Query gi|254780459|ref|YP_003064872.1| hypothetical protein CLIBASIA_01720 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 129
No_of_seqs 108 out of 275
Neff 6.5
Searched_HMMs 39220
Date Sun May 29 16:43:20 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780459.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 pfam09538 FYDLN_acid Protein o 100.0 3.1E-29 8E-34 199.8 5.4 48 1-48 1-48 (104)
2 TIGR02300 FYDLN_acid conserved 99.9 8.4E-28 2.1E-32 191.1 5.1 49 1-49 1-49 (157)
3 COG4530 Uncharacterized protei 99.9 1.3E-26 3.4E-31 183.7 4.0 126 1-128 1-128 (129)
4 smart00531 TFIIE Transcription 95.5 0.0095 2.4E-07 37.7 2.4 29 10-38 100-135 (147)
5 PRK10220 hypothetical protein; 95.4 0.0082 2.1E-07 38.1 1.8 30 11-40 5-34 (111)
6 pfam08271 TF_Zn_Ribbon TFIIB z 95.3 0.012 2.9E-07 37.2 2.2 30 10-39 1-32 (40)
7 PRK05654 acetyl-CoA carboxylas 95.0 0.0059 1.5E-07 39.0 0.2 32 9-40 30-63 (288)
8 pfam09986 DUF2225 Uncharacteri 94.9 0.016 4E-07 36.4 2.1 36 6-41 2-63 (214)
9 PRK00420 hypothetical protein; 94.5 0.026 6.6E-07 35.1 2.3 28 9-36 19-46 (107)
10 COG0846 SIR2 NAD-dependent pro 94.2 0.022 5.5E-07 35.5 1.5 29 10-38 123-159 (250)
11 PRK02625 DNA-directed RNA poly 94.0 0.022 5.6E-07 35.5 1.3 33 9-43 68-100 (627)
12 COG1326 Uncharacterized archae 94.0 0.031 7.9E-07 34.6 1.9 27 10-38 7-42 (201)
13 pfam07282 Transposase_35 Putat 93.0 0.061 1.6E-06 32.8 2.1 36 4-39 23-59 (69)
14 COG1645 Uncharacterized Zn-fin 93.0 0.043 1.1E-06 33.7 1.3 26 10-37 29-55 (131)
15 CHL00018 rpoC1 RNA polymerase 92.9 0.044 1.1E-06 33.7 1.3 35 9-45 66-103 (668)
16 PRK00564 hypA hydrogenase nick 92.9 0.06 1.5E-06 32.8 1.9 28 8-35 70-97 (117)
17 COG1996 RPC10 DNA-directed RNA 92.8 0.05 1.3E-06 33.3 1.4 27 10-36 7-34 (49)
18 PRK06450 threonine synthase; V 92.8 0.06 1.5E-06 32.8 1.8 28 9-39 3-30 (336)
19 COG0675 Transposase and inacti 92.5 0.078 2E-06 32.1 2.1 28 7-38 307-334 (364)
20 CHL00174 accD acetyl-CoA carbo 92.4 0.031 8E-07 34.6 -0.1 34 7-40 46-81 (305)
21 PRK07591 threonine synthase; V 92.4 0.067 1.7E-06 32.5 1.6 29 8-38 18-46 (422)
22 PRK08579 anaerobic ribonucleos 92.4 0.063 1.6E-06 32.7 1.5 23 10-35 567-589 (623)
23 PRK03824 hypA hydrogenase nick 92.3 0.064 1.6E-06 32.6 1.5 26 9-34 70-115 (135)
24 pfam08274 PhnA_Zn_Ribbon PhnA 92.3 0.073 1.9E-06 32.3 1.7 27 11-37 4-30 (30)
25 COG1066 Sms Predicted ATP-depe 92.2 0.079 2E-06 32.1 1.8 29 1-34 1-29 (456)
26 TIGR01405 polC_Gram_pos DNA po 92.1 0.082 2.1E-06 32.0 1.8 24 11-36 719-754 (1264)
27 TIGR00515 accD acetyl-CoA carb 91.9 0.043 1.1E-06 33.7 0.2 34 8-41 32-67 (292)
28 COG2816 NPY1 NTP pyrophosphohy 91.7 0.071 1.8E-06 32.4 1.1 29 8-36 110-139 (279)
29 TIGR00354 polC DNA polymerase 91.6 0.088 2.3E-06 31.8 1.5 25 9-38 679-703 (1173)
30 pfam10276 zf-CHCC Zinc-finger 91.6 0.085 2.2E-06 31.9 1.4 20 17-36 18-39 (40)
31 COG4391 Uncharacterized protei 91.6 0.13 3.3E-06 30.8 2.3 21 18-38 39-60 (62)
32 KOG2807 consensus 91.5 0.1 2.6E-06 31.4 1.8 30 7-39 274-303 (378)
33 COG1579 Zn-ribbon protein, pos 91.3 0.088 2.3E-06 31.8 1.3 29 8-36 196-231 (239)
34 pfam09723 CxxC_CxxC_SSSS Zinc 91.2 0.15 3.8E-06 30.4 2.4 25 11-35 7-35 (42)
35 smart00659 RPOLCX RNA polymera 91.2 0.11 2.8E-06 31.2 1.7 27 10-36 3-29 (44)
36 PRK12496 hypothetical protein; 91.2 0.078 2E-06 32.1 0.9 33 3-36 123-155 (166)
37 PRK03681 hypA hydrogenase nick 91.1 0.14 3.6E-06 30.5 2.1 27 9-35 70-96 (114)
38 COG2888 Predicted Zn-ribbon RN 91.0 0.1 2.6E-06 31.4 1.4 36 1-36 1-37 (61)
39 pfam03833 PolC_DP2 DNA polymer 91.0 0.11 2.7E-06 31.3 1.4 22 9-35 629-650 (852)
40 pfam09538 FYDLN_acid Protein o 90.8 0.32 8.2E-06 28.4 3.7 10 27-36 10-19 (104)
41 COG2816 NPY1 NTP pyrophosphohy 90.7 0.13 3.4E-06 30.7 1.7 23 4-31 124-146 (279)
42 COG4640 Predicted membrane pro 90.3 0.11 2.8E-06 31.2 1.0 26 10-38 2-27 (465)
43 PRK06260 threonine synthase; V 90.3 0.14 3.6E-06 30.5 1.6 29 10-39 4-32 (400)
44 TIGR02098 MJ0042_CXXC MJ0042 f 90.1 0.19 4.9E-06 29.8 2.1 28 10-37 3-38 (40)
45 PRK05978 hypothetical protein; 90.1 0.11 2.7E-06 31.3 0.8 34 5-38 30-65 (149)
46 PRK02995 DNA-directed RNA poly 90.1 0.16 4.1E-06 30.2 1.7 28 11-40 59-86 (1291)
47 PRK09001 DNA topoisomerase I; 90.1 0.2 5.1E-06 29.6 2.2 15 4-18 659-673 (869)
48 COG2888 Predicted Zn-ribbon RN 90.0 0.2 5E-06 29.7 2.1 32 4-35 22-59 (61)
49 pfam01155 HypA Hydrogenase exp 89.9 0.2 5.2E-06 29.6 2.1 26 9-35 69-94 (112)
50 PRK12380 hydrogenase nickel in 89.8 0.22 5.5E-06 29.4 2.2 27 8-35 69-95 (113)
51 COG0777 AccD Acetyl-CoA carbox 89.7 0.14 3.6E-06 30.6 1.2 34 7-40 26-61 (294)
52 TIGR01206 lysW lysine biosynth 89.6 0.28 7.1E-06 28.7 2.6 35 8-42 1-38 (54)
53 PRK00423 tfb transcription ini 89.6 0.24 6.2E-06 29.1 2.3 31 8-38 10-42 (310)
54 PRK12366 replication factor A; 89.2 0.2 5.2E-06 29.6 1.7 32 10-43 534-565 (649)
55 PRK06266 transcription initiat 89.1 0.13 3.4E-06 30.7 0.7 27 10-37 118-147 (178)
56 TIGR00373 TIGR00373 conserved 89.0 0.15 3.8E-06 30.4 0.9 26 11-36 113-140 (168)
57 pfam09297 zf-NADH-PPase NADH p 88.9 0.15 3.9E-06 30.4 0.8 20 1-20 13-32 (32)
58 COG2824 PhnA Uncharacterized Z 88.6 0.22 5.7E-06 29.3 1.5 31 10-40 4-34 (112)
59 pfam10571 UPF0547 Uncharacteri 88.5 0.22 5.6E-06 29.4 1.4 25 10-37 1-25 (26)
60 smart00834 CxxC_CXXC_SSSS Puta 88.4 0.26 6.6E-06 28.9 1.8 25 11-35 7-35 (41)
61 PRK00448 polC DNA polymerase I 88.4 0.27 7E-06 28.8 1.8 26 10-37 908-943 (1436)
62 PRK03754 DNA-directed RNA poly 87.9 0.22 5.7E-06 29.3 1.2 26 11-36 7-34 (49)
63 pfam05191 ADK_lid Adenylate ki 87.8 0.33 8.3E-06 28.3 2.0 28 9-36 1-31 (36)
64 LOAD_sir2 consensus 87.8 0.25 6.5E-06 29.0 1.4 34 8-41 117-158 (217)
65 COG1997 RPL43A Ribosomal prote 87.5 0.26 6.7E-06 28.9 1.3 29 8-38 34-65 (89)
66 TIGR00686 phnA alkylphosphonat 87.5 0.29 7.5E-06 28.6 1.6 32 10-41 3-34 (111)
67 cd01413 SIR2_Af2 SIR2_Af2: Arc 87.4 0.21 5.4E-06 29.5 0.8 31 9-39 113-149 (222)
68 COG1439 Predicted nucleic acid 87.4 0.26 6.7E-06 28.9 1.3 27 6-35 136-162 (177)
69 cd01412 SIRT5_Af1_CobB SIRT5_A 87.3 0.29 7.3E-06 28.7 1.4 33 9-41 109-145 (224)
70 PRK04023 DNA polymerase II lar 87.3 0.31 7.9E-06 28.5 1.6 21 9-34 633-653 (1128)
71 PRK00432 30S ribosomal protein 87.1 0.45 1.2E-05 27.4 2.3 29 8-36 22-52 (54)
72 COG1656 Uncharacterized conser 87.1 0.25 6.3E-06 29.1 1.0 29 10-38 98-142 (165)
73 pfam08996 zf-DNA_Pol DNA Polym 87.0 0.47 1.2E-05 27.4 2.4 35 8-42 17-61 (186)
74 PRK00481 NAD-dependent deacety 86.8 0.36 9.2E-06 28.0 1.7 32 9-40 122-156 (239)
75 pfam02146 SIR2 Sir2 family. Th 86.7 0.25 6.5E-06 29.0 0.9 32 9-40 104-142 (177)
76 pfam06677 Auto_anti-p27 Sjogre 86.2 0.49 1.2E-05 27.3 2.1 24 10-33 18-41 (41)
77 PRK11823 DNA repair protein Ra 86.2 0.47 1.2E-05 27.4 2.0 29 1-34 1-29 (454)
78 PRK02173 DNA-directed RNA poly 86.2 0.36 9.2E-06 28.1 1.4 30 11-40 65-99 (1438)
79 PRK00398 rpoP DNA-directed RNA 86.1 0.19 4.7E-06 29.8 -0.1 33 4-36 2-37 (52)
80 PRK09521 exosome complex RNA-b 86.1 0.36 9.1E-06 28.1 1.4 34 1-35 141-175 (187)
81 PRK09401 reverse gyrase; Revie 86.0 0.3 7.7E-06 28.5 1.0 24 10-36 678-701 (1176)
82 pfam04475 DUF555 Protein of un 85.9 0.33 8.4E-06 28.3 1.1 32 9-42 32-63 (102)
83 PRK09263 anaerobic ribonucleos 85.8 0.42 1.1E-05 27.7 1.6 25 10-34 642-667 (711)
84 PRK08271 anaerobic ribonucleos 85.7 0.4 1E-05 27.8 1.5 23 10-35 568-590 (625)
85 COG1571 Predicted DNA-binding 85.7 0.5 1.3E-05 27.2 2.0 34 8-41 349-382 (421)
86 COG2176 PolC DNA polymerase II 85.3 0.49 1.2E-05 27.2 1.8 25 10-36 915-949 (1444)
87 COG1545 Predicted nucleic-acid 85.1 0.43 1.1E-05 27.6 1.4 35 10-47 30-64 (140)
88 pfam03604 DNA_RNApol_7kD DNA d 84.9 0.46 1.2E-05 27.4 1.5 26 11-36 2-27 (32)
89 PRK07111 anaerobic ribonucleos 84.7 0.49 1.2E-05 27.3 1.5 21 10-34 648-668 (703)
90 PRK04023 DNA polymerase II lar 84.6 0.53 1.4E-05 27.0 1.7 13 7-19 643-655 (1128)
91 TIGR00354 polC DNA polymerase 84.4 0.46 1.2E-05 27.4 1.3 23 10-35 1091-1115(1173)
92 KOG2462 consensus 84.4 0.68 1.7E-05 26.4 2.1 33 4-36 125-171 (279)
93 PRK05580 primosome assembly pr 84.3 0.73 1.9E-05 26.2 2.3 31 6-36 410-441 (699)
94 cd01407 SIR2-fam SIR2 family o 84.3 0.47 1.2E-05 27.4 1.3 32 9-40 109-147 (218)
95 COG1110 Reverse gyrase [DNA re 84.3 0.4 1E-05 27.8 1.0 22 11-35 696-717 (1187)
96 COG1198 PriA Primosomal protei 84.0 0.67 1.7E-05 26.4 2.0 23 9-35 462-484 (730)
97 pfam03966 Trm112p Trm112p-like 83.7 0.46 1.2E-05 27.4 1.1 30 10-39 8-45 (47)
98 cd01410 SIRT7 SIRT7: Eukaryoti 83.5 0.55 1.4E-05 26.9 1.4 32 8-39 94-133 (206)
99 pfam05876 Terminase_GpA Phage 83.4 0.7 1.8E-05 26.3 1.9 29 11-39 202-242 (552)
100 TIGR02642 phage_xxxx uncharact 83.2 0.55 1.4E-05 26.9 1.3 33 2-34 175-207 (270)
101 PRK08402 replication factor A; 83.2 0.4 1E-05 27.8 0.6 29 11-39 216-245 (357)
102 COG1594 RPB9 DNA-directed RNA 83.1 0.86 2.2E-05 25.8 2.2 33 9-41 2-37 (113)
103 PRK05333 NAD-dependent deacety 82.5 0.33 8.4E-06 28.3 -0.1 14 26-39 179-192 (285)
104 COG1675 TFA1 Transcription ini 82.2 0.56 1.4E-05 26.9 1.0 25 10-37 114-143 (176)
105 pfam09862 DUF2089 Protein of u 82.0 0.55 1.4E-05 26.9 0.9 23 12-37 1-23 (113)
106 COG3364 Zn-ribbon containing p 81.9 0.35 8.8E-06 28.2 -0.1 26 10-35 3-29 (112)
107 PRK00241 nudC NADH pyrophospha 81.7 0.83 2.1E-05 25.9 1.7 29 8-36 99-128 (257)
108 cd01408 SIRT1 SIRT1: Eukaryoti 81.7 0.53 1.3E-05 27.0 0.7 32 8-39 115-153 (235)
109 TIGR00622 ssl1 transcription f 81.7 0.77 2E-05 26.0 1.6 28 11-41 3-30 (112)
110 cd00729 rubredoxin_SM Rubredox 81.4 1.2 3E-05 24.9 2.4 26 9-35 2-27 (34)
111 PRK08329 threonine synthase; V 81.4 0.81 2.1E-05 25.9 1.6 25 11-38 3-27 (348)
112 PRK00133 metG methionyl-tRNA s 81.3 0.92 2.3E-05 25.6 1.8 34 8-45 138-171 (666)
113 PRK03922 hypothetical protein; 81.2 0.72 1.8E-05 26.2 1.3 32 9-41 33-64 (113)
114 PRK13130 H/ACA RNA-protein com 81.1 0.78 2E-05 26.0 1.4 23 9-36 5-27 (54)
115 PRK13902 alaS lanyl-tRNA synth 81.0 0.71 1.8E-05 26.2 1.2 26 8-33 17-44 (898)
116 cd00350 rubredoxin_like Rubred 80.9 1.3 3.2E-05 24.7 2.4 26 9-35 1-26 (33)
117 PRK08197 threonine synthase; V 80.7 0.92 2.3E-05 25.6 1.7 29 8-38 5-33 (402)
118 COG3357 Predicted transcriptio 80.4 0.74 1.9E-05 26.2 1.1 27 11-37 60-87 (97)
119 PRK05638 threonine synthase; V 80.2 1.1 2.8E-05 25.1 1.9 28 8-38 1-28 (443)
120 PRK00762 hypA hydrogenase nick 80.0 0.8 2E-05 26.0 1.2 27 9-36 70-102 (124)
121 smart00647 IBR In Between Ring 79.9 1.3 3.4E-05 24.6 2.3 29 8-36 17-50 (64)
122 TIGR01351 adk adenylate kinase 79.8 1.2 3.1E-05 24.8 2.1 27 9-35 135-167 (232)
123 PRK00241 nudC NADH pyrophospha 79.6 0.75 1.9E-05 26.1 0.9 25 2-31 111-135 (257)
124 TIGR00416 sms DNA repair prote 79.5 0.95 2.4E-05 25.5 1.4 37 1-41 1-39 (481)
125 PRK12286 rpmF 50S ribosomal pr 79.3 1.1 2.8E-05 25.1 1.7 21 10-34 28-48 (59)
126 KOG2923 consensus 78.7 0.87 2.2E-05 25.7 1.0 25 11-36 24-54 (67)
127 cd01411 SIR2H SIR2H: Uncharact 78.6 0.8 2E-05 25.9 0.8 31 9-39 118-149 (225)
128 TIGR00143 hypF [NiFe] hydrogen 78.4 0.49 1.3E-05 27.2 -0.3 26 10-35 153-183 (799)
129 COG0484 DnaJ DnaJ-class molecu 78.3 1.2 3.1E-05 24.9 1.6 29 6-34 139-167 (371)
130 PRK11032 hypothetical protein; 78.1 1.3 3.3E-05 24.7 1.7 27 10-37 125-154 (160)
131 pfam01485 IBR IBR domain. The 77.5 1.7 4.2E-05 24.0 2.2 27 10-36 19-50 (64)
132 PRK12286 rpmF 50S ribosomal pr 77.2 0.95 2.4E-05 25.5 0.9 11 26-36 27-37 (59)
133 pfam01363 FYVE FYVE zinc finge 76.6 1.5 3.9E-05 24.2 1.8 28 9-37 9-36 (68)
134 COG5216 Uncharacterized conser 76.6 1.2 3.1E-05 24.8 1.3 25 11-36 24-54 (67)
135 COG1328 NrdD Oxygen-sensitive 76.3 1.3 3.3E-05 24.7 1.3 23 10-35 642-664 (700)
136 pfam04135 Nop10p Nucleolar RNA 76.1 1.6 4E-05 24.1 1.7 22 9-35 5-26 (53)
137 COG0068 HypF Hydrogenase matur 76.0 0.62 1.6E-05 26.6 -0.4 25 12-36 154-183 (750)
138 COG1998 RPS31 Ribosomal protei 75.9 1.2 3E-05 24.9 1.1 29 8-36 18-48 (51)
139 TIGR00375 TIGR00375 conserved 75.8 0.91 2.3E-05 25.6 0.5 34 4-37 240-277 (384)
140 smart00064 FYVE Protein presen 75.7 1.2 3.1E-05 24.8 1.1 34 3-37 1-37 (68)
141 COG2260 Predicted Zn-ribbon RN 75.2 1.5 3.8E-05 24.3 1.4 23 9-36 5-27 (59)
142 COG5151 SSL1 RNA polymerase II 75.1 0.93 2.4E-05 25.6 0.3 29 9-40 308-336 (421)
143 PRK09603 DNA-directed RNA poly 75.0 1.6 4E-05 24.2 1.5 21 15-36 1451-1472(2890)
144 pfam00406 ADK Adenylate kinase 74.9 1.5 3.8E-05 24.3 1.4 30 6-35 119-151 (186)
145 KOG2593 consensus 74.4 1.2 3.1E-05 24.8 0.8 28 11-38 130-165 (436)
146 PRK07225 DNA-directed RNA poly 74.1 2.2 5.6E-05 23.3 2.1 25 10-34 545-570 (605)
147 KOG2907 consensus 73.9 0.93 2.4E-05 25.6 0.1 37 9-45 7-44 (116)
148 cd01409 SIRT4 SIRT4: Eukaryoti 73.8 1.9 4.7E-05 23.7 1.6 15 27-41 170-184 (260)
149 COG3809 Uncharacterized protei 73.7 2.9 7.3E-05 22.6 2.6 27 10-36 2-31 (88)
150 COG1405 SUA7 Transcription ini 73.6 2.6 6.6E-05 22.8 2.3 33 10-42 2-36 (285)
151 PRK08270 anaerobic ribonucleos 72.8 2.2 5.5E-05 23.3 1.8 23 10-36 626-648 (681)
152 PRK08166 NADH dehydrogenase su 72.8 1.4 3.5E-05 24.5 0.7 18 17-34 216-233 (858)
153 pfam11672 DUF3268 Protein of u 72.3 1.5 3.8E-05 24.3 0.8 10 27-36 32-41 (102)
154 COG1096 Predicted RNA-binding 72.1 2.4 6.1E-05 23.0 1.8 31 4-35 143-174 (188)
155 pfam01783 Ribosomal_L32p Ribos 72.0 2.2 5.6E-05 23.2 1.7 20 10-33 27-46 (56)
156 pfam06524 NOA36 NOA36 protein. 72.0 6 0.00015 20.6 3.9 28 10-38 183-221 (314)
157 PRK00415 rps27e 30S ribosomal 71.7 2.9 7.3E-05 22.5 2.2 29 8-36 10-40 (59)
158 TIGR02605 CxxC_CxxC_SSSS putat 71.6 2.3 5.9E-05 23.1 1.7 25 11-35 7-36 (43)
159 PRK05823 consensus 71.3 3.6 9.1E-05 22.0 2.6 11 8-18 600-610 (691)
160 pfam09845 DUF2072 Zn-ribbon co 70.8 1.6 4E-05 24.1 0.7 27 10-36 2-29 (121)
161 PRK11827 hypothetical protein; 70.7 2.3 6E-05 23.1 1.6 31 9-39 8-39 (60)
162 pfam01927 DUF82 Protein of unk 70.1 1.9 5E-05 23.6 1.0 26 11-36 92-133 (146)
163 pfam12172 DUF35_N Rubredoxin-l 70.0 2.9 7.5E-05 22.5 1.9 22 10-34 12-33 (37)
164 TIGR01374 soxD sarcosine oxida 69.9 2.4 6.2E-05 23.0 1.5 16 27-42 2-17 (85)
165 COG1327 Predicted transcriptio 69.6 1.5 3.9E-05 24.2 0.4 39 8-46 27-71 (156)
166 smart00661 RPOL9 RNA polymeras 69.6 3 7.5E-05 22.5 1.9 32 10-41 1-35 (52)
167 cd01675 RNR_III Class III ribo 69.4 2.6 6.7E-05 22.8 1.6 22 11-35 520-541 (555)
168 cd00296 SIR2 SIR2 superfamily 69.3 2.5 6.5E-05 22.9 1.5 32 9-40 113-148 (222)
169 COG5257 GCD11 Translation init 68.9 2.9 7.3E-05 22.6 1.7 25 8-36 56-82 (415)
170 KOG1818 consensus 68.4 2.2 5.5E-05 23.3 1.0 34 3-37 159-192 (634)
171 PRK00349 uvrA excinuclease ABC 68.1 3.2 8.1E-05 22.3 1.8 37 6-42 249-297 (944)
172 cd04476 RPA1_DBD_C RPA1_DBD_C: 67.9 2.7 6.9E-05 22.7 1.4 27 10-36 35-61 (166)
173 COG5349 Uncharacterized protei 67.5 1.7 4.3E-05 24.0 0.3 33 5-37 17-51 (126)
174 pfam06044 DRP Dam-replacing fa 67.4 2.4 6.2E-05 23.0 1.1 32 10-41 32-68 (254)
175 TIGR02349 DnaJ_bact chaperone 67.4 3.2 8.2E-05 22.3 1.7 27 8-34 170-196 (386)
176 TIGR01031 rpmF_bact ribosomal 67.1 3.1 7.8E-05 22.4 1.5 22 9-34 27-48 (56)
177 KOG3623 consensus 67.0 2.7 6.9E-05 22.7 1.2 33 5-37 277-320 (1007)
178 PRK03564 formate dehydrogenase 67.0 4.7 0.00012 21.2 2.4 35 4-38 181-224 (307)
179 COG0423 GRS1 Glycyl-tRNA synth 66.7 2.3 5.8E-05 23.2 0.8 27 11-37 90-140 (558)
180 PRK07141 DNA topoisomerase I; 66.6 7.8 0.0002 19.9 3.5 43 11-53 567-617 (622)
181 cd00065 FYVE FYVE domain; Zinc 66.3 2.5 6.5E-05 22.9 1.0 26 10-36 3-28 (57)
182 PTZ00088 adenylate kinase 1; P 65.7 3.4 8.6E-05 22.1 1.5 29 6-34 123-162 (225)
183 PRK03976 rpl37ae 50S ribosomal 65.2 3.9 0.0001 21.7 1.8 30 7-38 34-66 (90)
184 COG0498 ThrC Threonine synthas 65.2 2.1 5.5E-05 23.3 0.4 29 10-39 6-34 (411)
185 pfam01475 FUR Ferric uptake re 64.7 4 0.0001 21.7 1.7 34 5-38 54-92 (120)
186 COG2051 RPS27A Ribosomal prote 64.4 4.4 0.00011 21.4 1.9 28 9-36 19-48 (67)
187 COG1040 ComFC Predicted amidop 64.2 0.94 2.4E-05 25.5 -1.6 27 10-39 25-51 (225)
188 pfam01780 Ribosomal_L37ae Ribo 64.1 3.4 8.5E-05 22.1 1.3 30 7-38 33-65 (90)
189 PRK04338 N(2),N(2)-dimethylgua 63.8 5.3 0.00014 20.9 2.3 32 5-37 235-266 (376)
190 TIGR02487 NrdD anaerobic ribon 63.8 3.6 9.2E-05 22.0 1.4 25 10-35 591-618 (655)
191 PRK10767 chaperone protein Dna 63.1 4.7 0.00012 21.2 1.9 32 5-36 137-168 (376)
192 PRK00464 nrdR transcriptional 62.5 3.2 8.2E-05 22.2 0.9 39 9-47 28-72 (149)
193 PRK05258 DNA-directed RNA poly 62.2 4.2 0.00011 21.5 1.5 27 11-39 59-85 (1204)
194 PHA02325 hypothetical protein 61.6 4.2 0.00011 21.5 1.4 14 25-38 4-17 (79)
195 KOG1088 consensus 61.6 3.3 8.5E-05 22.1 0.9 12 27-38 99-110 (124)
196 pfam04216 FdhE Protein involve 61.5 4.3 0.00011 21.5 1.4 30 8-37 165-202 (283)
197 COG1933 Archaeal DNA polymeras 61.5 2.1 5.4E-05 23.4 -0.1 27 9-38 167-195 (253)
198 COG2835 Uncharacterized conser 61.5 5.1 0.00013 21.0 1.8 30 10-39 9-39 (60)
199 PRK10996 thioredoxin 2; Provis 61.0 5.1 0.00013 21.0 1.7 23 9-35 2-31 (139)
200 smart00350 MCM minichromosome 60.8 6.4 0.00016 20.4 2.2 25 10-34 38-69 (509)
201 pfam09332 Mcm10 Mcm10 replicat 60.4 8.1 0.00021 19.8 2.7 42 7-48 283-328 (346)
202 PTZ00255 60S ribosomal protein 60.1 4.5 0.00012 21.3 1.3 30 7-38 34-66 (90)
203 COG2401 ABC-type ATPase fused 59.7 3.3 8.4E-05 22.2 0.6 28 11-41 132-159 (593)
204 cd01121 Sms Sms (bacterial rad 59.3 5.1 0.00013 21.0 1.5 21 11-34 2-22 (372)
205 PRK08493 NADH dehydrogenase su 59.3 4 0.0001 21.6 1.0 19 18-36 231-249 (819)
206 KOG2879 consensus 58.9 3 7.7E-05 22.4 0.3 30 9-38 239-288 (298)
207 COG1885 Uncharacterized protei 58.5 3 7.6E-05 22.4 0.2 23 19-41 42-64 (115)
208 pfam10083 DUF2321 Uncharacteri 57.9 4.8 0.00012 21.2 1.2 30 9-38 39-80 (158)
209 pfam02005 TRM N2,N2-dimethylgu 57.8 6.6 0.00017 20.3 1.9 33 5-37 235-269 (375)
210 COG1241 MCM2 Predicted ATPase 57.7 6.9 0.00017 20.2 1.9 23 10-32 130-157 (682)
211 KOG4451 consensus 57.7 1.9 5E-05 23.6 -0.9 34 10-52 250-283 (286)
212 COG1503 eRF1 Peptide chain rel 57.3 4.6 0.00012 21.3 1.0 28 11-38 329-360 (411)
213 pfam07754 DUF1610 Domain of un 57.0 4.7 0.00012 21.2 1.0 12 25-36 9-20 (26)
214 PRK09129 NADH dehydrogenase su 56.9 4.7 0.00012 21.3 1.0 17 18-34 211-227 (777)
215 TIGR03670 rpoB_arch DNA-direct 56.0 7.7 0.0002 19.9 1.9 23 11-33 540-563 (599)
216 COG5516 Conserved protein cont 55.9 4.9 0.00013 21.1 0.9 34 2-35 141-180 (196)
217 KOG4718 consensus 54.9 4.5 0.00011 21.4 0.6 28 10-38 195-228 (235)
218 KOG0978 consensus 54.8 1.4 3.7E-05 24.4 -1.9 29 11-41 645-693 (698)
219 COG1499 NMD3 NMD protein affec 54.7 6.8 0.00017 20.3 1.5 27 12-38 24-55 (355)
220 pfam03367 zf-ZPR1 ZPR1 zinc-fi 54.6 3.9 0.0001 21.7 0.3 25 11-36 3-40 (160)
221 PRK07860 NADH dehydrogenase su 54.6 4.9 0.00013 21.1 0.8 18 17-34 228-245 (809)
222 pfam00471 Ribosomal_L33 Riboso 54.1 7.4 0.00019 20.0 1.6 27 8-34 4-40 (48)
223 pfam04981 NMD3 NMD3 family. Th 53.8 3.1 7.9E-05 22.4 -0.4 33 6-38 10-47 (237)
224 cd04511 Nudix_Hydrolase_4 Memb 53.6 4.4 0.00011 21.4 0.4 31 12-45 1-31 (130)
225 KOG2324 consensus 53.0 6.6 0.00017 20.4 1.2 22 10-34 228-255 (457)
226 PRK08174 DNA topoisomerase III 52.7 13 0.00034 18.5 2.7 32 9-40 615-652 (670)
227 COG4888 Uncharacterized Zn rib 52.7 9 0.00023 19.5 1.9 34 6-39 19-59 (104)
228 pfam10146 zf-C4H2 Zinc finger- 52.7 3.9 0.0001 21.7 0.0 33 11-52 186-218 (220)
229 KOG4080 consensus 52.7 3.5 8.8E-05 22.1 -0.3 23 10-36 94-116 (176)
230 COG0272 Lig NAD-dependent DNA 51.2 7.2 0.00018 20.1 1.2 12 25-36 403-414 (667)
231 pfam07975 C1_4 TFIIH C1-like d 51.0 8 0.0002 19.8 1.4 27 11-37 1-30 (48)
232 smart00532 LIGANc Ligase N fam 51.0 7.2 0.00018 20.1 1.1 11 26-36 399-409 (441)
233 PRK04011 peptide chain release 50.9 11 0.00028 18.9 2.1 26 11-36 329-358 (409)
234 TIGR02386 rpoC_TIGR DNA-direct 50.9 8 0.0002 19.8 1.4 32 12-48 53-86 (1552)
235 COG5134 Uncharacterized conser 50.3 5.1 0.00013 21.0 0.3 20 18-37 68-90 (272)
236 COG1379 PHP family phosphoeste 49.8 3.5 9E-05 22.0 -0.6 34 4-37 239-276 (403)
237 PRK12268 methionyl-tRNA synthe 49.8 12 0.0003 18.8 2.1 31 11-45 143-173 (558)
238 cd02008 TPP_IOR_alpha Thiamine 49.7 7.9 0.0002 19.8 1.2 13 23-35 1-13 (178)
239 PRK11788 hypothetical protein; 49.3 7.6 0.00019 19.9 1.1 23 9-34 354-376 (389)
240 pfam04161 Arv1 Arv1-like famil 49.1 5.3 0.00013 20.9 0.2 27 11-37 2-35 (194)
241 PRK00279 adk adenylate kinase; 49.0 9.6 0.00024 19.3 1.5 29 8-36 126-157 (215)
242 pfam09567 RE_MamI MamI restric 48.7 5 0.00013 21.1 0.0 23 10-35 89-111 (350)
243 pfam01667 Ribosomal_S27e Ribos 48.0 13 0.00034 18.4 2.2 29 8-36 6-36 (55)
244 COG5560 UBP12 Ubiquitin C-term 48.0 3.4 8.7E-05 22.1 -0.9 44 6-49 405-451 (823)
245 TIGR00100 hypA hydrogenase nic 48.0 8.4 0.00021 19.7 1.1 26 10-35 79-108 (128)
246 COG0333 RpmF Ribosomal protein 47.7 6.6 0.00017 20.4 0.5 21 10-34 28-48 (57)
247 KOG4139 consensus 47.5 4.7 0.00012 21.2 -0.3 18 6-23 296-313 (520)
248 PRK11866 2-oxoacid ferredoxin 47.3 7.2 0.00018 20.1 0.7 25 16-40 5-29 (286)
249 PRK09462 fur ferric uptake reg 47.2 14 0.00035 18.4 2.1 33 6-38 65-102 (148)
250 COG1655 Uncharacterized protei 47.1 6.1 0.00016 20.5 0.3 14 6-19 16-29 (267)
251 pfam02150 RNA_POL_M_15KD RNA p 47.0 6.3 0.00016 20.5 0.3 30 10-39 2-33 (35)
252 pfam05766 NinG Bacteriophage L 46.8 4.8 0.00012 21.2 -0.3 29 8-36 5-34 (188)
253 pfam09526 DUF2387 Probable met 46.7 10 0.00026 19.2 1.3 26 11-36 10-40 (61)
254 pfam08882 Acetone_carb_G Aceto 46.4 7.2 0.00018 20.1 0.6 14 28-41 70-83 (106)
255 PRK02935 hypothetical protein; 46.3 7.4 0.00019 20.0 0.6 25 10-35 70-94 (117)
256 pfam11023 DUF2614 Protein of u 46.2 7.5 0.00019 20.0 0.6 25 10-35 70-94 (114)
257 PRK07956 ligA NAD-dependent DN 46.1 9.3 0.00024 19.4 1.1 24 8-31 403-427 (668)
258 PRK08566 DNA-directed RNA poly 45.8 3.7 9.4E-05 21.9 -1.0 12 24-35 143-154 (881)
259 COG0735 Fur Fe2+/Zn2+ uptake r 45.7 14 0.00035 18.4 1.9 31 9-39 72-106 (145)
260 pfam08646 Rep_fac-A_C Replicat 45.5 12 0.00032 18.7 1.6 28 10-37 19-48 (146)
261 PHA00733 hypothetical protein 45.4 5.3 0.00014 20.9 -0.2 28 10-37 93-129 (147)
262 cd00924 Cyt_c_Oxidase_Vb Cytoc 45.1 13 0.00033 18.6 1.7 26 15-40 67-93 (97)
263 pfam10080 DUF2318 Predicted me 44.9 8.2 0.00021 19.8 0.6 32 11-42 37-68 (102)
264 pfam12387 Peptidase_C74 Pestiv 44.9 7.9 0.0002 19.8 0.6 25 10-38 163-187 (200)
265 TIGR01384 TFS_arch transcripti 44.6 8.2 0.00021 19.8 0.6 28 11-38 2-32 (111)
266 pfam06676 DUF1178 Protein of u 44.0 13 0.00033 18.6 1.5 33 11-44 7-50 (145)
267 PTZ00083 40S ribosomal protein 44.0 15 0.00038 18.2 1.8 26 11-36 37-64 (85)
268 COG0375 HybF Zn finger protein 44.0 9.8 0.00025 19.3 0.9 24 11-35 72-95 (115)
269 TIGR03676 aRF1/eRF1 peptide ch 43.8 17 0.00045 17.7 2.2 26 11-36 322-352 (403)
270 cd00730 rubredoxin Rubredoxin; 43.8 12 0.00031 18.7 1.4 29 6-35 15-43 (50)
271 COG3877 Uncharacterized protei 43.7 10 0.00027 19.1 1.0 25 10-37 7-31 (122)
272 pfam11789 zf-Nse Zinc-finger o 43.7 12 0.00032 18.6 1.4 33 10-46 12-44 (57)
273 TIGR00108 eRF peptide chain re 43.4 13 0.00034 18.4 1.6 30 9-38 332-372 (425)
