 SFTCPYCGK 10 (54)
T ss_pred CcCCCCCCC
Confidence 467999996
No 357
>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=36.33 E-value=19 Score=22.00 Aligned_cols=8 Identities=25% Similarity=0.999 Sum_probs=6.6
Q ss_pred CCCCCCCC
Q 030755 4 AFCSDCKK 11 (172)
Q Consensus 4 ~~C~~Cg~ 11 (172)
..||+||.
T Consensus 42 ~~CPNCgG 49 (57)
T PF06906_consen 42 GVCPNCGG 49 (57)
T ss_pred CcCcCCCC
Confidence 57999997
No 358
>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=36.21 E-value=27 Score=21.27 Aligned_cols=23 Identities=22% Similarity=0.862 Sum_probs=13.3
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
.|.-||. .. +. --.-.|..||.=
T Consensus 17 ~CrRCG~-~s--yH--~qK~~CasCGyp 39 (55)
T PF01907_consen 17 LCRRCGR-RS--YH--IQKKTCASCGYP 39 (55)
T ss_dssp E-TTTSS-EE--EE--TTTTEETTTBTT
T ss_pred eecccCC-ee--ee--cCCCcccccCCC
Confidence 4777886 22 22 346678888864
No 359
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.13 E-value=37 Score=20.68 Aligned_cols=28 Identities=14% Similarity=0.394 Sum_probs=17.8
Q ss_pred CCCCCCC-ceeEeCCCCceEeCCCcceec
Q 030755 7 SDCKKHT-EVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 7 ~~Cg~~~-~i~~D~~~G~~vC~~CG~V~~ 34 (172)
-.||.+. .|+.--..=.+-|.+||.++-
T Consensus 17 H~Cg~NrwkIiRvGaDIkikC~nC~h~vm 45 (60)
T COG4481 17 HACGTNRWKIIRVGADIKIKCENCGHSVM 45 (60)
T ss_pred CccccceEEEEEecCcEEEEecCCCcEEE
Confidence 3577532 344433445678999999984
No 360
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=35.86 E-value=12 Score=32.34 Aligned_cols=30 Identities=27% Similarity=0.745 Sum_probs=22.9
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
..+|..||.. ++...-...|.+||.-++..
T Consensus 5 ~~rc~~cg~~----f~~a~~~~~c~~cGl~lp~~ 34 (411)
T COG0498 5 SLRCLKCGRE----FSQALLQGLCPDCGLFLPAE 34 (411)
T ss_pred EeecCCCCcc----hhhHHhhCcCCcCCcccccc
Confidence 4689999962 44445588999999999754
No 361
>PF04221 RelB: RelB antitoxin; InterPro: IPR007337 Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. Several toxin/antitoxin pairs may occur in a single species. RelE and RelB form a toxin-antitoxin system; RelE represses translation, probably through binding ribosomes [, ]. RelB stably binds RelE, presumably deactivating it.; PDB: 2KC8_B 2K29_A.
Probab=35.73 E-value=81 Score=20.45 Aligned_cols=30 Identities=17% Similarity=0.197 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHhcCCcHHHHHHHH-HHHHHHhhC
Q 030755 107 LAFKTIATMSDRLGLVATIKDRAN-EIYKKVEDQ 139 (172)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~~v~~~A~-~i~~~a~~~ 139 (172)
+.......+++.+||+.+ .|+ .+|+.+...
T Consensus 11 ~lK~~a~~il~~~Glt~s---~ai~~fl~qiv~~ 41 (83)
T PF04221_consen 11 ELKEEAEAILEELGLTLS---DAINMFLKQIVRE 41 (83)
T ss_dssp HHHHHHHHHHHHTT--HH---HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCHH---HHHHHHHHHHHHh
Confidence 345566777788888752 222 245555443
No 362
>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=35.72 E-value=17 Score=34.61 Aligned_cols=22 Identities=27% Similarity=0.552 Sum_probs=16.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
.+||.||.. +=...|..||.-.
T Consensus 626 RKCPkCG~y--------Tlk~rCP~CG~~T 647 (1095)
T TIGR00354 626 RKCPQCGKE--------SFWLKCPVCGELT 647 (1095)
T ss_pred EECCCCCcc--------cccccCCCCCCcc
Confidence 589999973 2367899999763
No 363
>PRK14068 exodeoxyribonuclease VII small subunit; Provisional
Probab=35.30 E-value=63 Score=20.95 Aligned_cols=36 Identities=6% Similarity=0.172 Sum_probs=27.8
Q ss_pred hhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhh
Q 030755 103 RGLILAFKTIATMSDRLGLVATIKDRANEIYKKVED 138 (172)
Q Consensus 103 ~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~ 138 (172)
.+...++..+..|...|.=++--.+.+..+|++...
T Consensus 6 ~sfEeal~~Le~IV~~LE~gdl~Leesl~lyeeG~~ 41 (76)
T PRK14068 6 QSFEEMMQELEQIVQKLDNETVSLEESLDLYQRGMK 41 (76)
T ss_pred cCHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 456788899999999987776667778888877654
No 364
>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=35.14 E-value=26 Score=29.02 Aligned_cols=11 Identities=45% Similarity=0.908 Sum_probs=9.9
Q ss_pred CCCCCCCCCCC
Q 030755 1 MTDAFCSDCKK 11 (172)
Q Consensus 1 ~~~~~C~~Cg~ 11 (172)
|....||.|++
T Consensus 1 md~~~CP~Ck~ 11 (309)
T TIGR00570 1 MDDQGCPRCKT 11 (309)
T ss_pred CCCCCCCcCCC
Confidence 78889999997
No 365
>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=35.01 E-value=21 Score=19.70 Aligned_cols=13 Identities=38% Similarity=0.749 Sum_probs=9.4
Q ss_pred CCCCCCCCCCc-eeE
Q 030755 4 AFCSDCKKHTE-VVF 17 (172)
Q Consensus 4 ~~C~~Cg~~~~-i~~ 17 (172)
..||.|++ ++ ++.
T Consensus 6 v~CP~C~s-~~~v~k 19 (36)
T PF03811_consen 6 VHCPRCQS-TEGVKK 19 (36)
T ss_pred eeCCCCCC-CCccee
Confidence 57999998 45 443
No 366
>PHA02540 61 DNA primase; Provisional
Probab=34.97 E-value=39 Score=28.35 Aligned_cols=29 Identities=17% Similarity=0.327 Sum_probs=22.7
Q ss_pred CCCCCCCCC------CceeEeCCCC--ceEeCCCcce
Q 030755 4 AFCSDCKKH------TEVVFDHSAG--DTVCSECGLV 32 (172)
Q Consensus 4 ~~C~~Cg~~------~~i~~D~~~G--~~vC~~CG~V 32 (172)
..||.|+-. +...+.++.| ..-|=+||.=
T Consensus 28 ~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa~ 64 (337)
T PHA02540 28 FRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGYH 64 (337)
T ss_pred ecCCCCCCccccCcCCcEEEeccCCceEEEecCCCCC
Confidence 369999962 2477788888 9999999963
No 367
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=34.93 E-value=21 Score=34.88 Aligned_cols=30 Identities=37% Similarity=0.822 Sum_probs=23.4
Q ss_pred CCCCCCCCCCceeEeCCCCc------eEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGD------TVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~------~vC~~CG~V~~ 34 (172)
..||+|+- .+++.|.+.|. --|..||.=+.
T Consensus 915 Y~Cp~Cky-~Ef~~d~svgsGfDLpdK~CPkCg~pl~ 950 (1444)
T COG2176 915 YLCPECKY-SEFIDDGSVGSGFDLPDKDCPKCGTPLK 950 (1444)
T ss_pred ccCCCCce-eeeecCCCcCCCCCCCCCCCCcCCCccc
Confidence 47999997 68888776553 46999999874
No 368
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=34.92 E-value=35 Score=23.63 Aligned_cols=31 Identities=23% Similarity=0.574 Sum_probs=19.9
Q ss_pred CCCCCCCCC----CceeEeCCCC--ceEeCCCcceec
Q 030755 4 AFCSDCKKH----TEVVFDHSAG--DTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~----~~i~~D~~~G--~~vC~~CG~V~~ 34 (172)
..|+.|.+. .+...-...+ .+.|..||.+..
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 369999972 1222223334 567999999975
No 369
>PF06150 ChaB: ChaB; InterPro: IPR009317 This family of proteins contain a conserved 60 residue region. This protein is known as ChaB in Escherichia coli and is found next to ChaA, which is a cation transporter protein. ChaB may be regulate ChaA function in some way.; PDB: 1SG7_A.
Probab=34.92 E-value=43 Score=20.44 Aligned_cols=15 Identities=20% Similarity=0.372 Sum_probs=9.6
Q ss_pred HHHHHHHHHHhhCcC
Q 030755 127 DRANEIYKKVEDQKS 141 (172)
Q Consensus 127 ~~A~~i~~~a~~~~~ 141 (172)
+.|.+||.++++.-+
T Consensus 11 ~~Aq~if~~afn~a~ 25 (57)
T PF06150_consen 11 EHAQRIFRKAFNSAW 25 (57)
T ss_dssp SHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 567777777766543
No 370
>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=34.88 E-value=16 Score=22.50 Aligned_cols=13 Identities=46% Similarity=0.871 Sum_probs=10.3
Q ss_pred ceEeCCCcceecc
Q 030755 23 DTVCSECGLVLES 35 (172)
Q Consensus 23 ~~vC~~CG~V~~e 35 (172)
.+||..||.=+.|
T Consensus 4 ~lvCSTCGrDlSe 16 (63)
T PF05864_consen 4 QLVCSTCGRDLSE 16 (63)
T ss_pred eeeecccCCcchH
Confidence 5799999987753
No 371
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=34.84 E-value=25 Score=30.36 Aligned_cols=24 Identities=29% Similarity=0.530 Sum_probs=15.1
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.|++|+.. . ..+...|..||.++.
T Consensus 223 ~C~~Cd~l---~---~~~~a~CpRC~~~L~ 246 (419)
T PRK15103 223 SCSCCTAI---L---PADQPVCPRCHTKGY 246 (419)
T ss_pred cCCCCCCC---C---CCCCCCCCCCCCcCc
Confidence 48888862 1 124457888888774
No 372
>PF01397 Terpene_synth: Terpene synthase, N-terminal domain; InterPro: IPR001906 Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C10) synthases, sesquiterpene (C15) synthases and the diterpene (C20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf []. Tpsa includes vetispiridiene synthase Q39979 from SWISSPROT, 5-epi- aristolochene synthase, Q40577 from SWISSPROT and (+)-delta-cadinene synthase P93665 from SWISSPROT . Tpsb includes (-)-limonene synthase, Q40322 from SWISSPROT. Tpsc includes copalyl diphosphate synthase (kaurene synthase A), O04408 from SWISSPROT. Tpsd includes taxadiene synthase, Q41594 from SWISSPROT, pinene synthase, O24475 from SWISSPROT and myrcene synthase, O24474 from SWISSPROT. Tpse includes ent-kaurene synthase B Q39548 from SWISSPROT. Tpsf includes linalool synthase Q9ZPN5 from SWISSPROT. In the fungus Phaeosphaeria sp. (strain L487) the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein [].; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 2ONH_A 2ONG_B 3P5R_A 3P5P_A 3N0F_A 3N0G_B 3PYB_A 3PYA_A 3G4F_A 3G4D_B ....
Probab=34.83 E-value=2e+02 Score=21.80 Aligned_cols=62 Identities=19% Similarity=0.206 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCC-CHHHHHHHHHHHHHHhCCCCCCcc
Q 030755 107 LAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGR-NQDALLAACLYIACRQEDKPRTVK 169 (172)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr-~~~~~aAAclYiacR~~~~~~tl~ 169 (172)
.-+..|..+ .+|||.-...++-..++..++......+. .......|..|-..|++|.+++..
T Consensus 48 ~~L~lID~l-qRLGi~yhFe~EI~~~L~~i~~~~~~~~~~~~dL~~~AL~FRLLRqhGy~VS~D 110 (183)
T PF01397_consen 48 EKLELIDTL-QRLGISYHFEDEIKEILDSIYRSWDEDNEEIDDLYTTALRFRLLRQHGYYVSSD 110 (183)
T ss_dssp HHHHHHHHH-HHTTCGGGGHHHHHHHHHHHHHTTTTTSHTSSCHHHHHHHHHHHHHTT----GG
T ss_pred HHHHHHHHH-HHcCCcHHHHHHHHHHHHHHhhhccccccccCchhHHHHHHHHHHHcCCcccHH
Confidence 334445444 68999988888888888888776544431 126788888899999999998753
No 373
>PRK14063 exodeoxyribonuclease VII small subunit; Provisional
Probab=34.82 E-value=59 Score=21.03 Aligned_cols=36 Identities=11% Similarity=0.077 Sum_probs=28.0
Q ss_pred hhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhh
Q 030755 103 RGLILAFKTIATMSDRLGLVATIKDRANEIYKKVED 138 (172)
Q Consensus 103 ~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~ 138 (172)
.+...++..+..|.++|.=++--.+.+..+|++...