274 PRK08620 DNA topoisomerase III 43.3 17 0.00043 17.8 2.1 13 25-37 647-659 (726)
275 COG1592 Rubrerythrin [Energy p 43.0 10 0.00026 19.2 0.9 10 27-36 135-144 (166)
276 pfam00684 DnaJ_CXXCXGXG DnaJ c 42.8 18 0.00047 17.6 2.2 29 6-34 8-36 (79)
277 pfam10071 DUF2310 Zn-ribbon-co 42.4 9.8 0.00025 19.3 0.7 13 27-39 222-234 (259)
278 pfam02591 DUF164 Putative zinc 42.4 8.3 0.00021 19.7 0.4 28 8-35 21-55 (56)
279 PRK11595 gluconate periplasmic 42.3 9.2 0.00023 19.5 0.6 24 10-36 21-44 (227)
280 pfam06906 DUF1272 Protein of u 42.3 9.9 0.00025 19.3 0.7 11 27-37 42-52 (57)
281 TIGR02390 RNA_pol_rpoA1 DNA-di 42.1 4.6 0.00012 21.3 -1.0 28 18-45 139-166 (901)
282 PTZ00303 phosphatidylinositol 42.0 13 0.00033 18.5 1.3 33 3-35 450-490 (1374)
283 COG1779 C4-type Zn-finger prot 41.8 11 0.00027 19.0 0.9 37 1-37 6-54 (201)
284 KOG3014 consensus 41.7 10 0.00026 19.2 0.7 15 5-19 29-47 (257)
285 PRK12336 translation initiatio 41.6 25 0.00065 16.8 2.8 28 10-37 99-130 (201)
286 pfam07503 zf-HYPF HypF finger. 41.0 5.7 0.00015 20.7 -0.6 28 11-38 1-33 (35)
287 KOG3084 consensus 40.9 14 0.00034 18.4 1.2 29 9-37 150-184 (345)
288 pfam01215 COX5B Cytochrome c o 40.7 16 0.0004 18.0 1.6 25 16-40 70-95 (99)
289 TIGR00575 dnlj DNA ligase, NAD 40.5 12 0.00031 18.7 1.0 14 24-37 409-422 (706)
290 pfam11781 RRN7 RNA polymerase 40.4 12 0.00031 18.7 0.9 30 7-36 6-35 (36)
291 PRK10436 hypothetical protein; 40.3 13 0.00032 18.6 1.0 31 6-36 349-392 (461)
292 TIGR02109 PQQ_syn_pqqE coenzym 40.1 12 0.0003 18.8 0.8 14 24-37 16-29 (363)
293 COG4031 Predicted metal-bindin 40.0 14 0.00034 18.4 1.1 20 11-35 2-21 (227)
294 pfam11706 zf-CGNR CGNR zinc fi 39.5 17 0.00044 17.8 1.6 26 10-35 3-34 (44)
295 PRK07726 DNA topoisomerase III 39.4 19 0.00049 17.5 1.9 27 11-38 632-663 (716)
296 pfam07191 DUF1407 Protein of u 39.3 16 0.00042 17.9 1.5 27 7-37 15-41 (70)
297 pfam12230 PRP21_like_P Pre-mRN 39.1 13 0.00032 18.6 0.9 16 26-41 162-177 (223)
298 pfam08792 A2L_zn_ribbon A2L zi 38.8 9.7 0.00025 19.3 0.3 28 10-37 4-32 (33)
299 PRK09919 hypothetical protein; 38.8 12 0.0003 18.8 0.7 17 25-41 7-23 (114)
300 TIGR00280 L37a ribosomal prote 38.5 12 0.00031 18.7 0.7 29 7-37 34-65 (92)
301 PRK12267 methionyl-tRNA synthe 38.5 15 0.00039 18.1 1.2 27 11-37 127-154 (644)
302 KOG0909 consensus 38.3 22 0.00056 17.1 2.0 45 6-50 158-224 (500)
303 TIGR02676 cas_provis_2 CRISPR- 37.1 12 0.00032 18.6 0.6 10 27-36 973-982 (1104)
304 PRK12860 transcriptional activ 37.1 23 0.00058 17.1 1.9 37 10-46 135-171 (189)
305 COG0551 TopA Zn-finger domain 37.0 21 0.00054 17.3 1.7 11 7-17 58-68 (140)
306 TIGR02387 rpoC1_cyan DNA-direc 36.9 15 0.00038 18.2 0.9 29 12-42 64-92 (625)
307 pfam04423 Rad50_zn_hook Rad50 36.8 13 0.00034 18.4 0.7 14 28-41 22-35 (54)
308 PRK04173 glycyl-tRNA synthetas 36.5 15 0.00038 18.2 0.9 25 11-35 90-137 (460)
309 COG3677 Transposase and inacti 36.3 19 0.00047 17.6 1.4 34 8-41 29-68 (129)
310 COG5595 Zn-ribbon-containing, 36.2 13 0.00034 18.4 0.6 12 27-38 219-230 (256)
311 COG1867 TRM1 N2,N2-dimethylgua 36.1 22 0.00056 17.1 1.7 34 5-38 236-269 (380)
312 pfam10605 3HBOH 3HB-oligomer h 35.8 11 0.00029 18.9 0.2 22 4-25 164-191 (689)
313 PRK02244 DNA-directed RNA poly 35.8 16 0.0004 18.0 0.9 12 25-36 18-29 (44)
314 TIGR02865 spore_II_E stage II 35.5 14 0.00035 18.4 0.6 11 8-18 378-388 (794)
315 cd07153 Fur_like Ferric uptake 35.4 24 0.00061 16.9 1.8 25 15-39 58-86 (116)
316 pfam09237 GAGA GAGA factor. Me 35.4 5.8 0.00015 20.7 -1.3 17 21-37 19-35 (54)
317 PRK05778 2-oxoglutarate ferred 35.0 19 0.00049 17.5 1.3 26 16-41 7-33 (306)
318 KOG1597 consensus 34.9 23 0.00058 17.0 1.6 30 11-40 2-35 (308)
319 pfam09706 Cas_CXXC_CXXC CRISPR 34.5 14 0.00035 18.4 0.5 18 19-36 44-61 (69)
320 pfam06221 zf-C2HC5 Putative zi 34.4 12 0.00031 18.7 0.1 27 10-36 16-42 (54)
321 TIGR00781 ccoO cytochrome c ox 34.3 14 0.00036 18.3 0.5 13 5-24 96-108 (234)
322 KOG1812 consensus 34.1 20 0.00052 17.3 1.3 26 10-37 307-334 (384)
323 TIGR00595 priA primosomal prot 34.0 20 0.00051 17.4 1.2 24 9-36 253-276 (524)
324 PRK08173 DNA topoisomerase III 33.9 28 0.00071 16.5 2.0 27 11-38 626-652 (857)
325 PRK00635 excinuclease ABC subu 33.7 26 0.00067 16.7 1.8 27 7-33 242-275 (1809)
326 COG2093 DNA-directed RNA polym 33.5 18 0.00047 17.6 1.0 24 9-35 4-27 (64)
327 cd02037 MRP-like MRP (Multiple 33.1 22 0.00057 17.1 1.3 16 22-37 128-143 (169)
328 COG3813 Uncharacterized protei 32.9 13 0.00034 18.5 0.2 15 23-37 38-52 (84)
329 PRK10391 oriC-binding nucleoid 32.8 16 0.0004 18.0 0.5 18 10-27 47-64 (71)
330 PRK00085 recO DNA repair prote 32.8 26 0.00067 16.7 1.7 26 10-35 151-181 (235)
331 KOG3608 consensus 32.6 2.8 7.2E-05 22.6 -3.3 34 11-44 209-255 (467)
332 KOG0119 consensus 32.6 21 0.00054 17.2 1.2 34 9-42 261-301 (554)
333 COG3880 Modulator of heat shoc 32.6 3.1 7.9E-05 22.3 -3.1 38 3-40 62-106 (176)
334 COG5270 PUA domain (predicted 32.4 22 0.00056 17.2 1.2 32 10-41 27-58 (202)
335 KOG2684 consensus 32.3 17 0.00045 17.7 0.7 27 9-35 203-236 (412)
336 KOG3576 consensus 32.3 5.6 0.00014 20.8 -1.8 26 11-36 147-183 (267)
337 KOG1734 consensus 31.9 11 0.00027 19.1 -0.5 15 28-42 272-286 (328)
338 PRK00912 ribonuclease P protei 31.8 16 0.00041 18.0 0.5 12 16-27 3-14 (237)
339 PRK00366 ispG 4-hydroxy-3-meth 31.5 16 0.00041 18.0 0.4 29 11-41 254-283 (367)
340 PRK00750 lysK lysyl-tRNA synth 31.4 42 0.0011 15.4 2.5 30 11-40 184-220 (513)
341 pfam01428 zf-AN1 AN1-like Zinc 31.3 21 0.00053 17.3 1.0 20 15-38 6-25 (43)
342 COG1029 FwdB Formylmethanofura 31.0 17 0.00045 17.7 0.5 12 25-36 4-15 (429)
343 pfam06827 zf-FPG_IleRS Zinc fi 31.0 26 0.00066 16.7 1.4 24 11-34 3-29 (30)
344 TIGR03031 cas_csx12 CRISPR-ass 31.0 18 0.00047 17.6 0.6 10 27-36 761-770 (802)
345 pfam01753 zf-MYND MYND finger. 30.7 35 0.00088 15.9 2.0 21 12-36 1-21 (39)
346 pfam08421 Methyltransf_13 Hypo 30.7 28 0.00072 16.5 1.6 17 12-28 1-21 (78)
347 pfam04551 GcpE GcpE protein. I 30.7 17 0.00043 17.8 0.4 27 13-41 245-272 (345)
348 pfam04035 consensus 30.7 21 0.00053 17.3 0.9 22 10-35 2-23 (60)
349 pfam08772 NOB1_Zn_bind Nin one 30.4 21 0.00053 17.3 0.8 23 11-35 11-33 (73)
350 pfam10058 DUF2296 Predicted in 30.2 15 0.00037 18.2 0.0 14 23-36 16-29 (51)
351 PRK00566 DNA-directed RNA poly 30.1 27 0.00069 16.6 1.4 13 25-37 70-82 (1284)
352 KOG1859 consensus 30.1 29 0.00073 16.4 1.5 24 11-34 675-716 (1096)
353 COG0143 MetG Methionyl-tRNA sy 30.0 31 0.00078 16.2 1.6 34 11-45 128-174 (558)
354 KOG3053 consensus 30.0 14 0.00036 18.3 -0.1 38 8-45 48-90 (293)
355 pfam04959 ARS2 Arsenite-resist 30.0 19 0.00049 17.5 0.6 11 9-19 77-87 (211)
356 COG1013 PorB Pyruvate:ferredox 29.9 19 0.00047 17.6 0.5 19 25-43 14-32 (294)
357 pfam12523 DUF3725 Protein of u 29.6 15 0.00039 18.1 0.0 22 14-35 47-68 (74)
358 PRK00595 rpmG 50S ribosomal pr 29.5 30 0.00076 16.3 1.5 28 7-34 8-45 (53)
359 COG5220 TFB3 Cdk activating ki 29.4 4.3 0.00011 21.5 -2.8 24 10-35 37-62 (314)
360 pfam09855 DUF2082 Nucleic-acid 28.9 21 0.00054 17.2 0.6 26 11-36 2-47 (64)
361 PRK07220 DNA topoisomerase I; 28.8 49 0.0013 15.0 2.6 11 25-35 634-644 (740)
362 KOG2906 consensus 28.8 33 0.00085 16.0 1.7 40 11-50 3-45 (105)
363 COG5017 Uncharacterized conser 28.7 11 0.00029 18.9 -0.8 12 14-25 5-16 (161)
364 KOG2071 consensus 28.6 20 0.0005 17.5 0.4 12 10-21 419-430 (579)
365 pfam11709 Mit_ribos_Mrp51 Mito 28.5 29 0.00074 16.4 1.3 17 1-17 46-62 (302)
366 TIGR01054 rgy reverse gyrase; 28.5 25 0.00063 16.8 0.9 27 11-37 756-786 (1843)
367 KOG4537 consensus 28.5 9.7 0.00025 19.3 -1.1 27 10-36 41-67 (178)
368 KOG2989 consensus 28.4 17 0.00043 17.8 0.1 14 24-37 75-88 (253)
369 TIGR02026 BchE magnesium-proto 28.1 31 0.00079 16.2 1.4 25 14-38 466-490 (506)
370 TIGR02159 PA_CoA_Oxy4 phenylac 28.1 27 0.00069 16.6 1.1 19 18-36 103-121 (152)
371 COG3464 Transposase and inacti 27.7 37 0.00093 15.8 1.7 28 10-37 39-88 (402)
372 pfam04997 RNA_pol_Rpb1_1 RNA p 27.6 30 0.00076 16.3 1.2 12 9-20 54-65 (330)
373 PRK11295 hypothetical protein; 27.3 15 0.00038 18.2 -0.4 22 22-43 20-41 (115)
374 COG2023 RPR2 RNase P subunit R 27.2 30 0.00076 16.3 1.2 28 9-36 56-92 (105)
375 COG2993 CcoO Cbb3-type cytochr 27.1 22 0.00056 17.1 0.5 17 5-21 98-117 (227)
376 COG4049 Uncharacterized protei 26.8 16 0.0004 18.0 -0.3 11 27-37 18-28 (65)
377 KOG3352 consensus 26.6 38 0.00096 15.7 1.6 25 15-39 121-146 (153)
378 TIGR02986 restrict_Alw26I type 26.5 26 0.00066 16.7 0.7 11 10-20 86-96 (461)
379 COG4306 Uncharacterized protei 26.1 20 0.00051 17.4 0.1 31 8-38 38-80 (160)
380 TIGR00411 redox_disulf_1 redox 26.1 25 0.00065 16.7 0.7 11 25-35 7-17 (82)
381 COG0178 UvrA Excinuclease ATPa 26.0 42 0.0011 15.4 1.7 36 7-42 243-290 (935)
382 cd00022 BIR Baculoviral inhibi 25.9 34 0.00086 16.0 1.2 19 19-37 26-45 (69)
383 KOG3475 consensus 25.9 13 0.00034 18.5 -0.8 29 4-34 6-39 (92)
384 pfam05280 FlhC Flagellar trans 25.9 55 0.0014 14.7 2.3 32 11-42 136-167 (176)
385 pfam06750 DiS_P_DiS Bacterial 25.9 24 0.0006 17.0 0.4 33 9-41 27-67 (86)
386 pfam10367 Vps39_2 Vacuolar sor 25.9 20 0.0005 17.4 0.0 14 6-19 75-88 (109)
387 pfam09889 DUF2116 Uncharacteri 25.8 25 0.00063 16.8 0.6 14 28-41 5-18 (59)
388 KOG3507 consensus 25.8 31 0.00078 16.3 1.0 28 9-36 20-47 (62)
389 TIGR00201 comF comF family pro 25.7 34 0.00088 15.9 1.3 21 12-36 1-22 (207)
390 PRK11088 rrmA 23S rRNA methylt 25.7 37 0.00094 15.8 1.4 27 11-39 4-30 (272)
391 COG4957 Predicted transcriptio 25.2 12 0.00032 18.7 -1.1 15 10-24 77-91 (148)
392 cd03038 GST_N_etherase_LigE GS 24.9 37 0.00095 15.7 1.3 18 17-34 1-21 (84)
393 pfam04780 DUF629 Protein of un 24.7 19 0.00047 17.6 -0.3 10 12-21 60-69 (466)
394 PRK11670 putative ATPase; Prov 24.6 35 0.00089 15.9 1.1 15 10-24 281-295 (369)
395 PRK07758 hypothetical protein; 24.3 23 0.00059 17.0 0.2 30 9-40 7-36 (95)
396 TIGR03318 YdfZ_fam putative se 24.2 29 0.00073 16.4 0.6 12 17-28 1-12 (65)
397 COG5415 Predicted integral mem 24.1 46 0.0012 15.2 1.7 30 8-37 191-225 (251)
398 pfam10013 DUF2256 Uncharacteri 24.1 35 0.00088 15.9 1.0 11 27-37 9-19 (42)
399 KOG0478 consensus 24.0 43 0.0011 15.4 1.5 27 11-37 266-297 (804)
400 pfam06090 Ins_P5_2-kin Inosito 24.0 13 0.00032 18.6 -1.2 32 3-34 125-166 (301)
401 PRK05452 anaerobic nitric oxid 23.9 32 0.00082 16.1 0.8 13 7-19 423-435 (479)
402 COG3972 Superfamily I DNA and 23.7 24 0.00062 16.9 0.2 15 3-17 237-251 (660)
403 COG5525 Bacteriophage tail ass 23.5 23 0.00059 17.0 0.0 28 11-38 229-271 (611)
404 PRK13796 GTP-binding protein Y 23.5 37 0.00094 15.8 1.1 10 27-36 5-14 (367)
405 cd00162 RING RING-finger (Real 23.4 34 0.00086 16.0 0.9 24 11-38 1-24 (45)
406 pfam05207 zf-CSL CSL zinc fing 23.4 47 0.0012 15.1 1.6 27 9-36 18-50 (55)
407 TIGR02474 pec_lyase pectate ly 23.3 24 0.00061 16.9 0.1 22 12-33 284-317 (356)
408 pfam02433 FixO Cytochrome C ox 23.0 29 0.00075 16.4 0.5 17 5-21 96-115 (226)
409 pfam05443 ROS_MUCR ROS/MUCR tr 22.7 17 0.00042 17.9 -0.8 14 9-22 70-83 (130)
410 KOG4317 consensus 22.7 45 0.0011 15.2 1.4 25 7-36 5-29 (383)
411 COG3478 Predicted nucleic-acid 22.6 31 0.00078 16.3 0.5 26 11-36 6-51 (68)
412 pfam05290 Baculo_IE-1 Baculovi 22.3 8.9 0.00023 19.5 -2.3 30 10-39 105-134 (141)
413 pfam10825 DUF2752 Protein of u 22.3 30 0.00075 16.3 0.4 10 26-35 9-18 (52)
414 PRK04351 hypothetical protein; 22.2 65 0.0017 14.2 2.5 30 6-36 95-124 (151)
415 TIGR02443 TIGR02443 conserved 21.8 36 0.00091 15.9 0.7 25 11-35 11-40 (63)
416 COG1781 PyrI Aspartate carbamo 21.8 46 0.0012 15.2 1.3 26 16-41 123-150 (153)
417 pfam04438 zf-HIT HIT zinc fing 21.8 38 0.00096 15.7 0.8 10 26-35 13-22 (30)
418 pfam05605 Di19 Drought induced 21.7 36 0.00091 15.9 0.7 12 25-36 62-73 (210)
419 PRK08351 DNA-directed RNA poly 21.6 35 0.0009 15.9 0.7 24 9-37 3-27 (61)
420 PRK09628 oorB 2-oxoglutarate-a 21.6 27 0.00069 16.6 0.1 24 18-41 7-31 (281)
421 pfam03811 Ins_element1 Inserti 21.5 49 0.0013 15.0 1.4 33 10-42 6-45 (88)
422 COG4694 Uncharacterized protei 21.4 32 0.0008 16.2 0.4 15 22-36 274-288 (758)
423 pfam06478 Corona_RPol_N Corona 21.4 38 0.00096 15.7 0.8 22 16-37 201-222 (355)
424 TIGR02187 GlrX_arch Glutaredox 21.2 32 0.00082 16.1 0.4 10 27-36 157-166 (237)
425 TIGR00398 metG methionyl-tRNA 21.2 65 0.0016 14.3 1.9 33 9-45 143-175 (573)
426 COG3024 Uncharacterized protei 21.1 39 0.00098 15.6 0.8 11 26-36 7-17 (65)
427 pfam06170 DUF983 Protein of un 20.8 36 0.00092 15.8 0.6 13 24-36 6-18 (86)
428 COG2956 Predicted N-acetylgluc 20.7 42 0.0011 15.4 0.9 21 11-34 356-376 (389)
429 COG2804 PulE Type II secretory 20.7 35 0.0009 15.9 0.5 25 9-33 395-431 (500)
430 pfam10609 ParA ParA/MinD ATPas 20.6 55 0.0014 14.7 1.5 16 23-38 62-77 (81)
431 cd03530 Rieske_NirD_small_Baci 20.6 70 0.0018 14.0 2.5 33 9-41 39-73 (98)
432 COG0267 RpmG Ribosomal protein 20.5 34 0.00087 16.0 0.4 29 7-35 5-43 (50)
433 pfam04641 Rtf2 Replication ter 20.5 53 0.0013 14.8 1.4 11 28-38 146-156 (254)
434 COG2995 PqiA Uncharacterized p 20.4 64 0.0016 14.3 1.8 30 6-35 15-47 (418)
435 KOG3816 consensus 20.4 23 0.00059 17.0 -0.5 24 11-34 476-508 (526)
436 COG5222 Uncharacterized conser 20.3 35 0.0009 15.9 0.4 27 10-40 275-301 (427)
437 PRK06393 rpoE DNA-directed RNA 20.3 40 0.001 15.6 0.7 21 10-35 6-26 (64)
438 smart00714 LITAF Possible memb 20.2 60 0.0015 14.5 1.6 12 26-37 3-14 (67)
439 KOG3854 consensus 20.1 30 0.00076 16.3 0.0 38 4-41 403-444 (505)
440 KOG2231 consensus 20.0 48 0.0012 15.1 1.1 30 7-36 19-51 (669)
441 TIGR00155 pqiA_fam integral me 20.0 35 0.0009 15.9 0.4 29 9-37 226-259 (421)
No 1
>pfam09538 FYDLN_acid Protein of unknown function (FYDLN_acid). 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=99.95 E-value=3.1e-29 Score=199.82 Aligned_cols=48 Identities=52% Similarity=0.814 Sum_probs=42.8
Q ss_pred CCCHHHCCCCCCCCCCCEEEECCCCCCCCCCCCCEECHHHHHCCCCCC
Q ss_conf 975222783117888874421488872277898715323310123443
Q gi|254780459|r 1 MAKPELGTKRTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFEAPTSPE 48 (129)
Q Consensus 1 MaK~elG~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~~~~~~~ 48 (129)
|||+|||+||+||+||+|||||||+||+||+||++|.+..+++++.++
T Consensus 1 m~k~e~g~kr~c~~c~~~fydl~k~p~~cp~cg~~~~~~~~k~~~~~~ 48 (104)
T pfam09538 1 MAKPEWGTKRTCPTCGKRFYDLNKDPIVCPKCGEEVPPEVAKSRAPAA 48 (104)
T ss_pred CCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCC
T ss_conf 970021676547888882112798987189988874632133446667
No 2
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300; 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=99.94 E-value=8.4e-28 Score=191.08 Aligned_cols=49 Identities=53% Similarity=0.948 Sum_probs=47.1
Q ss_pred CCCHHHCCCCCCCCCCCEEEECCCCCCCCCCCCCEECHHHHHCCCCCCC
Q ss_conf 9752227831178888744214888722778987153233101234434
Q gi|254780459|r 1 MAKPELGTKRTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFEAPTSPEK 49 (129)
Q Consensus 1 MaK~elG~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~~~~~~~~ 49 (129)
||||+||||||||+||.|||||||.||||||||..|+++.++++|+.|.
T Consensus 1 mAkpdLGtKrIcP~tg~KFYDLNr~P~vsPytGe~~p~~~~~~~r~~~~ 49 (157)
T TIGR02300 1 MAKPDLGTKRICPETGKKFYDLNRDPVVSPYTGEQFPLEEVLKSRRVRV 49 (157)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCHHHHHCCCEEEE
T ss_conf 9887678622068777722000789534177887047543004540257
No 3
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.93 E-value=1.3e-26 Score=183.72 Aligned_cols=126 Identities=41% Similarity=0.587 Sum_probs=74.2
Q ss_pred CCCHHHCCCCCCCCCCCEEEECCCCCCCCCCCCCEECHHHHHCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCC
Q ss_conf 97522278311788887442148887227789871532331012344344333212234--5433211000112233210
Q gi|254780459|r 1 MAKPELGTKRTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFEAPTSPEKEKEICSLEEE--TEVKPFVKHTSEEEEESPI 78 (129)
Q Consensus 1 MaK~elG~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~ 78 (129)
||||+||+|||||+||+|||||||+||||||||..|+.+.+..+...+++....+.... .......+..+....+...
T Consensus 1 mAk~eLGtKridPetg~KFYDLNrdPiVsPytG~s~P~s~fe~~t~~~~~e~e~E~~~kEvD~~~~e~e~VsledaD~d~ 80 (129)
T COG4530 1 MAKPELGTKRIDPETGKKFYDLNRDPIVSPYTGKSYPRSYFEETTPDAAAEEEEEEVVKEVDAENEEVEVVSLEDADDDP 80 (129)
T ss_pred CCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCC
T ss_conf 97644465321834243212037786236765550628998750502445677888887630233543056402355776
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 00123454432101123433333222223456653211244677875235
Q gi|254780459|r 79 SKEEDDTSLDMEYVQEMDLDDDDDFLEQNDTDTDTDVVDMDISIPDDADE 128 (129)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~~dddd~~leeeDeddD~D~id~di~~~dd~de 128 (129)
...++.....++...+...++++.||+.++ ++.+.+++.|.++.++++
T Consensus 81 ~GgDDlpDl~dDeDvd~~~ddDdtFLedee--ddDdd~s~iiGv~gdd~e 128 (129)
T COG4530 81 KGGDDLPDLGDDEDVDLDDDDDDTFLEDEE--DDDDDVSGIIGVPGDDEE 128 (129)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCHHHCCCCCCCCCCC
T ss_conf 677766554653223357787654324544--343013303258888777
No 4
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=95.47 E-value=0.0095 Score=37.72 Aligned_cols=29 Identities=14% Similarity=0.296 Sum_probs=20.5
Q ss_pred CCCCCCCCEEEECCC-------CCCCCCCCCCEECH
Q ss_conf 117888874421488-------87227789871532
Q gi|254780459|r 10 RTCPDTGKRFYDLNK-------QVIVSPYTQNSWPL 38 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk-------~PiiCP~CG~e~~~ 38 (129)
=+||+|++||=.|.= .--+||.||++...
T Consensus 100 Y~C~~C~~ryt~~eA~~l~~~~~~F~Cp~Cg~~L~~ 135 (147)
T smart00531 100 YKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEE 135 (147)
T ss_pred EECCCCCCEECHHHHHHHCCCCCCEECCCCCCEEEE
T ss_conf 889999978629999884189983788999999887
No 5
>PRK10220 hypothetical protein; Provisional
Probab=95.36 E-value=0.0082 Score=38.13 Aligned_cols=30 Identities=17% Similarity=0.423 Sum_probs=25.5
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCEECHHH
Q ss_conf 178888744214888722778987153233
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNSWPLAY 40 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~ 40 (129)
.||.|+.-|-=-...-.+||.||.||.+..
T Consensus 5 ~CP~C~seytYedg~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHEWNDAE 34 (111)
T ss_pred CCCCCCCCCEECCCCEEECCCCCCCCCCCC
T ss_conf 699898924382799789977647479765
No 6
>pfam08271 TF_Zn_Ribbon TFIIB zinc-binding. The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.
Probab=95.26 E-value=0.012 Score=37.22 Aligned_cols=30 Identities=17% Similarity=0.285 Sum_probs=25.4
Q ss_pred CCCCCCCCE--EEECCCCCCCCCCCCCEECHH
Q ss_conf 117888874--421488872277898715323
Q gi|254780459|r 10 RTCPDTGKR--FYDLNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 10 R~C~~Cg~K--FYDlnk~PiiCP~CG~e~~~~ 39 (129)
..||.||.+ +||..+--++|+.||..+.-.
T Consensus 1 ~~Cp~Cg~~~~~~D~~~Ge~vC~~CG~Vlee~ 32 (40)
T pfam08271 1 MKCPNCGSTEIVFDYERGEYVCTECGLVLEDN 32 (40)
T ss_pred CCCCCCCCCCEEEECCCCCEECCCCCEEEECC
T ss_conf 93887999706772778978705797190002
No 7
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=95.01 E-value=0.0059 Score=38.98 Aligned_cols=32 Identities=22% Similarity=0.486 Sum_probs=27.8
Q ss_pred CCCCCCCCCEEE--ECCCCCCCCCCCCCEECHHH
Q ss_conf 311788887442--14888722778987153233
Q gi|254780459|r 9 KRTCPDTGKRFY--DLNKQVIVSPYTQNSWPLAY 40 (129)
Q Consensus 9 KR~C~~Cg~KFY--Dlnk~PiiCP~CG~e~~~~~ 40 (129)
=..||+||.-.| ||.+.=-|||+||.-|....
T Consensus 30 W~kCp~C~~~i~~~dL~~n~~VCp~C~~H~ri~a 63 (288)
T PRK05654 30 WTKCPSCGQVLYRKELEANLNVCPKCGHHMRISA 63 (288)
T ss_pred CCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCH
T ss_conf 2228776503509999983878929979863199
No 8
>pfam09986 DUF2225 Uncharacterized protein conserved in bacteria (DUF2225). This domain, found in various hypothetical bacterial proteins, has no known function.
Probab=94.92 E-value=0.016 Score=36.40 Aligned_cols=36 Identities=25% Similarity=0.286 Sum_probs=25.2
Q ss_pred HCCCCCCCCCCCEEE----------------ECCC----------CCCCCCCCCCEECHHHH
Q ss_conf 278311788887442----------------1488----------87227789871532331
Q gi|254780459|r 6 LGTKRTCPDTGKRFY----------------DLNK----------QVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 6 lG~KR~C~~Cg~KFY----------------Dlnk----------~PiiCP~CG~e~~~~~~ 41 (129)
|-+|-+||-||.+|. ||.. .++|||.||-.+-...+
T Consensus 2 y~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~inP~~Y~v~vCp~CgyAa~~~~F 63 (214)
T pfam09986 2 YDKKIVCPVCNNEFKTKKVKSSGLRLIKRDSDFCIKYKGINPYFYDVWVCPHCGYAAFESDF 63 (214)
T ss_pred CCCEEECCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCCCCEEEEEEECCCCCCCCCHHHH
T ss_conf 86500489999845356887378255322264333368789723401699999854640103
No 9
>PRK00420 hypothetical protein; Validated
Probab=94.46 E-value=0.026 Score=35.07 Aligned_cols=28 Identities=21% Similarity=0.523 Sum_probs=23.9
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 3117888874421488872277898715
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
-++||.||+-.|-|.---+.||.||.++
T Consensus 19 ~~~C~~Cg~plf~~k~G~~~Cp~cgk~~ 46 (107)
T PRK00420 19 DKHCPVCGLPLFELKDGEVVCPNHGKVI 46 (107)
T ss_pred HHHCCCCCCCEEECCCCCEECCCCCCEE
T ss_conf 5137657984057489877689898743
No 10
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=94.24 E-value=0.022 Score=35.55 Aligned_cols=29 Identities=17% Similarity=0.358 Sum_probs=21.7
Q ss_pred CCCCCCCCEEEEC-------CCCCCCCCCCCC-EECH
Q ss_conf 1178888744214-------888722778987-1532
Q gi|254780459|r 10 RTCPDTGKRFYDL-------NKQVIVSPYTQN-SWPL 38 (129)
Q Consensus 10 R~C~~Cg~KFYDl-------nk~PiiCP~CG~-e~~~ 38 (129)
-.|..||.+||.- +..|..||+||. .+-|
T Consensus 123 ~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~~lrP 159 (250)
T COG0846 123 VRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGPVLRP 159 (250)
T ss_pred EEECCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf 5766875736521433310347998687679962468
No 11
>PRK02625 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=94.05 E-value=0.022 Score=35.50 Aligned_cols=33 Identities=12% Similarity=0.176 Sum_probs=24.9
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCEECHHHHHC
Q ss_conf 31178888744214888722778987153233101
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFEA 43 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~~ 43 (129)
.-.|. || ||.-.+..-++|+.||.||......+
T Consensus 68 d~eC~-CG-Kyk~~k~kg~vCe~CGVEvt~S~VRR 100 (627)
T PRK02625 68 DWECH-CG-KYKRVRHRGIVCERCGVEVTESRVRR 100 (627)
T ss_pred CCEEE-CC-CCCCCCCCCEECCCCCCCCCCCCCCC
T ss_conf 83771-88-72130328716687685734352110
No 12
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=93.98 E-value=0.031 Score=34.57 Aligned_cols=27 Identities=15% Similarity=0.377 Sum_probs=19.4
Q ss_pred CCCCCCCCEEEEC--------CCC-CCCCCCCCCEECH
Q ss_conf 1178888744214--------888-7227789871532
Q gi|254780459|r 10 RTCPDTGKRFYDL--------NKQ-VIVSPYTQNSWPL 38 (129)
Q Consensus 10 R~C~~Cg~KFYDl--------nk~-PiiCP~CG~e~~~ 38 (129)
-.||+|| |=.. ... -+-|+.||+.|+.
T Consensus 7 ~~Cp~Cg--~eev~hEVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 7 IECPSCG--SEEVSHEVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred EECCCCC--CCHHHHHHHHHCCCCEEEECCCCCCEEEC
T ss_conf 8899987--40346788873497527984578748401
No 13
>pfam07282 Transposase_35 Putative transposase DNA-binding domain. This putative domain is found at the C-terminus of a large number of transposase proteins. This domain contains four conserved cysteines suggestive of a zinc binding domain. Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesize this domain is DNA-binding.
Probab=93.02 E-value=0.061 Score=32.79 Aligned_cols=36 Identities=17% Similarity=0.147 Sum_probs=26.8
Q ss_pred HHHCCCCCCCCCCCEEEE-CCCCCCCCCCCCCEECHH
Q ss_conf 222783117888874421-488872277898715323
Q gi|254780459|r 4 PELGTKRTCPDTGKRFYD-LNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 4 ~elG~KR~C~~Cg~KFYD-lnk~PiiCP~CG~e~~~~ 39 (129)
++++|=++||.||.+=-. ++..--.||.||...+-.
T Consensus 23 ~~~~TS~~C~~Cg~~~~~~~~~r~~~C~~Cg~~~~rD 59 (69)
T pfam07282 23 NPAYTSKTCSVCGHKNKESLSGRTFKCPNCGFVADRD 59 (69)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCEECCH
T ss_conf 9998864279998998674888789899899689959
No 14
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=93.01 E-value=0.043 Score=33.72 Aligned_cols=26 Identities=19% Similarity=0.474 Sum_probs=21.4
Q ss_pred CCCCCCCCEEEECCCC-CCCCCCCCCEEC
Q ss_conf 1178888744214888-722778987153
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQ-VIVSPYTQNSWP 37 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~-PiiCP~CG~e~~ 37 (129)
.+||.||+=.|= |+ -+.||.||..+.
T Consensus 29 ~hCp~Cg~PLF~--KdG~v~CPvC~~~~~ 55 (131)
T COG1645 29 KHCPKCGTPLFR--KDGEVFCPVCGYREV 55 (131)
T ss_pred HHCCCCCCCCEE--ECCEEECCCCCCEEE
T ss_conf 448655883163--089587777776677
No 15
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=92.92 E-value=0.044 Score=33.65 Aligned_cols=35 Identities=6% Similarity=0.078 Sum_probs=23.7
Q ss_pred CCCCCCCCCEEEEC---CCCCCCCCCCCCEECHHHHHCCC
Q ss_conf 31178888744214---88872277898715323310123
Q gi|254780459|r 9 KRTCPDTGKRFYDL---NKQVIVSPYTQNSWPLAYFEAPT 45 (129)
Q Consensus 9 KR~C~~Cg~KFYDl---nk~PiiCP~CG~e~~~~~~~~~~ 45 (129)
.-.|. || ||.=+ ....++|+.||.||......+.|
T Consensus 66 d~eC~-CG-KYK~i~~~k~~g~vCerCGVEvt~S~VRR~R 103 (668)
T CHL00018 66 SGICA-CG-NYRVIGDEKEDPKFCEQCGVEFVDSRIRRYR 103 (668)
T ss_pred CCEEE-CC-CCCCCCCCCCCCCCCCCCCCCCCCCHHHHHC
T ss_conf 86675-87-7522465565762468778360401666750
No 16
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=92.89 E-value=0.06 Score=32.85 Aligned_cols=28 Identities=14% Similarity=0.118 Sum_probs=20.2
Q ss_pred CCCCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 8311788887442148887227789871
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
.+-.|++||..|.--...-..||.||..
T Consensus 70 ~~~~C~~Cg~~f~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 70 VELECKDCSHVFKPNALDYGVCEKCHSK 97 (117)
T ss_pred CEEECCCCCCEEECCCCCCCCCCCCCCC
T ss_conf 7899100899882277406859098899
No 17
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=92.79 E-value=0.05 Score=33.34 Aligned_cols=27 Identities=19% Similarity=0.279 Sum_probs=22.0
Q ss_pred CCCCCCCCEEEEC-CCCCCCCCCCCCEE
Q ss_conf 1178888744214-88872277898715
Q gi|254780459|r 10 RTCPDTGKRFYDL-NKQVIVSPYTQNSW 36 (129)
Q Consensus 10 R~C~~Cg~KFYDl-nk~PiiCP~CG~e~ 36 (129)
=.|..||++|=.+ +...|-||+||.-+
T Consensus 7 Y~C~~Cg~~~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 7 YKCARCGREVELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEHHHCCCEEEHHHCCCCEECCCCCCEE
T ss_conf 9934558850001035744579888579
No 18
>PRK06450 threonine synthase; Validated
Probab=92.77 E-value=0.06 Score=32.82 Aligned_cols=28 Identities=14% Similarity=0.211 Sum_probs=20.9
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCEECHH
Q ss_conf 3117888874421488872277898715323
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~ 39 (129)
|-.|+.||..| +- .+..||.||.-+...
T Consensus 3 ~l~C~~CG~~~-~~--~~~~C~~Cgg~l~~~ 30 (336)
T PRK06450 3 KVRCIRCGKER-EG--EELRCKKCGGPFEIE 30 (336)
T ss_pred EEECCCCCCCC-CC--CCEECCCCCCEEEEE
T ss_conf 58878558888-98--875889999878998
No 19
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.51 E-value=0.078 Score=32.14 Aligned_cols=28 Identities=25% Similarity=0.351 Sum_probs=23.9
Q ss_pred CCCCCCCCCCCEEEECCCCCCCCCCCCCEECH
Q ss_conf 78311788887442148887227789871532
Q gi|254780459|r 7 GTKRTCPDTGKRFYDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 7 G~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~ 38 (129)
-|-.+||.||. |...-..||.||..++-
T Consensus 307 ~tS~~C~~cg~----~~~r~~~C~~cg~~~~r 334 (364)
T COG0675 307 YTSKTCPCCGH----LSGRLFKCPRCGFVHDR 334 (364)
T ss_pred CCCCCCCCCCC----CCCCEEECCCCCCEECC
T ss_conf 87777887787----47854888998974065
No 20
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=92.39 E-value=0.031 Score=34.56 Aligned_cols=34 Identities=9% Similarity=0.014 Sum_probs=27.9
Q ss_pred CCCCCCCCCCCEEE--ECCCCCCCCCCCCCEECHHH
Q ss_conf 78311788887442--14888722778987153233
Q gi|254780459|r 7 GTKRTCPDTGKRFY--DLNKQVIVSPYTQNSWPLAY 40 (129)
Q Consensus 7 G~KR~C~~Cg~KFY--Dlnk~PiiCP~CG~e~~~~~ 40 (129)
+.=..||+|+.-.| ||.+.=-|||+||.-|....
T Consensus 46 nLW~KCp~C~~~iy~kdLe~Nl~VCp~C~~H~ri~a 81 (305)
T CHL00174 46 HLWVQCENCYGLNYKKFLKSKMNICEQCGYHLKMSS 81 (305)
T ss_pred CCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCH
T ss_conf 746549876622459999983989929979973399
No 21
>PRK07591 threonine synthase; Validated
Probab=92.38 E-value=0.067 Score=32.53 Aligned_cols=29 Identities=17% Similarity=0.308 Sum_probs=21.9
Q ss_pred CCCCCCCCCCEEEECCCCCCCCCCCCCEECH
Q ss_conf 8311788887442148887227789871532
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~ 38 (129)
+.-.|+.||++| +.. ....||.||..+..
T Consensus 18 t~L~C~~CG~~y-~~~-~~~~C~~Cg~~L~v 46 (422)
T PRK07591 18 TALKCRECGAEY-PLE-PLHVCEECFGPLEV 46 (422)
T ss_pred CEEECCCCCCCC-CCC-CCCCCCCCCCEEEE
T ss_conf 465876647916-986-54667779998898
No 22
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=92.37 E-value=0.063 Score=32.70 Aligned_cols=23 Identities=17% Similarity=0.294 Sum_probs=16.1
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 11788887442148887227789871
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
-+|+.||.++.-+. -.||.||..
T Consensus 567 d~C~~CGy~~~g~~---~~CP~CG~~ 589 (623)
T PRK08579 567 TVCNRCGRSTTGLY---TRCPRCGSE 589 (623)
T ss_pred CCCCCCCCCCCCCC---CCCCCCCCC
T ss_conf 33588998177776---559099696
No 23
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=92.30 E-value=0.064 Score=32.65 Aligned_cols=26 Identities=12% Similarity=0.229 Sum_probs=17.6
Q ss_pred CCCCCCCCCEE-----E---------ECCCCC------CCCCCCCC
Q ss_conf 31178888744-----2---------148887------22778987
Q gi|254780459|r 9 KRTCPDTGKRF-----Y---------DLNKQV------IVSPYTQN 34 (129)
Q Consensus 9 KR~C~~Cg~KF-----Y---------Dlnk~P------iiCP~CG~ 34 (129)
.-.|.+||..| | +|.=-| +.||+||.
T Consensus 70 ~~~C~~Cg~ef~~~~~~~~~~~~~~~~~h~~pe~~~~~~~CP~Cgs 115 (135)
T PRK03824 70 VLKCRNCGYEWSLKEVKDKLDEEIREAIHFIPEVVHAFLKCPKCGS 115 (135)
T ss_pred EEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 6892338987244433321000001111234212355662909989
No 24
>pfam08274 PhnA_Zn_Ribbon PhnA Zinc-Ribbon.
Probab=92.30 E-value=0.073 Score=32.31 Aligned_cols=27 Identities=19% Similarity=0.524 Sum_probs=24.3
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCEEC
Q ss_conf 178888744214888722778987153
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e~~ 37 (129)
.||.|+.-|-=-...-.|||.||.||.
T Consensus 4 ~Cp~C~seytY~d~~~~vCpeC~hEw~ 30 (30)
T pfam08274 4 KCPLCNSEYTYEDGALLVCPECAHEWS 30 (30)
T ss_pred CCCCCCCCCEECCCCEEECCCCCCCCC
T ss_conf 788789812474799979975456569
No 25
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=92.18 E-value=0.079 Score=32.09 Aligned_cols=29 Identities=28% Similarity=0.247 Sum_probs=24.6
Q ss_pred CCCHHHCCCCCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 9752227831178888744214888722778987
Q gi|254780459|r 1 MAKPELGTKRTCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 1 MaK~elG~KR~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
|||.. ++-+|++||. ...|--=-||.||+
T Consensus 1 MaK~~--t~f~C~~CG~---~s~KW~GkCp~Cg~ 29 (456)
T COG1066 1 MAKKK--TAFVCQECGY---VSPKWLGKCPACGA 29 (456)
T ss_pred CCCCC--CEEECCCCCC---CCCCCCCCCCCCCC
T ss_conf 99766--2788445788---78621555988787
No 26
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-positive type; InterPro: IPR006308 These are the polypeptide chains of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence and poorly alignable. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0005737 cytoplasm.
Probab=92.15 E-value=0.082 Score=32.01 Aligned_cols=24 Identities=13% Similarity=0.340 Sum_probs=19.1
Q ss_pred CCCCCCCEEEECCCCCC----------CCCCCC--CEE
Q ss_conf 17888874421488872----------277898--715
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVI----------VSPYTQ--NSW 36 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~Pi----------iCP~CG--~e~ 36 (129)
+||+| ||..|.+++- .||+|| +-+
T Consensus 719 ~Cp~C--ky~Ef~~D~~~~~GfDLp~K~CP~Cgak~pl 754 (1264)
T TIGR01405 719 LCPNC--KYSEFVTDGSVGSGFDLPDKDCPKCGAKAPL 754 (1264)
T ss_pred CCCCC--CEEEEECCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 08787--3553003787788776857888888877763
No 27
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit; InterPro: IPR000438 Fatty acid synthesis involves a set of reactions, commencing with carboxylation of acetyl-CoA to malonyl-CoA. This is an irreversible reaction, catalysed by the acetyl-CoA carboxylase complex (6.4.1.2 from EC); a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase and two non-identical carboxyl transferase subunits (alpha and beta) in a 2:2 association . The reaction involves two steps: Biotin carrier protein + ATP + HCO_3^- = Carboxybiotin carrier protein + ADP + P_i Carboxybiotin carrier protein + Acetyl-CoA = Malonyl-CoA + Biotin carrier protein In the first step, biotin carboxylase catalyses the carboxylation of the carrier protein to form an intermediate. Next, the transcarboxylase complex transfers the carboxyl group from the intermediate to acetyl-CoA forming malonyl-CoA.; GO: 0003989 acetyl-CoA carboxylase activity, 0006633 fatty acid biosynthetic process, 0009317 acetyl-CoA carboxylase complex.
Probab=91.93 E-value=0.043 Score=33.70 Aligned_cols=34 Identities=18% Similarity=0.416 Sum_probs=28.1
Q ss_pred CCCCCCCCCCEEE--ECCCCCCCCCCCCCEECHHHH
Q ss_conf 8311788887442--148887227789871532331
Q gi|254780459|r 8 TKRTCPDTGKRFY--DLNKQVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 8 ~KR~C~~Cg~KFY--Dlnk~PiiCP~CG~e~~~~~~ 41 (129)
.=--||+|+.-.| +|.|+=-|||+||.-|....-
T Consensus 32 ~wtKCp~C~~~~Y~keL~~n~~VC~~C~hH~R~~A~ 67 (292)
T TIGR00515 32 VWTKCPKCGQLLYTKELQRNLSVCLKCDHHFRMDAR 67 (292)
T ss_pred CEECCCHHHHHHHHHHHHCCCEECCCCCCCCCCCHH
T ss_conf 300144243443466530355574237987746879
No 28
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=91.72 E-value=0.071 Score=32.38 Aligned_cols=29 Identities=21% Similarity=0.331 Sum_probs=21.0
Q ss_pred CCCCCCCCCCEEEECCC-CCCCCCCCCCEE
Q ss_conf 83117888874421488-872277898715
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNK-QVIVSPYTQNSW 36 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk-~PiiCP~CG~e~ 36 (129)
+-|.|+.||+|-|---- .-.+||+||+.+
T Consensus 110 ~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 110 SHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred HCCCCCCCCCCCCCCCCCEEEECCCCCCCC
T ss_conf 376777789807435673245579888700
No 29
>TIGR00354 polC DNA polymerase II, large subunit DP2; InterPro: IPR004475 This family represents the large subunit, DP2, 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.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006308 DNA catabolic process.
Probab=91.63 E-value=0.088 Score=31.80 Aligned_cols=25 Identities=28% Similarity=0.400 Sum_probs=14.6
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCEECH
Q ss_conf 311788887442148887227789871532
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~ 38 (129)
-|.||+||+.=. -.+||.||+-...
T Consensus 679 ~~~CP~Cgk~s~-----~~~Cp~CG~~te~ 703 (1173)
T TIGR00354 679 IAKCPSCGKESL-----YRVCPVCGEKTEL 703 (1173)
T ss_pred CCCCCCCCCCCE-----EEECCCCCCEEEE
T ss_conf 121887664000-----0145778854544
No 30
>pfam10276 zf-CHCC Zinc-finger domain. This is a short zinc-finger domain conserved from fungi to humans. It is Cx8Hx14Cx2C.
Probab=91.61 E-value=0.085 Score=31.92 Aligned_cols=20 Identities=15% Similarity=0.492 Sum_probs=16.8
Q ss_pred CEEEECCCC--CCCCCCCCCEE
Q ss_conf 744214888--72277898715
Q gi|254780459|r 17 KRFYDLNKQ--VIVSPYTQNSW 36 (129)
Q Consensus 17 ~KFYDlnk~--PiiCP~CG~e~ 36 (129)
.-|++|.+. +++|||||.-|
T Consensus 18 ~V~l~l~~~~~~~~C~YC~~~f 39 (40)
T pfam10276 18 RVYINLDDETGPVECPYCGLRF 39 (40)
T ss_pred EEEEECCCCCCEEECCCCCCCC
T ss_conf 9988868999978899878691
No 31
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=91.57 E-value=0.13 Score=30.82 Aligned_cols=21 Identities=29% Similarity=0.673 Sum_probs=16.9
Q ss_pred EEEECCCC-CCCCCCCCCEECH
Q ss_conf 44214888-7227789871532
Q gi|254780459|r 18 RFYDLNKQ-VIVSPYTQNSWPL 38 (129)
Q Consensus 18 KFYDlnk~-PiiCP~CG~e~~~ 38 (129)
-|-++... -++|||||+-|..
T Consensus 39 V~L~mg~~gev~CPYC~t~y~l 60 (62)
T COG4391 39 VFLDMGDEGEVVCPYCSTRYRL 60 (62)
T ss_pred EEEECCCCCCEECCCCCCEEEE
T ss_conf 9887277874826766627874
No 32
>KOG2807 consensus
Probab=91.51 E-value=0.1 Score=31.38 Aligned_cols=30 Identities=20% Similarity=0.304 Sum_probs=24.5
Q ss_pred CCCCCCCCCCCEEEECCCCCCCCCCCCCEECHH
Q ss_conf 783117888874421488872277898715323
Q gi|254780459|r 7 GTKRTCPDTGKRFYDLNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 7 G~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~ 39 (129)
|.--.||.|++|.-.| |+.||-||......
T Consensus 274 ~~Gy~CP~CkakvCsL---P~eCpiC~ltLVss 303 (378)
T KOG2807 274 GGGYFCPQCKAKVCSL---PIECPICSLTLVSS 303 (378)
T ss_pred CCCEECCCCCCEEECC---CCCCCCCCEEEECC
T ss_conf 5855678656754258---75577454067545
No 33
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=91.33 E-value=0.088 Score=31.80 Aligned_cols=29 Identities=17% Similarity=0.398 Sum_probs=23.1
Q ss_pred CCCCCCCCCCEEEEC------CC-CCCCCCCCCCEE
Q ss_conf 831178888744214------88-872277898715
Q gi|254780459|r 8 TKRTCPDTGKRFYDL------NK-QVIVSPYTQNSW 36 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDl------nk-~PiiCP~CG~e~ 36 (129)
.+|+|-.|.++.+.- ++ .++.||+||...
T Consensus 196 ~g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRIL 231 (239)
T COG1579 196 EGRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRIL 231 (239)
T ss_pred CCCCCCCCEEEECHHHHHHHHCCCCCCCCCCCCHHH
T ss_conf 587035772451688998874489975287611367
No 34
>pfam09723 CxxC_CxxC_SSSS Zinc ribbon domain. 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=91.20 E-value=0.15 Score=30.38 Aligned_cols=25 Identities=28% Similarity=0.507 Sum_probs=20.3
Q ss_pred CCCCCCCEEEECCC----CCCCCCCCCCE
Q ss_conf 17888874421488----87227789871
Q gi|254780459|r 11 TCPDTGKRFYDLNK----QVIVSPYTQNS 35 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk----~PiiCP~CG~e 35 (129)
.|..||..|=-|-+ .++.||.||..
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~C~~~ 35 (42)
T pfam09723 7 RCEDCGHTFEVLQKISDAPLATCPECGST 35 (42)
T ss_pred EECCCCCEEEEEEECCCCCCCCCCCCCCC
T ss_conf 94889998999986579988769799998
No 35
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=91.19 E-value=0.11 Score=31.20 Aligned_cols=27 Identities=15% Similarity=0.111 Sum_probs=23.6
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 117888874421488872277898715
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
-+|-.||++|--=-++||-|++||.-+
T Consensus 3 Y~Cg~C~~~~~i~~~d~irC~~CG~RI 29 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGYRI 29 (44)
T ss_pred EECCCCCCCCCCCCCCCEECCCCCCEE
T ss_conf 886768982313779966506487477
No 36
>PRK12496 hypothetical protein; Provisional
Probab=91.18 E-value=0.078 Score=32.15 Aligned_cols=33 Identities=18% Similarity=0.079 Sum_probs=22.4
Q ss_pred CHHHCCCCCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 5222783117888874421488872277898715
Q gi|254780459|r 3 KPELGTKRTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 3 K~elG~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
|.-|-=+..|+.||+.| +-|..-=.||.||...
T Consensus 123 k~~~~W~~~C~gC~~~~-~~~~~~~~C~~CGs~l 155 (166)
T PRK12496 123 KKVIKWKYVCKGCKKMY-PENYPDEVCDVCGSPV 155 (166)
T ss_pred CEEEEEEEECCCCCCCC-CCCCCCCCCCCCCCHH
T ss_conf 11368999999878717-7889988387889899
No 37
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=91.10 E-value=0.14 Score=30.55 Aligned_cols=27 Identities=15% Similarity=0.162 Sum_probs=21.3
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 311788887442148887227789871
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
+-.|++||..|.=....-..||.||..
T Consensus 70 ~~~C~~C~~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 70 ECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred EEECCCCCCEEEECCCCCCCCCCCCCC
T ss_conf 899655998554067767739088399
No 38
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.00 E-value=0.1 Score=31.38 Aligned_cols=36 Identities=17% Similarity=0.194 Sum_probs=22.5
Q ss_pred CCCHHHCCCCCCCCCCCEE-EECCCCCCCCCCCCCEE
Q ss_conf 9752227831178888744-21488872277898715
Q gi|254780459|r 1 MAKPELGTKRTCPDTGKRF-YDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 1 MaK~elG~KR~C~~Cg~KF-YDlnk~PiiCP~CG~e~ 36 (129)
|++-+.+...+|.|||... -.=+-.--.||.||.+.
T Consensus 1 ~~~~~~~~~~~CtSCg~~i~p~e~~v~F~CPnCGe~~ 37 (61)
T COG2888 1 MAAMEMKDPPVCTSCGREIAPGETAVKFPCPNCGEVE 37 (61)
T ss_pred CCCCCCCCCCEECCCCCEECCCCCEEEEECCCCCCEE
T ss_conf 9531125885212378770468750086489998242
No 39
>pfam03833 PolC_DP2 DNA polymerase II large subunit DP2.
Probab=90.98 E-value=0.11 Score=31.27 Aligned_cols=22 Identities=27% Similarity=0.391 Sum_probs=17.9
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 311788887442148887227789871
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
.|+||+||+.=| -++||.||+.
T Consensus 629 ~R~C~~Cg~~t~-----~~~C~~CG~~ 650 (852)
T pfam03833 629 FRRCPSCGKESP-----ESTCPKCGSR 650 (852)
T ss_pred EEECCCCCCCCC-----CCCCCCCCCC
T ss_conf 038889999778-----7149999982
No 40
>pfam09538 FYDLN_acid Protein of unknown function (FYDLN_acid). Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=90.81 E-value=0.32 Score=28.38 Aligned_cols=10 Identities=10% Similarity=0.205 Sum_probs=8.0
Q ss_pred CCCCCCCCEE
Q ss_conf 2277898715
Q gi|254780459|r 27 IVSPYTQNSW 36 (129)
Q Consensus 27 iiCP~CG~e~ 36 (129)
-+||+||+-|
T Consensus 10 r~c~~c~~~f 19 (104)
T pfam09538 10 RTCPTCGKRF 19 (104)
T ss_pred CCCCCCCCCC
T ss_conf 5478888821
No 41
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=90.67 E-value=0.13 Score=30.71 Aligned_cols=23 Identities=30% Similarity=0.637 Sum_probs=18.4
Q ss_pred HHHCCCCCCCCCCCEEEECCCCCCCCCC
Q ss_conf 2227831178888744214888722778
Q gi|254780459|r 4 PELGTKRTCPDTGKRFYDLNKQVIVSPY 31 (129)
Q Consensus 4 ~elG~KR~C~~Cg~KFYDlnk~PiiCP~ 31 (129)
.+=|.||+||+||..|| |-|+|.
T Consensus 124 ~~~g~~~~C~~cg~~~f-----PR~dP~ 146 (279)
T COG2816 124 REGGWARVCPKCGHEHF-----PRIDPC 146 (279)
T ss_pred CCCCEEEECCCCCCCCC-----CCCCCE
T ss_conf 56732455798887007-----988976
No 42
>COG4640 Predicted membrane protein [Function unknown]
Probab=90.34 E-value=0.11 Score=31.23 Aligned_cols=26 Identities=12% Similarity=0.336 Sum_probs=19.1
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEECH
Q ss_conf 11788887442148887227789871532
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~~ 38 (129)
|.||.||.. -+-+-.-||.||+.|.-
T Consensus 2 ~fC~kcG~q---k~Ed~~qC~qCG~~~t~ 27 (465)
T COG4640 2 KFCPKCGSQ---KAEDDVQCTQCGHKFTS 27 (465)
T ss_pred CCCCCCCCC---CCCCCCCCCCCCCCCCC
T ss_conf 766444653---23455001114884776
No 43
>PRK06260 threonine synthase; Validated
Probab=90.34 E-value=0.14 Score=30.52 Aligned_cols=29 Identities=14% Similarity=0.335 Sum_probs=22.0
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEECHH
Q ss_conf 117888874421488872277898715323
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~ 39 (129)
-.|..||.+| +.+..+..||.||.-+...
T Consensus 4 L~C~~CG~~~-~~~~~~~~Cp~Cg~~L~v~ 32 (400)
T PRK06260 4 LKCIECGAEY-DPDEIIYTCPECGGLLEVK 32 (400)
T ss_pred EECCCCCCCC-CCCCCCCCCCCCCCEEEEE
T ss_conf 9979998958-9977675688789867887
No 44
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain; InterPro: IPR011723 Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, 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. (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries). This entry represents a region, which contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterised gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility . More information about these proteins can be found at Protein of the Month: Zinc Fingers ..
Probab=90.13 E-value=0.19 Score=29.75 Aligned_cols=28 Identities=14% Similarity=0.387 Sum_probs=20.6
Q ss_pred CCCCCCCCEEE------ECCCC--CCCCCCCCCEEC
Q ss_conf 11788887442------14888--722778987153
Q gi|254780459|r 10 RTCPDTGKRFY------DLNKQ--VIVSPYTQNSWP 37 (129)
Q Consensus 10 R~C~~Cg~KFY------Dlnk~--PiiCP~CG~e~~ 37 (129)
-+||+|.|.|| =.|.. -+=|++||+.|.
T Consensus 3 ~~CP~C~t~y~V~~~~~G~~g~kv~VrC~~C~~~~~ 38 (40)
T TIGR02098 3 IQCPNCKTSYRVDDSQLGANGRKVKVRCGKCGHVWT 38 (40)
T ss_pred EECCCCCCEEEEECCCCCCCCCEEEEEECCCCEEEE
T ss_conf 568998506888433478789878888189970786
No 45
>PRK05978 hypothetical protein; Provisional
Probab=90.09 E-value=0.11 Score=31.31 Aligned_cols=34 Identities=21% Similarity=0.281 Sum_probs=28.6
Q ss_pred HHCCCCCCCCCCC--EEEECCCCCCCCCCCCCEECH
Q ss_conf 2278311788887--442148887227789871532
Q gi|254780459|r 5 ELGTKRTCPDTGK--RFYDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 5 elG~KR~C~~Cg~--KFYDlnk~PiiCP~CG~e~~~ 38 (129)
-.|.++.||+||. -|-=+-|-.-.|+.||.+|..
T Consensus 30 ~RGlr~rCP~CG~G~LF~gyLkv~~~C~~CG~dl~~ 65 (149)
T PRK05978 30 WRGFRGRCPHCGEGKLFRAFLKPVDHCSACGEDFTH 65 (149)
T ss_pred HHHHCCCCCCCCCCHHHHHHCCCCCCCHHCCCCCCC
T ss_conf 988737598999941564216676550130852124
No 46
>PRK02995 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=90.08 E-value=0.16 Score=30.19 Aligned_cols=28 Identities=14% Similarity=0.170 Sum_probs=21.3
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCEECHHH
Q ss_conf 178888744214888722778987153233
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNSWPLAY 40 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~ 40 (129)
-| .|| ||-=.+-.-|+|..||.++....
T Consensus 59 eC-~Cg-kyk~~~~kg~~C~~Cgvevt~~~ 86 (1291)
T PRK02995 59 EC-YCG-KYKRVRFKGIICERCGVEVTRAK 86 (1291)
T ss_pred EE-ECC-CCCCCCCCCCCCCCCCCEECCCC
T ss_conf 67-178-61332469877699986505575
No 47
>PRK09001 DNA topoisomerase I; Validated
Probab=90.08 E-value=0.2 Score=29.62 Aligned_cols=15 Identities=40% Similarity=0.791 Sum_probs=11.9
Q ss_pred HHHCCCCCCCCCCCE
Q ss_conf 222783117888874
Q gi|254780459|r 4 PELGTKRTCPDTGKR 18 (129)
Q Consensus 4 ~elG~KR~C~~Cg~K 18 (129)
..|..||.||.||+-
T Consensus 659 ~~l~~~~~c~~c~~~ 673 (869)
T PRK09001 659 NALRAKRRCPKCGTA 673 (869)
T ss_pred HHHHHCCCCCCCCCC
T ss_conf 665414547743550
No 48
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.02 E-value=0.2 Score=29.68 Aligned_cols=32 Identities=25% Similarity=0.363 Sum_probs=24.2
Q ss_pred HHHCCCCCCCCCC-CEEEECCC-----CCCCCCCCCCE
Q ss_conf 2227831178888-74421488-----87227789871
Q gi|254780459|r 4 PELGTKRTCPDTG-KRFYDLNK-----QVIVSPYTQNS 35 (129)
Q Consensus 4 ~elG~KR~C~~Cg-~KFYDlnk-----~PiiCP~CG~e 35 (129)
-|-++|-.||+|| .--|--.| .|-+||+||.+
T Consensus 22 ~e~~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 22 GETAVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGFE 59 (61)
T ss_pred CCCEEEEECCCCCCEEEEHHHHHHHCCCCEECCCCCCC
T ss_conf 87500864899982424105668774994478876753
No 49
>pfam01155 HypA Hydrogenase expression/synthesis hypA family. Four conserved cysteines lie either side of the least conserved region.
Probab=89.86 E-value=0.2 Score=29.59 Aligned_cols=26 Identities=23% Similarity=0.446 Sum_probs=20.4
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 311788887442148887227789871
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
+-.|++||..|- +......||.||..
T Consensus 69 ~~~C~~Cg~~~~-~~~~~~~CP~Cgs~ 94 (112)
T pfam01155 69 VARCRDCGQEFE-LEERFFRCPKCGSL 94 (112)
T ss_pred EEECCCCCCEEC-CCCCCCCCCCCCCC
T ss_conf 489989997142-57776799089799
No 50
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=89.80 E-value=0.22 Score=29.42 Aligned_cols=27 Identities=11% Similarity=0.179 Sum_probs=21.0
Q ss_pred CCCCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 8311788887442148887227789871
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
.+-.|.+||..|- +...-..||.||..
T Consensus 69 ~~~~C~~C~~~~~-~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 69 AQAWCWDCSQVVE-IHQHDAQCPHCHGE 95 (113)
T ss_pred CEEECCCCCCEEE-CCCCCCCCCCCCCC
T ss_conf 5799655999872-47888839069799
No 51
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=89.71 E-value=0.14 Score=30.55 Aligned_cols=34 Identities=24% Similarity=0.521 Sum_probs=27.8
Q ss_pred CCCCCCCCCCCEEE--ECCCCCCCCCCCCCEECHHH
Q ss_conf 78311788887442--14888722778987153233
Q gi|254780459|r 7 GTKRTCPDTGKRFY--DLNKQVIVSPYTQNSWPLAY 40 (129)
Q Consensus 7 G~KR~C~~Cg~KFY--Dlnk~PiiCP~CG~e~~~~~ 40 (129)
|.=..||+||.--| ||.+.--+||+||.-+....
T Consensus 26 ~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~A 61 (294)
T COG0777 26 GLWTKCPSCGEMLYRKELESNLKVCPKCGHHMRISA 61 (294)
T ss_pred CCEEECCCCCCEEEHHHHHHHHHCCCCCCCCCCCCH
T ss_conf 835477875535468878733232655676465699
No 52
>TIGR01206 lysW lysine biosynthesis protein LysW; InterPro: IPR005906 This very small, poorly characterised protein in Thermus thermophilus has been shown to be essential for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate.; GO: 0019878 lysine biosynthetic process via aminoadipic acid.