T Consensus 5 ~sfEeal~~LE~Iv~~LE~~~l~Leesl~lyeeG~~ 40 (76)
T PRK14063 5 LSFEEAISQLEHLVSKLEQGDVPLEEAISYFKEGME 40 (76)
T ss_pred cCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence 456778899999999987776667888888877654
No 374
>PF02609 Exonuc_VII_S: Exonuclease VII small subunit; InterPro: IPR003761 Exonuclease VII is composed of two non-identical subunits; one large subunit and 4 small ones []. This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield nucleoside 5'-phosphates.; GO: 0008855 exodeoxyribonuclease VII activity, 0006308 DNA catabolic process, 0009318 exodeoxyribonuclease VII complex; PDB: 1VP7_F.
Probab=34.73 E-value=67 Score=18.98 Aligned_cols=32 Identities=13% Similarity=0.202 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhh
Q 030755 107 LAFKTIATMSDRLGLVATIKDRANEIYKKVED 138 (172)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~ 138 (172)
+++..++.+..+|.=++--.+.+..+|+++..
T Consensus 3 e~~~~Le~Iv~~Le~~~~sLdes~~lyeeg~~ 34 (53)
T PF02609_consen 3 EAMERLEEIVEKLESGELSLDESLKLYEEGME 34 (53)
T ss_dssp HHHHHHHHHHHHHHTT-S-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 46677788888877666667778888877654
No 375
>COG4393 Predicted membrane protein [Function unknown]
Probab=34.69 E-value=23 Score=29.79 Aligned_cols=26 Identities=15% Similarity=0.521 Sum_probs=20.0
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
.|--||- .-. -.+.|+++|..|+.++
T Consensus 336 AC~iCGd-~GY--v~e~dqvICv~C~Vrm 361 (405)
T COG4393 336 ACDICGD-QGY--VMEGDQVICVRCDVRM 361 (405)
T ss_pred HHHhccc-cce--EeECCEEEEEEccEEE
Confidence 5888995 333 3457999999999987
No 376
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=34.67 E-value=16 Score=25.55 Aligned_cols=8 Identities=25% Similarity=0.642 Sum_probs=4.9
Q ss_pred CCCCCCCC
Q 030755 5 FCSDCKKH 12 (172)
Q Consensus 5 ~C~~Cg~~ 12 (172)
.|+.|+..
T Consensus 54 ~C~~C~G~ 61 (111)
T PLN03165 54 VCRFCVGS 61 (111)
T ss_pred CCCCCcCc
Confidence 56666653
No 377
>PRK05667 dnaG DNA primase; Validated
Probab=34.61 E-value=41 Score=30.31 Aligned_cols=27 Identities=15% Similarity=0.320 Sum_probs=23.3
Q ss_pred CCCCCCCC-CceeEeCCCCceEeCCCcc
Q 030755 5 FCSDCKKH-TEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 5 ~C~~Cg~~-~~i~~D~~~G~~vC~~CG~ 31 (172)
.||.|+.. +++.+++..|...|-.||.
T Consensus 38 ~CPfH~ektpSf~V~~~k~~~~CF~Cg~ 65 (580)
T PRK05667 38 LCPFHDEKTPSFTVSPDKQFYHCFGCGA 65 (580)
T ss_pred cCCCCCCCCCceEEECCCCeEEECCCCC
Confidence 59999964 4788889999999999996
No 378
>PF05819 NolX: NolX protein; InterPro: IPR008718 This family consists of Rhizobium NolX and Xanthomonas HrpF proteins. The interaction between the plant pathogen Xanthomonas campestris pv. vesicatoria (strain 85-10) and its host plants is controlled by hrp genes (hypersensitive reaction and pathogenicity), which encode a type III protein secretion system. Among type III-secreted proteins are avirulence proteins, effectors involved in the induction of plant defence reactions. HrpF is dispensable for protein secretion but required for AvrBs3 recognition in planta, is thought to function as a translocator of effector proteins into the host cell []. NolX, a Glycine max (Soybean) cultivar specificity protein, is secreted by a type III secretion system (TTSS) and shows homology to HrpF. It is not known whether NolX functions at the bacterium-plant interface or acts inside the host cell. NolX is expressed in planta only during the early stages of nodule development [].; GO: 0009877 nodulation
Probab=34.59 E-value=70 Score=28.44 Aligned_cols=54 Identities=22% Similarity=0.222 Sum_probs=42.3
Q ss_pred chhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHH
Q 030755 101 PDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIAC 159 (172)
Q Consensus 101 ~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiac 159 (172)
+.-+..+|++++-++.+. ||..+-. +-|+++++..--.||-|..|+||+=|+.-
T Consensus 362 svMT~nDA~RELYrYSdy--LPK~L~~---~~f~~IVdG~s~tgKcPPQViAAAqyF~~ 415 (624)
T PF05819_consen 362 SVMTENDAMRELYRYSDY--LPKNLSL---EDFKQIVDGDSKTGKCPPQVIAAAQYFVD 415 (624)
T ss_pred cccchhHHHHHHHHhhhc--cccccCH---HHHHhHhcCccccCCCCHHHHHHHHHHHh
Confidence 345668899999999885 4765544 36888888887889999999999999874
No 379
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=34.50 E-value=34 Score=19.38 Aligned_cols=20 Identities=30% Similarity=0.652 Sum_probs=12.5
Q ss_pred ceeEeCC--CCceEeCCCccee
Q 030755 14 EVVFDHS--AGDTVCSECGLVL 33 (172)
Q Consensus 14 ~i~~D~~--~G~~vC~~CG~V~ 33 (172)
.+..+.. .+..+|.-||+..
T Consensus 18 rVyl~l~~~~~~~~CpYCg~~y 39 (40)
T PF10276_consen 18 RVYLNLDDEPGPVVCPYCGTRY 39 (40)
T ss_dssp CEEEE-TTTTCEEEETTTTEEE
T ss_pred eEEEecCCCCCeEECCCCCCEE
Confidence 3444433 3569999999753
No 380
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=34.42 E-value=15 Score=22.54 Aligned_cols=13 Identities=46% Similarity=0.871 Sum_probs=10.3
Q ss_pred ceEeCCCcceecc
Q 030755 23 DTVCSECGLVLES 35 (172)
Q Consensus 23 ~~vC~~CG~V~~e 35 (172)
.+||..||.=+.|
T Consensus 4 ~lVCsTCGrDlSe 16 (63)
T PHA03082 4 QLVCSTCGRDLSE 16 (63)
T ss_pred eeeecccCcchhH
Confidence 5799999987753
No 381
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=34.36 E-value=20 Score=32.73 Aligned_cols=24 Identities=33% Similarity=0.830 Sum_probs=14.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..||+|+.. | ..|+ .|..||..++
T Consensus 140 g~cp~C~~~-----d-~~g~-~ce~cg~~~~ 163 (673)
T PRK00133 140 GTCPKCGAE-----D-QYGD-NCEVCGATYS 163 (673)
T ss_pred cccCCCCCc-----c-cCCc-hhhhccccCC
Confidence 358888873 2 2344 3777776554
No 382
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=34.28 E-value=31 Score=31.20 Aligned_cols=29 Identities=21% Similarity=0.456 Sum_probs=17.1
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
+..||.|++...++. ..+--.+|..-|.+
T Consensus 2 ~~~C~~C~g~G~i~v-~~e~c~vc~gtG~~ 30 (715)
T COG1107 2 IKKCPECGGKGKIVV-GEEECPVCHGTGFS 30 (715)
T ss_pred CccccccCCCceEee-eeeecccccccccc
Confidence 468999998544443 22334455555666
No 383
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=33.87 E-value=20 Score=30.23 Aligned_cols=25 Identities=24% Similarity=0.635 Sum_probs=18.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
.+||+|..+ + ...-...|.+||.--
T Consensus 58 ~kC~~c~~~-~----~y~~~~~C~~cg~~~ 82 (415)
T COG5257 58 YKCPECYRP-E----CYTTEPKCPNCGAET 82 (415)
T ss_pred EeCCCCCCC-c----ccccCCCCCCCCCCc
Confidence 579999973 2 234477899999755
No 384
>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=33.83 E-value=29 Score=31.43 Aligned_cols=28 Identities=29% Similarity=0.718 Sum_probs=21.2
Q ss_pred CCCCC--CCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSD--CKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~--Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..||. |... +.+...|.+.|..|+....
T Consensus 475 ~ACp~~~CnKK---V~~~~~g~~~CekC~~~~~ 504 (608)
T TIGR00617 475 RACPSEDCNKK---VVDQGDGTYRCEKCNKNFA 504 (608)
T ss_pred ccCChhhCCCc---cccCCCCCEECCCCCCCCC
Confidence 36987 9873 3455679999999998764
No 385
>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=33.70 E-value=37 Score=18.06 Aligned_cols=25 Identities=16% Similarity=0.578 Sum_probs=12.2
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCC
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSEC 29 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~C 29 (172)
.|+.++...-.++=...+..+|..|
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C 26 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDC 26 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhc
Confidence 5777875222222234445555555
No 386
>PRK14066 exodeoxyribonuclease VII small subunit; Provisional
Probab=33.44 E-value=64 Score=20.84 Aligned_cols=35 Identities=11% Similarity=0.070 Sum_probs=26.1
Q ss_pred hHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhh
Q 030755 104 GLILAFKTIATMSDRLGLVATIKDRANEIYKKVED 138 (172)
Q Consensus 104 ~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~ 138 (172)
+...++..+..|..+|.=++--.+.++.+|.+...
T Consensus 5 ~fEeal~~LE~IV~~LE~g~l~Leesl~lyeeG~~ 39 (75)
T PRK14066 5 KFETALKKLEEVVKKLEGGELSLDDSLKAFEEGVK 39 (75)
T ss_pred cHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence 46778888899988887666666777777777654
No 387
>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=33.31 E-value=21 Score=27.16 Aligned_cols=34 Identities=24% Similarity=0.498 Sum_probs=16.1
Q ss_pred CCCCCCCCCCceeEeC---------CCCceEeCCCcceecccccc
Q 030755 4 AFCSDCKKHTEVVFDH---------SAGDTVCSECGLVLESHSID 39 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~---------~~G~~vC~~CG~V~~e~~i~ 39 (172)
..||.|+.. ..++. ....+.|..|+..+....|.
T Consensus 19 ~~C~~C~~~--~~f~g~~~~~~~~~~~~~~~C~~C~~~~~~~~l~ 61 (188)
T PF08996_consen 19 LTCPSCGTE--FEFPGVFEEDGDDVSPSGLQCPNCSTPLSPASLV 61 (188)
T ss_dssp EE-TTT--E--EEE-SSS--SSEEEETTEEEETTT--B--HHHHH
T ss_pred eECCCCCCC--ccccccccCCccccccCcCcCCCCCCcCCHHHHH
Confidence 369999973 22322 24578999999977554443
No 388
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=33.17 E-value=23 Score=32.16 Aligned_cols=21 Identities=29% Similarity=0.736 Sum_probs=13.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
..|+.||.... + ...|..||.
T Consensus 560 ~~C~~CGy~g~-~------~~~CP~CG~ 580 (618)
T PRK14704 560 DRCKCCSYHGV-I------GNECPSCGN 580 (618)
T ss_pred eecCCCCCCCC-c------CccCcCCCC
Confidence 47999986211 1 268999986
No 389
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=33.14 E-value=19 Score=22.50 Aligned_cols=12 Identities=33% Similarity=0.805 Sum_probs=10.4
Q ss_pred eEeCCCcceecc
Q 030755 24 TVCSECGLVLES 35 (172)
Q Consensus 24 ~vC~~CG~V~~e 35 (172)
+.|-.||.|+.+
T Consensus 5 vRCFTCGkvi~~ 16 (62)
T PRK04016 5 VRCFTCGKVIAE 16 (62)
T ss_pred eEecCCCCChHH
Confidence 679999999974
No 390
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=32.68 E-value=59 Score=21.16 Aligned_cols=31 Identities=13% Similarity=0.243 Sum_probs=24.0
Q ss_pred HHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCC
Q 030755 112 IATMSDRLGLVATIKDRANEIYKKVEDQKSSRGR 145 (172)
Q Consensus 112 I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr 145 (172)
+..++..|++|. +.+..+.-.+...+.++|+
T Consensus 63 ~~~ia~~l~~~~---~~vE~~l~~~I~~~~i~~~ 93 (105)
T PF01399_consen 63 ISEIAKALQLSE---EEVESILIDLISNGLIKAK 93 (105)
T ss_dssp HHHHHHHHTCCH---HHHHHHHHHHHHTTSSEEE
T ss_pred hHHHHHHhccch---HHHHHHHHHHHHCCCEEEE
Confidence 577899999998 6666677788777777764
No 391
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=32.68 E-value=80 Score=17.75 Aligned_cols=29 Identities=24% Similarity=0.433 Sum_probs=18.7
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCC
Q 030755 111 TIATMSDRLGLVATIKDRANEIYKKVEDQKSS 142 (172)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~ 142 (172)
...+++..++++...+.. ++++..+.|++
T Consensus 19 t~~ela~~~~is~~tv~~---~l~~L~~~g~I 47 (48)
T PF13412_consen 19 TQKELAEKLGISRSTVNR---YLKKLEEKGLI 47 (48)
T ss_dssp -HHHHHHHHTS-HHHHHH---HHHHHHHTTSE
T ss_pred CHHHHHHHhCCCHHHHHH---HHHHHHHCcCc
Confidence 466788999999755444 66666666654
No 392
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=32.53 E-value=18 Score=29.09 Aligned_cols=23 Identities=30% Similarity=0.725 Sum_probs=14.1
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
..+|.+||+. | ..=+.-|.+||.