Probab=89.65 E-value=0.28 Score=28.75 Aligned_cols=35 Identities=17% Similarity=0.317 Sum_probs=28.1
Q ss_pred CCCCCCCCCCEEEECCC---CCCCCCCCCCEECHHHHH
Q ss_conf 83117888874421488---872277898715323310
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNK---QVIVSPYTQNSWPLAYFE 42 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk---~PiiCP~CG~e~~~~~~~ 42 (129)
.|..||.||+..-=-|- .=++|+.||++|....+-
T Consensus 1 ~~~~~P~~GA~i~L~N~ELg~lV~c~~~G~ElEVVsld 38 (54)
T TIGR01206 1 MKAECPECGAEIELENPELGELVVCDECGAELEVVSLD 38 (54)
T ss_pred CCCCCCCCCCEEEECCCCCCCEEECCCCCCEEEEEECC
T ss_conf 95468876755674088766167528999306873058
No 53
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=89.62 E-value=0.24 Score=29.12 Aligned_cols=31 Identities=23% Similarity=0.395 Sum_probs=25.4
Q ss_pred CCCCCCCCCCE--EEECCCCCCCCCCCCCEECH
Q ss_conf 83117888874--42148887227789871532
Q gi|254780459|r 8 TKRTCPDTGKR--FYDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 8 ~KR~C~~Cg~K--FYDlnk~PiiCP~CG~e~~~ 38 (129)
.+-.||+||.. .||...--++|-.||..+.-
T Consensus 10 ~~~kCp~Cg~~~ii~D~~~G~~vC~~CG~Vi~e 42 (310)
T PRK00423 10 EELRCPECGSDKLIYDYERGEIVCADCGYVIEE 42 (310)
T ss_pred CEEECCCCCCCCEEEECCCCCEECCCCCCEEEC
T ss_conf 735898986985356789987753028876113
No 54
>PRK12366 replication factor A; Reviewed
Probab=89.22 E-value=0.2 Score=29.59 Aligned_cols=32 Identities=19% Similarity=0.224 Sum_probs=23.3
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEECHHHHHC
Q ss_conf 1178888744214888722778987153233101
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFEA 43 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~~ 43 (129)
-.||+|+.|- .+...--+||.||.. .|..++.
T Consensus 534 ~~CP~C~krv-~~~e~~y~C~~cGev-eP~~ll~ 565 (649)
T PRK12366 534 TLCPNCRKRV-NLVDNKYVCEECGEV-EPNELLV 565 (649)
T ss_pred EECCCCCCEE-EECCCCEECCCCCCC-CCCEEEE
T ss_conf 7286667605-645882527767874-7764899
No 55
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=89.11 E-value=0.13 Score=30.72 Aligned_cols=27 Identities=15% Similarity=0.333 Sum_probs=19.9
Q ss_pred CCCCCCCCEEEECCC---CCCCCCCCCCEEC
Q ss_conf 117888874421488---8722778987153
Q gi|254780459|r 10 RTCPDTGKRFYDLNK---QVIVSPYTQNSWP 37 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk---~PiiCP~CG~e~~ 37 (129)
=+||+|+.|| .|.- .--+||.||..+.
T Consensus 118 Y~C~~c~~R~-tFeeAme~~F~CP~CG~~Le 147 (178)
T PRK06266 118 FVCPNGHPKF-TFDEAMEYGFRCPQCGEMLE 147 (178)
T ss_pred EECCCCCCCC-CHHHHHHCCCCCCCCCCCCE
T ss_conf 8889998300-59999883996999988663
No 56
>TIGR00373 TIGR00373 conserved hypothetical protein TIGR00373; InterPro: IPR005241 This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain. .
Probab=89.05 E-value=0.15 Score=30.40 Aligned_cols=26 Identities=23% Similarity=0.446 Sum_probs=19.0
Q ss_pred CCCCCCCEE-EECCC-CCCCCCCCCCEE
Q ss_conf 178888744-21488-872277898715
Q gi|254780459|r 11 TCPDTGKRF-YDLNK-QVIVSPYTQNSW 36 (129)
Q Consensus 11 ~C~~Cg~KF-YDlnk-~PiiCP~CG~e~ 36 (129)
+||+|..|| |+=-- ---+||.||+-.
T Consensus 113 ~CpN~~vrftf~eAme~nFtCP~CG~~l 140 (168)
T TIGR00373 113 VCPNMNVRFTFDEAMELNFTCPECGAML 140 (168)
T ss_pred EECCCEEEEEHHHHHCCCCCCCCCCCHH
T ss_conf 7138405740422311679883313232
No 57
>pfam09297 zf-NADH-PPase NADH pyrophosphatase zinc ribbon domain. This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure.
Probab=88.90 E-value=0.15 Score=30.37 Aligned_cols=20 Identities=35% Similarity=0.669 Sum_probs=14.9
Q ss_pred CCCHHHCCCCCCCCCCCEEE
Q ss_conf 97522278311788887442
Q gi|254780459|r 1 MAKPELGTKRTCPDTGKRFY 20 (129)
Q Consensus 1 MaK~elG~KR~C~~Cg~KFY 20 (129)
|.....|.+|+||+||..+|
T Consensus 13 t~~~~~g~~r~C~~Cg~~~y 32 (32)
T pfam09297 13 TEPAEGGWARVCPSCGHEHY 32 (32)
T ss_pred CCCCCCCCEEECCCCCCCCC
T ss_conf 75077851766887676659
No 58
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=88.63 E-value=0.22 Score=29.33 Aligned_cols=31 Identities=13% Similarity=0.372 Sum_probs=23.5
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEECHHH
Q ss_conf 1178888744214888722778987153233
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWPLAY 40 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~ 40 (129)
..||.|+.-|-==.-.-.+||.|+.+|.+..
T Consensus 4 p~cp~c~sEytYed~~~~~cpec~~ew~~~~ 34 (112)
T COG2824 4 PPCPKCNSEYTYEDGGQLICPECAHEWNENE 34 (112)
T ss_pred CCCCCCCCCEEEECCCEEECCHHCCCCCCCC
T ss_conf 8897567711893685676740013255232
No 59
>pfam10571 UPF0547 Uncharacterized protein family UPF0547. This domain contains a zinc-ribbon motif.
Probab=88.46 E-value=0.22 Score=29.36 Aligned_cols=25 Identities=20% Similarity=0.493 Sum_probs=19.4
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEEC
Q ss_conf 1178888744214888722778987153
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~ 37 (129)
++||.|++.- --.-.+||.||.+|.
T Consensus 1 K~CP~C~~~v---p~~~~~Cp~CG~~F~ 25 (26)
T pfam10571 1 KTCPECGAEV---PLAAKICPHCGYEFK 25 (26)
T ss_pred CCCCCCCCCC---CHHCCCCCCCCCCCC
T ss_conf 9687554836---400344778885555
No 60
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=88.45 E-value=0.26 Score=28.93 Aligned_cols=25 Identities=28% Similarity=0.488 Sum_probs=20.2
Q ss_pred CCCCCCCEEEECCC----CCCCCCCCCCE
Q ss_conf 17888874421488----87227789871
Q gi|254780459|r 11 TCPDTGKRFYDLNK----QVIVSPYTQNS 35 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk----~PiiCP~CG~e 35 (129)
.|.+||..|==|-+ .++.||.||+.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EECCCCCEEEEEEECCCCCCCCCCCCCCC
T ss_conf 96899997999986578878858689992
No 61
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=88.37 E-value=0.27 Score=28.80 Aligned_cols=26 Identities=27% Similarity=0.441 Sum_probs=16.7
Q ss_pred CCCCCCCC-EE---------EECCCCCCCCCCCCCEEC
Q ss_conf 11788887-44---------214888722778987153
Q gi|254780459|r 10 RTCPDTGK-RF---------YDLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 10 R~C~~Cg~-KF---------YDlnk~PiiCP~CG~e~~ 37 (129)
-+||+|.- .| |||- .-.||.||+-+.
T Consensus 908 Y~Cp~Cky~ef~~~g~~~sGyDLp--dk~CP~Cg~~l~ 943 (1436)
T PRK00448 908 YVCPNCKYSEFFTDGSVGSGYDLP--DKDCPKCGTKLK 943 (1436)
T ss_pred CCCCCCCCHHCCCCCCCCCCCCCC--CCCCCCCCCCCC
T ss_conf 257655400002466546577786--566864343002
No 62
>PRK03754 DNA-directed RNA polymerase subunit P; Provisional
Probab=87.90 E-value=0.22 Score=29.33 Aligned_cols=26 Identities=23% Similarity=0.561 Sum_probs=21.3
Q ss_pred CCCCCCCEE-EECCC-CCCCCCCCCCEE
Q ss_conf 178888744-21488-872277898715
Q gi|254780459|r 11 TCPDTGKRF-YDLNK-QVIVSPYTQNSW 36 (129)
Q Consensus 11 ~C~~Cg~KF-YDlnk-~PiiCP~CG~e~ 36 (129)
.|..||+-| .||.- ..+-||+||.-+
T Consensus 7 rcakcgkev~ldl~~~revrcpycgski 34 (49)
T PRK03754 7 RCAKCGREVKLDLSTTRDLRCPYCGSKI 34 (49)
T ss_pred HHHHCCCEEEEEHHHHHHCCCCCCCCEE
T ss_conf 7765383036412323310377767754
No 63
>pfam05191 ADK_lid Adenylate kinase, active site lid. 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 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.
Probab=87.83 E-value=0.33 Score=28.32 Aligned_cols=28 Identities=18% Similarity=0.242 Sum_probs=21.5
Q ss_pred CCCCCCCCCEEEECCC---CCCCCCCCCCEE
Q ss_conf 3117888874421488---872277898715
Q gi|254780459|r 9 KRTCPDTGKRFYDLNK---QVIVSPYTQNSW 36 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk---~PiiCP~CG~e~ 36 (129)
-|+|++||+-|--+.+ .+-+|-.||.++
T Consensus 1 Rr~C~~Cg~~Yn~~~~pPk~~g~CD~cg~~L 31 (36)
T pfam05191 1 RRVCPSCGRIYHVKFNPPKVEGVCDKCGGEL 31 (36)
T ss_pred CCCCCCCCCHHCCCCCCCCCCCCCCCCCCEE
T ss_conf 9574888751134556988788267989992
No 64
>LOAD_sir2 consensus
Probab=87.77 E-value=0.25 Score=29.00 Aligned_cols=34 Identities=18% Similarity=0.243 Sum_probs=23.4
Q ss_pred CCCCCCCCCCEEE--------ECCCCCCCCCCCCCEECHHHH
Q ss_conf 8311788887442--------148887227789871532331
Q gi|254780459|r 8 TKRTCPDTGKRFY--------DLNKQVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 8 ~KR~C~~Cg~KFY--------Dlnk~PiiCP~CG~e~~~~~~ 41 (129)
.+-.|.+|+.+|- .....+..||.||..+-|...
T Consensus 117 ~~~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~C~g~lrP~Vv 158 (217)
T LOAD_sir2 117 AKERCTSCGKEYPREEVVERIGLKNTPPKCPDCGGLLKPDIV 158 (217)
T ss_pred CEEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCEECCCEE
T ss_conf 758838999938889988888605899988545898687378
No 65
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=87.55 E-value=0.26 Score=28.92 Aligned_cols=29 Identities=14% Similarity=0.295 Sum_probs=22.6
Q ss_pred CCCCCCCCCCEEEECCCC---CCCCCCCCCEECH
Q ss_conf 831178888744214888---7227789871532
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNKQ---VIVSPYTQNSWPL 38 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk~---PiiCP~CG~e~~~ 38 (129)
.|++||+||.+ =+.|- -=.|.+||..|.-
T Consensus 34 ~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRT--TVKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred CCCCCCCCCCC--CEEEECCCEEECCCCCCEECC
T ss_conf 47769978974--045523675871788873026
No 66
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA; InterPro: IPR004624 This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage . This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA ..
Probab=87.50 E-value=0.29 Score=28.61 Aligned_cols=32 Identities=13% Similarity=0.275 Sum_probs=27.5
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEECHHHH
Q ss_conf 11788887442148887227789871532331
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~ 41 (129)
-.||.|...|.=-...-.+||.|+.+|.-...
T Consensus 3 p~cpkc~~~y~y~d~~~~~cp~c~~eW~~~e~ 34 (111)
T TIGR00686 3 PPCPKCNSEYTYHDGGNLICPDCGYEWNDNEP 34 (111)
T ss_pred CCCCCCCCCEEEECCCEEECCCCCCCCCCCCC
T ss_conf 88888775414306850332200122465555
No 67
>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=87.37 E-value=0.21 Score=29.46 Aligned_cols=31 Identities=13% Similarity=0.191 Sum_probs=21.5
Q ss_pred CCCCCCCCCEEE------ECCCCCCCCCCCCCEECHH
Q ss_conf 311788887442------1488872277898715323
Q gi|254780459|r 9 KRTCPDTGKRFY------DLNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 9 KR~C~~Cg~KFY------Dlnk~PiiCP~CG~e~~~~ 39 (129)
+-.|++||.+|- -....+..||.||..+-|.
T Consensus 113 ~~~C~~C~~~~~~~~~~~~~~~~~P~C~~C~g~lrP~ 149 (222)
T cd01413 113 TAYCVNCGSKYDLEEVKYAKKHEVPRCPKCGGIIRPD 149 (222)
T ss_pred EEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 5782899983778898777525899774558833675
No 68
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=87.37 E-value=0.26 Score=28.90 Aligned_cols=27 Identities=11% Similarity=0.113 Sum_probs=21.6
Q ss_pred HCCCCCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 278311788887442148887227789871
Q gi|254780459|r 6 LGTKRTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 6 lG~KR~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
..-+.+|..|++.|= ..-=+||.||..
T Consensus 136 ~~w~~rC~GC~~~f~---~~~~~Cp~CG~~ 162 (177)
T COG1439 136 RKWRLRCHGCKRIFP---EPKDFCPICGSP 162 (177)
T ss_pred EEEEEEEECCCEECC---CCCCCCCCCCCC
T ss_conf 535689845752508---988807789991
No 69
>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=87.29 E-value=0.29 Score=28.66 Aligned_cols=33 Identities=9% Similarity=0.055 Sum_probs=23.4
Q ss_pred CCCCCCCCCEEEECC----CCCCCCCCCCCEECHHHH
Q ss_conf 311788887442148----887227789871532331
Q gi|254780459|r 9 KRTCPDTGKRFYDLN----KQVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 9 KR~C~~Cg~KFYDln----k~PiiCP~CG~e~~~~~~ 41 (129)
+-.|+.|+.+|+..- +.+..||.||...-|...
T Consensus 109 ~~~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~lrP~vV 145 (224)
T cd01412 109 RVRCSSCGYVGENNEEIPEEELPRCPKCGGLLRPGVV 145 (224)
T ss_pred EEEECCCCCCCCCCCCCCCCCCCCCCCCCCEECCCEE
T ss_conf 6998999898855222123679977467997055377
No 70
>PRK04023 DNA polymerase II large subunit; Validated
Probab=87.27 E-value=0.31 Score=28.48 Aligned_cols=21 Identities=29% Similarity=0.700 Sum_probs=13.0
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 31178888744214888722778987
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
.|+||+||+.=| -+.||.||+
T Consensus 633 ~R~Cp~Cg~eT~-----~~~C~~CG~ 653 (1128)
T PRK04023 633 NRKCPSCGKETF-----YRRCPFCGT 653 (1128)
T ss_pred EEECCCCCCCCC-----CCCCCCCCC
T ss_conf 028899998357-----557877799
No 71
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=87.10 E-value=0.45 Score=27.45 Aligned_cols=29 Identities=17% Similarity=0.315 Sum_probs=23.1
Q ss_pred CCCCCCCCCCE-EEECCCCCCCCCCCCC-EE
Q ss_conf 83117888874-4214888722778987-15
Q gi|254780459|r 8 TKRTCPDTGKR-FYDLNKQVIVSPYTQN-SW 36 (129)
Q Consensus 8 ~KR~C~~Cg~K-FYDlnk~PiiCP~CG~-e~ 36 (129)
+++.||.||.- |-=-.++-..|=+||. ||
T Consensus 22 ~~k~CPrCG~GvfmA~H~dR~~CGKCgyTef 52 (54)
T PRK00432 22 KNKFCPRCGPGVFMAEHKDRWACGKCGYTEF 52 (54)
T ss_pred CCCCCCCCCCCEEEEECCCCCCCCCCCCEEE
T ss_conf 6785979999464012588766358667464
No 72
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=87.07 E-value=0.25 Score=29.06 Aligned_cols=29 Identities=10% Similarity=0.313 Sum_probs=23.8
Q ss_pred CCCCCCCCEEEECCCCCCC----------------CCCCCCEECH
Q ss_conf 1178888744214888722----------------7789871532
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIV----------------SPYTQNSWPL 38 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~Pii----------------CP~CG~e~~~ 38 (129)
-.||-|+..--.+-|..+. ||+||..|=+
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~ 142 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWK 142 (165)
T ss_pred CCCCCCCCEECCCCHHHHHHCCCHHHHHCCCCEEECCCCCCCCCC
T ss_conf 327434978010767777520652442020014677997623267
No 73
>pfam08996 zf-DNA_Pol DNA Polymerase alpha zinc finger. 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. 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.
Probab=87.01 E-value=0.47 Score=27.35 Aligned_cols=35 Identities=26% Similarity=0.380 Sum_probs=23.9
Q ss_pred CCCCCCCCCCEEE-----ECCC---CC--CCCCCCCCEECHHHHH
Q ss_conf 8311788887442-----1488---87--2277898715323310
Q gi|254780459|r 8 TKRTCPDTGKRFY-----DLNK---QV--IVSPYTQNSWPLAYFE 42 (129)
Q Consensus 8 ~KR~C~~Cg~KFY-----Dlnk---~P--iiCP~CG~e~~~~~~~ 42 (129)
.+-.||+||+.|. .-+. .| +.||+|++.|.+..+.
T Consensus 17 l~l~Cp~C~~~~~f~gv~~~~~~~~~~sg~~C~~C~~~~~~~~i~ 61 (186)
T pfam08996 17 LKLKCPSCGTEFPFPGIFASSGERVTPSGLQCPKCNALIPLAQIV 61 (186)
T ss_pred EEEECCCCCCCEECCCEECCCCCCEEECCCCCCCCCCCCCHHHHH
T ss_conf 597899999845778864068983306868896987918899999
No 74
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=86.79 E-value=0.36 Score=28.05 Aligned_cols=32 Identities=9% Similarity=0.051 Sum_probs=22.1
Q ss_pred CCCCCCCCCEEEE---CCCCCCCCCCCCCEECHHH
Q ss_conf 3117888874421---4888722778987153233
Q gi|254780459|r 9 KRTCPDTGKRFYD---LNKQVIVSPYTQNSWPLAY 40 (129)
Q Consensus 9 KR~C~~Cg~KFYD---lnk~PiiCP~CG~e~~~~~ 40 (129)
+-.|+.||.+|.- -...+..||.||...-|..
T Consensus 122 ~~~C~~C~~~~~~~~~~~~~~p~C~~Cgg~lrP~V 156 (239)
T PRK00481 122 RARCTKCGQTYDLDEVDLEPPPRCPKCGGILRPDV 156 (239)
T ss_pred EEEECCCCCCCCHHHHHCCCCCCCCCCCCEECCCE
T ss_conf 01708998985166630257998856799746422
No 75
>pfam02146 SIR2 Sir2 family. This region is characteristic of Silent information regulator 2 (Sir2) proteins, or sirtuins. These are protein deacetylases that depend on nicotine adenine dinucleotide (NAD). They are found in many subcellular locations, including the nucleus, cytoplasm and mitochondria. Eukaryotic forms play in important role in the regulation of transcriptional repression. Moreover, they are involved in microtubule organisation and DNA damage repair processes.
Probab=86.74 E-value=0.25 Score=29.00 Aligned_cols=32 Identities=13% Similarity=0.058 Sum_probs=22.6
Q ss_pred CCCCCCCCCEEEE-------CCCCCCCCCCCCCEECHHH
Q ss_conf 3117888874421-------4888722778987153233
Q gi|254780459|r 9 KRTCPDTGKRFYD-------LNKQVIVSPYTQNSWPLAY 40 (129)
Q Consensus 9 KR~C~~Cg~KFYD-------lnk~PiiCP~CG~e~~~~~ 40 (129)
+-.|++|+.+|.- ....+..||.||..+-|..
T Consensus 104 ~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg~lrP~V 142 (177)
T pfam02146 104 KARCVSCHKKYTGETLPERIDAAKVPKCDKCGGLLKPDI 142 (177)
T ss_pred EEECCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCE
T ss_conf 558789999188899998876016998767899647857
No 76
>pfam06677 Auto_anti-p27 Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). This family consists of several Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) sequences. 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=86.23 E-value=0.49 Score=27.25 Aligned_cols=24 Identities=21% Similarity=0.620 Sum_probs=21.5
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCC
Q ss_conf 117888874421488872277898
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQ 33 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG 33 (129)
.+||.||+-.+-+..-.+.||.|+
T Consensus 18 ~~C~~Cg~pLf~~k~g~~~Cp~C~ 41 (41)
T pfam06677 18 EHCPKCGTPLFRLKDGKVFCPSCE 41 (41)
T ss_pred CCCCCCCCEEEECCCCCEECCCCC
T ss_conf 325456983058489999578779
No 77
>PRK11823 DNA repair protein RadA; Provisional
Probab=86.22 E-value=0.47 Score=27.38 Aligned_cols=29 Identities=28% Similarity=0.293 Sum_probs=23.1
Q ss_pred CCCHHHCCCCCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 9752227831178888744214888722778987
Q gi|254780459|r 1 MAKPELGTKRTCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 1 MaK~elG~KR~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
|||.. +.-+|++||..|. |--=-||.||+
T Consensus 1 MaK~k--~~y~C~~CG~~~~---kW~GkCp~C~~ 29 (454)
T PRK11823 1 MAKAK--TAYVCQECGAESP---KWLGRCPACGA 29 (454)
T ss_pred CCCCC--CEEECCCCCCCCC---CCCEECCCCCC
T ss_conf 99888--7179988999788---71435879898
No 78
>PRK02173 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=86.21 E-value=0.36 Score=28.07 Aligned_cols=30 Identities=13% Similarity=0.284 Sum_probs=19.7
Q ss_pred CCCCCCCEEEECCCCCC-----CCCCCCCEECHHH
Q ss_conf 17888874421488872-----2778987153233
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVI-----VSPYTQNSWPLAY 40 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~Pi-----iCP~CG~e~~~~~ 40 (129)
-|+.||+||-=.++.-| +|+.||.++....
T Consensus 65 eC~~Cgk~~~~~~~~~~c~~~~~C~~~gvev~~~~ 99 (1438)
T PRK02173 65 KCPICGRKYKKSNENQLCIATKECKIEKPEILPKI 99 (1438)
T ss_pred CCHHCCCCCCEEECCEECCCCCCCCCCCEEECCCE
T ss_conf 21100771124116855356761788886948254
No 79
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=86.13 E-value=0.19 Score=29.83 Aligned_cols=33 Identities=21% Similarity=0.285 Sum_probs=25.7
Q ss_pred HHHCCCCCCCCCCCEEEE--CCCC-CCCCCCCCCEE
Q ss_conf 222783117888874421--4888-72277898715
Q gi|254780459|r 4 PELGTKRTCPDTGKRFYD--LNKQ-VIVSPYTQNSW 36 (129)
Q Consensus 4 ~elG~KR~C~~Cg~KFYD--lnk~-PiiCP~CG~e~ 36 (129)
++-+.+-.|..||+.|-+ |++- -|-||+||.-+
T Consensus 2 ~~~~~~Y~C~rCg~~fs~~el~~lPgirCPyCGyrI 37 (52)
T PRK00398 2 AEERKLYRCGRCGRTFSKEELEILPGVRCPYCGFKI 37 (52)
T ss_pred CCHHHEEEHHCCCCCCCHHHHHHCCCCCCCCCCCEE
T ss_conf 233223430014476079898447786557568389
No 80
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=86.06 E-value=0.36 Score=28.09 Aligned_cols=34 Identities=15% Similarity=0.286 Sum_probs=26.8
Q ss_pred CCCHHHCCCCC-CCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 97522278311-788887442148887227789871
Q gi|254780459|r 1 MAKPELGTKRT-CPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 1 MaK~elG~KR~-C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
++.++||.=.. |++||.-.. -...-+.||.||..
T Consensus 141 t~~~eLGVv~A~C~~cg~~m~-~~~~~~~Cp~cg~~ 175 (187)
T PRK09521 141 TKGKDLGVIKALCSRCRTPLV-KKGNTLKCPNCGNV 175 (187)
T ss_pred ECCCCCEEEEEECCCCCCCEE-EECCEEECCCCCCE
T ss_conf 538884499995776788586-73999999999998
No 81
>PRK09401 reverse gyrase; Reviewed
Probab=86.03 E-value=0.3 Score=28.53 Aligned_cols=24 Identities=25% Similarity=0.436 Sum_probs=19.2
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 117888874421488872277898715
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
..|.+||..|-|-- -.||.||...
T Consensus 678 krC~~cg~qft~~~---~~cP~Cgs~~ 701 (1176)
T PRK09401 678 KRCRDCGHQFTDES---DRCPRCGSTN 701 (1176)
T ss_pred HHHHHCCCCCCCCC---CCCCCCCCCC
T ss_conf 67753586012466---6688778887
No 82
>pfam04475 DUF555 Protein of unknown function (DUF555). Family of uncharacterized, hypothetical archaeal proteins.
Probab=85.93 E-value=0.33 Score=28.30 Aligned_cols=32 Identities=16% Similarity=0.234 Sum_probs=26.2
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCEECHHHHH
Q ss_conf 3117888874421488872277898715323310
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFE 42 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~ 42 (129)
||.=| ..+|-+..---.+||+||.+|++....
T Consensus 32 krLn~--~l~~VeIevG~~~cP~Cge~~~~afvv 63 (102)
T pfam04475 32 KRLNP--KLDFVEIEVGSTACPKCGEELESVFVV 63 (102)
T ss_pred HHHCC--CCCEEEEECCCCCCCCCCCCCCCEEEE
T ss_conf 86498--988799825751088767866747898
No 83
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=85.84 E-value=0.42 Score=27.68 Aligned_cols=25 Identities=16% Similarity=0.328 Sum_probs=14.1
Q ss_pred CCCCCCCCE-EEECCCCCCCCCCCCC
Q ss_conf 117888874-4214888722778987
Q gi|254780459|r 10 RTCPDTGKR-FYDLNKQVIVSPYTQN 34 (129)
Q Consensus 10 R~C~~Cg~K-FYDlnk~PiiCP~CG~ 34 (129)
-+|+.||-. =+-.+.....||.||.
T Consensus 642 d~C~~CGy~Ge~~~~~~g~~CP~CG~ 667 (711)
T PRK09263 642 DECYECGFTGEFECTEKGFTCPKCGN 667 (711)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 65667897662357778980939999
No 84
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=85.73 E-value=0.4 Score=27.77 Aligned_cols=23 Identities=13% Similarity=0.130 Sum_probs=16.3
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 11788887442148887227789871
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
.+||+|+ +|.-.. --.||.||.+
T Consensus 568 siC~~ch--gy~~Ge-~~~CP~CG~~ 590 (625)
T PRK08271 568 TICNEGH--AIDKRT-GKRCPVCGSE 590 (625)
T ss_pred EECCCCC--CCCCCC-CCCCCCCCCC
T ss_conf 3788999--885776-8839899897
No 85
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=85.66 E-value=0.5 Score=27.19 Aligned_cols=34 Identities=12% Similarity=0.171 Sum_probs=27.8
Q ss_pred CCCCCCCCCCEEEECCCCCCCCCCCCCEECHHHH
Q ss_conf 8311788887442148887227789871532331
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~ 41 (129)
.|-+||.||.+-==.+|.=--||+||+-+.-...
T Consensus 349 ~~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~~ 382 (421)
T COG1571 349 VNPVCPRCGGRMKSAGRNGFRCKKCGTRARETLI 382 (421)
T ss_pred CCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf 1788976677131167898526642661775532
No 86
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=85.31 E-value=0.49 Score=27.25 Aligned_cols=25 Identities=12% Similarity=0.254 Sum_probs=17.0
Q ss_pred CCCCCCCCEEEECCC----------CCCCCCCCCCEE
Q ss_conf 117888874421488----------872277898715
Q gi|254780459|r 10 RTCPDTGKRFYDLNK----------QVIVSPYTQNSW 36 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk----------~PiiCP~CG~e~ 36 (129)
-+||+|. |..|.. .+=.||+||+-+
T Consensus 915 Y~Cp~Ck--y~Ef~~d~svgsGfDLpdK~CPkCg~pl 949 (1444)
T COG2176 915 YLCPECK--YSEFIDDGSVGSGFDLPDKDCPKCGTPL 949 (1444)
T ss_pred CCCCCCC--EEEEECCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 3288874--0466237876778888999898679943
No 87
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=85.14 E-value=0.43 Score=27.57 Aligned_cols=35 Identities=14% Similarity=0.298 Sum_probs=22.3
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEECHHHHHCCCCC
Q ss_conf 11788887442148887227789871532331012344
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFEAPTSP 47 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~~~~~~ 47 (129)
..|++||..||== -..||.||..-..+...-+.++
T Consensus 30 ~kC~~CG~v~~PP---r~~Cp~C~~~~~~E~vels~~G 64 (140)
T COG1545 30 TKCKKCGRVYFPP---RAYCPKCGSETELEWVELSGEG 64 (140)
T ss_pred EECCCCCCEECCC---CCCCCCCCCCCCEEEEEECCCE
T ss_conf 6837898188198---2338788997844799939976
No 88
>pfam03604 DNA_RNApol_7kD DNA directed RNA polymerase, 7 kDa subunit.
Probab=84.94 E-value=0.46 Score=27.42 Aligned_cols=26 Identities=12% Similarity=0.041 Sum_probs=22.5
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 17888874421488872277898715
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
+|-.||++|=--.++||.|..||.-+
T Consensus 2 iCg~Cg~~~~i~~~d~irC~eCG~RI 27 (32)
T pfam03604 2 ICGECGAEVELKPGDPIRCKECGHRI 27 (32)
T ss_pred CCCCCCCCCCCCCCCCEECCCCCCEE
T ss_conf 54546773200899968711087388
No 89
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=84.70 E-value=0.49 Score=27.25 Aligned_cols=21 Identities=19% Similarity=0.184 Sum_probs=13.8
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 1178888744214888722778987
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
-+|+.||- . -. ---.||.||.
T Consensus 648 ~~C~~CGy--~-~~-~~~~CP~CG~ 668 (703)
T PRK07111 648 DYCKNCGY--Y-GV-INDKCPKCGS 668 (703)
T ss_pred CCCCCCCC--C-CC-CCCCCCCCCC
T ss_conf 65788998--2-88-7782919979
No 90
>PRK04023 DNA polymerase II large subunit; Validated
Probab=84.63 E-value=0.53 Score=27.02 Aligned_cols=13 Identities=31% Similarity=0.470 Sum_probs=7.7
Q ss_pred CCCCCCCCCCCEE
Q ss_conf 7831178888744
Q gi|254780459|r 7 GTKRTCPDTGKRF 19 (129)
Q Consensus 7 G~KR~C~~Cg~KF 19 (129)
..+++|+.||++=
T Consensus 643 T~~~~C~~CG~~T 655 (1128)
T PRK04023 643 TFYRRCPFCGTHT 655 (1128)
T ss_pred CCCCCCCCCCCCC
T ss_conf 5755787779966
No 91
>TIGR00354 polC DNA polymerase II, large subunit DP2; InterPro: IPR004475 This family represents the large subunit, DP2, 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.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006308 DNA catabolic process.
Probab=84.39 E-value=0.46 Score=27.44 Aligned_cols=23 Identities=4% Similarity=0.199 Sum_probs=10.7
Q ss_pred CCCCCCCCEEEECCCCCCC--CCCCCCE
Q ss_conf 1178888744214888722--7789871
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIV--SPYTQNS 35 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~Pii--CP~CG~e 35 (129)
-.|..||+|| .|=|+. ||+||.-
T Consensus 1091 vRCTkCn~KY---RRIPL~GkC~kCG~~ 1115 (1173)
T TIGR00354 1091 VRCTKCNAKY---RRIPLKGKCLKCGSN 1115 (1173)
T ss_pred CCCCCCCCCC---CCCCCCCCCCCCCCC
T ss_conf 1013586841---334786644466883
No 92
>KOG2462 consensus
Probab=84.36 E-value=0.68 Score=26.37 Aligned_cols=33 Identities=18% Similarity=0.458 Sum_probs=17.8
Q ss_pred HHHCCCCCCCCCCCEEEECC--------------CCCCCCCCCCCEE
Q ss_conf 22278311788887442148--------------8872277898715
Q gi|254780459|r 4 PELGTKRTCPDTGKRFYDLN--------------KQVIVSPYTQNSW 36 (129)
Q Consensus 4 ~elG~KR~C~~Cg~KFYDln--------------k~PiiCP~CG~e~ 36 (129)
+-...+-+|+.||+.|=-.- |.--.||+||..|
T Consensus 125 ~~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~Y 171 (279)
T KOG2462 125 AAKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVY 171 (279)
T ss_pred CCCCCCEECCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCEE
T ss_conf 12477321355365212445510111014542355455478898422
No 93
>PRK05580 primosome assembly protein PriA; Validated
Probab=84.33 E-value=0.73 Score=26.19 Aligned_cols=31 Identities=10% Similarity=0.057 Sum_probs=18.9
Q ss_pred HCCCCCCCCCCCEE-EECCCCCCCCCCCCCEE
Q ss_conf 27831178888744-21488872277898715
Q gi|254780459|r 6 LGTKRTCPDTGKRF-YDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 6 lG~KR~C~~Cg~KF-YDlnk~PiiCP~CG~e~ 36 (129)
=|..-.||+|+... |-.+...+.|.+||...
T Consensus 410 Cg~~~~C~~C~~~L~~h~~~~~l~Ch~Cg~~~ 441 (699)
T PRK05580 410 CGWVARCPHCDGPLTLHRAGRRLRCHHCGYQE 441 (699)
T ss_pred CCCEEECCCCCCEEEECCCCCCEECCCCCCCC
T ss_conf 19945656789863420689833226468836
No 94
>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=84.30 E-value=0.47 Score=27.37 Aligned_cols=32 Identities=16% Similarity=0.271 Sum_probs=22.7
Q ss_pred CCCCCCCCCEEEE------C-CCCCCCCCCCCCEECHHH
Q ss_conf 3117888874421------4-888722778987153233
Q gi|254780459|r 9 KRTCPDTGKRFYD------L-NKQVIVSPYTQNSWPLAY 40 (129)
Q Consensus 9 KR~C~~Cg~KFYD------l-nk~PiiCP~CG~e~~~~~ 40 (129)
+-.|.+|+.+|.- + ...+..||.||..+-|..
T Consensus 109 ~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg~lrP~V 147 (218)
T cd01407 109 RVRCTKCGKEYPRDELQADIDREEVPRCPKCGGLLRPDV 147 (218)
T ss_pred EEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCCEECCCE
T ss_conf 489799999676788877762489998867899964317
No 95
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=84.29 E-value=0.4 Score=27.77 Aligned_cols=22 Identities=27% Similarity=0.575 Sum_probs=19.1
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 1788887442148887227789871
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
.|..||..|-+. .+ .||+||..