T Consensus 82 l~~C~~CGa~---V---~~~e~~Cp~C~S 104 (314)
T PF09567_consen 82 LGKCNNCGAN---V---SRLEESCPNCGS 104 (314)
T ss_pred hhhhccccce---e---eehhhcCCCCCc
Confidence 3568888863 1 123566888875
No 393
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=32.46 E-value=33 Score=26.57 Aligned_cols=36 Identities=19% Similarity=0.257 Sum_probs=23.6
Q ss_pred CCCCCCCCCCceeEe---CCCCceEeCCCcceecccccccC
Q 030755 4 AFCSDCKKHTEVVFD---HSAGDTVCSECGLVLESHSIDET 41 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D---~~~G~~vC~~CG~V~~e~~i~~~ 41 (172)
..|..|+.. ...+ .......|..||-++..+++-.+
T Consensus 110 ~~C~~C~~~--~~~~~~~~~~~~p~C~~Cgg~lrp~Vv~fg 148 (224)
T cd01412 110 VRCSSCGYV--GENNEEIPEEELPRCPKCGGLLRPGVVWFG 148 (224)
T ss_pred cccCCCCCC--CCcchhhhccCCCCCCCCCCccCCceEECC
Confidence 579999863 1111 12345789999999987776444
No 394
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=32.31 E-value=16 Score=30.82 Aligned_cols=11 Identities=18% Similarity=0.782 Sum_probs=8.6
Q ss_pred CCCCCCCCCCC
Q 030755 2 TDAFCSDCKKH 12 (172)
Q Consensus 2 ~~~~C~~Cg~~ 12 (172)
.+..|+.||.+
T Consensus 5 ~~~~C~~CGr~ 15 (355)
T COG1499 5 STILCVRCGRS 15 (355)
T ss_pred cccEeccCCCc
Confidence 45689999974
No 395
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=32.31 E-value=22 Score=26.50 Aligned_cols=37 Identities=24% Similarity=0.372 Sum_probs=20.6
Q ss_pred CCCCCCCCCCceeEe-----CCCCceEeCCCcceecccccccC
Q 030755 4 AFCSDCKKHTEVVFD-----HSAGDTVCSECGLVLESHSIDET 41 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D-----~~~G~~vC~~CG~V~~e~~i~~~ 41 (172)
..|..|+.. ....+ .......|..||-++..+++..|
T Consensus 106 ~~C~~C~~~-~~~~~~~~~~~~~~~~~C~~C~~~lrp~vv~fg 147 (178)
T PF02146_consen 106 LRCSKCGKE-YDREDIVDSIDEEEPPRCPKCGGLLRPDVVLFG 147 (178)
T ss_dssp EEETTTSBE-EEGHHHHHHHHTTSSCBCTTTSCBEEEEE--BT
T ss_pred eeecCCCcc-ccchhhcccccccccccccccCccCCCCeeecC
Confidence 368888862 11100 12334578888888887776543
No 396
>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=32.23 E-value=31 Score=19.00 Aligned_cols=24 Identities=17% Similarity=0.468 Sum_probs=14.8
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 2 ~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
+...|+.|+. .. -.++|.+|+..|
T Consensus 2 ~~~~C~~H~~-~~-------~~~~C~~C~~~~ 25 (42)
T PF00643_consen 2 QEPKCPEHPE-EP-------LSLFCEDCNEPL 25 (42)
T ss_dssp SSSB-SSTTT-SB-------EEEEETTTTEEE
T ss_pred cCccCccCCc-cc-------eEEEecCCCCcc
Confidence 4567999986 32 246677777665
No 397
>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=32.16 E-value=26 Score=27.12 Aligned_cols=38 Identities=21% Similarity=0.343 Sum_probs=23.3
Q ss_pred CCCCCCCCCCceeE---e-CCCCceEeCCCcceecccccccC
Q 030755 4 AFCSDCKKHTEVVF---D-HSAGDTVCSECGLVLESHSIDET 41 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~---D-~~~G~~vC~~CG~V~~e~~i~~~ 41 (172)
..|..|+....... . .......|..||-++..+++-.|
T Consensus 110 ~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~lrP~Vv~fg 151 (218)
T cd01407 110 VRCTKCGKEYPRDELQADIDREEVPRCPKCGGLLRPDVVFFG 151 (218)
T ss_pred ceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCccCCCeEECC
Confidence 57999986311100 0 12235679999999988876544
No 398
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=32.07 E-value=27 Score=21.57 Aligned_cols=24 Identities=21% Similarity=0.636 Sum_probs=14.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
..|--||.. ..- .-.-+|..||.=
T Consensus 17 ~~CRRCGr~-syh----v~k~~CaaCGfg 40 (61)
T COG2126 17 IRCRRCGRR-SYH----VRKKYCAACGFG 40 (61)
T ss_pred ehhhhccch-hee----eccceecccCCC
Confidence 357778863 222 235578888865
No 399
>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
Probab=31.89 E-value=25 Score=30.30 Aligned_cols=29 Identities=31% Similarity=0.610 Sum_probs=18.2
Q ss_pred CCCCCCCCCceeEeC--CCCceEeCCCccee
Q 030755 5 FCSDCKKHTEVVFDH--SAGDTVCSECGLVL 33 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~--~~G~~vC~~CG~V~ 33 (172)
.|+.||...+-+... ..|..+|.+|=...
T Consensus 9 ~c~fc~~~~~~~~~~~~~~~~~ic~~c~~~~ 39 (413)
T TIGR00382 9 YCSFCGKSQDEVRKLIAGPGVYICDECIELC 39 (413)
T ss_pred ecCCCCCChhhcccccCCCCCcCCCchHHHH
Confidence 799999842222222 23468999996544
No 400
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=31.80 E-value=77 Score=21.09 Aligned_cols=35 Identities=17% Similarity=0.192 Sum_probs=23.6
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCC
Q 030755 110 KTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRG 144 (172)
Q Consensus 110 ~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~G 144 (172)
++|+.+++..+++...++.+.+-+-......+.+|
T Consensus 6 eli~~ia~~~~~s~~~v~~vv~~~~~~i~~~L~~g 40 (96)
T TIGR00987 6 EMSEYLFDELGLSKREAKELVELFFEEIRRALENG 40 (96)
T ss_pred HHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHcC
Confidence 47888899999998777766655555444434444
No 401
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=31.61 E-value=81 Score=20.84 Aligned_cols=35 Identities=20% Similarity=0.160 Sum_probs=22.5
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCC
Q 030755 110 KTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRG 144 (172)
Q Consensus 110 ~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~G 144 (172)
+.|+.+++.++|+...++.+.+.+-......+.+|
T Consensus 5 eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~~g 39 (90)
T PRK10753 5 QLIDVIADKAELSKTQAKAALESTLAAITESLKEG 39 (90)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHcC
Confidence 47888899999997666666655544443333333
No 402
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=31.59 E-value=34 Score=28.90 Aligned_cols=29 Identities=24% Similarity=0.433 Sum_probs=21.3
Q ss_pred CCCCCCCCCCCceeEe-CCCCceEeCCCcce
Q 030755 3 DAFCSDCKKHTEVVFD-HSAGDTVCSECGLV 32 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D-~~~G~~vC~~CG~V 32 (172)
..+|=+|+.+ +..+- ..=|..||.+|--.
T Consensus 19 Nk~CfeC~a~-NPQWvSvsyGIfICLECSG~ 48 (386)
T KOG0704|consen 19 NKKCFECGAP-NPQWVSVSYGIFICLECSGK 48 (386)
T ss_pred CCceeecCCC-CCCeEeecccEEEEEecCCc
Confidence 3579999984 55444 46899999999544
No 403
>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam
Probab=31.37 E-value=46 Score=25.72 Aligned_cols=20 Identities=30% Similarity=0.426 Sum_probs=17.5
Q ss_pred HHHHHhcCCcHHHHHHHHHH
Q 030755 113 ATMSDRLGLVATIKDRANEI 132 (172)
Q Consensus 113 ~~~~~~L~Lp~~v~~~A~~i 132 (172)
-.++..+|+|+.++++|.+|
T Consensus 196 ~~~a~~~g~~~~ii~rA~~~ 215 (216)
T cd03284 196 IEVARLAGLPEEVIERAREI 215 (216)
T ss_pred HHHHHHhCcCHHHHHHHHHh
Confidence 36788899999999999986
No 404
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=31.26 E-value=1.1e+02 Score=18.86 Aligned_cols=27 Identities=11% Similarity=0.073 Sum_probs=22.3
Q ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHH
Q 030755 108 AFKTIATMSDRLGLVATIKDRANEIYK 134 (172)
Q Consensus 108 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~ 134 (172)
-.+.|....+.+++|+.++..|+++..
T Consensus 17 e~~~i~~~~~~~~~~~evI~~ai~~a~ 43 (73)
T TIGR01446 17 EMEDLKYWLDEFGNSPELIKEALKEAV 43 (73)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 356788888999999999999988754
No 405
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=31.13 E-value=2e+02 Score=20.67 Aligned_cols=55 Identities=9% Similarity=-0.001 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhh---Cc--CCCCCCHHHHHHHHHHHHHHh
Q 030755 107 LAFKTIATMSDRLGLVATIKDRANEIYKKVED---QK--SSRGRNQDALLAACLYIACRQ 161 (172)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~---~~--~~~Gr~~~~~aAAclYiacR~ 161 (172)
...++|.++.....++..+.-.|.-+..++.. .. .+...+..-+..+|+.+|.+.
T Consensus 53 ~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~ 112 (149)
T PF08613_consen 53 SIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKF 112 (149)
T ss_dssp -HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhh
Confidence 36779999999999999999999988888877 22 134456777888888888764
No 406
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=30.98 E-value=82 Score=19.20 Aligned_cols=31 Identities=19% Similarity=0.314 Sum_probs=22.6
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCC
Q 030755 110 KTIATMSDRLGLVATIKDRANEIYKKVEDQKSSR 143 (172)
Q Consensus 110 ~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~ 143 (172)
..+.+|+..+++|...+.. +.+.+.++|++.
T Consensus 23 ~t~~eIa~~l~i~~~~v~~---~L~~L~~~GlV~ 53 (68)
T PF01978_consen 23 ATAEEIAEELGISRSTVYR---ALKSLEEKGLVE 53 (68)
T ss_dssp EEHHHHHHHHTSSHHHHHH---HHHHHHHTTSEE
T ss_pred CCHHHHHHHHCcCHHHHHH---HHHHHHHCCCEE
Confidence 3567899999999865554 666777777753
No 407
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=30.80 E-value=39 Score=15.74 Aligned_cols=10 Identities=30% Similarity=0.823 Sum_probs=7.2
Q ss_pred EeCCCcceec
Q 030755 25 VCSECGLVLE 34 (172)
Q Consensus 25 vC~~CG~V~~ 34 (172)
.|..||.+..
T Consensus 2 ~C~~C~~~f~ 11 (23)
T PF00096_consen 2 KCPICGKSFS 11 (23)
T ss_dssp EETTTTEEES
T ss_pred CCCCCCCccC
Confidence 5777877764
No 408
>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=30.64 E-value=22 Score=23.67 Aligned_cols=39 Identities=21% Similarity=0.330 Sum_probs=25.4
Q ss_pred CCCCCCCCCCc------eeEeCCCCceEeCCCcceecccccccCcc
Q 030755 4 AFCSDCKKHTE------VVFDHSAGDTVCSECGLVLESHSIDETSE 43 (172)
Q Consensus 4 ~~C~~Cg~~~~------i~~D~~~G~~vC~~CG~V~~e~~i~~~~e 43 (172)
+.|-+||.+-. +..+..+-...|..|-.|.+ -+.+.|-+
T Consensus 1 ~~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~-~i~~~gL~ 45 (88)
T PF12156_consen 1 MKCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQ-LIHENGLE 45 (88)
T ss_pred CCCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHH-HHHHcchH
Confidence 46999997421 11233345899999999974 56565554
No 409
>KOG1247 consensus Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=30.46 E-value=17 Score=31.58 Aligned_cols=11 Identities=27% Similarity=0.543 Sum_probs=5.4
Q ss_pred HHHHHHHHHHH
Q 030755 149 ALLAACLYIAC 159 (172)
Q Consensus 149 ~~aAAclYiac 159 (172)
.+++..+|++.