T Consensus 696 rC~dcg~q~~~~-~~--~cP~Cgs~ 717 (1187)
T COG1110 696 RCRDCGEQFVDS-ED--KCPRCGSR 717 (1187)
T ss_pred HHHHCCCEECCC-CC--CCCCCCCC
T ss_conf 885158440443-23--59887883
No 96
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=84.03 E-value=0.67 Score=26.43 Aligned_cols=23 Identities=13% Similarity=0.154 Sum_probs=15.0
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 311788887442148887227789871
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
+-.|.-||.. -+.|..||.||..
T Consensus 462 ~L~CH~Cg~~----~~~p~~Cp~Cgs~ 484 (730)
T COG1198 462 QLRCHYCGYQ----EPIPQSCPECGSE 484 (730)
T ss_pred EEEECCCCCC----CCCCCCCCCCCCC
T ss_conf 0670779998----9988779899997
No 97
>pfam03966 Trm112p Trm112p-like protein. 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. Trm112p is required for tRNA methylation in S. cerevisiae 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.
Probab=83.75 E-value=0.46 Score=27.42 Aligned_cols=30 Identities=23% Similarity=0.535 Sum_probs=25.0
Q ss_pred CCCCCCCCEE--------EECCCCCCCCCCCCCEECHH
Q ss_conf 1178888744--------21488872277898715323
Q gi|254780459|r 10 RTCPDTGKRF--------YDLNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 10 R~C~~Cg~KF--------YDlnk~PiiCP~CG~e~~~~ 39 (129)
-+||.|...- ||..+.-++||.||..|++.
T Consensus 8 L~CP~~kgpL~l~~~~~~~~~~egeLvC~~~~~~yPI~ 45 (47)
T pfam03966 8 LACPLCKGPLALVEVAGHYDIEEGELVCPECGLAYPIR 45 (47)
T ss_pred EECCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCC
T ss_conf 75557578342244434446112778623556024046
No 98
>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=83.51 E-value=0.55 Score=26.93 Aligned_cols=32 Identities=9% Similarity=0.019 Sum_probs=21.9
Q ss_pred CCCCCCCCCCEEE-E-------CCCCCCCCCCCCCEECHH
Q ss_conf 8311788887442-1-------488872277898715323
Q gi|254780459|r 8 TKRTCPDTGKRFY-D-------LNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 8 ~KR~C~~Cg~KFY-D-------lnk~PiiCP~CG~e~~~~ 39 (129)
.+-.|++||.+|- + ....+..||.||..+-|.
T Consensus 94 ~~~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~lrP~ 133 (206)
T cd01410 94 FIEVCKSCGPEYVRDDVVETRGDKETGRRCHACGGILKDT 133 (206)
T ss_pred CEEECCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf 7478889999275799998875447899882338970464
No 99
>pfam05876 Terminase_GpA Phage terminase large subunit (GpA). This family consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities.
Probab=83.41 E-value=0.7 Score=26.30 Aligned_cols=29 Identities=21% Similarity=0.257 Sum_probs=19.5
Q ss_pred CCCCCCCEEE--------ECCCCC----CCCCCCCCEECHH
Q ss_conf 1788887442--------148887----2277898715323
Q gi|254780459|r 11 TCPDTGKRFY--------DLNKQV----IVSPYTQNSWPLA 39 (129)
Q Consensus 11 ~C~~Cg~KFY--------Dlnk~P----iiCP~CG~e~~~~ 39 (129)
-||.||..|. +.+-.| .+||.||..+...
T Consensus 202 pCPhCg~~q~l~~~~l~w~~~~~p~~a~y~C~~Cg~~i~e~ 242 (552)
T pfam05876 202 PCPHCGEEQELRWERLKWDKGEAPETARYVCPHCGCVIEEH 242 (552)
T ss_pred ECCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCCCCCCHH
T ss_conf 89899986555005466479998553499898898888999
No 100
>TIGR02642 phage_xxxx uncharacterized phage protein; InterPro: IPR013464 This uncharacterised protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus (strain YJ016), Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to the phage lambda antitermination protein Q..
Probab=83.23 E-value=0.55 Score=26.94 Aligned_cols=33 Identities=18% Similarity=0.175 Sum_probs=27.4
Q ss_pred CCHHHCCCCCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 752227831178888744214888722778987
Q gi|254780459|r 2 AKPELGTKRTCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 2 aK~elG~KR~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
|..+-|.+++||.|-.==--+.+.|=.||.|+-
T Consensus 175 a~~~a~~~~~CP~C~Gtg~~~~~~P~~C~~C~G 207 (270)
T TIGR02642 175 AVAKAAESRKCPRCRGTGLRLRRQPEECDKCAG 207 (270)
T ss_pred HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 999874148879865667888977887777786
No 101
>PRK08402 replication factor A; Reviewed
Probab=83.23 E-value=0.4 Score=27.77 Aligned_cols=29 Identities=28% Similarity=0.621 Sum_probs=23.9
Q ss_pred CCCCCCCEE-EECCCCCCCCCCCCCEECHH
Q ss_conf 178888744-21488872277898715323
Q gi|254780459|r 11 TCPDTGKRF-YDLNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 11 ~C~~Cg~KF-YDlnk~PiiCP~CG~e~~~~ 39 (129)
.||.|+.|. ||-.-+--+||.||..-+..
T Consensus 216 ACPeC~rkvd~d~~~~~wiCpEhGeV~P~k 245 (357)
T PRK08402 216 ACPECKKKVDYDPGTDVWICPEHGEVQPIK 245 (357)
T ss_pred HCHHHHHCCCCCCCCCCEECCCCCCCCCEE
T ss_conf 482431102447887626676667747537
No 102
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=83.13 E-value=0.86 Score=25.75 Aligned_cols=33 Identities=18% Similarity=0.201 Sum_probs=26.1
Q ss_pred CCCCCCCCCEEEECC---CCCCCCCCCCCEECHHHH
Q ss_conf 311788887442148---887227789871532331
Q gi|254780459|r 9 KRTCPDTGKRFYDLN---KQVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 9 KR~C~~Cg~KFYDln---k~PiiCP~CG~e~~~~~~ 41 (129)
.|-||.||.--|==. ..-.+|++||.++.....
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~~Cgye~~~~~~ 37 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEASNK 37 (113)
T ss_pred CCCCCCCCCEEEEEECCCCCEEECCCCCCCCCCCCC
T ss_conf 522687668567857488847888887860003644
No 103
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=82.53 E-value=0.33 Score=28.29 Aligned_cols=14 Identities=14% Similarity=-0.007 Sum_probs=10.1
Q ss_pred CCCCCCCCCEECHH
Q ss_conf 72277898715323
Q gi|254780459|r 26 VIVSPYTQNSWPLA 39 (129)
Q Consensus 26 PiiCP~CG~e~~~~ 39 (129)
...||.||...-|.
T Consensus 179 ~P~C~~Cgg~lrP~ 192 (285)
T PRK05333 179 VPACPACGGILKPD 192 (285)
T ss_pred CCCCCCCCCCCCCC
T ss_conf 87888899981574
No 104
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=82.16 E-value=0.56 Score=26.88 Aligned_cols=25 Identities=16% Similarity=0.480 Sum_probs=19.4
Q ss_pred CCCCCCCCEE-----EECCCCCCCCCCCCCEEC
Q ss_conf 1178888744-----214888722778987153
Q gi|254780459|r 10 RTCPDTGKRF-----YDLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 10 R~C~~Cg~KF-----YDlnk~PiiCP~CG~e~~ 37 (129)
=+||.|.+|| +.++ -.||.||....
T Consensus 114 y~C~~~~~r~sfdeA~~~~---F~Cp~Cg~~L~ 143 (176)
T COG1675 114 YVCPNCHVKYSFDEAMELG---FTCPKCGEDLE 143 (176)
T ss_pred EECCCCCCCCCHHHHHHHC---CCCCCCCCHHH
T ss_conf 5677887731499999837---98887774244
No 105
>pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=81.96 E-value=0.55 Score=26.94 Aligned_cols=23 Identities=17% Similarity=0.323 Sum_probs=18.9
Q ss_pred CCCCCCEEEECCCCCCCCCCCCCEEC
Q ss_conf 78888744214888722778987153
Q gi|254780459|r 12 CPDTGKRFYDLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 12 C~~Cg~KFYDlnk~PiiCP~CG~e~~ 37 (129)
||.||.+ |.=+-+.||.||+++.
T Consensus 1 CPvCg~~---l~Vt~L~C~~C~t~ie 23 (113)
T pfam09862 1 CPVCGEE---LTVTRLECSKCGTTIE 23 (113)
T ss_pred CCCCCCC---EEEEEEECCCCCCEEE
T ss_conf 9989981---3899988489986797
No 106
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=81.95 E-value=0.35 Score=28.17 Aligned_cols=26 Identities=19% Similarity=0.327 Sum_probs=19.7
Q ss_pred CCCCCCCCEEEECCCC-CCCCCCCCCE
Q ss_conf 1178888744214888-7227789871
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQ-VIVSPYTQNS 35 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~-PiiCP~CG~e 35 (129)
++|..||+.|-|-.+. --=||+||.-
T Consensus 3 H~CtrCG~vf~~g~~~il~GCp~CG~n 29 (112)
T COG3364 3 HQCTRCGEVFDDGSEEILSGCPKCGCN 29 (112)
T ss_pred CEECCCCCCCCCCCHHHHCCCCCCCCH
T ss_conf 521404456365129988157201631
No 107
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=81.74 E-value=0.83 Score=25.86 Aligned_cols=29 Identities=14% Similarity=0.280 Sum_probs=19.5
Q ss_pred CCCCCCCCCCEEEECCC-CCCCCCCCCCEE
Q ss_conf 83117888874421488-872277898715
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNK-QVIVSPYTQNSW 36 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk-~PiiCP~CG~e~ 36 (129)
+-|-|+.||.+-.--.. .-..||.||+++
T Consensus 99 ~hrfC~~CG~~t~~~~~g~~~~C~~C~~~~ 128 (257)
T PRK00241 99 SHRFCGYCGHPTHPSKTEWAMLCPHCRERY 128 (257)
T ss_pred CCCCCCCCCCCCCCCCCCEEEECCCCCCCC
T ss_conf 798456567366338785069889998631
No 108
>cd01408 SIRT1 SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; 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, 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 nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
Probab=81.72 E-value=0.53 Score=27.05 Aligned_cols=32 Identities=16% Similarity=0.237 Sum_probs=21.8
Q ss_pred CCCCCCCCCCEEE------E-CCCCCCCCCCCCCEECHH
Q ss_conf 8311788887442------1-488872277898715323
Q gi|254780459|r 8 TKRTCPDTGKRFY------D-LNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 8 ~KR~C~~Cg~KFY------D-lnk~PiiCP~CG~e~~~~ 39 (129)
.+-.|++||.+|= . ++.....||.||..+-|.
T Consensus 115 ~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg~lrP~ 153 (235)
T cd01408 115 ATAHCIKCKHKYPGDWMREDIFNQEVPKCPRCGGLVKPD 153 (235)
T ss_pred CEEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf 878868999888889998887348888860238946887
No 109
>TIGR00622 ssl1 transcription factor ssl1; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C .; GO: 0006281 DNA repair, 0005634 nucleus.
Probab=81.68 E-value=0.77 Score=26.03 Aligned_cols=28 Identities=18% Similarity=0.313 Sum_probs=22.2
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCEECHHHH
Q ss_conf 1788887442148887227789871532331
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~ 41 (129)
-||.|-+|+=-| ||+||.||-......=
T Consensus 3 fCP~C~aKvC~L---P~eCp~C~L~LilstH 30 (112)
T TIGR00622 3 FCPRCKAKVCEL---PVECPICDLVLILSTH 30 (112)
T ss_pred CCCCCCCCCCCC---CCCCCCCCCEEECCHH
T ss_conf 288872522168---8563767702100011
No 110
>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=81.45 E-value=1.2 Score=24.94 Aligned_cols=26 Identities=15% Similarity=0.123 Sum_probs=19.8
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 311788887442148887227789871
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
+-+|+.||--+..- .-|-+||-||+-
T Consensus 2 ~w~C~vCGyi~~G~-~aP~~CPvC~~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGE-EAPEKCPICGAP 27 (34)
T ss_pred EEECCCCCCEEECC-CCCCCCCCCCCC
T ss_conf 68889899886888-798758699996
No 111
>PRK08329 threonine synthase; Validated
Probab=81.39 E-value=0.81 Score=25.91 Aligned_cols=25 Identities=12% Similarity=0.375 Sum_probs=18.7
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCEECH
Q ss_conf 1788887442148887227789871532
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e~~~ 38 (129)
.|+.||.+| + ..-+..|+ ||.-+..
T Consensus 3 ~C~~CG~~y-~-~~~~~~C~-cg~~l~v 27 (348)
T PRK08329 3 RCTKCGRTY-E-EKFRLRCT-CGGTLLV 27 (348)
T ss_pred CCCCCCCCC-C-CCCCEECC-CCCEEEE
T ss_conf 888787936-9-99977899-9997898
No 112
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=81.29 E-value=0.92 Score=25.57 Aligned_cols=34 Identities=18% Similarity=0.212 Sum_probs=20.9
Q ss_pred CCCCCCCCCCEEEECCCCCCCCCCCCCEECHHHHHCCC
Q ss_conf 83117888874421488872277898715323310123
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFEAPT 45 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~~~~ 45 (129)
.+-+||.||..= ..-=.|+.||..+.|..+..++
T Consensus 138 V~GtCP~C~~~~----~~GD~Ce~cG~~~~p~eL~~p~ 171 (666)
T PRK00133 138 VKGTCPKCGAED----QYGDNCEVCGATYSPTELINPK 171 (666)
T ss_pred EEEECCCCCCHH----HCCCCCCCCCCCCCCHHHCCCC
T ss_conf 420257778712----0487422456516734423864
No 113
>PRK03922 hypothetical protein; Provisional
Probab=81.23 E-value=0.72 Score=26.22 Aligned_cols=32 Identities=16% Similarity=0.292 Sum_probs=24.6
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCEECHHHH
Q ss_conf 311788887442148887227789871532331
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~ 41 (129)
||.=| -+.+|-+..---..||+||.+|++...
T Consensus 33 krLn~-~~l~yVeievG~~~cP~Cge~~~~afv 64 (113)
T PRK03922 33 KRLNP-EDLDYVEVEVGSTSCPKCGEPFDSAFV 64 (113)
T ss_pred HHCCC-CCCCEEEEECCCCCCCCCCCCCCCEEE
T ss_conf 54380-569769982575218877786674789
No 114
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=81.11 E-value=0.78 Score=26.02 Aligned_cols=23 Identities=30% Similarity=0.602 Sum_probs=18.5
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 3117888874421488872277898715
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
=|.|++||. |-|. -+||.||..-
T Consensus 5 irkC~~Cg~--YTL~---~~CP~CG~~t 27 (54)
T PRK13130 5 IRKCPKCGR--YTLK---ETCPECGGKT 27 (54)
T ss_pred HHHCCCCCC--EECC---CCCCCCCCCC
T ss_conf 651863564--3032---5286688726
No 115
>PRK13902 alaS lanyl-tRNA synthetase; Provisional
Probab=81.05 E-value=0.71 Score=26.25 Aligned_cols=26 Identities=15% Similarity=0.383 Sum_probs=21.6
Q ss_pred CCCCCCCCCCEEEECCCCCCCCC--CCC
Q ss_conf 83117888874421488872277--898
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNKQVIVSP--YTQ 33 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk~PiiCP--~CG 33 (129)
.+++|+.||.-|+=++..--+|+ -|.
T Consensus 17 ~r~~c~~c~~~fwt~d~~r~~cgd~~c~ 44 (898)
T PRK13902 17 ERKQCKKCGSYFWTLDPDRETCGDAPCD 44 (898)
T ss_pred EEEECCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 6626533377500579986778999888
No 116
>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=80.88 E-value=1.3 Score=24.73 Aligned_cols=26 Identities=27% Similarity=0.405 Sum_probs=20.5
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 311788887442148887227789871
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
|-+|+.||--| +=...|-+||-||+-
T Consensus 1 ~~~C~vCGyi~-~~~~~p~~CP~Cg~~ 26 (33)
T cd00350 1 KYVCPVCGYIY-DGEEAPWVCPVCGAP 26 (33)
T ss_pred CCCCCCCCCEE-ECCCCCCCCCCCCCC
T ss_conf 94888699887-578698728788997
No 117
>PRK08197 threonine synthase; Validated
Probab=80.68 E-value=0.92 Score=25.57 Aligned_cols=29 Identities=10% Similarity=0.287 Sum_probs=21.3
Q ss_pred CCCCCCCCCCEEEECCCCCCCCCCCCCEECH
Q ss_conf 8311788887442148887227789871532
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~ 38 (129)
++-.|+.||++| +.+.....|| ||..+..
T Consensus 5 ~~L~C~~Cg~~y-~~~~~~~~c~-Cg~~L~v 33 (402)
T PRK08197 5 SHLECSKCGDHY-DADQVHNLCK-CGGPLLV 33 (402)
T ss_pred CCCCCCCCCCCC-CCCCCEEECC-CCCEEEE
T ss_conf 635899998957-9988233389-9897988
No 118
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=80.37 E-value=0.74 Score=26.17 Aligned_cols=27 Identities=22% Similarity=0.423 Sum_probs=20.7
Q ss_pred CCCCCCCEEEECCC-CCCCCCCCCCEEC
Q ss_conf 17888874421488-8722778987153
Q gi|254780459|r 11 TCPDTGKRFYDLNK-QVIVSPYTQNSWP 37 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk-~PiiCP~CG~e~~ 37 (129)
.|-+||--|.+..= .|--||.|-.+|.
T Consensus 60 ~CkkCGfef~~~~ik~pSRCP~CKSE~I 87 (97)
T COG3357 60 RCKKCGFEFRDDKIKKPSRCPKCKSEWI 87 (97)
T ss_pred HHCCCCCCCCCCCCCCCCCCCCCHHHCC
T ss_conf 2222686236554678666985314304
No 119
>PRK05638 threonine synthase; Validated
Probab=80.17 E-value=1.1 Score=25.07 Aligned_cols=28 Identities=14% Similarity=0.366 Sum_probs=20.6
Q ss_pred CCCCCCCCCCEEEECCCCCCCCCCCCCEECH
Q ss_conf 8311788887442148887227789871532
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~ 38 (129)
.|-.|+.||+.| + +-.+..| .||.-+..
T Consensus 1 ~~LkC~~CG~~y-~-~~~~~~C-~CG~~L~v 28 (443)
T PRK05638 1 VKVKCPKCGREY-N-SYIPPFC-ICGEELEI 28 (443)
T ss_pred CCCCCCCCCCCC-C-CCCCCCC-CCCCEEEE
T ss_conf 968887647756-8-8899447-99982699
No 120
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=80.04 E-value=0.8 Score=25.95 Aligned_cols=27 Identities=15% Similarity=0.338 Sum_probs=16.3
Q ss_pred CCCCCCCCCEE----EECCCC-C-CCCCCCCCEE
Q ss_conf 31178888744----214888-7-2277898715
Q gi|254780459|r 9 KRTCPDTGKRF----YDLNKQ-V-IVSPYTQNSW 36 (129)
Q Consensus 9 KR~C~~Cg~KF----YDlnk~-P-iiCP~CG~e~ 36 (129)
.-.| +||.+| ..+.+. | ..||.||...
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~ 102 (124)
T PRK00762 70 ELEC-ECGYKGVVDEDEIDHYAAVMECPVCGNKH 102 (124)
T ss_pred EEEE-ECCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 5996-28995553321000256777191887977
No 121
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=79.86 E-value=1.3 Score=24.56 Aligned_cols=29 Identities=17% Similarity=0.239 Sum_probs=20.5
Q ss_pred CCCCCC--CCCCEEEE--C-CCCCCCCCCCCCEE
Q ss_conf 831178--88874421--4-88872277898715
Q gi|254780459|r 8 TKRTCP--DTGKRFYD--L-NKQVIVSPYTQNSW 36 (129)
Q Consensus 8 ~KR~C~--~Cg~KFYD--l-nk~PiiCP~CG~e~ 36 (129)
..|-|| .|+.-++- . +-..++||+||+.|
T Consensus 17 ~~~wCP~~~C~~~~~~~~~~~~~~v~C~~C~~~f 50 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSF 50 (64)
T ss_pred CCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCC
T ss_conf 9339929998700785678988766899998500
No 122
>TIGR01351 adk adenylate kinases; InterPro: IPR006259 Most members of this family are known or believed to be adenylate kinase. Adenylate kinase (ADK) 2.7.4.3 from EC converts ATP + AMP to ADP + ADP, that is, it uses ATP as a phosphate donor for AMP. Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). However, some members accept other nucleotide triphosphates as donors, and may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (2.7.4.10 from EC) is Q9UIJ7 from SWISSPROT, a GTP:AMP phosphotransferase that has been identified in bovine heart and human cells and derived from mitrochondrail GTP AMP that is specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate .This family is designated subfamily rather than equivalog for this reason. ADK has also been identified in different bacterial species and in yeast . Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge. ; GO: 0005524 ATP binding, 0016776 phosphotransferase activity phosphate group as acceptor, 0019201 nucleotide kinase activity, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=79.79 E-value=1.2 Score=24.82 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=19.6
Q ss_pred CCCCCCCCCEEEECCCCCCC------CCCCCCE
Q ss_conf 31178888744214888722------7789871
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIV------SPYTQNS 35 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~Pii------CP~CG~e 35 (129)
-|+||+||.=|=---+.|-+ |+-|+.+
T Consensus 135 R~~cp~cG~~Yh~~f~pPk~~gG~~~cD~~~~~ 167 (232)
T TIGR01351 135 RRICPSCGRVYHIKFNPPKVPGGENLCDDCGGE 167 (232)
T ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCC
T ss_conf 733067785561022788678767988644575
No 123
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=79.63 E-value=0.75 Score=26.12 Aligned_cols=25 Identities=20% Similarity=0.469 Sum_probs=20.0
Q ss_pred CCHHHCCCCCCCCCCCEEEECCCCCCCCCC
Q ss_conf 752227831178888744214888722778
Q gi|254780459|r 2 AKPELGTKRTCPDTGKRFYDLNKQVIVSPY 31 (129)
Q Consensus 2 aK~elG~KR~C~~Cg~KFYDlnk~PiiCP~ 31 (129)
....-|.+|.||+||..+| |-|+|.
T Consensus 111 ~~~~~g~~~~C~~C~~~~y-----Pri~Pa 135 (257)
T PRK00241 111 HPSKTEWAMLCPHCRERYY-----PRIAPC 135 (257)
T ss_pred CCCCCCEEEECCCCCCCCC-----CCCCCE
T ss_conf 3387850698899986316-----887976
No 124
>TIGR00416 sms DNA repair protein RadA; InterPro: IPR004504 RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair.
Probab=79.51 E-value=0.95 Score=25.49 Aligned_cols=37 Identities=22% Similarity=0.234 Sum_probs=26.1
Q ss_pred CCCHHHCCCCCCCCCCCEEEECCCCCCCCCCCCC--EECHHHH
Q ss_conf 9752227831178888744214888722778987--1532331
Q gi|254780459|r 1 MAKPELGTKRTCPDTGKRFYDLNKQVIVSPYTQN--SWPLAYF 41 (129)
Q Consensus 1 MaK~elG~KR~C~~Cg~KFYDlnk~PiiCP~CG~--e~~~~~~ 41 (129)
|||+= =+|=+|.+|| ||+-|===-||.|++ .|....+
T Consensus 1 mAK~P-k~~FvC~~CG---~~~p~W~G~C~~C~aw~t~~E~~~ 39 (481)
T TIGR00416 1 MAKAP-KSKFVCQSCG---AESPKWLGKCPACHAWNTLTEERL 39 (481)
T ss_pred CCCCC-CCCCCCCCCC---CCCHHHCCCCCCCCCCCHHHHHHH
T ss_conf 98888-7742022357---745046473888665313777877
No 125
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=79.29 E-value=1.1 Score=25.13 Aligned_cols=21 Identities=29% Similarity=0.491 Sum_probs=16.8
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 1178888744214888722778987
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
-.||+||. +.+.=-+||.||.
T Consensus 28 ~~C~~CG~----~~~~H~vC~~CG~ 48 (59)
T PRK12286 28 VECPNCGE----LKLPHRVCPSCGY 48 (59)
T ss_pred EECCCCCC----CCCCCEECCCCCE
T ss_conf 57889998----6547778898981
No 126
>KOG2923 consensus
Probab=78.71 E-value=0.87 Score=25.73 Aligned_cols=25 Identities=28% Similarity=0.501 Sum_probs=20.0
Q ss_pred CCCCCCCEEE------ECCCCCCCCCCCCCEE
Q ss_conf 1788887442------1488872277898715
Q gi|254780459|r 11 TCPDTGKRFY------DLNKQVIVSPYTQNSW 36 (129)
Q Consensus 11 ~C~~Cg~KFY------Dlnk~PiiCP~CG~e~ 36 (129)
-|| ||-||- -+|+..+.||+|.-.+
T Consensus 24 PCp-CGDrf~It~edL~~ge~Va~CpsCSL~I 54 (67)
T KOG2923 24 PCP-CGDRFQITLEDLENGEDVARCPSCSLII 54 (67)
T ss_pred CCC-CCCEEEECHHHHHCCCEEECCCCCEEEE
T ss_conf 777-8873365399986788063189966999
No 127
>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=78.61 E-value=0.8 Score=25.94 Aligned_cols=31 Identities=10% Similarity=-0.086 Sum_probs=21.6
Q ss_pred CCCCCCCCCEEEECC-CCCCCCCCCCCEECHH
Q ss_conf 311788887442148-8872277898715323
Q gi|254780459|r 9 KRTCPDTGKRFYDLN-KQVIVSPYTQNSWPLA 39 (129)
Q Consensus 9 KR~C~~Cg~KFYDln-k~PiiCP~CG~e~~~~ 39 (129)
+-.|+.|+.+|.-.. .....||.||..+-|.
T Consensus 118 ~~~C~~C~~~~~~~~~~~~p~C~~Cgg~lrP~ 149 (225)
T cd01411 118 RIYCTVCGKTVDWEEYLKSPYHAKCGGVIRPD 149 (225)
T ss_pred EEEECCCCCCCCHHHHCCCCCCCCCCCEECCC
T ss_conf 67838999867778805698876679982783
No 128
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF; InterPro: IPR004421 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesized as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins , , . Members of the HypF family are accessory proteins involved in hydrogenase maturation. They contain the following domains: acylphosphatase, zinc fingers (2 repeats), a YrdC-like domain, and a C-terminal domain with a putative O-carbamoyltransferase motif. The presence of CO and CN- ligands of the active site iron atoms is essential for [NiFe]-hydrogenase enzyme activity . Both ligands have been suggested to originate from carbamoylphosphate , which is required for maturation of [NiFe]-hydrogenases . Escherichia coli HypF interacts with carbamoylphosphate as a substrate and releases inorganic phosphate . In addition, HypF also cleaves ATP into AMP and pyrophosphate in the presence of carbamoylphosphate. This, and the fact that HypF catalyzes a carbamoylphosphate-dependent pyrophosphate ATP exchange reaction, suggest that the protein catalyzes the activation of carbamoylphosphate . The mechanism of action of HypF, as well as of its individual domains, is not yet clear. Mutations in any of the three major signature motifs, the acylphosphatase, the zinc fingers, and the O-carbamoyltransferase motif, can block carbamoylphosphate phosphatase activity. This indicates an integrated cooperativity between these domains in the cleavage reaction . The N-terminal acylphosphatase (ACP) domain is thought to support the conversion of carbamoylphosphate into CO and CN- , . Biochemical results demonstrating its ACP activity are not available , . ACPs are small enzymes that specifically catalyze the hydrolysis of carboxylphosphate bonds in acylphosphates, including carbamoylphosphate . Zinc fingers have been implicated in bivalent cation binding or as part of a chaperone domain interacting with the large subunit precursor, but experimental studies on such a function are lacking thus far. The YrdC-like domain is present in protein families with regulatory functions (IPR012200 from INTERPRO, IPR010923 from INTERPRO) and has been implicated in RNA binding . It is not clear what function it may have in members of the HypF family. A C-terminal domain is distantly related to peptidase M22, but contains a conserved O-carbamoyltransferase motif required for the carbamoylphosphate phosphatase activity . The function of this domain is not clear. Nomenclature note: the following names are used as synonyms of HypF: HupY in Azotobacter chroococcum, HupN in Rhizobium leguminosarum, HydA in Escherichia coli. In other organisms, these names are used to designate various "hydrogenase cluster" proteins unrelated to the members of this family. ; GO: 0030528 transcription regulator activity.
Probab=78.38 E-value=0.49 Score=27.24 Aligned_cols=26 Identities=35% Similarity=0.654 Sum_probs=15.6
Q ss_pred CCCCCCCCEEEE-CCC----CCCCCCCCCCE
Q ss_conf 117888874421-488----87227789871
Q gi|254780459|r 10 RTCPDTGKRFYD-LNK----QVIVSPYTQNS 35 (129)
Q Consensus 10 R~C~~Cg~KFYD-lnk----~PiiCP~CG~e 35 (129)
+.|+.|-.=|-| ++| .|+-||.||=.
T Consensus 153 pLC~~C~~EY~dP~DRRFHAQ~~aCP~CGP~ 183 (799)
T TIGR00143 153 PLCPDCEKEYKDPLDRRFHAQAIACPRCGPK 183 (799)
T ss_pred CCCHHHHHHCCCCCCCEEEECCCCCCCCCCC
T ss_conf 9884689970788763046446277335786
No 129
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=78.30 E-value=1.2 Score=24.87 Aligned_cols=29 Identities=10% Similarity=0.054 Sum_probs=21.6
Q ss_pred HCCCCCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 27831178888744214888722778987
Q gi|254780459|r 6 LGTKRTCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 6 lG~KR~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
+=+.++|+.|.-...-=+..|.+||.|+-
T Consensus 139 ~~~~~~C~~C~GsGak~gt~~~tC~tC~G 167 (371)
T COG0484 139 VTRSVTCSTCHGSGAKPGTDPKTCPTCNG 167 (371)
T ss_pred CCEEEECCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 45236788678988899999985788788
No 130
>PRK11032 hypothetical protein; Provisional
Probab=78.06 E-value=1.3 Score=24.70 Aligned_cols=27 Identities=7% Similarity=0.233 Sum_probs=18.8
Q ss_pred CCCCCCCCEEEECCCC--CCCCCCCCC-EEC
Q ss_conf 1178888744214888--722778987-153
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQ--VIVSPYTQN-SWP 37 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~--PiiCP~CG~-e~~ 37 (129)
-+|-+||.+ +-|++. -..||+||. +|.
T Consensus 125 LvC~~Cg~~-~~~~~~~~ippCp~Cg~~~F~ 154 (160)
T PRK11032 125 LVCEKCHHH-LAFYTPEVLPLCPKCGHDQFQ 154 (160)
T ss_pred EEHHHCCCE-EEEECCCCCCCCCCCCCCEEE
T ss_conf 657428987-787468779888779997674
No 131
>pfam01485 IBR IBR domain. The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (pfam00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organisms. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease.
Probab=77.51 E-value=1.7 Score=24.02 Aligned_cols=27 Identities=15% Similarity=0.340 Sum_probs=19.7
Q ss_pred CCCCC--CCCEEEECC--CCC-CCCCCCCCEE
Q ss_conf 11788--887442148--887-2277898715
Q gi|254780459|r 10 RTCPD--TGKRFYDLN--KQV-IVSPYTQNSW 36 (129)
Q Consensus 10 R~C~~--Cg~KFYDln--k~P-iiCP~CG~e~ 36 (129)
|-||+ |+.-++=-. ..+ +.||+||.+|
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 50 (64)
T pfam01485 19 KWCPTPDCGNIIEKTDGGSQNIVTCSKCGTEF 50 (64)
T ss_pred CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCC
T ss_conf 69909998804784788888832998999476
No 132
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=77.21 E-value=0.95 Score=25.49 Aligned_cols=11 Identities=9% Similarity=0.096 Sum_probs=5.8
Q ss_pred CCCCCCCCCEE
Q ss_conf 72277898715
Q gi|254780459|r 26 VIVSPYTQNSW 36 (129)
Q Consensus 26 PiiCP~CG~e~ 36 (129)
-+.||.||.-.
T Consensus 27 ~~~C~~CG~~~ 37 (59)
T PRK12286 27 LVECPNCGELK 37 (59)
T ss_pred EEECCCCCCCC
T ss_conf 45788999865
No 133
>pfam01363 FYVE FYVE zinc finger. 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 Zn++ 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. We have included members which do not conserve these histidine residues but are clearly related.
Probab=76.61 E-value=1.5 Score=24.21 Aligned_cols=28 Identities=14% Similarity=0.191 Sum_probs=23.2
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCEEC
Q ss_conf 31178888744214888722778987153
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~ 37 (129)
=..|+.|+++| -|-+.--.|..||..|=
T Consensus 9 ~~~C~~C~~~F-~~~~RrHhCR~CG~v~C 36 (68)
T pfam01363 9 VTNCMGCGKPF-SFFRRRHHCRNCGRIFC 36 (68)
T ss_pred CCCCCCCCCCC-CCCCCCCCCCCCCCEEC
T ss_conf 89484879901-28331231433696807
No 134
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=76.61 E-value=1.2 Score=24.80 Aligned_cols=25 Identities=36% Similarity=0.565 Sum_probs=18.8
Q ss_pred CCCCCCCEEE----EC--CCCCCCCCCCCCEE
Q ss_conf 1788887442----14--88872277898715
Q gi|254780459|r 11 TCPDTGKRFY----DL--NKQVIVSPYTQNSW 36 (129)
Q Consensus 11 ~C~~Cg~KFY----Dl--nk~PiiCP~CG~e~ 36 (129)
-|| ||-||- || +...+.||+|.-.+
T Consensus 24 PCP-CGDRFeIsLeDl~~GE~VArCPSCSLiv 54 (67)
T COG5216 24 PCP-CGDRFEISLEDLRNGEVVARCPSCSLIV 54 (67)
T ss_pred CCC-CCCEEEEEHHHHHCCCEEEECCCCEEEE
T ss_conf 478-8877578877853986688769851899
No 135
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=76.30 E-value=1.3 Score=24.66 Aligned_cols=23 Identities=13% Similarity=0.125 Sum_probs=15.0
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 11788887442148887227789871
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
++|..||. +|++-.+ .||+||..
T Consensus 642 ~~C~~cg~-~~~~~~~--~Cp~CG~~ 664 (700)
T COG1328 642 SVCNRCGY-SGEGLRT--RCPKCGSE 664 (700)
T ss_pred EEECCCCC-CCCCCCC--CCCCCCCC
T ss_conf 05114796-6455646--58887873
No 136
>pfam04135 Nop10p Nucleolar RNA-binding protein, Nop10p family. Nop10p is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10p is probably necessary for the stability of these RNPs.
Probab=76.14 E-value=1.6 Score=24.15 Aligned_cols=22 Identities=27% Similarity=0.549 Sum_probs=18.1
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 311788887442148887227789871
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
-|.|+.|+ -|=|+. .||.||..
T Consensus 5 ~r~c~~c~--~YTLk~---~cp~cG~~ 26 (53)
T pfam04135 5 LRKCPGCR--VYTLKD---KCPECGGP 26 (53)
T ss_pred HHHCCCCC--CEECCC---CCCCCCCC
T ss_conf 54088999--676778---46889884
No 137
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=76.00 E-value=0.62 Score=26.63 Aligned_cols=25 Identities=36% Similarity=0.578 Sum_probs=13.9
Q ss_pred CCCCCCEEEE-CCC----CCCCCCCCCCEE
Q ss_conf 7888874421-488----872277898715
Q gi|254780459|r 12 CPDTGKRFYD-LNK----QVIVSPYTQNSW 36 (129)
Q Consensus 12 C~~Cg~KFYD-lnk----~PiiCP~CG~e~ 36 (129)
|+.|-..|=| +|| .|+-||.||-.+
T Consensus 154 C~~C~~EY~dp~nRRfHAQp~aCp~CGP~~ 183 (750)
T COG0068 154 CPFCDKEYKDPLNRRFHAQPIACPKCGPHL 183 (750)
T ss_pred CHHHHHHHCCCCCCCCCCCCCCCCCCCCCE
T ss_conf 877898736934344114665576668872
No 138
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=75.93 E-value=1.2 Score=24.92 Aligned_cols=29 Identities=21% Similarity=0.313 Sum_probs=23.9
Q ss_pred CCCCCCCCCC-EEEECCCCCCCCCCCCC-EE
Q ss_conf 8311788887-44214888722778987-15
Q gi|254780459|r 8 TKRTCPDTGK-RFYDLNKQVIVSPYTQN-SW 36 (129)
Q Consensus 8 ~KR~C~~Cg~-KFYDlnk~PiiCP~CG~-e~ 36 (129)
++|.||.||. -|-=.-++-..|-+||- +|
T Consensus 18 k~~~CPrCG~gvfmA~H~dR~~CGkCgyTe~ 48 (51)
T COG1998 18 KNRFCPRCGPGVFMADHKDRWACGKCGYTEF 48 (51)
T ss_pred CCCCCCCCCCCCHHHHCCCEEEECCCCCEEE
T ss_conf 1452888888434341576067435452366
No 139
>TIGR00375 TIGR00375 conserved hypothetical protein TIGR00375; InterPro: IPR005287 This family of conserved hypothetical proteins has no known function. .
Probab=75.84 E-value=0.91 Score=25.61 Aligned_cols=34 Identities=21% Similarity=0.339 Sum_probs=26.1
Q ss_pred HHHCCCC--CCCCCCCEEEE--CCCCCCCCCCCCCEEC
Q ss_conf 2227831--17888874421--4888722778987153
Q gi|254780459|r 4 PELGTKR--TCPDTGKRFYD--LNKQVIVSPYTQNSWP 37 (129)
Q Consensus 4 ~elG~KR--~C~~Cg~KFYD--lnk~PiiCP~CG~e~~ 37 (129)
|.||+=+ .|..|+++|-= =.+--.-||+||..|.
T Consensus 240 P~LGKYh~TAC~~C~~~~~~E~a~~~~~~CpkCgg~ik 277 (384)
T TIGR00375 240 PKLGKYHLTACEKCYERYKSEDAKKADAKCPKCGGKIK 277 (384)
T ss_pred CCCCHHHHHHHHHCCCCCCCCCHHHHHCCCCCCCCEEE
T ss_conf 33231577788754764664002555246979786055
No 140
>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 COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=75.19 E-value=1.5 Score=24.26 Aligned_cols=23 Identities=30% Similarity=0.606 Sum_probs=18.2
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 3117888874421488872277898715
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
=|.|+.||. |-|. =+||.||...
T Consensus 5 ~rkC~~cg~--YTLk---e~Cp~CG~~t 27 (59)
T COG2260 5 IRKCPKCGR--YTLK---EKCPVCGGDT 27 (59)
T ss_pred HHCCCCCCC--EEEC---CCCCCCCCCC
T ss_conf 431767881--4611---3377888745
No 142
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=75.11 E-value=0.93 Score=25.55 Aligned_cols=29 Identities=21% Similarity=0.272 Sum_probs=22.7
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCEECHHH
Q ss_conf 31178888744214888722778987153233
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNSWPLAY 40 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~ 40 (129)
---||.|-+|---| ||.||.|........
T Consensus 308 Gy~CP~CktkVCsL---Pi~CP~Csl~Lilst 336 (421)
T COG5151 308 GYECPVCKTKVCSL---PISCPICSLQLILST 336 (421)
T ss_pred CEECCCCCCEEECC---CCCCCCHHHHHHHHH
T ss_conf 42177432503047---766762147899888
No 143
>PRK09603 DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=75.02 E-value=1.6 Score=24.17 Aligned_cols=21 Identities=10% Similarity=0.045 Sum_probs=7.8
Q ss_pred CCCEEEECCCCCC-CCCCCCCEE
Q ss_conf 8874421488872-277898715
Q gi|254780459|r 15 TGKRFYDLNKQVI-VSPYTQNSW 36 (129)
Q Consensus 15 Cg~KFYDlnk~Pi-iCP~CG~e~ 36 (129)
|| ||-=..-.-| +|-+||.++
T Consensus 1451 cg-kyk~~~~~g~~vc~~cgvev 1472 (2890)
T PRK09603 1451 CG-KYKKPRFKDIGTCEKCGVAI 1472 (2890)
T ss_pred CC-CCCCCCCCCCEECCCCCCEE
T ss_conf 78-75430258975758787286
No 144
>pfam00406 ADK Adenylate kinase.
Probab=74.94 E-value=1.5 Score=24.26 Aligned_cols=30 Identities=20% Similarity=0.358 Sum_probs=21.4
Q ss_pred HCCCCCCCCCCCEE---EECCCCCCCCCCCCCE
Q ss_conf 27831178888744---2148887227789871
Q gi|254780459|r 6 LGTKRTCPDTGKRF---YDLNKQVIVSPYTQNS 35 (129)
Q Consensus 6 lG~KR~C~~Cg~KF---YDlnk~PiiCP~CG~e 35 (129)
+-..|+||.||.-| |.=-+.|..|..||..
T Consensus 119 l~~R~~~~~~g~~y~~~~~pp~~~~~~~~~~~~ 151 (186)
T pfam00406 119 LTGRRIHPNSGRSYHLEFNPPKVPGKDDVTGEP 151 (186)
T ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 976641556688156667895213645444223
No 145
>KOG2593 consensus
Probab=74.37 E-value=1.2 Score=24.80 Aligned_cols=28 Identities=14% Similarity=0.270 Sum_probs=22.7
Q ss_pred CCCCCCCEEEEC--------CCCCCCCCCCCCEECH
Q ss_conf 178888744214--------8887227789871532
Q gi|254780459|r 11 TCPDTGKRFYDL--------NKQVIVSPYTQNSWPL 38 (129)
Q Consensus 11 ~C~~Cg~KFYDl--------nk~PiiCP~CG~e~~~ 38 (129)
.||+|++||-+| -..--.|-.||+++..
T Consensus 130 ~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelve 165 (436)
T KOG2593 130 VCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVE 165 (436)
T ss_pred CCCCCCCCHHHHHHHHHHCCCCCEEEEECCCCCHHC
T ss_conf 387412411266787752146766987247970210
No 146
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=74.13 E-value=2.2 Score=23.26 Aligned_cols=25 Identities=20% Similarity=0.468 Sum_probs=16.6
Q ss_pred CCCCCCCC-EEEECCCCCCCCCCCCC
Q ss_conf 11788887-44214888722778987
Q gi|254780459|r 10 RTCPDTGK-RFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 10 R~C~~Cg~-KFYDlnk~PiiCP~CG~ 34 (129)
.+|.+||. -+|+.++.-..|+.|+.
T Consensus 545 ~vC~~CG~i~~~~~~~~~~~C~~C~~ 570 (605)
T PRK07225 545 YVCAKCGMIAIYDKKRNMKYCPICGE 570 (605)
T ss_pred EECCCCCCEEEEECCCCCEECCCCCC
T ss_conf 73105797024303579748989899
No 147
>KOG2907 consensus
Probab=73.92 E-value=0.93 Score=25.55 Aligned_cols=37 Identities=19% Similarity=0.300 Sum_probs=29.8
Q ss_pred CCCCCCCCCEEEECCCCCCC-CCCCCCEECHHHHHCCC
Q ss_conf 31178888744214888722-77898715323310123
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIV-SPYTQNSWPLAYFEAPT 45 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~Pii-CP~CG~e~~~~~~~~~~ 45 (129)
--.|+.||.-.|=.+..+-+ |+-|+.+|++..+...+
T Consensus 7 ~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~~~~~~~ 44 (116)
T KOG2907 7 LDFCSDCGSLLEEPSAQSTVLCIRCKIEYPVSQFSGLV 44 (116)
T ss_pred CCHHHHHHHHCCCCCCCCCEEECCCCCCCCHHHHCCEE
T ss_conf 31556665342164556746730110227877837716
No 148
>cd01409 SIRT4 SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 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=73.81 E-value=1.9 Score=23.71 Aligned_cols=15 Identities=0% Similarity=-0.301 Sum_probs=10.5
Q ss_pred CCCCCCCCEECHHHH
Q ss_conf 227789871532331
Q gi|254780459|r 27 IVSPYTQNSWPLAYF 41 (129)
Q Consensus 27 iiCP~CG~e~~~~~~ 41 (129)
..||.||..+-|...
T Consensus 170 P~C~~C~g~lrP~VV 184 (260)
T cd01409 170 PECERCGGVLKPDVV 184 (260)
T ss_pred CCCCCCCCEECCCEE
T ss_conf 888778999277578
No 149
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.72 E-value=2.9 Score=22.57 Aligned_cols=27 Identities=19% Similarity=0.400 Sum_probs=20.9
Q ss_pred CCCCCCCCEEEECCCCCC---CCCCCCCEE
Q ss_conf 117888874421488872---277898715
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVI---VSPYTQNSW 36 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~Pi---iCP~CG~e~ 36 (129)
-.||+||.-.-=--|.-| -||.|+..|
T Consensus 2 llCP~C~v~l~~~~rs~vEiD~CPrCrGVW 31 (88)
T COG3809 2 LLCPICGVELVMSVRSGVEIDYCPRCRGVW 31 (88)
T ss_pred CCCCCCCCEEEEEEECCCEEEECCCCCCEE
T ss_conf 646757845666432383243077656176
No 150
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=73.60 E-value=2.6 Score=22.82 Aligned_cols=33 Identities=18% Similarity=0.317 Sum_probs=26.5
Q ss_pred CCCCCCCCE--EEECCCCCCCCCCCCCEECHHHHH
Q ss_conf 117888874--421488872277898715323310
Q gi|254780459|r 10 RTCPDTGKR--FYDLNKQVIVSPYTQNSWPLAYFE 42 (129)
Q Consensus 10 R~C~~Cg~K--FYDlnk~PiiCP~CG~e~~~~~~~ 42 (129)
..||.||.- -+|+-+--++|-.||.......+.
T Consensus 2 ~~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~~~id 36 (285)
T COG1405 2 MSCPECGSTNIITDYERGEIVCADCGLVLEDSLID 36 (285)
T ss_pred CCCCCCCCCCCEEECCCCEEEECCCCEEECCCCCC
T ss_conf 98999997411130668718833697785553125
No 151
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=72.79 E-value=2.2 Score=23.30 Aligned_cols=23 Identities=22% Similarity=0.354 Sum_probs=15.1
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 117888874421488872277898715
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
.+|+.||. +.-.--.||.||...
T Consensus 626 ~~C~~CGy----~~ge~~~CP~CG~~~ 648 (681)
T PRK08270 626 SICPKHGY----LAGEHEFCPKCGKET 648 (681)
T ss_pred CCCCCCCC----CCCCCCCCCCCCCCC
T ss_conf 86788997----778867493998967
No 152
>PRK08166 NADH dehydrogenase subunit G; Validated
Probab=72.77 E-value=1.4 Score=24.51 Aligned_cols=18 Identities=11% Similarity=0.108 Sum_probs=15.0
Q ss_pred CEEEECCCCCCCCCCCCC
Q ss_conf 744214888722778987
Q gi|254780459|r 17 KRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 17 ~KFYDlnk~PiiCP~CG~ 34 (129)
.|.+||.+.|=|||+||.
T Consensus 216 ~R~wdl~~~~SvC~~Cgv 233 (858)
T PRK08166 216 NRKWDMQFAPSICQHCSV 233 (858)
T ss_pred CCCHHCEECCEECCCCCC
T ss_conf 772221137634688877
No 153
>pfam11672 DUF3268 Protein of unknown function (DUF3268). This family of proteins has no known function.
Probab=72.31 E-value=1.5 Score=24.30 Aligned_cols=10 Identities=0% Similarity=-0.233 Sum_probs=5.3
Q ss_pred CCCCCCCCEE
Q ss_conf 2277898715
Q gi|254780459|r 27 IVSPYTQNSW 36 (129)
Q Consensus 27 iiCP~CG~e~ 36 (129)
-+|+.|++-+
T Consensus 32 y~C~~C~AyV 41 (102)
T pfam11672 32 YLCTGCDAYV 41 (102)
T ss_pred EECCCCCCEE
T ss_conf 8889998547
No 154
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=72.09 E-value=2.4 Score=23.05 Aligned_cols=31 Identities=16% Similarity=0.355 Sum_probs=22.3
Q ss_pred HHHCC-CCCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 22278-311788887442148887227789871
Q gi|254780459|r 4 PELGT-KRTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 4 ~elG~-KR~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
++||. +-.|+.|+.-..= ...-+.||+||..
T Consensus 143 ~dlGVI~A~CsrC~~~L~~-~~~~l~Cp~Cg~t 174 (188)
T COG1096 143 NDLGVIYARCSRCRAPLVK-KGNMLKCPNCGNT 174 (188)
T ss_pred CCCEEEEEECCCCCCCEEE-CCCEEECCCCCCE
T ss_conf 8616999983677762088-4759988877987
No 155
>pfam01783 Ribosomal_L32p Ribosomal L32p protein family.
Probab=72.02 E-value=2.2 Score=23.24 Aligned_cols=20 Identities=30% Similarity=0.539 Sum_probs=15.3
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCC
Q ss_conf 117888874421488872277898
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQ 33 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG 33 (129)
-+||+||. +.+.=-+||.||
T Consensus 27 ~~c~~cg~----~~l~H~vc~~cg 46 (56)
T pfam01783 27 VECPNCGE----LKLPHRVCPSCG 46 (56)
T ss_pred EECCCCCC----CCCCCEECCCCC
T ss_conf 58889998----535877889898
No 156
>pfam06524 NOA36 NOA36 protein. This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.
Probab=72.02 E-value=6 Score=20.61 Aligned_cols=28 Identities=14% Similarity=0.146 Sum_probs=18.0
Q ss_pred CCCCCCCCEE-----------EECCCCCCCCCCCCCEECH
Q ss_conf 1178888744-----------2148887227789871532
Q gi|254780459|r 10 RTCPDTGKRF-----------YDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 10 R~C~~Cg~KF-----------YDlnk~PiiCP~CG~e~~~ 38 (129)
..|+-|-+=| |+-| .||.||+||.+...
T Consensus 183 ySCLrCK~C~CddHvrrKg~Ky~k~-k~~pCPKCg~~t~e 221 (314)
T pfam06524 183 YSCLRCKVCCCNDHVRRKGFKYDKD-KNLPCPKCGYPTTE 221 (314)
T ss_pred EEECCEEEEECHHHHHCCCEEECCC-CCCCCCCCCCCCCC
T ss_conf 1320113476100332024022168-88899877884422
No 157
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=71.75 E-value=2.9 Score=22.55 Aligned_cols=29 Identities=21% Similarity=0.322 Sum_probs=22.7
Q ss_pred CCCCCCCCCCEEEECCC--CCCCCCCCCCEE
Q ss_conf 83117888874421488--872277898715
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNK--QVIVSPYTQNSW 36 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk--~PiiCP~CG~e~ 36 (129)
.|-.||.||.-=-=|.+ +++.|..||+..
T Consensus 10 lkVkC~~C~neqivFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 10 LKVKCPDCGNEQVIFSHASTVVRCLVCGRTL 40 (59)
T ss_pred EEEECCCCCCEEEEEECCCCEEECCCCCCEE
T ss_conf 9879999998679981377279975468777
No 158
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family; 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=71.56 E-value=2.3 Score=23.13 Aligned_cols=25 Identities=24% Similarity=0.493 Sum_probs=19.2
Q ss_pred CCCCCCCEEEECCC---C-CC-CCCCCCCE
Q ss_conf 17888874421488---8-72-27789871
Q gi|254780459|r 11 TCPDTGKRFYDLNK---Q-VI-VSPYTQNS 35 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk---~-Pi-iCP~CG~e 35 (129)
.|-+||..|==|-| . |+ +||.||..
T Consensus 7 ~C~~Cg~~fe~~Qk~sD~~pl~~CP~C~~~ 36 (43)
T TIGR02605 7 RCTSCGHQFEVLQKISDEEPLTTCPACGGP 36 (43)
T ss_pred EECCCCCCEEEEECCCCCCCCCCCCCCCCC
T ss_conf 346899814566504775534478767876
No 159
>PRK05823 consensus
Probab=71.35 E-value=3.6 Score=21.96 Aligned_cols=11 Identities=27% Similarity=0.697 Sum_probs=7.6
Q ss_pred CCCCCCCCCCE
Q ss_conf 83117888874
Q gi|254780459|r 8 TKRTCPDTGKR 18 (129)
Q Consensus 8 ~KR~C~~Cg~K 18 (129)
+.+.||.||..
T Consensus 600 ~~~~CP~Cg~~ 610 (691)
T PRK05823 600 VGRDCPKCASD 610 (691)
T ss_pred CCCCCCCCCCC
T ss_conf 79989888982
No 160
>pfam09845 DUF2072 Zn-ribbon containing protein (DUF2072). This archaeal protein has no known function.
Probab=70.75 E-value=1.6 Score=24.13 Aligned_cols=27 Identities=22% Similarity=0.303 Sum_probs=20.9
Q ss_pred CCCCCCCCEEEECCCC-CCCCCCCCCEE
Q ss_conf 1178888744214888-72277898715
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQ-VIVSPYTQNSW 36 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~-PiiCP~CG~e~ 36 (129)
+.|..||+-|=|=-+. --=||.||.-+
T Consensus 2 H~C~~C~~~f~dgs~e~l~GCp~Cg~~~ 29 (121)
T pfam09845 2 HRCTKCGKIFEDGSTEILKGCPSCGGKK 29 (121)
T ss_pred CCCCCCCCCCCCCCHHHHCCCCCCCCCE
T ss_conf 6057177874665689874674348844
No 161
>PRK11827 hypothetical protein; Provisional
Probab=70.74 E-value=2.3 Score=23.09 Aligned_cols=31 Identities=23% Similarity=0.533 Sum_probs=25.7
Q ss_pred CCCCCCCCCE-EEECCCCCCCCCCCCCEECHH
Q ss_conf 3117888874-421488872277898715323
Q gi|254780459|r 9 KRTCPDTGKR-FYDLNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 9 KR~C~~Cg~K-FYDlnk~PiiCP~CG~e~~~~ 39 (129)
--+||.|..+ +||-.+..+||-.++--|++.
T Consensus 8 ILvCP~ckg~L~yd~~~~ELic~~~~LAyPIr 39 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLAFPLR 39 (60)
T ss_pred EEECCCCCCCCEECCCCCEEEECCCCEECCCC
T ss_conf 25577889903398768988606647426553
No 162
>pfam01927 DUF82 Protein of unknown function DUF82. This prokaryotic protein family has no known function. The protein contains four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=70.09 E-value=1.9 Score=23.58 Aligned_cols=26 Identities=12% Similarity=0.225 Sum_probs=13.7
Q ss_pred CCCCCCCEEEECCCC----------------CCCCCCCCCEE
Q ss_conf 178888744214888----------------72277898715
Q gi|254780459|r 11 TCPDTGKRFYDLNKQ----------------VIVSPYTQNSW 36 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~----------------PiiCP~CG~e~ 36 (129)
.|+.|+....-.-|. =-.||+||..|
T Consensus 92 RC~~CN~~L~~v~k~~v~~~vp~~v~~~~~~F~~C~~CgkvY 133 (146)
T pfam01927 92 RCLKCNGPLEPVSKEEVAGRVPPYVYERYDEFWRCPKCGRVY 133 (146)
T ss_pred CCCCCCCCCEECCHHHHHHHCCCHHHHCCCCEEECCCCCCEE
T ss_conf 565679899581878985456720222588147789999981
No 163
>pfam12172 DUF35_N Rubredoxin-like zinc ribbon domain (DUF35_N). This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in a hypothetical protein from Mycobacterium tuberculosis. 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.
Probab=70.00 E-value=2.9 Score=22.49 Aligned_cols=22 Identities=23% Similarity=0.409 Sum_probs=16.9
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 1178888744214888722778987
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
..|++||.-||=- . .+||+||.
T Consensus 12 ~rC~~Cg~~~fPp--r-~~C~~C~~ 33 (37)
T pfam12172 12 QRCRDCGTVRFPP--R-PVCPHCGS 33 (37)
T ss_pred CCCCCCCCEEECC--C-CCCCCCCC
T ss_conf 5467899858489--7-77866376
No 164
>TIGR01374 soxD sarcosine oxidase, delta subunit family; InterPro: IPR006279 These sequences represent the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Mesorhizobium loti and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate . Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process.
Probab=69.94 E-value=2.4 Score=22.99 Aligned_cols=16 Identities=25% Similarity=0.360 Sum_probs=10.4
Q ss_pred CCCCCCCCEECHHHHH
Q ss_conf 2277898715323310
Q gi|254780459|r 27 IVSPYTQNSWPLAYFE 42 (129)
Q Consensus 27 iiCP~CG~e~~~~~~~ 42 (129)
|.||+||..=+...+.
T Consensus 2 I~CP~CGE~R~e~EF~ 17 (85)
T TIGR01374 2 IPCPYCGEPRDETEFT 17 (85)
T ss_pred CCCCCCCCCCCCCCCC
T ss_conf 6488998978712211
No 165
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=69.64 E-value=1.5 Score=24.20 Aligned_cols=39 Identities=18% Similarity=0.364 Sum_probs=26.3
Q ss_pred CCCCCCCCCCEEEECCCC----CCCCCCCCC--EECHHHHHCCCC
Q ss_conf 831178888744214888----722778987--153233101234
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNKQ----VIVSPYTQN--SWPLAYFEAPTS 46 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk~----PiiCP~CG~--e~~~~~~~~~~~ 46 (129)
-.|.|++||.||--|-+- |+|=-+-|. .|+...+++.-.
T Consensus 27 RRReC~~C~~RFTTfE~~El~~~~VvKkdg~Re~F~r~Kl~~gl~ 71 (156)
T COG1327 27 RRRECLECGERFTTFERAELRPLIVVKKDGRREPFDREKLRRGLI 71 (156)
T ss_pred HHHCCCCCCCCCCHHHEEEECCCEEECCCCCCCCCCHHHHHHHHH
T ss_conf 401165215644412124331305887589708788899998999
No 166
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=69.56 E-value=3 Score=22.47 Aligned_cols=32 Identities=19% Similarity=0.286 Sum_probs=23.6
Q ss_pred CCCCCCCCEEEE---CCCCCCCCCCCCCEECHHHH
Q ss_conf 117888874421---48887227789871532331
Q gi|254780459|r 10 RTCPDTGKRFYD---LNKQVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 10 R~C~~Cg~KFYD---lnk~PiiCP~CG~e~~~~~~ 41 (129)
|.||.||--.|= =++.-..|++||.+++....
T Consensus 1 kFCp~C~n~l~p~~~~~~~~~~C~~C~y~~~~~~~ 35 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCCCEEEEEECCCCEEEECCCCCCCCCCCCC
T ss_conf 97865288876853699538974899984366886
No 167
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=69.41 E-value=2.6 Score=22.80 Aligned_cols=22 Identities=18% Similarity=0.157 Sum_probs=15.2
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 1788887442148887227789871
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
+|+.||.+.= +.-=.||.||..
T Consensus 520 ~C~~CG~~~~---~~~~~CP~CG~~ 541 (555)
T cd01675 520 ICNDCGYIGE---GEGFKCPKCGSE 541 (555)
T ss_pred ECCCCCCCCC---CCCCCCCCCCCC
T ss_conf 7789998275---678769098396
No 168
>cd00296 SIR2 SIR2 superfamily 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. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic
Probab=69.33 E-value=2.5 Score=22.87 Aligned_cols=32 Identities=13% Similarity=0.157 Sum_probs=22.3
Q ss_pred CCCCCCCCCEEEE----CCCCCCCCCCCCCEECHHH
Q ss_conf 3117888874421----4888722778987153233
Q gi|254780459|r 9 KRTCPDTGKRFYD----LNKQVIVSPYTQNSWPLAY 40 (129)
Q Consensus 9 KR~C~~Cg~KFYD----lnk~PiiCP~CG~e~~~~~ 40 (129)
+-.|..|+.+|.. ....+..||.||..+-|..
T Consensus 113 ~~~C~~C~~~~~~~~~~~~~~~~~c~~C~g~lrp~v 148 (222)
T cd00296 113 RVRCTSCGKEYPRDEVLEREKPPRCPKCGGLLRPDV 148 (222)
T ss_pred EEECCCCCCCCCHHHHHCCCCCCCCCCCCCEECCCE
T ss_conf 227089989587678640357898646799944024
No 169
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=68.86 E-value=2.9 Score=22.56 Aligned_cols=25 Identities=12% Similarity=0.166 Sum_probs=18.1
Q ss_pred CCCCCCCCCC--EEEECCCCCCCCCCCCCEE
Q ss_conf 8311788887--4421488872277898715
Q gi|254780459|r 8 TKRTCPDTGK--RFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 8 ~KR~C~~Cg~--KFYDlnk~PiiCP~CG~e~ 36 (129)
+=|.||+|+. .|| .-..||+||++-
T Consensus 56 ~i~kC~~c~~~~~y~----~~~~C~~cg~~~ 82 (415)
T COG5257 56 KIYKCPECYRPECYT----TEPKCPNCGAET 82 (415)
T ss_pred CEEECCCCCCCCCCC----CCCCCCCCCCCC
T ss_conf 457577778876623----478777789973
No 170
>KOG1818 consensus
Probab=68.38 E-value=2.2 Score=23.30 Aligned_cols=34 Identities=12% Similarity=0.117 Sum_probs=30.5
Q ss_pred CHHHCCCCCCCCCCCEEEECCCCCCCCCCCCCEEC
Q ss_conf 52227831178888744214888722778987153
Q gi|254780459|r 3 KPELGTKRTCPDTGKRFYDLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 3 K~elG~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~ 37 (129)
-|+|--++.|.-|-++|==|||.- .|=.||-.|-
T Consensus 159 ~pdW~D~~~C~rCr~~F~~~~rkH-HCr~CG~vFC 192 (634)
T KOG1818 159 APDWIDSEECLRCRVKFGLTNRKH-HCRNCGQVFC 192 (634)
T ss_pred CCCCCCCCCCCEEEEEEEECCCCC-CCCCCCHHHC
T ss_conf 855434420111234410015653-4300210222
No 171
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=68.13 E-value=3.2 Score=22.28 Aligned_cols=37 Identities=14% Similarity=0.191 Sum_probs=25.3
Q ss_pred HCCCCCCCCCCCEEE-------ECCCCCCCCCCCC-----CEECHHHHH
Q ss_conf 278311788887442-------1488872277898-----715323310
Q gi|254780459|r 6 LGTKRTCPDTGKRFY-------DLNKQVIVSPYTQ-----NSWPLAYFE 42 (129)
Q Consensus 6 lG~KR~C~~Cg~KFY-------Dlnk~PiiCP~CG-----~e~~~~~~~ 42 (129)
+-++..||.||..|. =||-.-=-||.|. ..|+++.+.
T Consensus 249 fS~~~~Cp~cG~sf~e~sP~lFSFNSP~GACp~C~GlG~~~~iD~~lvI 297 (944)
T PRK00349 249 FSENFACPVCGFSIPELEPRLFSFNSPFGACPTCDGLGVKLEFDPDLVV 297 (944)
T ss_pred ECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECHHHHC
T ss_conf 1113478887865687881446899998828677887269775789944
No 172
>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=67.90 E-value=2.7 Score=22.69 Aligned_cols=27 Identities=15% Similarity=0.239 Sum_probs=22.9
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 117888874421488872277898715
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
..||.|.+|-.+-+-.--.|++|+..+
T Consensus 35 ~AC~~C~KKv~~~~~~~y~C~~C~~~~ 61 (166)
T cd04476 35 PACPGCNKKVVEEGNGTYRCEKCNKSV 61 (166)
T ss_pred HHHHHHCCEEEECCCCEEECCCCCCCC
T ss_conf 431514838285799749862239978
No 173
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.45 E-value=1.7 Score=23.97 Aligned_cols=33 Identities=21% Similarity=0.345 Sum_probs=28.0
Q ss_pred HHCCCCCCCCCC--CEEEECCCCCCCCCCCCCEEC
Q ss_conf 227831178888--744214888722778987153
Q gi|254780459|r 5 ELGTKRTCPDTG--KRFYDLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 5 elG~KR~C~~Cg--~KFYDlnk~PiiCP~CG~e~~ 37 (129)
.-|.|-.||.|| .-|--|-|.-..|-.||.++.
T Consensus 17 ~~Gl~grCP~CGeGrLF~gFLK~~p~C~aCG~dyg 51 (126)
T COG5349 17 KRGLRGRCPRCGEGRLFRGFLKVVPACEACGLDYG 51 (126)
T ss_pred HHHHCCCCCCCCCCHHHHHHCCCCCHHHHCCCCCC
T ss_conf 88746779988983254201453743666064115
No 174
>pfam06044 DRP Dam-replacing family. Dam-replacing protein (DRP) is an 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.
Probab=67.45 E-value=2.4 Score=23.01 Aligned_cols=32 Identities=19% Similarity=0.376 Sum_probs=21.6
Q ss_pred CCCCCCCCE---EEECCCC--CCCCCCCCCEECHHHH
Q ss_conf 117888874---4214888--7227789871532331
Q gi|254780459|r 10 RTCPDTGKR---FYDLNKQ--VIVSPYTQNSWPLAYF 41 (129)
Q Consensus 10 R~C~~Cg~K---FYDlnk~--PiiCP~CG~e~~~~~~ 41 (129)
--||+||.. =|-=|+. --.||.|..+|.+.+.
T Consensus 32 ~yCP~Cg~~~l~~~~NN~PVaDFyC~~C~e~yELKsK 68 (254)
T pfam06044 32 GYCPNCGSNPLSRFANNQPVADFYCPNCHEDYELKSK 68 (254)
T ss_pred CCCCCCCCCHHHHCCCCCCCCEEECCCCCHHHHHHCC
T ss_conf 8799889722122337992330354774066600302
No 175
>TIGR02349 DnaJ_bact chaperone protein DnaJ; InterPro: IPR012724 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation . Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate. DnaJ comprises a 70-residue N-terminal domain (the J-domain); a 30-residue glycine-rich region (the G-domain); a central domain containing 4 repeats of a CxxCxGxG motif (the CRR-domain); and a 120-170 residue C-terminal region. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins , either together or separately. This entry mostly consists of bacterial forms of DnaJ. The three components of the DnaK-DnaJ-GrpE system are typically encoded by consecutive genes. DnaJ homologues occur in many genomes, typically not encoded near DnaK and GrpE-like genes. Most such proteins are not included in this family, though some chloroplast homologues are included; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding, 0009408 response to heat.
Probab=67.43 E-value=3.2 Score=22.25 Aligned_cols=27 Identities=7% Similarity=0.007 Sum_probs=19.2
Q ss_pred CCCCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 831178888744214888722778987
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
.+..|++|.=-=|.=+.+|.+||.||=
T Consensus 170 ~~~~C~~C~GsGA~~g~~~~tC~~C~G 196 (386)
T TIGR02349 170 RLESCETCHGSGAKPGTDPKTCPTCGG 196 (386)
T ss_pred EEEECCCCCCCCCCCCCCCEECCCCCC
T ss_conf 566268887611108888547877897
No 176
>TIGR01031 rpmF_bact ribosomal protein L32; 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 of 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.
Probab=67.13 E-value=3.1 Score=22.36 Aligned_cols=22 Identities=23% Similarity=0.378 Sum_probs=15.3
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 31178888744214888722778987
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
--.||+||. |...=-|||.||.
T Consensus 27 ~v~C~~CGe----~~~pHrvC~~CG~ 48 (56)
T TIGR01031 27 LVVCPNCGE----YKLPHRVCPSCGY 48 (56)
T ss_pred CCCCCCCCC----CCCCEEECCCCCC
T ss_conf 542677888----5355020288886
No 177
>KOG3623 consensus
Probab=67.02 E-value=2.7 Score=22.70 Aligned_cols=33 Identities=21% Similarity=0.385 Sum_probs=25.4
Q ss_pred HHCCCCCCCCCCCEEE-----------ECCCCCCCCCCCCCEEC
Q ss_conf 2278311788887442-----------14888722778987153
Q gi|254780459|r 5 ELGTKRTCPDTGKRFY-----------DLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 5 elG~KR~C~~Cg~KFY-----------Dlnk~PiiCP~CG~e~~ 37 (129)
.+-.|--|+.||+-|- --+-.|--||.|+.-|.