T Consensus 490 ~~a~nii~lvs 500 (567)
T KOG1247|consen 490 GLAANIIYLVS 500 (567)
T ss_pred ehhhHHHHHHH
Confidence 44555555543
No 410
>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=30.39 E-value=33 Score=30.48 Aligned_cols=32 Identities=28% Similarity=0.602 Sum_probs=19.6
Q ss_pred CCCCCCCCCceeEeCC---CCceEeCCCcceecccc
Q 030755 5 FCSDCKKHTEVVFDHS---AGDTVCSECGLVLESHS 37 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~---~G~~vC~~CG~V~~e~~ 37 (172)
.||+||.....+++.. +=.+.| .||.-.+-.+
T Consensus 170 ic~~cGrv~~~~~~~~~~~~v~Y~c-~cG~~g~~~~ 204 (515)
T TIGR00467 170 FCENCGRDTTTVNNYDNEYSIEYSC-ECGNQESVDI 204 (515)
T ss_pred ecCCcCccCceEEEecCCceEEEEc-CCCCEEEEee
Confidence 6999998532333332 345668 4998865433
No 411
>PRK00279 adk adenylate kinase; Reviewed
Probab=30.36 E-value=38 Score=25.83 Aligned_cols=29 Identities=28% Similarity=0.665 Sum_probs=18.3
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
.||.||..-++.+++....-.|..||.-+
T Consensus 129 ~~~~~g~~~~~~~~~p~~~~~~~~~~~~l 157 (215)
T PRK00279 129 ICPACGRTYHVKFNPPKVEGKCDVCGEEL 157 (215)
T ss_pred ccCccCCcccccCCCCCCcCcCcCCCCcc
Confidence 57777765456666655556677777444
No 412
>PRK07217 replication factor A; Reviewed
Probab=30.12 E-value=27 Score=28.97 Aligned_cols=22 Identities=32% Similarity=0.671 Sum_probs=15.6
Q ss_pred CCCCC--CCCCCceeEeCCCCceEeCCCccee
Q 030755 4 AFCSD--CKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~--Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
..||+ |+.. + ..-.|..||.|=
T Consensus 189 ~rCP~~~C~Rv---l-----~~g~C~~HG~ve 212 (311)
T PRK07217 189 KRCPEEDCTRV---L-----QNGRCSEHGKVE 212 (311)
T ss_pred ecCCccccCcc---c-----cCCCCCCCCCcC
Confidence 47999 9873 2 224899999774
No 413
>KOG1252 consensus Cystathionine beta-synthase and related enzymes [Amino acid transport and metabolism]
Probab=30.09 E-value=85 Score=26.54 Aligned_cols=42 Identities=21% Similarity=0.194 Sum_probs=30.8
Q ss_pred cHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHHHhCCCCC
Q 030755 122 VATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPR 166 (172)
Q Consensus 122 p~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiacR~~~~~~ 166 (172)
|+..+..|++| +.+.+++-|-+.-.-++|+|++|-|.++..+
T Consensus 290 ~d~A~~~Ar~L---a~eeGll~G~SSGan~~aAl~~a~~~en~~k 331 (362)
T KOG1252|consen 290 SDEAIEMARRL---ALEEGLLVGISSGANVAAALKLAKRPENAGK 331 (362)
T ss_pred CHHHHHHHHHH---HHhhCeeecccchHHHHHHHHHHhccccCCc
Confidence 45555555554 3456888888888999999999999876543
No 414
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=29.97 E-value=26 Score=21.54 Aligned_cols=23 Identities=30% Similarity=0.728 Sum_probs=11.8
Q ss_pred CCCCCCCCCceeEeCCCC-ceEeCCCcc
Q 030755 5 FCSDCKKHTEVVFDHSAG-DTVCSECGL 31 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G-~~vC~~CG~ 31 (172)
.|.+||. |+ =..+| .--|..||.
T Consensus 20 NCl~CGk---Ii-C~~Eg~~~pC~fCg~ 43 (57)
T PF06221_consen 20 NCLNCGK---II-CEQEGPLGPCPFCGT 43 (57)
T ss_pred cccccCh---hh-cccccCcCcCCCCCC
Confidence 4666664 22 22455 566666663
No 415
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=29.48 E-value=27 Score=34.60 Aligned_cols=23 Identities=35% Similarity=0.624 Sum_probs=17.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
.+||.||.. .=...|..||.-++
T Consensus 675 ~~Cp~Cg~~--------~~~~~Cp~CG~~~~ 697 (1627)
T PRK14715 675 FKCPKCGKV--------GLYHVCPFCGTRVE 697 (1627)
T ss_pred eeCCCCCCc--------cccccCcccCCccc
Confidence 579999973 22678999998754
No 416
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=29.40 E-value=32 Score=28.39 Aligned_cols=28 Identities=25% Similarity=0.554 Sum_probs=22.0
Q ss_pred CCCCCCCCCC-CceeEeCCCCceEeCCCc
Q 030755 3 DAFCSDCKKH-TEVVFDHSAGDTVCSECG 30 (172)
Q Consensus 3 ~~~C~~Cg~~-~~i~~D~~~G~~vC~~CG 30 (172)
..-||.|... .-.++--.+|-++|.+|=
T Consensus 48 lleCPvC~~~l~~Pi~QC~nGHlaCssC~ 76 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPPIFQCDNGHLACSSCR 76 (299)
T ss_pred hccCchhhccCcccceecCCCcEehhhhh
Confidence 4579999963 234667789999999998
No 417
>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=29.26 E-value=33 Score=26.70 Aligned_cols=38 Identities=16% Similarity=0.398 Sum_probs=22.6
Q ss_pred CCCCCCCCCCceeE--eC-CCCceEeCCCcceecccccccC
Q 030755 4 AFCSDCKKHTEVVF--DH-SAGDTVCSECGLVLESHSIDET 41 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~--D~-~~G~~vC~~CG~V~~e~~i~~~ 41 (172)
..|..|+..-.... .. ......|..||-++..+++-.|
T Consensus 114 ~~C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg~lrP~Vv~fg 154 (222)
T cd01413 114 AYCVNCGSKYDLEEVKYAKKHEVPRCPKCGGIIRPDVVLFG 154 (222)
T ss_pred ceECCCCCCcchhHHHHhccCCCCcCCCCCCccCCCEEECC
Confidence 56999986311100 01 1234679999999887776544
No 418
>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=29.19 E-value=34 Score=19.05 Aligned_cols=30 Identities=20% Similarity=0.472 Sum_probs=19.4
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
...|..|+.. +..... .+-|..|+.++-..
T Consensus 11 ~~~C~~C~~~---i~~~~~-~~~C~~C~~~~H~~ 40 (49)
T smart00109 11 PTKCCVCRKS---IWGSFQ-GLRCSWCKVKCHKK 40 (49)
T ss_pred CCCccccccc---cCcCCC-CcCCCCCCchHHHH
Confidence 3579999973 222223 47799999987433
No 419
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=29.16 E-value=52 Score=20.21 Aligned_cols=27 Identities=19% Similarity=0.379 Sum_probs=15.6
Q ss_pred CCCCCC-ceeEeCCCCceEeCCCcceec
Q 030755 8 DCKKHT-EVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 8 ~Cg~~~-~i~~D~~~G~~vC~~CG~V~~ 34 (172)
-||++. .++.--..=.+-|..||..+.
T Consensus 15 PCG~~~Wei~R~GaDikikC~gCg~~im 42 (57)
T PF06107_consen 15 PCGSNEWEIIRIGADIKIKCLGCGRQIM 42 (57)
T ss_pred CCCCCEEEEEEccCcEEEEECCCCCEEE
Confidence 378732 222222233567999999884
No 420
>TIGR01505 tartro_sem_red 2-hydroxy-3-oxopropionate reductase. This model represents 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60), also called tartronate semialdehyde reductase. It follows glyoxylate carboligase and precedes glycerate kinase in D-glycerate pathway of glyoxylate degradation. The eventual product, 3-phosphoglycerate, is an intermediate of glycolysis and is readily metabolized. Tartronic semialdehyde, the substrate of this enzyme, may also come from other pathways, such as D-glucarate catabolism.
Probab=28.95 E-value=1.3e+02 Score=23.95 Aligned_cols=37 Identities=5% Similarity=0.081 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcC
Q 030755 105 LILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKS 141 (172)
Q Consensus 105 l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~ 141 (172)
+.+-...+.++++.++++..+.+.+.++|+.+.+.+.
T Consensus 235 ~~KDl~~~~~~a~~~g~~~~~~~~~~~~~~~a~~~g~ 271 (291)
T TIGR01505 235 HQKDLNLALDSAKAVGANLPNTATVQELFNTLRANGG 271 (291)
T ss_pred HHHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHhcCC
Confidence 3667788889999999999999999999999998773
No 421
>KOG4537 consensus Zn-ribbon-containing protein implicated in mitosis [Cell cycle control, cell division, chromosome partitioning; Defense mechanisms]
Probab=28.92 E-value=11 Score=28.09 Aligned_cols=29 Identities=24% Similarity=0.576 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 2 ~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
-...||.|+. - +. ........|..|-.-.
T Consensus 39 Lde~Cp~C~~-I-lm-~dr~~~~~CVsC~~~~ 67 (178)
T KOG4537|consen 39 LDEICPKCEK-I-LM-RDRDNPMFCVSCINDL 67 (178)
T ss_pred hhhhcchHHH-H-HH-hhccCceEEEeeeccc
Confidence 3468999997 2 33 4467789999998777
No 422
>PF14502 HTH_41: Helix-turn-helix domain
Probab=28.81 E-value=1.1e+02 Score=18.13 Aligned_cols=26 Identities=19% Similarity=0.295 Sum_probs=22.7
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHH
Q 030755 111 TIATMSDRLGLVATIKDRANEIYKKV 136 (172)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~~~a 136 (172)
.|.++++.++++.-.+..|..+++..
T Consensus 8 tI~e~~~~~~vs~GtiQ~Alk~Le~~ 33 (48)
T PF14502_consen 8 TISEYSEKFGVSRGTIQNALKFLEEN 33 (48)
T ss_pred CHHHHHHHhCcchhHHHHHHHHHHHC
Confidence 57889999999999999999888774
No 423
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=28.76 E-value=80 Score=23.06 Aligned_cols=46 Identities=20% Similarity=0.322 Sum_probs=32.7
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCC---CC--------CCHHHHHHHHHHHHH
Q 030755 111 TIATMSDRLGLVATIKDRANEIYKKVEDQKSS---RG--------RNQDALLAACLYIAC 159 (172)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~---~G--------r~~~~~aAAclYiac 159 (172)
.+..|+...++|+.+.++ |+.++.+.|++ +| |.++.|-..=||-|.
T Consensus 27 s~~~IA~~~~is~~~L~k---il~~L~kaGlV~S~rG~~GGy~Lar~~~~Isl~dVv~av 83 (150)
T COG1959 27 SSAEIAERQGISPSYLEK---ILSKLRKAGLVKSVRGKGGGYRLARPPEEITLGDVVRAL 83 (150)
T ss_pred cHHHHHHHhCcCHHHHHH---HHHHHHHcCCEEeecCCCCCccCCCChHHCcHHHHHHHh
Confidence 478899999999999888 66666666665 33 556766666666554
No 424
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=28.50 E-value=23 Score=31.39 Aligned_cols=29 Identities=28% Similarity=0.692 Sum_probs=22.3
Q ss_pred CCCCCCCCCCceeEe-CCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFD-HSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D-~~~G~~vC~~CG~V~ 33 (172)
..|-.||. .+.-+- ..+|.++|.+|=.|-
T Consensus 9 evC~DC~~-~dp~WASvnrGt~lC~eCcsvH 38 (669)
T KOG0818|consen 9 EVCADCSG-PDPSWASVNRGTFLCDECCSVH 38 (669)
T ss_pred hhhcccCC-CCCcceeecCceEehHhhhHHH
Confidence 57999998 444443 369999999998875
No 425
>PRK15461 NADH-dependent gamma-hydroxybutyrate dehydrogenase; Provisional
Probab=28.50 E-value=1.4e+02 Score=24.18 Aligned_cols=38 Identities=8% Similarity=0.121 Sum_probs=33.3
Q ss_pred hHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcC
Q 030755 104 GLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKS 141 (172)
Q Consensus 104 ~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~ 141 (172)
...+-.+.+.+.++.+++|..+.+.+.++|+.+.+.+.
T Consensus 237 ~~~KD~~l~~~~a~~~g~~~p~~~~~~~~~~~a~~~g~ 274 (296)
T PRK15461 237 LAHKDLGIALDVANQLHVPMPLGAASREVYSQARAAGR 274 (296)
T ss_pred HHHhhHHHHHHHHHHcCCCChHHHHHHHHHHHHHhcCC
Confidence 33667888999999999999999999999999998773
No 426
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=28.46 E-value=38 Score=23.11 Aligned_cols=20 Identities=10% Similarity=0.456 Sum_probs=16.6
Q ss_pred eeEeCCCCceEeCCCcceec
Q 030755 15 VVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 15 i~~D~~~G~~vC~~CG~V~~ 34 (172)
+++++.--.+||..|+..|.
T Consensus 3 f~y~~~~~vlIC~~C~~av~ 22 (109)
T PF12013_consen 3 FHYNPEYRVLICRQCQYAVQ 22 (109)
T ss_pred ceEcCcCCEEEeCCCCcccC
Confidence 46677788999999999874
No 427
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=28.38 E-value=1.2e+02 Score=18.89 Aligned_cols=23 Identities=17% Similarity=0.231 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHhcCCcHHHHHHH
Q 030755 107 LAFKTIATMSDRLGLVATIKDRA 129 (172)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~~v~~~A 129 (172)
+.+++|..+-..-|.|+.+.|-|
T Consensus 10 ~vL~~I~~~~~~~G~~Pt~rEIa 32 (65)
T PF01726_consen 10 EVLEFIREYIEENGYPPTVREIA 32 (65)
T ss_dssp HHHHHHHHHHHHHSS---HHHHH
T ss_pred HHHHHHHHHHHHcCCCCCHHHHH
Confidence 45556555555555555544433
No 428
>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=28.21 E-value=30 Score=19.52 Aligned_cols=30 Identities=23% Similarity=0.566 Sum_probs=19.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceeccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
..|..|+.. +.....-.+.|..|+.++-..