T Consensus 277 a~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFS 320 (1007)
T KOG3623 277 ALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFS 320 (1007)
T ss_pred HHHCCCCCCCCCHHHHHHHHHHHHHEEECCCCCCCCCCCCCCCC
T ss_conf 65404466411134545787776621005888867864123135
No 178
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=66.96 E-value=4.7 Score=21.25 Aligned_cols=35 Identities=17% Similarity=0.459 Sum_probs=22.1
Q ss_pred HHHCC-CCCCCCCCCEEE----ECC----CCCCCCCCCCCEECH
Q ss_conf 22278-311788887442----148----887227789871532
Q gi|254780459|r 4 PELGT-KRTCPDTGKRFY----DLN----KQVIVSPYTQNSWPL 38 (129)
Q Consensus 4 ~elG~-KR~C~~Cg~KFY----Dln----k~PiiCP~CG~e~~~ 38 (129)
.+.|- .++||-||..=. .+. ..=..|.-|+++|.-
T Consensus 181 ~~~~~~~~~CPvCGs~Pvasvv~~g~~~G~RyL~CslC~teW~~ 224 (307)
T PRK03564 181 AEYGEQRQYCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHV 224 (307)
T ss_pred CCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEECCCCCCCCCC
T ss_conf 78777788599889875145575068787068864877774021
No 179
>COG0423 GRS1 Glycyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=66.71 E-value=2.3 Score=23.17 Aligned_cols=27 Identities=22% Similarity=0.341 Sum_probs=19.3
Q ss_pred CCCCCCCEEE-------------ECC-----------CCCCCCCCCCCEEC
Q ss_conf 1788887442-------------148-----------88722778987153
Q gi|254780459|r 11 TCPDTGKRFY-------------DLN-----------KQVIVSPYTQNSWP 37 (129)
Q Consensus 11 ~C~~Cg~KFY-------------Dln-----------k~PiiCP~CG~e~~ 37 (129)
-|++||.+|- .-| +.-|.||.||..+.
T Consensus 90 ~c~~c~~~yRADHLiEe~l~~~~~~~~~~~e~~~ii~~~~ir~p~~g~~l~ 140 (558)
T COG0423 90 ECKKCGERYRADHLIEEYLGKDGHGNMSPEELTEIIREYDIRCPECGGELN 140 (558)
T ss_pred ECCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf 346245345336888987641034557878888888861775887688668
No 180
>PRK07141 DNA topoisomerase I; Validated
Probab=66.63 E-value=7.8 Score=19.89 Aligned_cols=43 Identities=19% Similarity=0.218 Sum_probs=25.4
Q ss_pred CCCCCCCEEE-ECCCC----CCCC---CCCCCEECHHHHHCCCCCCCCCCC
Q ss_conf 1788887442-14888----7227---789871532331012344344333
Q gi|254780459|r 11 TCPDTGKRFY-DLNKQ----VIVS---PYTQNSWPLAYFEAPTSPEKEKEI 53 (129)
Q Consensus 11 ~C~~Cg~KFY-Dlnk~----PiiC---P~CG~e~~~~~~~~~~~~~~~~~~ 53 (129)
.||.||.... =.+|. =+-| |.|.+.++.+...+.+|..+.++.
T Consensus 567 ~CP~Cg~~l~~r~~~~g~~~F~gCs~yp~Ck~t~~~~~~~~~~~~~~~~~~ 617 (622)
T PRK07141 567 SCPDCNGDLVYRNNRKGDQRFIGCSNFPNCRFTRSYEDAKKKKRFFKRKKK 617 (622)
T ss_pred CCCCCCCCEEEEECCCCCCEEEECCCCCCCCCCEECCCCCCCCCCCCCCCC
T ss_conf 887899822578736889869878999888881167888766656555665
No 181
>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=66.31 E-value=2.5 Score=22.88 Aligned_cols=26 Identities=19% Similarity=0.321 Sum_probs=22.1
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 117888874421488872277898715
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
..|..|+++|= |.+.-..|-.||..|
T Consensus 3 ~~C~~C~~~F~-~~~rrhhCr~CG~~~ 28 (57)
T cd00065 3 SSCMGCGKPFT-LTRRRHHCRNCGRIF 28 (57)
T ss_pred CCCCCCCCHHC-CCCCCCCCHHCCCHH
T ss_conf 90628888003-864561751454034
No 182
>PTZ00088 adenylate kinase 1; Provisional
Probab=65.68 E-value=3.4 Score=22.13 Aligned_cols=29 Identities=14% Similarity=0.230 Sum_probs=18.2
Q ss_pred HCCCCCCCCCCCEEE-------ECCCCC----CCCCCCCC
Q ss_conf 278311788887442-------148887----22778987
Q gi|254780459|r 6 LGTKRTCPDTGKRFY-------DLNKQV----IVSPYTQN 34 (129)
Q Consensus 6 lG~KR~C~~Cg~KFY-------Dlnk~P----iiCP~CG~ 34 (129)
+-..|+|+.||.-|= -||..| -.|..|+.
T Consensus 123 l~gRr~c~~cg~~Yni~~~~~~~~~~pp~~p~~~c~~c~g 162 (225)
T PTZ00088 123 ILGRRICHECDKNFNIAHIQDDPFDMPPILPPKDCEKCKG 162 (225)
T ss_pred HHCCEECCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 9706313334771101112344345777788764554589
No 183
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=65.22 E-value=3.9 Score=21.70 Aligned_cols=30 Identities=13% Similarity=0.267 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCEEEECCCC---CCCCCCCCCEECH
Q ss_conf 7831178888744214888---7227789871532
Q gi|254780459|r 7 GTKRTCPDTGKRFYDLNKQ---VIVSPYTQNSWPL 38 (129)
Q Consensus 7 G~KR~C~~Cg~KFYDlnk~---PiiCP~CG~e~~~ 38 (129)
-.|++||.||. --+.|. -=.|-+||..|.-
T Consensus 34 ~~ky~Cp~Cg~--~~vkR~a~GIW~C~kC~~~~aG 66 (90)
T PRK03976 34 RAKHVCPVCGR--PKVKRIATGIWQCRKCGAKFAG 66 (90)
T ss_pred HCCCCCCCCCC--CEEEEEEEEEEECCCCCCEEEC
T ss_conf 36864998999--7458888888888999988767
No 184
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=65.21 E-value=2.1 Score=23.32 Aligned_cols=29 Identities=17% Similarity=0.178 Sum_probs=21.8
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEECHH
Q ss_conf 117888874421488872277898715323
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~ 39 (129)
-.|.+||..|=+-.. ...||.||-.++..
T Consensus 6 ~rc~~cg~~f~~a~~-~~~c~~cGl~lp~~ 34 (411)
T COG0498 6 LRCLKCGREFSQALL-QGLCPDCGLFLPAE 34 (411)
T ss_pred EECCCCCCCHHHHHH-HCCCCCCCCCCCCC
T ss_conf 534777756656776-07577788616620
No 185
>pfam01475 FUR Ferric uptake regulator family. This family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes. This family is also known as the FUR family.
Probab=64.73 E-value=4 Score=21.68 Aligned_cols=34 Identities=24% Similarity=0.331 Sum_probs=25.1
Q ss_pred HHCC-CCCCCCCCCEEEECCCCC----CCCCCCCCEECH
Q ss_conf 2278-311788887442148887----227789871532
Q gi|254780459|r 5 ELGT-KRTCPDTGKRFYDLNKQV----IVSPYTQNSWPL 38 (129)
Q Consensus 5 elG~-KR~C~~Cg~KFYDlnk~P----iiCP~CG~e~~~ 38 (129)
+.|. .|+-..-|..+|+++... ++|-.||..++.
T Consensus 54 ~~gli~~~~~~~~~~~y~~~~~~~H~HliC~~Cg~v~ei 92 (120)
T pfam01475 54 EAGIVKRLNFEGGESRYELNQGHHHDHLICEKCGKVIEF 92 (120)
T ss_pred HCCCEEEEEECCCEEEEEECCCCCCCEEEECCCCCEEEE
T ss_conf 679469998479979997569997647998999999984
No 186
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=64.43 E-value=4.4 Score=21.41 Aligned_cols=28 Identities=18% Similarity=0.385 Sum_probs=21.5
Q ss_pred CCCCCCCCCEEEECCC--CCCCCCCCCCEE
Q ss_conf 3117888874421488--872277898715
Q gi|254780459|r 9 KRTCPDTGKRFYDLNK--QVIVSPYTQNSW 36 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk--~PiiCP~CG~e~ 36 (129)
+-.||.||-.--=|.+ +.+.|+.||+..
T Consensus 19 ~VkCpdC~N~q~vFshast~V~C~~CG~~l 48 (67)
T COG2051 19 RVKCPDCGNEQVVFSHASTVVTCLICGTTL 48 (67)
T ss_pred EEECCCCCCEEEEECCCCEEEEEECCCCEE
T ss_conf 988899997789952576089930156589
No 187
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=64.17 E-value=0.94 Score=25.51 Aligned_cols=27 Identities=7% Similarity=0.108 Sum_probs=22.9
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEECHH
Q ss_conf 117888874421488872277898715323
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~ 39 (129)
..|+.|++.|.-+.. .||-||..+...
T Consensus 25 ~~C~~C~~~~~~~~~---~C~~C~~~l~~~ 51 (225)
T COG1040 25 GLCSGCQADLPLIGN---LCPLCGLPLSSH 51 (225)
T ss_pred CCCHHHHHHHHHHHH---HHHHHHCCCCCC
T ss_conf 869455423467762---757875514443
No 188
>pfam01780 Ribosomal_L37ae Ribosomal L37ae protein family. This ribosomal protein is found in archaebacteria and eukaryotes. It contains four conserved cysteine residues that may bind to zinc.
Probab=64.08 E-value=3.4 Score=22.14 Aligned_cols=30 Identities=20% Similarity=0.282 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCEEEECCCCC---CCCCCCCCEECH
Q ss_conf 78311788887442148887---227789871532
Q gi|254780459|r 7 GTKRTCPDTGKRFYDLNKQV---IVSPYTQNSWPL 38 (129)
Q Consensus 7 G~KR~C~~Cg~KFYDlnk~P---iiCP~CG~e~~~ 38 (129)
=.|++||.||..= +.|.- =.|-+||..|.-
T Consensus 33 ~~ky~Cp~Cgk~~--vkR~a~GIW~C~~C~~~~aG 65 (90)
T pfam01780 33 HAKYTCPFCGKDA--VKRKAVGIWKCRKCGKTFAG 65 (90)
T ss_pred CCCCCCCCCCCCE--EEEEEEEEEECCCCCCEEEC
T ss_conf 2763089999887--78888888872798997778
No 189
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=63.85 E-value=5.3 Score=20.90 Aligned_cols=32 Identities=22% Similarity=0.193 Sum_probs=23.9
Q ss_pred HHCCCCCCCCCCCEEEECCCCCCCCCCCCCEEC
Q ss_conf 227831178888744214888722778987153
Q gi|254780459|r 5 ELGTKRTCPDTGKRFYDLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 5 elG~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~ 37 (129)
.+|.=-.|++||.+.. ....|-.||.||..+.
T Consensus 235 ~~G~v~~C~~C~~~~~-~~~~~~~C~~cg~~~~ 266 (376)
T PRK04338 235 NLGYVYHCPECGYREH-EYEFEKECPVCGYKVG 266 (376)
T ss_pred HCCEEEECCCCCCEEE-CCCCCCCCCCCCCCCE
T ss_conf 4874998899985432-2578877888898350
No 190
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase; InterPro: IPR012833 This entry is found in the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centred 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 (IPR012837 from INTERPRO). Together the two form an alpha-2/beta-2 heterodimer.; GO: 0008998 ribonucleoside-triphosphate reductase activity, 0016491 oxidoreductase activity.
Probab=63.76 E-value=3.6 Score=21.95 Aligned_cols=25 Identities=16% Similarity=0.244 Sum_probs=18.5
Q ss_pred CCCCCCCCEEEECCC---CCCCCCCCCCE
Q ss_conf 117888874421488---87227789871
Q gi|254780459|r 10 RTCPDTGKRFYDLNK---QVIVSPYTQNS 35 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk---~PiiCP~CG~e 35 (129)
++|-.|| .|=...- .=-.||+||..
T Consensus 591 ~~C~~Cg-~y~~~~~~t~~g~~CP~CGs~ 618 (655)
T TIGR02487 591 DVCEDCG-EYTGEGLNTEKGDKCPKCGSH 618 (655)
T ss_pred CEECCCC-CCHHCCCCCCCCCCCCCCCCC
T ss_conf 6525765-320000001155668898876
No 191
>PRK10767 chaperone protein DnaJ; Provisional
Probab=63.11 E-value=4.7 Score=21.23 Aligned_cols=32 Identities=16% Similarity=0.027 Sum_probs=25.4
Q ss_pred HHCCCCCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 22783117888874421488872277898715
Q gi|254780459|r 5 ELGTKRTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 5 elG~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
.+..++.|..|.-.-+--+..|..||.|+-.-
T Consensus 137 ~~~~~~~C~~C~G~G~~~~~~~~~C~~c~G~g 168 (376)
T PRK10767 137 RIPTLEECDVCHGSGAKPGTQPQTCPTCHGSG 168 (376)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 46666544667787767999886677667866
No 192
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=62.47 E-value=3.2 Score=22.24 Aligned_cols=39 Identities=18% Similarity=0.266 Sum_probs=23.6
Q ss_pred CCCCCCCCCEEEECCCC----CCCCCCCC--CEECHHHHHCCCCC
Q ss_conf 31178888744214888----72277898--71532331012344
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQ----VIVSPYTQ--NSWPLAYFEAPTSP 47 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~----PiiCP~CG--~e~~~~~~~~~~~~ 47 (129)
.|-|++||.||-=+-|- |.|==.=| ..|+...+.+.-..
T Consensus 28 RReC~~C~~RFTTyE~~e~~~l~VvKrdg~re~Fdr~Kl~~gi~~ 72 (149)
T PRK00464 28 RRECLACGKRFTTFERVELVPPLVIKKDGRREPFDREKLLRGLLR 72 (149)
T ss_pred EEECCCCCCEEEEHHHHCCCCCEEEECCCCCCCCCHHHHHHHHHH
T ss_conf 210677898420144510026579945998777779999999999
No 193
>PRK05258 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=62.23 E-value=4.2 Score=21.53 Aligned_cols=27 Identities=15% Similarity=0.223 Sum_probs=18.3
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCEECHH
Q ss_conf 17888874421488872277898715323
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~ 39 (129)
-|. || ||.=....=++|-.||.++...
T Consensus 59 ec~-cg-kyk~~~~~g~~C~~Cgve~~~~ 85 (1204)
T PRK05258 59 ECH-CG-KYKRVRYKGIVCDRCGVEVTRS 85 (1204)
T ss_pred EEC-CC-CCCCCCCCCCCCCCCCCCCCCC
T ss_conf 353-77-6122035985769999864518
No 194
>PHA02325 hypothetical protein
Probab=61.64 E-value=4.2 Score=21.54 Aligned_cols=14 Identities=14% Similarity=0.247 Sum_probs=8.6
Q ss_pred CCCCCCCCCCEECH
Q ss_conf 87227789871532
Q gi|254780459|r 25 QVIVSPYTQNSWPL 38 (129)
Q Consensus 25 ~PiiCP~CG~e~~~ 38 (129)
..-+||+||+.|--
T Consensus 4 ~~k~CpkCgA~Wi~ 17 (79)
T PHA02325 4 DTKTCPKCSAMWLD 17 (79)
T ss_pred CCCCCCCCCCEEEC
T ss_conf 65416777788688
No 195
>KOG1088 consensus
Probab=61.61 E-value=3.3 Score=22.15 Aligned_cols=12 Identities=33% Similarity=0.722 Sum_probs=7.1
Q ss_pred CCCCCCCCEECH
Q ss_conf 227789871532
Q gi|254780459|r 27 IVSPYTQNSWPL 38 (129)
Q Consensus 27 iiCP~CG~e~~~ 38 (129)
.+||.||+.|++
T Consensus 99 l~CpetG~vfpI 110 (124)
T KOG1088 99 LVCPETGRVFPI 110 (124)
T ss_pred EECCCCCCEEEC
T ss_conf 866888737652
No 196
>pfam04216 FdhE Protein involved in formate dehydrogenase formation. The function of these proteins is unknown. They may possibly be involved in the formation of formate dehydrogenase.
Probab=61.53 E-value=4.3 Score=21.46 Aligned_cols=30 Identities=13% Similarity=0.308 Sum_probs=14.1
Q ss_pred CCCCCCCCCCEEEE----C----CCCCCCCCCCCCEEC
Q ss_conf 83117888874421----4----888722778987153
Q gi|254780459|r 8 TKRTCPDTGKRFYD----L----NKQVIVSPYTQNSWP 37 (129)
Q Consensus 8 ~KR~C~~Cg~KFYD----l----nk~PiiCP~CG~e~~ 37 (129)
.+..||-||.+=.= . +..=..|..|+++|.
T Consensus 165 ~~~~CPvCGs~P~~s~~~~~~~~G~Ryl~Cs~C~teW~ 202 (283)
T pfam04216 165 QRGLCPVCGSAPVASVIRGGGAQGLRYLHCSLCETEWH 202 (283)
T ss_pred CCCCCCCCCCCCHHHEEECCCCCCCEEEECCCCCCCCC
T ss_conf 58969999981000113137878836886588878324
No 197
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=61.49 E-value=2.1 Score=23.35 Aligned_cols=27 Identities=15% Similarity=0.325 Sum_probs=19.9
Q ss_pred CCCCCCCCCEEEECCCCCC--CCCCCCCEECH
Q ss_conf 3117888874421488872--27789871532
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVI--VSPYTQNSWPL 38 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~Pi--iCP~CG~e~~~ 38 (129)
+-.|..|++|| +|-|+ .||+||.....
T Consensus 167 ~~rc~~c~~k~---rr~pl~g~c~kcg~~~~l 195 (253)
T COG1933 167 EFRCVKCNTKF---RRPPLDGKCPICGGKIVL 195 (253)
T ss_pred EEEHHHHHHHH---CCCCCCCCCCCCCCEEEE
T ss_conf 13557655453---679865414223884799
No 198
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=61.47 E-value=5.1 Score=21.02 Aligned_cols=30 Identities=27% Similarity=0.547 Sum_probs=23.7
Q ss_pred CCCCCCCC-EEEECCCCCCCCCCCCCEECHH
Q ss_conf 11788887-4421488872277898715323
Q gi|254780459|r 10 RTCPDTGK-RFYDLNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 10 R~C~~Cg~-KFYDlnk~PiiCP~CG~e~~~~ 39 (129)
-.||-|-. -.|+=-|.-++||.|+.-|++.
T Consensus 9 LaCP~~kg~L~~~~~~~~L~c~~~~~aYpI~ 39 (60)
T COG2835 9 LACPVCKGPLVYDEEKQELICPRCKLAYPIR 39 (60)
T ss_pred EECCCCCCCCEEECCCCEEEECCCCCEEECC
T ss_conf 6666758950681568989715348131334
No 199
>PRK10996 thioredoxin 2; Provisional
Probab=60.96 E-value=5.1 Score=21.02 Aligned_cols=23 Identities=9% Similarity=0.039 Sum_probs=15.0
Q ss_pred CCCCCCCCCEEEECCCCCC-------CCCCCCCE
Q ss_conf 3117888874421488872-------27789871
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVI-------VSPYTQNS 35 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~Pi-------iCP~CG~e 35 (129)
+-+||+||++ ||-|. .|=+|++.
T Consensus 2 ~~vC~~C~~~----Nrvp~~~~~~~~~Cg~C~~~ 31 (139)
T PRK10996 2 NTVCTHCQAI----NRIPDERIEDAAKCGRCGHD 31 (139)
T ss_pred EEECCCCCCC----CCCCCCCCCCCCCCCCCCCC
T ss_conf 7989775764----78896446799857878985
No 200
>smart00350 MCM minichromosome maintenance proteins.
Probab=60.76 E-value=6.4 Score=20.43 Aligned_cols=25 Identities=24% Similarity=0.303 Sum_probs=19.4
Q ss_pred CCCCCCCCEEEEC-----CCCCCCCC--CCCC
Q ss_conf 1178888744214-----88872277--8987
Q gi|254780459|r 10 RTCPDTGKRFYDL-----NKQVIVSP--YTQN 34 (129)
Q Consensus 10 R~C~~Cg~KFYDl-----nk~PiiCP--~CG~ 34 (129)
-.|+.||..||-. -..|..|| .|+.
T Consensus 38 f~C~~C~~~~~~~~~~~~~~~p~~C~~~~C~~ 69 (509)
T smart00350 38 FTCEKCGATLGPEIQSGRETEPTVCPPRECQS 69 (509)
T ss_pred EECCCCCCEEEEEECCCEECCCCCCCCCCCCC
T ss_conf 99489979986863288565887699766899
No 201
>pfam09332 Mcm10 Mcm10 replication factor. Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha.
Probab=60.43 E-value=8.1 Score=19.79 Aligned_cols=42 Identities=21% Similarity=0.345 Sum_probs=29.9
Q ss_pred CCCC--CCCCCCCEEEECCCCCC-CCCCCCC-EECHHHHHCCCCCC
Q ss_conf 7831--17888874421488872-2778987-15323310123443
Q gi|254780459|r 7 GTKR--TCPDTGKRFYDLNKQVI-VSPYTQN-SWPLAYFEAPTSPE 48 (129)
Q Consensus 7 G~KR--~C~~Cg~KFYDlnk~Pi-iCP~CG~-e~~~~~~~~~~~~~ 48 (129)
|.|| .|+.||.|--=|.|-|. .|.+||. -|.-..+++-+++.
T Consensus 283 a~KRFFkC~dC~~Rtisl~r~P~~~C~~Cg~~kweR~~M~~Ekkg~ 328 (346)
T pfam09332 283 AVKRFFKCPDCGNRTISLDRLPKKHCKNCGLFKWERDAMLKEKKGK 328 (346)
T ss_pred CEEEEEECCCCCCCEEEEECCCCCCCCCCCCCCEEEHHHHHHCCCC
T ss_conf 3332245688787445621076222323677511001134330667
No 202
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=60.11 E-value=4.5 Score=21.34 Aligned_cols=30 Identities=10% Similarity=0.066 Sum_probs=22.1
Q ss_pred CCCCCCCCCCCEEEECCCCC---CCCCCCCCEECH
Q ss_conf 78311788887442148887---227789871532
Q gi|254780459|r 7 GTKRTCPDTGKRFYDLNKQV---IVSPYTQNSWPL 38 (129)
Q Consensus 7 G~KR~C~~Cg~KFYDlnk~P---iiCP~CG~e~~~ 38 (129)
-.|.+||.||.. -+.|.- =.|-+||..|.-
T Consensus 34 ~~ky~Cp~Cgk~--~vkR~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 34 HARYFCSFCGKH--ATKRKAVGIWRCKGCSKTVAG 66 (90)
T ss_pred HCCCCCCCCCCC--EEEEEEEEEEECCCCCCEEEC
T ss_conf 177628999997--668888888876899998858
No 203
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=59.74 E-value=3.3 Score=22.17 Aligned_cols=28 Identities=11% Similarity=0.173 Sum_probs=20.2
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCEECHHHH
Q ss_conf 1788887442148887227789871532331
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~ 41 (129)
-|+.||+ +---|-.| +| +||.-+.+..+
T Consensus 132 ~c~~cg~-~iean~kp-~c-~cg~~~~~~ei 159 (593)
T COG2401 132 RCEKCGT-IIEANTKP-EC-KCGSHVHILEI 159 (593)
T ss_pred ECCHHCH-HHHHCCCC-CC-CCCCCEEEEEE
T ss_conf 0502110-02404885-55-78984489996
No 204
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=59.30 E-value=5.1 Score=21.01 Aligned_cols=21 Identities=19% Similarity=0.180 Sum_probs=16.7
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 178888744214888722778987
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
+|++||..|. |--=-||.||+
T Consensus 2 ~C~~CG~~~~---kW~GkCp~Cg~ 22 (372)
T cd01121 2 VCSECGYVSP---KWLGKCPECGE 22 (372)
T ss_pred CCCCCCCCCC---CCCEECCCCCC
T ss_conf 9988999788---72426979998
No 205
>PRK08493 NADH dehydrogenase subunit G; Validated
Probab=59.27 E-value=4 Score=21.64 Aligned_cols=19 Identities=16% Similarity=0.205 Sum_probs=15.4
Q ss_pred EEEECCCCCCCCCCCCCEE
Q ss_conf 4421488872277898715
Q gi|254780459|r 18 RFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 18 KFYDlnk~PiiCP~CG~e~ 36 (129)
+-+.|.|.+-+||+||.=-
T Consensus 231 r~w~~~k~~t~C~~CgvGC 249 (819)
T PRK08493 231 NAWELKKIPSTCPHCSAGC 249 (819)
T ss_pred CCCCCCCCCCCCCCCCCCC
T ss_conf 6640120044189888996
No 206
>KOG2879 consensus
Probab=58.86 E-value=3 Score=22.42 Aligned_cols=30 Identities=17% Similarity=0.431 Sum_probs=20.8
Q ss_pred CCCCCCCCCE---------------EEECCCCCC-----CCCCCCCEECH
Q ss_conf 3117888874---------------421488872-----27789871532
Q gi|254780459|r 9 KRTCPDTGKR---------------FYDLNKQVI-----VSPYTQNSWPL 38 (129)
Q Consensus 9 KR~C~~Cg~K---------------FYDlnk~Pi-----iCP~CG~e~~~ 38 (129)
+-+||-||.. ||=+++.-. .||.||+...+
T Consensus 239 ~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~ 288 (298)
T KOG2879 239 DTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEP 288 (298)
T ss_pred CCEEECCCCCCCCCEEECCCCCEEEHHHHHHHHCCHHHCCCCCCCCCCCC
T ss_conf 75500669999987310445640114556656410132216755887751
No 207
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=58.48 E-value=3 Score=22.44 Aligned_cols=23 Identities=9% Similarity=0.278 Sum_probs=14.2
Q ss_pred EEECCCCCCCCCCCCCEECHHHH
Q ss_conf 42148887227789871532331
Q gi|254780459|r 19 FYDLNKQVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 19 FYDlnk~PiiCP~CG~e~~~~~~ 41 (129)
|-+.-----.||.||+.|....+
T Consensus 42 yV~ie~G~t~CP~Cg~~~e~~fv 64 (115)
T COG1885 42 YVEIEVGSTSCPKCGEPFESAFV 64 (115)
T ss_pred EEEEECCCCCCCCCCCCCCEEEE
T ss_conf 69984365558877996631789
No 208
>pfam10083 DUF2321 Uncharacterized protein conserved in bacteria (DUF2321). Members of this family of hypothetical bacterial proteins have no known function.
Probab=57.85 E-value=4.8 Score=21.17 Aligned_cols=30 Identities=17% Similarity=0.410 Sum_probs=21.8
Q ss_pred CCCCCCCCCE----EE-----EC---CCCCCCCCCCCCEECH
Q ss_conf 3117888874----42-----14---8887227789871532
Q gi|254780459|r 9 KRTCPDTGKR----FY-----DL---NKQVIVSPYTQNSWPL 38 (129)
Q Consensus 9 KR~C~~Cg~K----FY-----Dl---nk~PiiCP~CG~e~~~ 38 (129)
=+.||+|++. || .| +.-|--|-+||.-|+=
T Consensus 39 I~~Cp~C~t~IrG~y~v~GV~~lg~~y~~PsyC~nCG~pyPW 80 (158)
T pfam10083 39 ITSCPHCSTPIRGFYYVDGVLGLGSDYDAPSYCHNCGKPFPW 80 (158)
T ss_pred HHHCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHCCCCCCC
T ss_conf 975868999867750268736448889995468747998883
No 209
>pfam02005 TRM N2,N2-dimethylguanosine tRNA methyltransferase. This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA. The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs. The enzyme is found in both eukaryotes and archaebacteria
Probab=57.82 E-value=6.6 Score=20.34 Aligned_cols=33 Identities=18% Similarity=0.140 Sum_probs=24.5
Q ss_pred HHCCCCCCCCCCCEEEECC--CCCCCCCCCCCEEC
Q ss_conf 2278311788887442148--88722778987153
Q gi|254780459|r 5 ELGTKRTCPDTGKRFYDLN--KQVIVSPYTQNSWP 37 (129)
Q Consensus 5 elG~KR~C~~Cg~KFYDln--k~PiiCP~CG~e~~ 37 (129)
.+|.=-.|++||.+.+-.+ +.+..||.||..+.
T Consensus 235 ~~g~v~~C~~C~~~~~~~~~~~~~~~c~~cg~~~~ 269 (375)
T pfam02005 235 KLGYVYHCSGCMNREVVTGIAKFKAECPHCGGRFH 269 (375)
T ss_pred HCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 28748988998652335787777776877898553
No 210
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=57.73 E-value=6.9 Score=20.23 Aligned_cols=23 Identities=13% Similarity=0.107 Sum_probs=16.2
Q ss_pred CCCCCCCCEEEEC----CC-CCCCCCCC
Q ss_conf 1178888744214----88-87227789
Q gi|254780459|r 10 RTCPDTGKRFYDL----NK-QVIVSPYT 32 (129)
Q Consensus 10 R~C~~Cg~KFYDl----nk-~PiiCP~C 32 (129)
-+|+.||.-+|=. +. .|..||+|
T Consensus 130 ~~C~~Cg~~~~~~~~~~~~~~~~~C~~~ 157 (682)
T COG1241 130 FECPKCGREVEVEQSEFRVEPPRECENC 157 (682)
T ss_pred EECCCCCCEEEEEECCCCCCCCCCCCCC
T ss_conf 9937899889998546651477558886
No 211
>KOG4451 consensus
Probab=57.66 E-value=1.9 Score=23.58 Aligned_cols=34 Identities=15% Similarity=0.450 Sum_probs=23.7
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEECHHHHHCCCCCCCCCC
Q ss_conf 1178888744214888722778987153233101234434433
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFEAPTSPEKEKE 52 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~~~~~~~~~~~ 52 (129)
.+|.||+.. .-|.-.|||-|-+- .++|.+++++.
T Consensus 250 K~ClsChqq---IHRNAPiCPlCKaK------sRSrNPKKpkr 283 (286)
T KOG4451 250 KVCLSCHQQ---IHRNAPICPLCKAK------SRSRNPKKPKR 283 (286)
T ss_pred HHHHHHHHH---HHCCCCCCCCHHHC------CCCCCCCCCCC
T ss_conf 589988888---85579877300100------13579887443
No 212
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=57.26 E-value=4.6 Score=21.27 Aligned_cols=28 Identities=14% Similarity=0.256 Sum_probs=17.0
Q ss_pred CCCCCCCEEEECCCC----CCCCCCCCCEECH
Q ss_conf 178888744214888----7227789871532
Q gi|254780459|r 11 TCPDTGKRFYDLNKQ----VIVSPYTQNSWPL 38 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~----PiiCP~CG~e~~~ 38 (129)
-||+||-++-=-.|. ...||.||.+..+
T Consensus 329 ~c~~~~~e~~~s~~~~~~~~~~~~~~~~e~~~ 360 (411)
T COG1503 329 KCPTCGYENLKSKREFEQKRFRCPECGSEMEE 360 (411)
T ss_pred CCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCH
T ss_conf 27774344441134443222368544653210
No 213
>pfam07754 DUF1610 Domain of unknown function (DUF1610). This zinc ribbon domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=57.01 E-value=4.7 Score=21.22 Aligned_cols=12 Identities=8% Similarity=-0.111 Sum_probs=7.1
Q ss_pred CCCCCCCCCCEE
Q ss_conf 872277898715
Q gi|254780459|r 25 QVIVSPYTQNSW 36 (129)
Q Consensus 25 ~PiiCP~CG~e~ 36 (129)
.+-.||+||...
T Consensus 9 ~~y~CPnCGf~~ 20 (26)
T pfam07754 9 VPYPCPNCGFXX 20 (26)
T ss_pred CCCCCCCCCCCC
T ss_conf 986689866301
No 214
>PRK09129 NADH dehydrogenase subunit G; Validated
Probab=56.89 E-value=4.7 Score=21.25 Aligned_cols=17 Identities=29% Similarity=0.454 Sum_probs=14.3
Q ss_pred EEEECCCCCCCCCCCCC
Q ss_conf 44214888722778987
Q gi|254780459|r 18 RFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 18 KFYDlnk~PiiCP~CG~ 34 (129)
|-++|.|.|=|||+||.