T Consensus 12 ~~C~~C~~~---i~~~~~~~~~C~~C~~~~H~~ 41 (50)
T cd00029 12 TFCDVCRKS---IWGLFKQGLRCSWCKVKCHKK 41 (50)
T ss_pred CChhhcchh---hhccccceeEcCCCCCchhhh
Confidence 468899872 333333456799999988544
No 429
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=28.12 E-value=22 Score=21.22 Aligned_cols=10 Identities=30% Similarity=0.873 Sum_probs=4.6
Q ss_pred EeCCCcceec
Q 030755 25 VCSECGLVLE 34 (172)
Q Consensus 25 vC~~CG~V~~ 34 (172)
.|..||.--.
T Consensus 30 ~C~~Cgh~w~ 39 (55)
T PF14311_consen 30 KCPKCGHEWK 39 (55)
T ss_pred ECCCCCCeeE
Confidence 3555544443
No 430
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=27.92 E-value=1.9e+02 Score=19.34 Aligned_cols=51 Identities=20% Similarity=0.214 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHH
Q 030755 106 ILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLY 156 (172)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclY 156 (172)
..+...+.....+++|+..-...-.++.+-+-+..-..--...+++-|.-|
T Consensus 45 ~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~y 95 (96)
T PF13335_consen 45 SEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALSY 95 (96)
T ss_pred HHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHhC
Confidence 457889999999999998777777777777766544444456777777644
No 431
>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=27.78 E-value=16 Score=30.87 Aligned_cols=33 Identities=27% Similarity=0.567 Sum_probs=16.1
Q ss_pred CCCCCCC-CCc--eeEeC--CCCceEeCCCcceecccc
Q 030755 5 FCSDCKK-HTE--VVFDH--SAGDTVCSECGLVLESHS 37 (172)
Q Consensus 5 ~C~~Cg~-~~~--i~~D~--~~G~~vC~~CG~V~~e~~ 37 (172)
.|++||. .+. +.+|. .+=.+.|..||...+-.+
T Consensus 176 iC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~i 213 (360)
T PF01921_consen 176 ICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVDI 213 (360)
T ss_dssp EETTTEE--EEEEEEE--SSSEEEEE--TTS---EEET
T ss_pred eccccCCcccceeeEeecCCCEEEEEecCCCCEEEEec
Confidence 5999998 222 23443 334578999999875444
No 432
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=27.73 E-value=1e+02 Score=20.37 Aligned_cols=30 Identities=10% Similarity=0.088 Sum_probs=21.6
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHhhC
Q 030755 110 KTIATMSDRLGLVATIKDRANEIYKKVEDQ 139 (172)
Q Consensus 110 ~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~ 139 (172)
+.|..+++..+|+..-++.+.+.+-.....
T Consensus 5 eli~~ia~~~~~s~~~~~~~v~~~~~~i~~ 34 (90)
T PRK10664 5 QLIDKIAAGADISKAAAGRALDAIIASVTE 34 (90)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 478889999999987766666655554443
No 433
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=27.59 E-value=87 Score=23.26 Aligned_cols=46 Identities=13% Similarity=0.330 Sum_probs=30.2
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCC---C--------CCHHHHHHHHHHHHH
Q 030755 111 TIATMSDRLGLVATIKDRANEIYKKVEDQKSSR---G--------RNQDALLAACLYIAC 159 (172)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~---G--------r~~~~~aAAclYiac 159 (172)
.++.|++.+++|..+++.. ++.+.+.|++. | |.|+.+-..=|+-|.
T Consensus 27 s~~eIA~~~~ip~~~l~kI---l~~L~~aGLv~s~rG~~GGy~Lar~p~~Itl~dIl~ai 83 (164)
T PRK10857 27 PLADISERQGISLSYLEQL---FSRLRKNGLVSSVRGPGGGYLLGKDASSIAVGEVISAV 83 (164)
T ss_pred cHHHHHHHHCcCHHHHHHH---HHHHHHCCCEEeCCCCCCCeeccCCHHHCCHHHHHHHH
Confidence 5678899999999988884 44444555542 3 556666555555444
No 434
>PRK03922 hypothetical protein; Provisional
Probab=27.57 E-value=59 Score=22.72 Aligned_cols=20 Identities=30% Similarity=0.652 Sum_probs=13.6
Q ss_pred eCCCCceEeCCCcceecccc
Q 030755 18 DHSAGDTVCSECGLVLESHS 37 (172)
Q Consensus 18 D~~~G~~vC~~CG~V~~e~~ 37 (172)
+-+-|...|..||.=++.-.
T Consensus 44 eievG~~~cP~cge~~~~af 63 (113)
T PRK03922 44 EVEVGLTICPKCGEPFDSAF 63 (113)
T ss_pred EEecCcccCCCCCCcCCcEE
Confidence 44678888888887765433
No 435
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=27.55 E-value=76 Score=20.42 Aligned_cols=35 Identities=14% Similarity=0.198 Sum_probs=22.8
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCC
Q 030755 110 KTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRG 144 (172)
Q Consensus 110 ~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~G 144 (172)
+.|+.++...+++...++.+.+-+-......+..|
T Consensus 5 eli~~ia~~~~~s~~~v~~vl~~~~~~i~~~L~~g 39 (90)
T PF00216_consen 5 ELIKRIAEKTGLSKKDVEAVLDALFDVIKEALKEG 39 (90)
T ss_dssp HHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 57888899999997666666655544444333333
No 436
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=27.51 E-value=31 Score=24.14 Aligned_cols=12 Identities=42% Similarity=0.935 Sum_probs=10.8
Q ss_pred ceEeCCCcceec
Q 030755 23 DTVCSECGLVLE 34 (172)
Q Consensus 23 ~~vC~~CG~V~~ 34 (172)
+..|.+||+-++
T Consensus 74 EyyCP~Cgt~le 85 (112)
T PF08882_consen 74 EYYCPGCGTQLE 85 (112)
T ss_pred EEECCCCcceeE
Confidence 578999999997
No 437
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=27.36 E-value=92 Score=20.76 Aligned_cols=22 Identities=14% Similarity=0.345 Sum_probs=15.8
Q ss_pred HHHHHHhcCCcHHHHHHHHHHH
Q 030755 112 IATMSDRLGLVATIKDRANEIY 133 (172)
Q Consensus 112 I~~~~~~L~Lp~~v~~~A~~i~ 133 (172)
|..|+++|++|..-++.|++.+
T Consensus 68 v~~I~~~l~~~~~~v~~al~~L 89 (102)
T PF08784_consen 68 VDEIAQQLGMSENEVRKALDFL 89 (102)
T ss_dssp HHHHHHHSTS-HHHHHHHHHHH
T ss_pred HHHHHHHhCcCHHHHHHHHHHH
Confidence 5568889999987777776654
No 438
>PRK08116 hypothetical protein; Validated
Probab=27.19 E-value=49 Score=26.54 Aligned_cols=28 Identities=29% Similarity=0.627 Sum_probs=16.4
Q ss_pred CCCCCCCCCCceeEeCCCCce----EeCCCcce
Q 030755 4 AFCSDCKKHTEVVFDHSAGDT----VCSECGLV 32 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~----vC~~CG~V 32 (172)
..||+||.....+++. .|.. +|-.|-.-
T Consensus 17 ~~C~~Cg~~~~~~~~~-~~~~~~~~~~c~C~~~ 48 (268)
T PRK08116 17 EYCEVCGKRIEKVVEL-LGKNRIVPIMCECERE 48 (268)
T ss_pred ccCcCCCCcceeeecc-cCcceecCCCCCChHH
Confidence 4799999854444442 2332 46677553
No 439
>TIGR01280 xseB exodeoxyribonuclease VII, small subunit. This protein is the small subunit for exodeoxyribonuclease VII. Exodeoxyribonuclease VII is made of a complex of four small subunits to one large subunit. The complex degrades single-stranded DNA into large acid-insoluble oligonucleotides. These nucleotides are then degraded further into acid-soluble oligonucleotides.
Probab=27.15 E-value=94 Score=19.51 Aligned_cols=34 Identities=9% Similarity=0.117 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhh
Q 030755 105 LILAFKTIATMSDRLGLVATIKDRANEIYKKVED 138 (172)
Q Consensus 105 l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~ 138 (172)
...++..+..|.++|.=++--.+.+..+|+++..
T Consensus 3 fEe~l~~Le~Iv~~LE~~~l~Leesl~lyeeG~~ 36 (67)
T TIGR01280 3 FEEALSELEQIVQKLESGDLALEEALNLFERGMA 36 (67)
T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence 3467778888888886666556777777776643
No 440
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=27.11 E-value=2.5e+02 Score=23.67 Aligned_cols=54 Identities=11% Similarity=0.064 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHhcCCc----HHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHHH
Q 030755 106 ILAFKTIATMSDRLGLV----ATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIAC 159 (172)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp----~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYiac 159 (172)
..++.+|+.|..++++. ..+..++..+.-......-.-+-.|..+|||.+..+.
T Consensus 180 VTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~ 237 (335)
T KOG0656|consen 180 VTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAAILSVS 237 (335)
T ss_pred CCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHHH
Confidence 35788999999999984 4566666655444333322335677788888665443
No 441
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.11 E-value=33 Score=31.91 Aligned_cols=21 Identities=29% Similarity=0.757 Sum_probs=14.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
..|+.||-. ..+ ...|..||-
T Consensus 681 ~~C~~CG~~-~~~------~~~CP~CG~ 701 (735)
T PRK07111 681 DRCPVCGYL-GVI------EDKCPKCGS 701 (735)
T ss_pred eecCCCCCC-CCc------CccCcCCCC
Confidence 479999952 211 268999996
No 442
>TIGR01692 HIBADH 3-hydroxyisobutyrate dehydrogenase. This enzyme belongs to the 3-hydroxyacid dehydrogenase family, sharing a common evolutionary origin and enzymatic mechanism with 6-phosphogluconate. HIBADH exhibits sequence similarity to the NAD binding domain of 6-phosphogluconate dehydrogenase above trusted (pfam03446).
Probab=27.05 E-value=1.4e+02 Score=23.83 Aligned_cols=38 Identities=11% Similarity=0.187 Sum_probs=32.9
Q ss_pred hHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcC
Q 030755 104 GLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKS 141 (172)
Q Consensus 104 ~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~ 141 (172)
.+.+-.+.+..++..+++|..+.+.+.++|+.+.+.+.
T Consensus 238 ~~~KDl~~~~~~a~~~g~~~p~~~~~~~~~~~a~~~g~ 275 (288)
T TIGR01692 238 LMLKDLGLAQDAAKSAGAPTPLGALARQLYSLFDDKGH 275 (288)
T ss_pred HHHhhHHHHHHHHHHcCCCChHHHHHHHHHHHHHhcCC
Confidence 34566788899999999999999999999999998774
No 443
>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=26.86 E-value=95 Score=16.44 Aligned_cols=27 Identities=22% Similarity=0.694 Sum_probs=16.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcce
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V 32 (172)
..|..|+. -+.+=+..-.+-|.-|..|
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 45777775 2444444556677777766
No 444
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=26.80 E-value=32 Score=29.90 Aligned_cols=15 Identities=40% Similarity=0.623 Sum_probs=8.4
Q ss_pred HHHHHHHHHhcCCcH
Q 030755 109 FKTIATMSDRLGLVA 123 (172)
Q Consensus 109 ~~~I~~~~~~L~Lp~ 123 (172)
...|+--+.+|++|.
T Consensus 132 ~~QiklRA~RL~~~~ 146 (456)
T COG1066 132 LQQIKLRADRLGLPT 146 (456)
T ss_pred HHHHHHHHHHhCCCc
Confidence 344555566677653
No 445
>KOG3430 consensus Dynein light chain type 1 [Cytoskeleton]
Probab=26.75 E-value=1.7e+02 Score=19.71 Aligned_cols=27 Identities=7% Similarity=0.012 Sum_probs=13.5
Q ss_pred hhhHHHHHHHHHHHHHhcC-CcHHHHHH
Q 030755 102 DRGLILAFKTIATMSDRLG-LVATIKDR 128 (172)
Q Consensus 102 e~~l~~~~~~I~~~~~~L~-Lp~~v~~~ 128 (172)
+..-.+|+..-...++++. .+.++...
T Consensus 15 ~~mq~~a~~~a~~al~~f~~~~k~iA~~ 42 (90)
T KOG3430|consen 15 EEMQQEAIELARQALEKFNVIEKDIAAF 42 (90)
T ss_pred hHHHHHHHHHHHHHHHHcCCChHHHHHH
Confidence 3334555555555566665 44444333
No 446
>PRK09709 exonuclease VIII; Reviewed
Probab=26.68 E-value=33 Score=32.31 Aligned_cols=27 Identities=26% Similarity=0.823 Sum_probs=20.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~ 39 (172)
..|..||. +|---|.+||.|+++....
T Consensus 526 ~~~~~~g~---------~~g~~~~d~~a~m~~~t~~ 552 (877)
T PRK09709 526 IVCNACGQ---------TGGDNCPDCGAVMGDATYQ 552 (877)
T ss_pred hhhccccc---------cCCCCCCchhhhccCcccc
Confidence 46899986 3666799999999875433
No 447
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=26.59 E-value=25 Score=29.62 Aligned_cols=29 Identities=24% Similarity=0.699 Sum_probs=18.9
Q ss_pred CCCCCCCC-CceeEeC-CCCceEeCCCccee
Q 030755 5 FCSDCKKH-TEVVFDH-SAGDTVCSECGLVL 33 (172)
Q Consensus 5 ~C~~Cg~~-~~i~~D~-~~G~~vC~~CG~V~ 33 (172)
-||.|+.+ ++++... .+=..-|..||.--
T Consensus 98 lC~~C~NPETel~itk~q~i~~~CkACG~r~ 128 (400)
T KOG2767|consen 98 LCPSCENPETELIITKKQTISLKCKACGFRS 128 (400)
T ss_pred eCcCCCCCceeEEecccchhhhHHHHcCCcc
Confidence 59999985 4554442 23345699999753
No 448
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=26.53 E-value=56 Score=16.96 Aligned_cols=10 Identities=50% Similarity=0.972 Sum_probs=5.8
Q ss_pred eEeCCCccee
Q 030755 24 TVCSECGLVL 33 (172)
Q Consensus 24 ~vC~~CG~V~ 33 (172)
..|..|+..|
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 3466666655
No 449
>PHA01748 hypothetical protein
Probab=26.49 E-value=1.6e+02 Score=17.96 Aligned_cols=28 Identities=14% Similarity=0.062 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHhcCCc-HHHHHHHHHHHH
Q 030755 107 LAFKTIATMSDRLGLV-ATIKDRANEIYK 134 (172)
Q Consensus 107 ~~~~~I~~~~~~L~Lp-~~v~~~A~~i~~ 134 (172)
+....|++++...|++ ..++..|.+.|-
T Consensus 12 el~~eld~~a~~~g~~RSE~Ir~Ai~~~~ 40 (60)
T PHA01748 12 DLLELLDRYAIKHGLNRSEAIRKAIEKMV 40 (60)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4567888999999987 467777766444
No 450
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=26.40 E-value=1.1e+02 Score=16.27 Aligned_cols=26 Identities=38% Similarity=0.489 Sum_probs=16.3
Q ss_pred HHHHHhcCCcHHHHHHHHHHHHHHhhCcC
Q 030755 113 ATMSDRLGLVATIKDRANEIYKKVEDQKS 141 (172)
Q Consensus 113 ~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~ 141 (172)
++|++.||+..+.+.+ +++++.+.|+
T Consensus 6 ~diA~~lG~t~ETVSR---~l~~l~~~gl 31 (32)
T PF00325_consen 6 QDIADYLGLTRETVSR---ILKKLERQGL 31 (32)
T ss_dssp HHHHHHHTS-HHHHHH---HHHHHHHTTS
T ss_pred HHHHHHhCCcHHHHHH---HHHHHHHcCC
Confidence 4688899998755544 5666555553
No 451
>PF06573 Churchill: Churchill protein; InterPro: IPR009508 This family consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signalling during neural development. The slow induction by FGF of a transcription factor (Churchill) in the neural plate in turn induces expression of Sip1 (Smad interacting protein-1), which inhibits mesodermal genes and sensitizes cells to later neural inducing factors [].; GO: 0008270 zinc ion binding, 0007275 multicellular organismal development, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2JOX_A.
Probab=26.33 E-value=31 Score=24.00 Aligned_cols=32 Identities=31% Similarity=0.805 Sum_probs=15.5
Q ss_pred CCCCCCCCCce--eE----eCCCC------ceEeCCCcceecccc
Q 030755 5 FCSDCKKHTEV--VF----DHSAG------DTVCSECGLVLESHS 37 (172)
Q Consensus 5 ~C~~Cg~~~~i--~~----D~~~G------~~vC~~CG~V~~e~~ 37 (172)
-|..|++ .++ +. ..+.| +-+|.+|+.||.++-
T Consensus 29 ~Ca~C~k-rdfv~i~nk~~~eedgeEivTY~HvC~nC~HvIA~HE 72 (112)
T PF06573_consen 29 GCASCQK-RDFVLISNKSIEEEDGEEIVTYDHVCKNCHHVIARHE 72 (112)
T ss_dssp --SSS---SS-EEEEEEEEEEETTEEEEEEEEEETTT--EEEEEE
T ss_pred hhhccCC-CCcEEEecccccccCCcEEEEeeeccCccceEEEeee
Confidence 5889997 332 11 12233 357999999998764
No 452
>KOG1129 consensus TPR repeat-containing protein [General function prediction only]
Probab=26.11 E-value=75 Score=27.07 Aligned_cols=30 Identities=17% Similarity=0.270 Sum_probs=14.8
Q ss_pred HHHHHHHHHHhhCcCCCCCCHHHHHHHHHH
Q 030755 127 DRANEIYKKVEDQKSSRGRNQDALLAACLY 156 (172)
Q Consensus 127 ~~A~~i~~~a~~~~~~~Gr~~~~~aAAclY 156 (172)
|.|.++|+++++.|...+.-.-.+.-.|+|
T Consensus 341 E~AlryYRRiLqmG~~speLf~NigLCC~y 370 (478)
T KOG1129|consen 341 EMALRYYRRILQMGAQSPELFCNIGLCCLY 370 (478)
T ss_pred HHHHHHHHHHHHhcCCChHHHhhHHHHHHh
Confidence 345555555555554444434445555555
No 453
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=25.88 E-value=1.2e+02 Score=19.60 Aligned_cols=35 Identities=14% Similarity=0.309 Sum_probs=23.6
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCC
Q 030755 110 KTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRG 144 (172)
Q Consensus 110 ~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~G 144 (172)
+.+..+++..+++...+....+-+-......+..|
T Consensus 5 eli~~ia~~~~~~~~~v~~vl~~l~~~i~~~L~~g 39 (90)
T smart00411 5 ELIDAIAEKAGLSKKDAKAAVDAFLEIITEALKKG 39 (90)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhCC
Confidence 57888899999998766666655555444444444
No 454
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=25.87 E-value=21 Score=34.36 Aligned_cols=24 Identities=21% Similarity=0.645 Sum_probs=15.1
Q ss_pred CCCCCCCCCCceeEeC-CCCceEeCCCc
Q 030755 4 AFCSDCKKHTEVVFDH-SAGDTVCSECG 30 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~-~~G~~vC~~CG 30 (172)
..||+||++ +--|. ..|.. |..|=
T Consensus 9 ~~CpNCGG~--isseRL~~glp-Ce~CL 33 (1187)
T COG1110 9 SSCPNCGGD--ISSERLEKGLP-CERCL 33 (1187)
T ss_pred ccCCCCCCc--CcHHHHhcCCC-chhcc
Confidence 469999983 33333 45544 88773
No 455
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=25.72 E-value=50 Score=30.37 Aligned_cols=32 Identities=19% Similarity=0.414 Sum_probs=20.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCC---Ccceecccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSE---CGLVLESHS 37 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~---CG~V~~e~~ 37 (172)
..||.||++ ++.+...-.+.|.+ |-.-+-..+
T Consensus 405 ~~CP~Cgs~--l~~~~~~~~~~C~n~~~C~aq~~~~l 439 (665)
T PRK07956 405 THCPVCGSE--LVRVEGEAVLRCTNGLSCPAQLKERL 439 (665)
T ss_pred CCCCCCCCE--eEecCCCeEEECCCCCCCHHHHHHHH
Confidence 479999983 55544445678974 755554444
No 456
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=25.61 E-value=1.3e+02 Score=17.07 Aligned_cols=29 Identities=14% Similarity=0.116 Sum_probs=19.7
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCC
Q 030755 111 TIATMSDRLGLVATIKDRANEIYKKVEDQKSS 142 (172)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~ 142 (172)
.+..+++.++++...+..+..-+. +.|++
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~---~~g~i 50 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLE---AEGLV 50 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH---HCCCE
Confidence 356788899999877777655444 44554
No 457
>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=25.48 E-value=1e+02 Score=24.24 Aligned_cols=32 Identities=19% Similarity=0.323 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhC
Q 030755 108 AFKTIATMSDRLGLVATIKDRANEIYKKVEDQ 139 (172)
Q Consensus 108 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~ 139 (172)
-...+..+++.||||..-++.=..+|+...++
T Consensus 164 ~~~~l~~l~~~L~ls~~kv~KDL~lYrsnLeK 195 (214)
T TIGR03060 164 LNEILKELSEALGLSYDRVEKDLDLYKSNLEK 195 (214)
T ss_pred HHHHHHHHHHHcCCCHHHHHhhHHHHHhHHHH
Confidence 34588999999999999999989999887654
No 458
>PHA02956 hypothetical protein; Provisional
Probab=25.37 E-value=45 Score=24.39 Aligned_cols=20 Identities=25% Similarity=0.793 Sum_probs=17.8
Q ss_pred CceeEeCCCCceEeCCCcce
Q 030755 13 TEVVFDHSAGDTVCSECGLV 32 (172)
Q Consensus 13 ~~i~~D~~~G~~vC~~CG~V 32 (172)
++++.|.+.|.++|..=|.+
T Consensus 107 nsiiidsssgkiicegigii 126 (189)
T PHA02956 107 NSIIIDSSSGKIICEGIGII 126 (189)
T ss_pred ceEEEecCCCcEEeecchHH
Confidence 47899999999999998876
No 459
>PRK09568 DNA primase large subunit; Reviewed
Probab=25.34 E-value=4e+02 Score=22.13 Aligned_cols=39 Identities=18% Similarity=0.129 Sum_probs=28.7
Q ss_pred hHHHHHHHHHH------HHHhcCCcHHHHHHHHHHHHHHhhCcCC
Q 030755 104 GLILAFKTIAT------MSDRLGLVATIKDRANEIYKKVEDQKSS 142 (172)
Q Consensus 104 ~l~~~~~~I~~------~~~~L~Lp~~v~~~A~~i~~~a~~~~~~ 142 (172)
.+.++.++|++ +...+.-+..++++|++-.+.+...+.+
T Consensus 10 Fl~~a~~~v~~~~~g~~L~~ll~~~~~~v~rA~eRv~~al~~~~~ 54 (306)
T PRK09568 10 FIKSLEDELKKYGGGITLSDLLLNSTTLIDQAKDRIQKIKSGEEL 54 (306)
T ss_pred ChHHHHHHHHhhcCCCcHHHHHcCcHHHHHHHHHHHHHHhccCCc
Confidence 45667777877 4556666788999998888888865544
No 460
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=25.31 E-value=2.8e+02 Score=21.97 Aligned_cols=55 Identities=24% Similarity=0.289 Sum_probs=36.2
Q ss_pred HHHHHHHhcCCc--HHHHHHHHHHHHHHhhC--cCCCCCCHHHHHHHHHHHHHHhCCCC
Q 030755 111 TIATMSDRLGLV--ATIKDRANEIYKKVEDQ--KSSRGRNQDALLAACLYIACRQEDKP 165 (172)
Q Consensus 111 ~I~~~~~~L~Lp--~~v~~~A~~i~~~a~~~--~~~~Gr~~~~~aAAclYiacR~~~~~ 165 (172)
.|.+++.+|||. +.+.+.|.+|.+...-+ +..-|-.-..-|.-|+=+|+-..++|
T Consensus 2 lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~ 60 (262)
T KOG4557|consen 2 LISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQII 60 (262)
T ss_pred cHHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhccc
Confidence 478899999994 67999999998876332 22233333445556666666555554
No 461
>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=25.29 E-value=35 Score=21.92 Aligned_cols=22 Identities=23% Similarity=0.543 Sum_probs=10.8
Q ss_pred eeEeCCCCceEeCCCcceeccc
Q 030755 15 VVFDHSAGDTVCSECGLVLESH 36 (172)
Q Consensus 15 i~~D~~~G~~vC~~CG~V~~e~ 36 (172)
+-.+++--..+|..||.++-..
T Consensus 38 ~~l~~~~kr~~Ck~C~~~liPG 59 (85)
T PF04032_consen 38 IRLPPEIKRTICKKCGSLLIPG 59 (85)
T ss_dssp ---STTCCCTB-TTT--B--CT
T ss_pred CCCChHHhcccccCCCCEEeCC
Confidence 3456677788999999998533
No 462
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=25.25 E-value=30 Score=29.56 Aligned_cols=25 Identities=16% Similarity=0.231 Sum_probs=16.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
..|+.||.. ++ ......|..||-.+
T Consensus 3 l~C~~Cg~~----~~-~~~~~~C~~c~g~l 27 (398)
T TIGR03844 3 LRCPGCGEV----LP-DHYTLSCPLDCGLL 27 (398)
T ss_pred EEeCCCCCc----cC-CccccCCCCCCCce
Confidence 579999973 23 23468898887444
No 463
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=25.19 E-value=1.3e+02 Score=18.07 Aligned_cols=24 Identities=17% Similarity=0.185 Sum_probs=17.8
Q ss_pred HHHHHHhcCCcHHHHHHHHHHHHH
Q 030755 112 IATMSDRLGLVATIKDRANEIYKK 135 (172)
Q Consensus 112 I~~~~~~L~Lp~~v~~~A~~i~~~ 135 (172)
...+++.++++...+.+|...+..
T Consensus 27 ~~~la~~~~vsr~tvr~al~~L~~ 50 (64)
T PF00392_consen 27 ERELAERYGVSRTTVREALRRLEA 50 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHhccCCcHHHHHHHHHHH
Confidence 457888999999888888766554
No 464
>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=25.18 E-value=1.2e+02 Score=19.78 Aligned_cols=23 Identities=22% Similarity=0.234 Sum_probs=17.2
Q ss_pred HHHHHHHHHhcCCcHHHHHHHHH
Q 030755 109 FKTIATMSDRLGLVATIKDRANE 131 (172)
Q Consensus 109 ~~~I~~~~~~L~Lp~~v~~~A~~ 131 (172)
....++++.+|||++..++.+..
T Consensus 11 ~~~wk~~~R~LGlse~~Id~ie~ 33 (80)
T cd08313 11 PRRWKEFVRRLGLSDNEIERVEL 33 (80)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHH
Confidence 45677888899999877766654
No 465
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=24.88 E-value=72 Score=16.45 Aligned_cols=25 Identities=32% Similarity=0.724 Sum_probs=17.3
Q ss_pred CCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 5 ~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
+|..|+.. .|... .+-|..|+.++.
T Consensus 2 ~C~~C~~~----~~~~~-~Y~C~~c~f~lh 26 (30)
T PF03107_consen 2 WCDVCRRK----IDGFY-FYHCSECCFTLH 26 (30)
T ss_pred CCCCCCCC----cCCCE-eEEeCCCCCeEc
Confidence 58889873 23333 789999997664
No 466
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=24.83 E-value=40 Score=30.31 Aligned_cols=17 Identities=12% Similarity=0.085 Sum_probs=12.7
Q ss_pred cCCcHHHHHHHHHHHHH
Q 030755 119 LGLVATIKDRANEIYKK 135 (172)
Q Consensus 119 L~Lp~~v~~~A~~i~~~ 135 (172)
+..|.+..+.+.++.+.
T Consensus 211 ~~~p~~~~ne~~~~i~~ 227 (558)
T COG0143 211 FIWPANRRNEVLNFLKE 227 (558)
T ss_pred ccCChHHHHHHHHHHHc
Confidence 45788888888886666
No 467
>PF08238 Sel1: Sel1 repeat; InterPro: IPR006597 Sel1-like repeats are tetratricopeptide repeat sequences originally identified in a Caenorhabditis elegans receptor molecule which is a key negative regulator of the Notch pathway []. Mammalian homologues have since been identified although these mainly pancreatic proteins have yet to have a function assigned.; PDB: 2XM6_A 3RJV_A 1OUV_A 1KLX_A.
Probab=24.81 E-value=1.1e+02 Score=15.74 Aligned_cols=20 Identities=25% Similarity=0.415 Sum_probs=15.2
Q ss_pred CCcHHHHHHHHHHHHHHhhCc
Q 030755 120 GLVATIKDRANEIYKKVEDQK 140 (172)
Q Consensus 120 ~Lp~~v~~~A~~i~~~a~~~~ 140 (172)
+++.+ .+.|..+|+++.+.|
T Consensus 19 g~~~d-~~~A~~~~~~Aa~~g 38 (39)
T PF08238_consen 19 GVPKD-YEKAFKWYEKAAEQG 38 (39)
T ss_dssp SSCHH-HHHHHHHHHHHHHTT
T ss_pred Ccccc-ccchHHHHHHHHHcc
Confidence 56664 788899999887764
No 468
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=24.75 E-value=42 Score=23.03 Aligned_cols=21 Identities=38% Similarity=0.787 Sum_probs=16.0
Q ss_pred EeCCCCceEeCCCcceecccc
Q 030755 17 FDHSAGDTVCSECGLVLESHS 37 (172)
Q Consensus 17 ~D~~~G~~vC~~CG~V~~e~~ 37 (172)
.|-+-|...|..||.-++.-.
T Consensus 41 VeIevG~~~cP~Cge~~~~a~ 61 (102)
T PF04475_consen 41 VEIEVGDTICPKCGEELDSAF 61 (102)
T ss_pred EEEecCcccCCCCCCccCceE
Confidence 455789999999998886443
No 469
>PF04391 DUF533: Protein of unknown function (DUF533); InterPro: IPR007486 Some family members may be secreted or integral membrane proteins.
Probab=24.75 E-value=79 Score=24.21 Aligned_cols=20 Identities=15% Similarity=0.258 Sum_probs=17.3
Q ss_pred HHHHHHHHHhcCCcHHHHHH
Q 030755 109 FKTIATMSDRLGLVATIKDR 128 (172)
Q Consensus 109 ~~~I~~~~~~L~Lp~~v~~~ 128 (172)
..|+..++..|+||+.++++
T Consensus 163 r~YL~~LA~aL~L~~~lv~~ 182 (188)
T PF04391_consen 163 RAYLDELAQALGLDPDLVAQ 182 (188)
T ss_pred HHHHHHHHHHhCcCHHHHHH
Confidence 46899999999999987765
No 470
>PRK13266 Thf1-like protein; Reviewed
Probab=24.65 E-value=1.1e+02 Score=24.31 Aligned_cols=32 Identities=16% Similarity=0.345 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhC
Q 030755 108 AFKTIATMSDRLGLVATIKDRANEIYKKVEDQ 139 (172)
Q Consensus 108 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~ 139 (172)
-...+..+++.||||..-++.=..+|+..+++
T Consensus 166 ~~~~l~~l~~~L~ls~~kv~KDL~lYrsnLeK 197 (225)
T PRK13266 166 LNEALKDISEGLGLSKEKVEKDLDLYRSNLEK 197 (225)
T ss_pred HHHHHHHHHHHcCCCHHHHHhhHHHHHhHHHH
Confidence 34688999999999999888888888876654
No 471
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=24.63 E-value=87 Score=22.15 Aligned_cols=47 Identities=21% Similarity=0.349 Sum_probs=32.1
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCC---C--------CCHHHHHHHHHHHHHH
Q 030755 111 TIATMSDRLGLVATIKDRANEIYKKVEDQKSSR---G--------RNQDALLAACLYIACR 160 (172)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~---G--------r~~~~~aAAclYiacR 160 (172)
.+..|++.+++|..+++.. ++++.+.|++. | |.++.+--+=||-+..
T Consensus 27 s~~~ia~~~~ip~~~l~ki---l~~L~~~glv~s~~G~~Ggy~l~~~~~~Itl~dv~~a~e 84 (135)
T TIGR02010 27 TLADISERQGISLSYLEQL---FAKLRKAGLVKSVRGPGGGYQLGRPAEDISVADIIDAVD 84 (135)
T ss_pred cHHHHHHHHCcCHHHHHHH---HHHHHHCCceEEEeCCCCCEeccCCHHHCcHHHHHHHhC
Confidence 5678899999999888874 44444445442 2 5577777777776653
No 472
>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=24.62 E-value=1.1e+02 Score=23.93 Aligned_cols=32 Identities=16% Similarity=0.357 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhC
Q 030755 108 AFKTIATMSDRLGLVATIKDRANEIYKKVEDQ 139 (172)
Q Consensus 108 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~ 139 (172)
-...+..+++.||||..-++.=..+|+..+++
T Consensus 161 ~~~~l~~l~~~l~ls~~kv~kDL~lYrsnLeK 192 (216)
T PF11264_consen 161 RPEALEKLSEALGLSKEKVEKDLDLYRSNLEK 192 (216)
T ss_pred HHHHHHHHHHHcCCCHHHHHhhHHHHHhHHHH
Confidence 45678899999999999888888888877654
No 473
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=24.62 E-value=1.1e+02 Score=21.37 Aligned_cols=29 Identities=14% Similarity=0.164 Sum_probs=20.9
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCC
Q 030755 111 TIATMSDRLGLVATIKDRANEIYKKVEDQKSS 142 (172)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~ 142 (172)
.+.+++..+++|...+....+ .+.+.|++
T Consensus 27 s~~eia~~l~is~~~v~~~l~---~L~~~Gli 55 (130)
T TIGR02944 27 SAAEIAEQTGLNAPTVSKILK---QLSLAGIV 55 (130)
T ss_pred cHHHHHHHHCcCHHHHHHHHH---HHHHCCcE
Confidence 577889999999988777444 44445655
No 474
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=24.60 E-value=45 Score=28.35 Aligned_cols=34 Identities=24% Similarity=0.451 Sum_probs=20.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceecccccccCccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEW 44 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~~~~ew 44 (172)
..|+.|+. ...+.. ...-.|..||. .....||=|
T Consensus 245 ~~C~~c~~-~~~~~~--~~~~~C~~c~~----~~~~~GPlW 278 (382)
T PRK04338 245 YYCPKCLY-REEVEG--LPPEECPVCGG----KFGTAGPLW 278 (382)
T ss_pred EECCCCCc-EEEecC--CCCCCCCCCCC----cceeccccc
Confidence 36999997 333322 23456888876 333566766
No 475
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=24.60 E-value=15 Score=31.84 Aligned_cols=27 Identities=30% Similarity=0.781 Sum_probs=17.9
Q ss_pred CCCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 3 ~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
...||.|++. |--.+-.--|.=||.|+
T Consensus 180 V~~CP~Ca~~----F~l~rRrHHCRLCG~Vm 206 (505)
T KOG1842|consen 180 VQFCPECANS----FGLTRRRHHCRLCGRVM 206 (505)
T ss_pred ccccccccch----hhhHHHhhhhhhcchHH
Confidence 3579999973 22334455677777776
No 476
>PRK11559 garR tartronate semialdehyde reductase; Provisional
Probab=24.43 E-value=1.9e+02 Score=23.12 Aligned_cols=37 Identities=11% Similarity=0.114 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcC
Q 030755 105 LILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKS 141 (172)
Q Consensus 105 l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~ 141 (172)
..+-.+.+.+.+..+++|..+.+.+.++|+.+.+.+.
T Consensus 238 ~~KDl~~~~~~a~~~g~~~p~~~~~~~~~~~~~~~g~ 274 (296)
T PRK11559 238 HIKDLANALDTSHGVGAPLPLTAAVMEMMQALKADGL 274 (296)
T ss_pred HHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHhcCC
Confidence 3455777889999999999999999999999998773
No 477
>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=24.40 E-value=54 Score=30.06 Aligned_cols=32 Identities=16% Similarity=0.323 Sum_probs=20.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCC--Ccceecccc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSE--CGLVLESHS 37 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~--CG~V~~e~~ 37 (172)
..||.||++ ++.+...-.+.|.+ |-.-+-..+
T Consensus 393 ~~CP~C~s~--l~~~~~~~~~~C~n~~C~aq~~~~l 426 (652)
T TIGR00575 393 THCPSCGSP--LVKIEEEAVIRCPNLNCPAQRVERI 426 (652)
T ss_pred CCCCCCCCE--eEecCCcEEEEECCCCCHHHHHHHh
Confidence 479999983 55554445678874 655444444
No 478
>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=24.39 E-value=33 Score=25.89 Aligned_cols=23 Identities=26% Similarity=0.635 Sum_probs=16.4
Q ss_pred CCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 6 CSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 6 C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
|+.||.. +. .+..+|.+|+.-+.
T Consensus 1 C~~C~~~--~~----~~~~~C~~C~~~~~ 23 (190)
T TIGR00201 1 CSLCGRP--YQ----SVHALCRQCGSWRT 23 (190)
T ss_pred CCccccc--cc----cccCCchhhCCccc
Confidence 9999973 22 13579999987664
No 479
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=24.36 E-value=33 Score=23.17 Aligned_cols=13 Identities=23% Similarity=0.843 Sum_probs=10.4
Q ss_pred eEeCCCcceeccc
Q 030755 24 TVCSECGLVLESH 36 (172)
Q Consensus 24 ~vC~~CG~V~~e~ 36 (172)
..|.+||.+..+.
T Consensus 59 a~CkkCGfef~~~ 71 (97)
T COG3357 59 ARCKKCGFEFRDD 71 (97)
T ss_pred hhhcccCcccccc
Confidence 4699999998653
No 480
>TIGR01070 mutS1 DNA mismatch repair protein MutS.
Probab=24.32 E-value=94 Score=29.42 Aligned_cols=28 Identities=21% Similarity=0.344 Sum_probs=24.2
Q ss_pred HHHHHhcCCcHHHHHHHHHHHHHHhhCc
Q 030755 113 ATMSDRLGLVATIKDRANEIYKKVEDQK 140 (172)
Q Consensus 113 ~~~~~~L~Lp~~v~~~A~~i~~~a~~~~ 140 (172)
-.+|...|||+.|+++|.++.+......
T Consensus 758 i~VA~laGlP~~VI~rA~~il~~le~~~ 785 (840)
T TIGR01070 758 LAVAALAGLPKEVIARARQILTQLEARS 785 (840)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHhcc
Confidence 3678889999999999999999987543
No 481
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=24.28 E-value=36 Score=22.89 Aligned_cols=23 Identities=26% Similarity=0.793 Sum_probs=15.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
..|.-||.. ..- --.-.|..||.
T Consensus 17 tlCrRCG~~-syH----~qK~~CasCGy 39 (91)
T PTZ00073 17 TLCRRCGKR-SFH----VQKKRCASCGY 39 (91)
T ss_pred chhcccCcc-ccc----cccccchhcCC
Confidence 469999973 322 23556999998
No 482
>PRK15059 tartronate semialdehyde reductase; Provisional
Probab=24.07 E-value=1.9e+02 Score=23.36 Aligned_cols=38 Identities=8% Similarity=0.036 Sum_probs=33.1
Q ss_pred hHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcC
Q 030755 104 GLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKS 141 (172)
Q Consensus 104 ~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~ 141 (172)
...+-.+.+.+.++.+++|..+.+.+.++|+.+.+.+.
T Consensus 234 ~~~KDl~l~~~~a~~~g~~~p~~~~~~~~~~~a~~~g~ 271 (292)
T PRK15059 234 LHQKDLNLALQSAKALALNLPNTATCQELFNTCAANGG 271 (292)
T ss_pred HHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHhcCC
Confidence 44667888889999999999999999999999988764
No 483
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=23.98 E-value=1.4e+02 Score=18.97 Aligned_cols=35 Identities=17% Similarity=0.338 Sum_probs=22.6
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCC
Q 030755 110 KTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRG 144 (172)
Q Consensus 110 ~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~G 144 (172)
+.+..++...+++...+....+.+-......+..|
T Consensus 4 ~l~~~ia~~~~~~~~~v~~vl~~~~~~i~~~L~~g 38 (87)
T cd00591 4 ELIEAIAEKTGLSKKDAEAAVDAFLDVITEALAKG 38 (87)
T ss_pred HHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHhCC
Confidence 46888899999997666666555554444333333
No 484
>PRK14069 exodeoxyribonuclease VII small subunit; Provisional
Probab=23.85 E-value=1.1e+02 Score=20.88 Aligned_cols=37 Identities=8% Similarity=0.150 Sum_probs=26.6
Q ss_pred hhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhh
Q 030755 102 DRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVED 138 (172)
Q Consensus 102 e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~ 138 (172)
+.+...++..+..|..+|.=++--.+.++.+|.....
T Consensus 7 ~~sFEeal~~LEeIV~~LEsgdl~LEesl~lyeeGv~ 43 (95)
T PRK14069 7 KISFEDALRELEQIAEKLERQDFSLEESLKAYERGME 43 (95)
T ss_pred CCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence 4456788888999988887666556777777766543
No 485
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.84 E-value=57 Score=28.19 Aligned_cols=28 Identities=21% Similarity=0.593 Sum_probs=19.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCccee
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~ 33 (172)
..||.|+.+ |..+..=....|+.||.-.
T Consensus 369 krCP~C~v~--IEr~eGCnKM~C~~c~~~f 396 (445)
T KOG1814|consen 369 KRCPKCKVV--IERSEGCNKMHCTKCGTYF 396 (445)
T ss_pred CCCCcccce--eecCCCccceeeccccccc
Confidence 579999962 4444445577888888754
No 486
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=23.82 E-value=1.8e+02 Score=18.40 Aligned_cols=42 Identities=7% Similarity=0.156 Sum_probs=35.9
Q ss_pred hhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCC
Q 030755 102 DRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSR 143 (172)
Q Consensus 102 e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~ 143 (172)
+-+..++++....+|+..++++--..+..++...+...+++.
T Consensus 22 ~~~~~~vy~~Y~~~c~~~~~~~l~~~~~~~~l~~L~~~gli~ 63 (87)
T cd08768 22 EATTGEVYEVYEELCEEIGVDPLTQRRISDLLSELEMLGLLE 63 (87)
T ss_pred CccHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHHHcCCeE
Confidence 456788999999999999999878888889999988888764
No 487
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=23.78 E-value=78 Score=29.65 Aligned_cols=26 Identities=19% Similarity=0.346 Sum_probs=21.7
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHH
Q 030755 111 TIATMSDRLGLVATIKDRANEIYKKV 136 (172)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~~~a 136 (172)
+--.++..+|||+.|+++|.+++...
T Consensus 484 ~a~~iA~~~Glp~~ii~~A~~~~~~~ 509 (771)
T TIGR01069 484 YAFEIAQRYGIPHFIIEQAKTFYGEF 509 (771)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHHhh
Confidence 34468899999999999999998754
No 488
>PLN03131 hypothetical protein; Provisional
Probab=23.73 E-value=56 Score=29.83 Aligned_cols=31 Identities=13% Similarity=0.290 Sum_probs=22.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcceec
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~ 34 (172)
..|-.||...---....-|..||..|.-|-.
T Consensus 24 k~CADCga~~P~WASiNlGIFICi~CSGIHR 54 (705)
T PLN03131 24 RRCINCNSLGPQFVCTNFWTFICMTCSGIHR 54 (705)
T ss_pred CccccCCCCCCCeeEeccceEEchhchhhhc
Confidence 5799999842222334579999999988864
No 489
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=23.34 E-value=1.5e+02 Score=18.06 Aligned_cols=24 Identities=17% Similarity=0.392 Sum_probs=17.5
Q ss_pred HHHHHHHHHhcCCcHHHHHHHHHHHHH
Q 030755 109 FKTIATMSDRLGLVATIKDRANEIYKK 135 (172)
Q Consensus 109 ~~~I~~~~~~L~Lp~~v~~~A~~i~~~ 135 (172)
.-.|..+|.+++++. ++|.++|++
T Consensus 5 v~~Ie~~A~~~~~s~---~ea~~~~~~ 28 (62)
T PF12668_consen 5 VFCIEEFAKKLNISG---EEAYNYFKR 28 (62)
T ss_pred HHHHHHHHHHHCcCH---HHHHHHHHH
Confidence 457899999999996 455555554
No 490
>TIGR01795 CM_mono_cladeE monofunctional chorismate mutase, alpha proteobacterial type. The alpha proteobacterial members are trusted because the pathways of CM are evident and there is only one plausible CM in the genome. In S. coelicolor, however, there is another aparrent monofunctional CM.
Probab=23.31 E-value=2.4e+02 Score=18.87 Aligned_cols=31 Identities=6% Similarity=0.086 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhh
Q 030755 105 LILAFKTIATMSDRLGLVATIKDRANEIYKKVED 138 (172)
Q Consensus 105 l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~ 138 (172)
....+..+...+..+||++.+++. ||+.+.+
T Consensus 50 e~~vl~~~~~~a~~~gl~p~~~e~---i~~~i~~ 80 (94)
T TIGR01795 50 EDYQIARLRRLAIDAGLDPEFAEK---FLNFIVT 80 (94)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHH---HHHHHHH
Confidence 356678889999999999988765 5655543
No 491
>COG2979 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.31 E-value=91 Score=24.47 Aligned_cols=22 Identities=18% Similarity=0.315 Sum_probs=18.7
Q ss_pred HHHHHHHHHhcCCcHHHHHHHH
Q 030755 109 FKTIATMSDRLGLVATIKDRAN 130 (172)
Q Consensus 109 ~~~I~~~~~~L~Lp~~v~~~A~ 130 (172)
+.|++.++.+|+||+.+++.-.
T Consensus 194 r~YL~~La~~L~L~dalvd~lE 215 (225)
T COG2979 194 RSYLNALAGALGLPDALVDHLE 215 (225)
T ss_pred HHHHHHHHHHhCCCHHHHHHHH
Confidence 4689999999999999888743
No 492
>smart00351 PAX Paired Box domain.
Probab=23.30 E-value=1.9e+02 Score=20.20 Aligned_cols=58 Identities=16% Similarity=0.078 Sum_probs=31.7
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCC-----CCCHHHHH-HHHHHH-HHHhCCCCCCcccc
Q 030755 111 TIATMSDRLGLVATIKDRANEIYKKVEDQKSSR-----GRNQDALL-AACLYI-ACRQEDKPRTVKGT 171 (172)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~-----Gr~~~~~a-AAclYi-acR~~~~~~tl~ei 171 (172)
....+|..|+++...+..-.+-| .+.|.+. |+++..+. ....+| ....++-..|+.||
T Consensus 35 s~~~iA~~~gvs~~tV~kwi~r~---~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el 99 (125)
T smart00351 35 RPCDISRQLCVSHGCVSKILGRY---YETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEI 99 (125)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHH---HHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHH
Confidence 46789999999997776644444 4333332 32332221 222232 24555555677765
No 493
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=23.25 E-value=37 Score=25.50 Aligned_cols=33 Identities=27% Similarity=0.484 Sum_probs=20.9
Q ss_pred CCCCCCCCCCCCC-c--eeEeCCCCceEeCCCcceec
Q 030755 1 MTDAFCSDCKKHT-E--VVFDHSAGDTVCSECGLVLE 34 (172)
Q Consensus 1 ~~~~~C~~Cg~~~-~--i~~D~~~G~~vC~~CG~V~~ 34 (172)
|+.+.|--||+.. . .+.-...-..||.+|+ -++
T Consensus 1 m~~~~CEiCG~~i~~~~~v~vegsel~VC~~Ca-k~G 36 (165)
T COG1813 1 MSGMGCELCGREIDKPIKVKVEGAELTVCDDCA-KFG 36 (165)
T ss_pred CCCcceeccccccCCCeeEEeecceeehhHHHH-Hhc
Confidence 6677799999741 1 1111234467999999 554
No 494
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=23.22 E-value=52 Score=27.45 Aligned_cols=25 Identities=28% Similarity=0.664 Sum_probs=16.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEeC--CCc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCS--ECG 30 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~--~CG 30 (172)
..||.||+++ ......+...|. .|-
T Consensus 151 kFCp~CG~~t--kp~e~g~k~~Cs~~~C~ 177 (345)
T KOG3084|consen 151 KFCPGCGSPT--KPEEAGTKLQCSDETCP 177 (345)
T ss_pred ccCcccCCCc--ccccCCccceeecccCC
Confidence 4799999853 233456667777 555
No 495
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=23.22 E-value=1.8e+02 Score=17.48 Aligned_cols=35 Identities=3% Similarity=0.182 Sum_probs=24.3
Q ss_pred HHHHHHHHHHhcCCcHH-HHHHHHHHHHHHhhCcCC
Q 030755 108 AFKTIATMSDRLGLVAT-IKDRANEIYKKVEDQKSS 142 (172)
Q Consensus 108 ~~~~I~~~~~~L~Lp~~-v~~~A~~i~~~a~~~~~~ 142 (172)
..+.++.+++..+.++. +.+....++..+.+++++
T Consensus 32 ~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~~glI 67 (68)
T PF05402_consen 32 VEEIVDALAEEYDVDPEEAEEDVEEFLEQLREKGLI 67 (68)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT--
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCcCc
Confidence 34577788899999975 677777888888887764
No 496
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=23.12 E-value=27 Score=21.81 Aligned_cols=13 Identities=31% Similarity=0.736 Sum_probs=10.2
Q ss_pred eEeCCCcceeccc
Q 030755 24 TVCSECGLVLESH 36 (172)
Q Consensus 24 ~vC~~CG~V~~e~ 36 (172)
+-|=+||.||.+.
T Consensus 5 iRCFsCGkvi~~~ 17 (63)
T COG1644 5 VRCFSCGKVIGHK 17 (63)
T ss_pred eEeecCCCCHHHH
Confidence 4589999999743
No 497
>PRK07220 DNA topoisomerase I; Validated
Probab=23.01 E-value=80 Score=29.39 Aligned_cols=26 Identities=19% Similarity=0.532 Sum_probs=15.1
Q ss_pred CCCCCCCCCCceeEeCCCC----ceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFDHSAG----DTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G----~~vC~~CG~ 31 (172)
..||.||. ..+... ..| ++.|..|..
T Consensus 636 ~~Cp~Cg~-~~~k~~-~~g~~~~~~~Cp~C~~ 665 (740)
T PRK07220 636 KVCEAHGL-NHIRII-NGGKRPWDLGCPQCNF 665 (740)
T ss_pred CCCCCCCC-ceEEEE-ecCCccceeeCCCCCC
Confidence 46888875 333333 223 567877775
No 498
>PRK09401 reverse gyrase; Reviewed
Probab=22.94 E-value=27 Score=34.29 Aligned_cols=25 Identities=20% Similarity=0.502 Sum_probs=16.5
Q ss_pred CCCCCCCCCCceeEeC-CCCceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFDH-SAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~-~~G~~vC~~CG~ 31 (172)
..||+||++ +.|. -.--+.|..|=-
T Consensus 8 ~~cpnc~g~---i~~~rl~~g~~c~~cl~ 33 (1176)
T PRK09401 8 NSCPNCGGD---ISDERLEKGLPCEKCLP 33 (1176)
T ss_pred ccCCCCCCc---CcHhHHhcCCcChhhCC
Confidence 369999984 3333 233488999864
No 499
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=22.90 E-value=48 Score=29.91 Aligned_cols=22 Identities=32% Similarity=0.736 Sum_probs=12.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEeCCCcc
Q 030755 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (172)
Q Consensus 4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~ 31 (172)
..|+.||-.... ....|..||-
T Consensus 525 ~~C~~CG~~g~~------~~~~CP~Cgs 546 (579)
T TIGR02487 525 DVCEDCGYTGEG------LNDKCPKCGS 546 (579)
T ss_pred ccCCCCCCCCCC------CCCcCcCCCC
Confidence 468888852110 1147888885
No 500
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=22.89 E-value=39 Score=20.04 Aligned_cols=11 Identities=27% Similarity=0.909 Sum_probs=8.8
Q ss_pred ceEeCCCccee
Q 030755 23 DTVCSECGLVL 33 (172)
Q Consensus 23 ~~vC~~CG~V~ 33 (172)
.++|.+||.-.
T Consensus 4 ~l~C~dCg~~F 14 (49)
T PF13451_consen 4 TLTCKDCGAEF 14 (49)
T ss_pred eEEcccCCCeE
Confidence 58999999754
Done!