T Consensus 211 R~wel~~~~TiC~~C~v 227 (777)
T PRK09129 211 RTWELSRRKSVSPHDSL 227 (777)
T ss_pred CCEEEEECCEECCCCCC
T ss_conf 74010367866788887
No 215
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=55.96 E-value=7.7 Score=19.93 Aligned_cols=23 Identities=22% Similarity=0.388 Sum_probs=8.6
Q ss_pred CCCCCCCE-EEECCCCCCCCCCCC
Q ss_conf 17888874-421488872277898
Q gi|254780459|r 11 TCPDTGKR-FYDLNKQVIVSPYTQ 33 (129)
Q Consensus 11 ~C~~Cg~K-FYDlnk~PiiCP~CG 33 (129)
+|.+||.- +|+.++.-..|+.||
T Consensus 540 vC~~CG~i~~~~~~~~~~~C~~C~ 563 (599)
T TIGR03670 540 VCENCGHIAWEDKRKGTAYCPVCG 563 (599)
T ss_pred EECCCCCCEEEECCCCCEECCCCC
T ss_conf 402678403541357974898889
No 216
>COG5516 Conserved protein containing a Zn-ribbon-like motif, possibly RNA-binding [General function prediction only]
Probab=55.85 E-value=4.9 Score=21.12 Aligned_cols=34 Identities=21% Similarity=0.276 Sum_probs=24.4
Q ss_pred CCHHHCCCCCCCC--CCCEEEECCCC--CCCCC--CCCCE
Q ss_conf 7522278311788--88744214888--72277--89871
Q gi|254780459|r 2 AKPELGTKRTCPD--TGKRFYDLNKQ--VIVSP--YTQNS 35 (129)
Q Consensus 2 aK~elG~KR~C~~--Cg~KFYDlnk~--PiiCP--~CG~e 35 (129)
+-.+.|.-||||+ |+--|||=.|. --=|- -||.-
T Consensus 141 ad~~~~rlRiC~n~gCtwlFvDrSRnrsRrWCsMa~CGNR 180 (196)
T COG5516 141 ADGDFQRLRICPNPGCTWLFVDRSRNRSRRWCSMAVCGNR 180 (196)
T ss_pred CCCCHHHEEECCCCCCEEEEEECCHHHCCCHHHHHHHCCH
T ss_conf 0875232466699994389874440110210236652374
No 217
>KOG4718 consensus
Probab=54.88 E-value=4.5 Score=21.36 Aligned_cols=28 Identities=14% Similarity=0.369 Sum_probs=22.8
Q ss_pred CCCCCCCCEEEE------CCCCCCCCCCCCCEECH
Q ss_conf 117888874421------48887227789871532
Q gi|254780459|r 10 RTCPDTGKRFYD------LNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 10 R~C~~Cg~KFYD------lnk~PiiCP~CG~e~~~ 38 (129)
|.|-+||.+||= |.+ --+||.||--|.-
T Consensus 195 ~rCg~c~i~~h~~c~qty~q~-~~~cphc~d~w~h 228 (235)
T KOG4718 195 IRCGSCNIQYHRGCIQTYLQR-RDICPHCGDLWTH 228 (235)
T ss_pred ECCCCCCCHHHHHHHHHHHCC-CCCCCCHHCCCCC
T ss_conf 204765302212789998602-6769841014476
No 218
>KOG0978 consensus
Probab=54.79 E-value=1.4 Score=24.37 Aligned_cols=29 Identities=14% Similarity=0.206 Sum_probs=17.3
Q ss_pred CCCCCCCEEEE--------------------CCCCCCCCCCCCCEECHHHH
Q ss_conf 17888874421--------------------48887227789871532331
Q gi|254780459|r 11 TCPDTGKRFYD--------------------LNKQVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 11 ~C~~Cg~KFYD--------------------lnk~PiiCP~CG~e~~~~~~ 41 (129)
.||.|.+||=| .. -=-||+||+.|-+.-+
T Consensus 645 kCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etR--qRKCP~Cn~aFganDv 693 (698)
T KOG0978 645 KCSVCNTRWKDAVITKCGHVFCEECVQTRYETR--QRKCPKCNAAFGANDV 693 (698)
T ss_pred ECCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHH--CCCCCCCCCCCCCCCC
T ss_conf 287766755668998320688899888899885--4879998888785311
No 219
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=54.75 E-value=6.8 Score=20.27 Aligned_cols=27 Identities=15% Similarity=-0.117 Sum_probs=15.1
Q ss_pred CCCCCCEEEECCCCC-----CCCCCCCCEECH
Q ss_conf 788887442148887-----227789871532
Q gi|254780459|r 12 CPDTGKRFYDLNKQV-----IVSPYTQNSWPL 38 (129)
Q Consensus 12 C~~Cg~KFYDlnk~P-----iiCP~CG~e~~~ 38 (129)
|+.|=..=|.+-+.| .+|+.||+-|.+
T Consensus 24 C~dC~~~~~~~~~ip~~~~v~~C~~Cga~~~~ 55 (355)
T COG1499 24 CGDCYVETTPLIEIPDEVNVEVCRHCGAYRIR 55 (355)
T ss_pred CHHHHHCCCCCCCCCCCEEEEECCCCCCCCCC
T ss_conf 67787504622038873578987767870489
No 220
>pfam03367 zf-ZPR1 ZPR1 zinc-finger domain. The zinc-finger protein ZPR1 is ubiquitous among eukaryotes. It is indeed known to be an essential protein in yeast. In quiescent cells, ZPR1 is localized to the cytoplasm. But in proliferating cells treated with EGF or with other mitogens, ZPR1 accumulates in the nucleolus. ZPR1 interacts with the cytoplasmic domain of the inactive EGF receptor (EGFR) and is thought to inhibit the basal protein tyrosine kinase activity of EGFR. This interaction is disrupted when cells are treated with EGF, though by themselves, inactive EGFRs are not sufficient to sequester ZPR1 to the cytoplasm. Upon stimulation by EGF, ZPR1 directly binds the eukaryotic translation elongation factor-1alpha (eEF-1alpha) to form ZPR1/eEF-1alpha complexes. These move into the nucleus, localising particularly at the nucleolus. Indeed, the interaction between ZPR1 and eEF-1alpha has been shown to be essential for normal cellular proliferation, and ZPR1 is thought to be involved
Probab=54.64 E-value=3.9 Score=21.70 Aligned_cols=25 Identities=16% Similarity=0.235 Sum_probs=14.7
Q ss_pred CCCCCCCE----EEECCCCC---------CCCCCCCCEE
Q ss_conf 17888874----42148887---------2277898715
Q gi|254780459|r 11 TCPDTGKR----FYDLNKQV---------IVSPYTQNSW 36 (129)
Q Consensus 11 ~C~~Cg~K----FYDlnk~P---------iiCP~CG~e~ 36 (129)
-||+||.. ++ +-+-| ..||.||.-.
T Consensus 3 ~Cp~Cg~~g~t~~~-~~~IP~F~evii~sf~C~~CGyr~ 40 (160)
T pfam03367 3 DCPVCGGEGTTRMK-LTDIPYFREVIIMSFICEHCGYRS 40 (160)
T ss_pred CCCCCCCCCEEEEE-EECCCCCCEEEEEEEECCCCCCEE
T ss_conf 79889988779999-964898642899999999999882
No 221
>PRK07860 NADH dehydrogenase subunit G; Validated
Probab=54.62 E-value=4.9 Score=21.11 Aligned_cols=18 Identities=22% Similarity=0.180 Sum_probs=14.4
Q ss_pred CEEEECCCCCCCCCCCCC
Q ss_conf 744214888722778987
Q gi|254780459|r 17 KRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 17 ~KFYDlnk~PiiCP~CG~ 34 (129)
+|-++|.+.|=|||+||.
T Consensus 228 aR~Wel~~~~TvC~~C~v 245 (809)
T PRK07860 228 ARPFDLVSTPSVCEHCAS 245 (809)
T ss_pred CCCEEEEECCEECCCCCC
T ss_conf 774365762214688776
No 222
>pfam00471 Ribosomal_L33 Ribosomal protein L33.
Probab=54.14 E-value=7.4 Score=20.03 Aligned_cols=27 Identities=22% Similarity=0.386 Sum_probs=21.0
Q ss_pred CCCCCCCCCCEEEECCCCCC----------CCCCCCC
Q ss_conf 83117888874421488872----------2778987
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNKQVI----------VSPYTQN 34 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk~Pi----------iCP~CG~ 34 (129)
++-.|..||.+||=-.|.+- -||.|+.
T Consensus 4 i~L~ct~c~~~nY~t~KNk~~~~erLelkKycp~c~k 40 (48)
T pfam00471 4 ITLECTECGGRNYTTTKNKRNTPERLELKKYCPKCRK 40 (48)
T ss_pred EEEEEECCCCEEEEECCCCCCCCCEEEEECCCCCCCC
T ss_conf 9999837887537762676889541789702844265
No 223
>pfam04981 NMD3 NMD3 family. The NMD3 protein is involved in nonsense mediated mRNA decay. This amino 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=53.80 E-value=3.1 Score=22.36 Aligned_cols=33 Identities=18% Similarity=0.142 Sum_probs=26.2
Q ss_pred HCCCCCCCCCCCEEEECCCC-----CCCCCCCCCEECH
Q ss_conf 27831178888744214888-----7227789871532
Q gi|254780459|r 6 LGTKRTCPDTGKRFYDLNKQ-----VIVSPYTQNSWPL 38 (129)
Q Consensus 6 lG~KR~C~~Cg~KFYDlnk~-----PiiCP~CG~e~~~ 38 (129)
-..-+.|++|=.+-++|-+- -.+||+||.-+.+
T Consensus 10 ~~~~~mC~~C~~~~~~i~~ip~~~~v~~C~~Cg~~~~~ 47 (237)
T pfam04981 10 PLIDGLCPDCYRERVDITEIPEELTVVVCRDCGRYLIP 47 (237)
T ss_pred CCCCCCCHHHHHCCCCEEECCCEEEEEECCCCCCEECC
T ss_conf 77356666787105765998985899999999879508
No 224
>cd04511 Nudix_Hydrolase_4 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, U=I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specifici
Probab=53.60 E-value=4.4 Score=21.43 Aligned_cols=31 Identities=19% Similarity=0.330 Sum_probs=18.1
Q ss_pred CCCCCCEEEECCCCCCCCCCCCCEECHHHHHCCC
Q ss_conf 7888874421488872277898715323310123
Q gi|254780459|r 12 CPDTGKRFYDLNKQVIVSPYTQNSWPLAYFEAPT 45 (129)
Q Consensus 12 C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~~~~ 45 (129)
||+||.-|| .+|.++-.+=-...-..++.+|
T Consensus 1 C~~Cg~~~y---~nP~~~v~~ii~~~~kILLvrR 31 (130)
T cd04511 1 CPDCGYIHY---QNPKIIVGCVPEWEGKVLLCRR 31 (130)
T ss_pred CCCCCCEEC---CCCCEEEEEEEEECCEEEEEEC
T ss_conf 979996305---9997899999986999999940
No 225
>KOG2324 consensus
Probab=53.04 E-value=6.6 Score=20.35 Aligned_cols=22 Identities=27% Similarity=0.684 Sum_probs=15.5
Q ss_pred CCCCCCCCEEEECCC------CCCCCCCCCC
Q ss_conf 117888874421488------8722778987
Q gi|254780459|r 10 RTCPDTGKRFYDLNK------QVIVSPYTQN 34 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk------~PiiCP~CG~ 34 (129)
-+||+|| |--|- .|+.||+|..
T Consensus 228 ~~C~~C~---~s~n~e~~~~sk~~~Cp~C~~ 255 (457)
T KOG2324 228 MSCPSCG---YSKNSEDLDLSKIASCPKCNE 255 (457)
T ss_pred EECCCCC---CCCCHHHHCCCCCCCCCCCCC
T ss_conf 4467677---557601213776566876567
No 226
>PRK08174 DNA topoisomerase III; Validated
Probab=52.70 E-value=13 Score=18.47 Aligned_cols=32 Identities=22% Similarity=0.370 Sum_probs=19.9
Q ss_pred CCCCCCCCCEEEECC-C--CCCCC---CCCCCEECHHH
Q ss_conf 311788887442148-8--87227---78987153233
Q gi|254780459|r 9 KRTCPDTGKRFYDLN-K--QVIVS---PYTQNSWPLAY 40 (129)
Q Consensus 9 KR~C~~Cg~KFYDln-k--~PiiC---P~CG~e~~~~~ 40 (129)
-+.||.||..-.--+ | .=+-| |.|-..++...
T Consensus 615 ~~~CP~Cg~~l~~r~~k~G~F~gCs~yP~Ck~t~p~~~ 652 (670)
T PRK08174 615 SPACPQCGAPTRQRNGKSGPFWGCSRYPDCKGTLPVDS 652 (670)
T ss_pred CCCCCCCCCEEEEEECCCCCEEECCCCCCCCCCCCCCC
T ss_conf 99787899750367068873786999988888522899
No 227
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=52.69 E-value=9 Score=19.51 Aligned_cols=34 Identities=24% Similarity=0.251 Sum_probs=26.0
Q ss_pred HCCCCCCCCCCCEEEE-------CCCCCCCCCCCCCEECHH
Q ss_conf 2783117888874421-------488872277898715323
Q gi|254780459|r 6 LGTKRTCPDTGKRFYD-------LNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 6 lG~KR~C~~Cg~KFYD-------lnk~PiiCP~CG~e~~~~ 39 (129)
|-++-+||-||.---= +|+--++|-.||..|.-+
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~e 59 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECE 59 (104)
T ss_pred CCCEEECCCCCCEEEEEEEEEECCCEEEEECCCCCCEEEEE
T ss_conf 88357168558723557889742745689714575537882
No 228
>pfam10146 zf-C4H2 Zinc finger-containing protein. This is a family of proteins which appears to have a highly conserved zinc finger domain at the C terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members are annotated as being tumour-associated antigen HCA127 in humans but this could not confirmed.
Probab=52.68 E-value=3.9 Score=21.72 Aligned_cols=33 Identities=15% Similarity=0.436 Sum_probs=22.6
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCEECHHHHHCCCCCCCCCC
Q ss_conf 178888744214888722778987153233101234434433
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFEAPTSPEKEKE 52 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~~~~~~~~~~~ 52 (129)
+|+||+-. .-|.-.|||-|-+- .++|.+.+++.
T Consensus 186 ~ClSChQQ---IHRNAPICPlCKAK------SRSrNPKKpKr 218 (220)
T pfam10146 186 VCLSCHQQ---IHRNAPICPLCKAK------SRSRNPKKPKR 218 (220)
T ss_pred HHHHHHHH---HHCCCCCCCCCCCC------CCCCCCCCCCC
T ss_conf 66618988---85579777423343------45789999888
No 229
>KOG4080 consensus
Probab=52.68 E-value=3.5 Score=22.05 Aligned_cols=23 Identities=22% Similarity=0.472 Sum_probs=14.9
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 117888874421488872277898715
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
++||.||- +...-.+|++|=.-+
T Consensus 94 ~~CP~CGh----~k~a~~LC~~Cy~kV 116 (176)
T KOG4080 94 NTCPACGH----IKPAHTLCDYCYAKV 116 (176)
T ss_pred CCCCCCCC----CCCCCCCHHHHHHHH
T ss_conf 43754576----441452079999999
No 230
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=51.18 E-value=7.2 Score=20.09 Aligned_cols=12 Identities=8% Similarity=-0.039 Sum_probs=5.7
Q ss_pred CCCCCCCCCCEE
Q ss_conf 872277898715
Q gi|254780459|r 25 QVIVSPYTQNSW 36 (129)
Q Consensus 25 ~PiiCP~CG~e~ 36 (129)
.|-.||.||+.+
T Consensus 403 ~P~~CP~C~s~l 414 (667)
T COG0272 403 FPTHCPVCGSEL 414 (667)
T ss_pred CCCCCCCCCCEE
T ss_conf 999798899976
No 231
>pfam07975 C1_4 TFIIH C1-like domain. The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterized by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C (pfam00130).
Probab=51.03 E-value=8 Score=19.82 Aligned_cols=27 Identities=19% Similarity=0.212 Sum_probs=21.3
Q ss_pred CCCCCCCEEEECCC---CCCCCCCCCCEEC
Q ss_conf 17888874421488---8722778987153
Q gi|254780459|r 11 TCPDTGKRFYDLNK---QVIVSPYTQNSWP 37 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk---~PiiCP~CG~e~~ 37 (129)
.|..|..+|.+... ..-.||+|...|=
T Consensus 1 ~C~gCq~~f~~~~~~~~~~y~C~~C~~~FC 30 (48)
T pfam07975 1 FCYGCQQKLPDGINKTSSVYRCPKCKNVFC 30 (48)
T ss_pred CCCCCCCCCCCCCCCCCCEEECCCCCCCCC
T ss_conf 951215516787777543388956687610
No 232
>smart00532 LIGANc Ligase N family.
Probab=50.97 E-value=7.2 Score=20.09 Aligned_cols=11 Identities=9% Similarity=0.012 Sum_probs=5.9
Q ss_pred CCCCCCCCCEE
Q ss_conf 72277898715
Q gi|254780459|r 26 VIVSPYTQNSW 36 (129)
Q Consensus 26 PiiCP~CG~e~ 36 (129)
|-.||.||+..
T Consensus 399 P~~CP~C~s~l 409 (441)
T smart00532 399 PTHCPSCGSEL 409 (441)
T ss_pred CCCCCCCCCEE
T ss_conf 99898997983
No 233
>PRK04011 peptide chain release factor 1; Provisional
Probab=50.94 E-value=11 Score=18.94 Aligned_cols=26 Identities=15% Similarity=0.175 Sum_probs=12.1
Q ss_pred CCCCCCCEEEECCCC----CCCCCCCCCEE
Q ss_conf 178888744214888----72277898715
Q gi|254780459|r 11 TCPDTGKRFYDLNKQ----VIVSPYTQNSW 36 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~----PiiCP~CG~e~ 36 (129)
.|++|+..+-..-+. --.||+||...
T Consensus 329 ~c~~c~~~~~~~~~~~~~~~~~cp~cg~~~ 358 (409)
T PRK04011 329 KCNNCGYEEEKTVKEEEPKTGTCPKCGSAL 358 (409)
T ss_pred ECCCCCCEEEEECCCCCCCCCCCCCCCCCC
T ss_conf 759987178872153322346897557510
No 234
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit; InterPro: IPR012754 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 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry represents the beta-prime subunit, RpoC, found in most bacteria. It excludes some, mainly cyanobacterial, species where RpoC is replaced by two homologous proteins that include an additional domain. One arm of the "claw" is predominantly formed by this subunit, the other being predominantly formed by the beta subunit. The active site of the enzyme is defined by three invariant aspartate residues within the beta-prime subunit .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=50.93 E-value=8 Score=19.83 Aligned_cols=32 Identities=9% Similarity=0.126 Sum_probs=21.7
Q ss_pred CCCCCCEEEECC--CCCCCCCCCCCEECHHHHHCCCCCC
Q ss_conf 788887442148--8872277898715323310123443
Q gi|254780459|r 12 CPDTGKRFYDLN--KQVIVSPYTQNSWPLAYFEAPTSPE 48 (129)
Q Consensus 12 C~~Cg~KFYDln--k~PiiCP~CG~e~~~~~~~~~~~~~ 48 (129)
|. || ||==++ -.=++|=+||-|+.. .+.||-|
T Consensus 53 C~-CG-KYK~~rPmyKGvvCerCGVEVT~---skVRRER 86 (1552)
T TIGR02386 53 CY-CG-KYKKVRPMYKGVVCERCGVEVTE---SKVRRER 86 (1552)
T ss_pred EC-CC-CCCCCCCCCCCEEEECCCCEEEE---EEEECCC
T ss_conf 05-67-53223756575176017817941---1640232
No 235
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=50.30 E-value=5.1 Score=21.02 Aligned_cols=20 Identities=15% Similarity=0.069 Sum_probs=14.1
Q ss_pred EEEEC---CCCCCCCCCCCCEEC
Q ss_conf 44214---888722778987153
Q gi|254780459|r 18 RFYDL---NKQVIVSPYTQNSWP 37 (129)
Q Consensus 18 KFYDl---nk~PiiCP~CG~e~~ 37 (129)
|+|+- .|.-|+||.||..+.
T Consensus 68 K~y~~~kiYRf~I~C~~C~n~i~ 90 (272)
T COG5134 68 KSYYTTKIYRFSIKCHLCSNPID 90 (272)
T ss_pred CCCCCEEEEEEEEECCCCCCCEE
T ss_conf 43111367999997467777305
No 236
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=49.83 E-value=3.5 Score=22.01 Aligned_cols=34 Identities=18% Similarity=0.297 Sum_probs=23.4
Q ss_pred HHHCCCC--CCCCCCCEEE--ECCCCCCCCCCCCCEEC
Q ss_conf 2227831--1788887442--14888722778987153
Q gi|254780459|r 4 PELGTKR--TCPDTGKRFY--DLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 4 ~elG~KR--~C~~Cg~KFY--Dlnk~PiiCP~CG~e~~ 37 (129)
|.||+=. .|..|.+||- +..+----||+||..+.
T Consensus 239 P~LGKY~~TAC~rC~t~y~le~A~~~~wrCpkCGg~ik 276 (403)
T COG1379 239 PRLGKYHLTACSRCYTRYSLEEAKSLRWRCPKCGGKIK 276 (403)
T ss_pred CCCCCHHHHHHHHHHHCCCCCHHHHHCCCCCCCCCCHH
T ss_conf 11130647889876004675545540646862366010
No 237
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=49.80 E-value=12 Score=18.78 Aligned_cols=31 Identities=16% Similarity=0.078 Sum_probs=14.8
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCEECHHHHHCCC
Q ss_conf 17888874421488872277898715323310123
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFEAPT 45 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~~~~ 45 (129)
+||.||..- -.--.|-.||..+.+..++.++
T Consensus 143 ~cP~c~~~~----~~Gd~ce~cg~~~~~~dli~p~ 173 (558)
T PRK12268 143 TCPYCGYEK----ARGDQCDNCGALLDPTDLINPR 173 (558)
T ss_pred CCCCCCCCC----CCCCHHHHCCCCCCHHHHCCCC
T ss_conf 067768743----5673253247647857724885
No 238
>cd02008 TPP_IOR_alpha Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as indolepyruvate or phenylpyruvate, which are generated by the transamination of aromatic amino acids, to the corresponding aryl acetyl-CoA.
Probab=49.73 E-value=7.9 Score=19.84 Aligned_cols=13 Identities=8% Similarity=0.031 Sum_probs=10.9
Q ss_pred CCCCCCCCCCCCE
Q ss_conf 8887227789871
Q gi|254780459|r 23 NKQVIVSPYTQNS 35 (129)
Q Consensus 23 nk~PiiCP~CG~e 35 (129)
.|.|..||.||.-
T Consensus 1 pRpp~~CpGCgh~ 13 (178)
T cd02008 1 PRPPGLCPGCPHR 13 (178)
T ss_pred CCCCCCCCCCCCC
T ss_conf 9788868899985
No 239
>PRK11788 hypothetical protein; Provisional
Probab=49.32 E-value=7.6 Score=19.94 Aligned_cols=23 Identities=17% Similarity=0.252 Sum_probs=18.7
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 31178888744214888722778987
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
.-.|.+||-+-.-|- =-||+|..
T Consensus 354 ~Y~C~~CGF~~~~~~---WqCPsC~~ 376 (389)
T PRK11788 354 RYRCRNCGFTARTLY---WHCPSCKA 376 (389)
T ss_pred CEECCCCCCCCCCEE---EECCCCCC
T ss_conf 976999999888314---57909998
No 240
>pfam04161 Arv1 Arv1-like family. Arv1 is a transmembrane protein with potential zinc-binding motifs. ARV1 is a novel mediator of eukaryotic sterol homeostasis.
Probab=49.13 E-value=5.3 Score=20.93 Aligned_cols=27 Identities=11% Similarity=0.287 Sum_probs=17.5
Q ss_pred CCCCCCCE----EEECC---CCCCCCCCCCCEEC
Q ss_conf 17888874----42148---88722778987153
Q gi|254780459|r 11 TCPDTGKR----FYDLN---KQVIVSPYTQNSWP 37 (129)
Q Consensus 11 ~C~~Cg~K----FYDln---k~PiiCP~CG~e~~ 37 (129)
+|-+||.+ |-..+ -..-.||+||...+
T Consensus 2 iCi~C~~~~~~ly~~y~~~~i~l~~C~~C~~~~D 35 (194)
T pfam04161 2 ICIECGRPVKSLYKKYSSGNIKLTDCPNCNEVAD 35 (194)
T ss_pred EEEECCCCHHHHHHHCCCCCEEEEECCCCCCCCC
T ss_conf 8766899605688410798479866875254353
No 241
>PRK00279 adk adenylate kinase; Reviewed
Probab=49.03 E-value=9.6 Score=19.34 Aligned_cols=29 Identities=21% Similarity=0.251 Sum_probs=17.5
Q ss_pred CCCCCCCCCCEEEECC---CCCCCCCCCCCEE
Q ss_conf 8311788887442148---8872277898715
Q gi|254780459|r 8 TKRTCPDTGKRFYDLN---KQVIVSPYTQNSW 36 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDln---k~PiiCP~CG~e~ 36 (129)
..|+||.||.-|==.. +.+..|+.||...
T Consensus 126 ~R~~~~~~g~~y~~~~~pp~~~~~~~~~~~~l 157 (215)
T PRK00279 126 GRRICPACGRTYHVKFNPPKVEGKCDVTGEEL 157 (215)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 11567556764554578988666455433202
No 242
>pfam09567 RE_MamI MamI restriction endonuclease. This family includes the MamI (recognizes and cleaves GATNN^NNATC) restriction endonuclease.
Probab=48.66 E-value=5 Score=21.08 Aligned_cols=23 Identities=22% Similarity=0.401 Sum_probs=17.2
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 11788887442148887227789871
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
+.|.+||++--=| ..-||+||..
T Consensus 89 g~C~~Cgs~V~~l---E~eCPsCgSt 111 (350)
T pfam09567 89 GKCNDCGSEVKAL---ELECPSCAAA 111 (350)
T ss_pred CCCCCCCHHHHHH---HHCCCCCCCC
T ss_conf 1000001356556---5228766654
No 243
>pfam01667 Ribosomal_S27e Ribosomal protein S27.
Probab=48.04 E-value=13 Score=18.43 Aligned_cols=29 Identities=14% Similarity=0.190 Sum_probs=21.5
Q ss_pred CCCCCCCCCCEEEEC--CCCCCCCCCCCCEE
Q ss_conf 831178888744214--88872277898715
Q gi|254780459|r 8 TKRTCPDTGKRFYDL--NKQVIVSPYTQNSW 36 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDl--nk~PiiCP~CG~e~ 36 (129)
.|-.||.|+.-=-=| -.+++.|..||+.+
T Consensus 6 ~~VkCp~C~n~~~vFshA~t~V~C~~Cg~~L 36 (55)
T pfam01667 6 LDVKCPGCGNITTVFSHAQTVVKCIICGKVL 36 (55)
T ss_pred EEEECCCCCCEEEEEECCCEEEECCCCCCEE
T ss_conf 8849999997568971487178855448786
No 244
>COG5560 UBP12 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=48.03 E-value=3.4 Score=22.08 Aligned_cols=44 Identities=14% Similarity=0.028 Sum_probs=33.3
Q ss_pred HCCCCCCCCCCCEEEECCCCCCCCCCCCC---EECHHHHHCCCCCCC
Q ss_conf 27831178888744214888722778987---153233101234434
Q gi|254780459|r 6 LGTKRTCPDTGKRFYDLNKQVIVSPYTQN---SWPLAYFEAPTSPEK 49 (129)
Q Consensus 6 lG~KR~C~~Cg~KFYDlnk~PiiCP~CG~---e~~~~~~~~~~~~~~ 49 (129)
.-+||.|.-----|.-+-|+-++||.||+ .|+|-.-+...-+++
T Consensus 405 ~H~kRNdSiItdLFqgmyKSTL~Cp~C~~vsitfDPfmdlTLPLPvs 451 (823)
T COG5560 405 EHLKRNDSIITDLFQGMYKSTLTCPGCGSVSITFDPFMDLTLPLPVS 451 (823)
T ss_pred HHHHCCCCCHHHHHHHHHHCEEECCCCCCEEEEECCHHHCCCCCCHH
T ss_conf 98743742089998888652465567674456415423111357443
No 245
>TIGR00100 hypA hydrogenase nickel insertion protein HypA; 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 Methanococcus jannaschii. ; GO: 0016151 nickel ion binding, 0006464 protein modification process.
Probab=47.96 E-value=8.4 Score=19.70 Aligned_cols=26 Identities=12% Similarity=0.189 Sum_probs=17.5
Q ss_pred CCCCCCCCEEEEC-CCC---CCCCCCCCCE
Q ss_conf 1178888744214-888---7227789871
Q gi|254780459|r 10 RTCPDTGKRFYDL-NKQ---VIVSPYTQNS 35 (129)
Q Consensus 10 R~C~~Cg~KFYDl-nk~---PiiCP~CG~e 35 (129)
--|..|+.-|-=. .+- -|.||.|+..
T Consensus 79 ~~C~~C~~~~~~~~~~~~~F~~~CP~C~g~ 108 (128)
T TIGR00100 79 CRCEDCSEEVEPEIDELDEFEVRCPKCHGI 108 (128)
T ss_pred EEEEECCCCCEECCCCCCCEEEECCCCCCC
T ss_conf 998108801200101321325565899895
No 246
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=47.70 E-value=6.6 Score=20.35 Aligned_cols=21 Identities=19% Similarity=0.270 Sum_probs=14.2
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 1178888744214888722778987
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
-.|++||.. ...=-|||+||.
T Consensus 28 ~~c~~cG~~----~l~Hrvc~~cg~ 48 (57)
T COG0333 28 SVCPNCGEY----KLPHRVCLKCGY 48 (57)
T ss_pred EECCCCCCE----ECCCEECCCCCC
T ss_conf 035678860----157547486776
No 247
>KOG4139 consensus
Probab=47.52 E-value=4.7 Score=21.25 Aligned_cols=18 Identities=44% Similarity=1.005 Sum_probs=12.5
Q ss_pred HCCCCCCCCCCCEEEECC
Q ss_conf 278311788887442148
Q gi|254780459|r 6 LGTKRTCPDTGKRFYDLN 23 (129)
Q Consensus 6 lG~KR~C~~Cg~KFYDln 23 (129)
-+.|-.||-|+-+||+|+
T Consensus 296 ~~~~GrCpfc~~~~~~L~ 313 (520)
T KOG4139 296 ITSKGRCPFCGERYYDLS 313 (520)
T ss_pred CCCCCCCCCCCCHHHHHH
T ss_conf 145620566601677767
No 248
>PRK11866 2-oxoacid ferredoxin oxidoreductase subunit beta; Provisional
Probab=47.29 E-value=7.2 Score=20.12 Aligned_cols=25 Identities=20% Similarity=0.077 Sum_probs=17.4
Q ss_pred CCEEEECCCCCCCCCCCCCEECHHH
Q ss_conf 8744214888722778987153233
Q gi|254780459|r 16 GKRFYDLNKQVIVSPYTQNSWPLAY 40 (129)
Q Consensus 16 g~KFYDlnk~PiiCP~CG~e~~~~~ 40 (129)
-.|=|.-++.|+-||+||.-.....
T Consensus 5 ~~~dy~~~~~~~WCpGCG~~~Il~a 29 (286)
T PRK11866 5 KPNDYAVKRPPIWCPGCGNYGILEA 29 (286)
T ss_pred CHHHCCCCCCCCCCCCCCCHHHHHH
T ss_conf 8678088999866899971899999
No 249
>PRK09462 fur ferric uptake regulator; Provisional
Probab=47.17 E-value=14 Score=18.42 Aligned_cols=33 Identities=18% Similarity=0.288 Sum_probs=23.4
Q ss_pred HCC-CCCCCCCCCEEEECCCCC----CCCCCCCCEECH
Q ss_conf 278-311788887442148887----227789871532
Q gi|254780459|r 6 LGT-KRTCPDTGKRFYDLNKQV----IVSPYTQNSWPL 38 (129)
Q Consensus 6 lG~-KR~C~~Cg~KFYDlnk~P----iiCP~CG~e~~~ 38 (129)
.|. .|+-..=|..+|.++..+ ++|=.||..++.
T Consensus 65 ~Glv~~~~~~~g~~~ye~~~~~hH~HliC~~CG~i~e~ 102 (148)
T PRK09462 65 AGIVTRHNFEGGKSVFELTQQHHHDHLICLDCGKVIEF 102 (148)
T ss_pred CCCEEEEEECCCCEEEEECCCCCCCEEEECCCCCEEEE
T ss_conf 89679999759957998169887567999999899885
No 250
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.06 E-value=6.1 Score=20.53 Aligned_cols=14 Identities=21% Similarity=0.536 Sum_probs=11.0
Q ss_pred HCCCCCCCCCCCEE
Q ss_conf 27831178888744
Q gi|254780459|r 6 LGTKRTCPDTGKRF 19 (129)
Q Consensus 6 lG~KR~C~~Cg~KF 19 (129)
|-.+..||-|++||
T Consensus 16 ~kk~ieCPvC~tkF 29 (267)
T COG1655 16 YKKTIECPVCNTKF 29 (267)
T ss_pred HHCEECCCCCCCHH
T ss_conf 64211467655301
No 251
>pfam02150 RNA_POL_M_15KD RNA polymerases M/15 Kd subunit.
Probab=46.97 E-value=6.3 Score=20.48 Aligned_cols=30 Identities=13% Similarity=0.137 Sum_probs=19.3
Q ss_pred CCCCCCCCEEEECCCCCC--CCCCCCCEECHH
Q ss_conf 117888874421488872--277898715323
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVI--VSPYTQNSWPLA 39 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~Pi--iCP~CG~e~~~~ 39 (129)
|.||.||--.|==+..-- .|-.||.+|+..
T Consensus 2 ~FCp~C~NlL~~~~~k~~~~~Cr~C~y~~p~~ 33 (35)
T pfam02150 2 IFCPKCGNLLLPKEDKEGRNACRQCGYEEPAD 33 (35)
T ss_pred CCCHHHCCCCCCCCCHHHHHHHHHCCCCCCCC
T ss_conf 03400067535551212057786068777443
No 252
>pfam05766 NinG Bacteriophage Lambda NinG protein. NinG or Rap is involved in recombination. Rap (recombination adept with plasmid) increases lambda-by-plasmid recombination catalysed by Escherichia coli's RecBCD pathway.
Probab=46.78 E-value=4.8 Score=21.19 Aligned_cols=29 Identities=21% Similarity=0.230 Sum_probs=22.7
Q ss_pred CCCCCCCCCCEEEECCCCCCC-CCCCCCEE
Q ss_conf 831178888744214888722-77898715
Q gi|254780459|r 8 TKRTCPDTGKRFYDLNKQVIV-SPYTQNSW 36 (129)
Q Consensus 8 ~KR~C~~Cg~KFYDlnk~Pii-CP~CG~e~ 36 (129)
.-|.|-.||.+|-=+.-.-.+ ||.||..+
T Consensus 5 k~kkCk~C~~~F~p~~~~q~vCsp~Ca~~~ 34 (188)
T pfam05766 5 KPKKCKVCGVYFVPARSGQKVCSPECALAL 34 (188)
T ss_pred CCCCCCCCCCCCCCCCCCCEECCHHHHHHH
T ss_conf 887464156853677777313288999999
No 253
>pfam09526 DUF2387 Probable metal-binding protein (DUF2387). 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=46.73 E-value=10 Score=19.20 Aligned_cols=26 Identities=8% Similarity=0.120 Sum_probs=19.1
Q ss_pred CCCCCCC-----EEEECCCCCCCCCCCCCEE
Q ss_conf 1788887-----4421488872277898715
Q gi|254780459|r 11 TCPDTGK-----RFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 11 ~C~~Cg~-----KFYDlnk~PiiCP~CG~e~ 36 (129)
+||+|+. -|.+-+..-+.|=+||..-
T Consensus 10 vCP~C~~~D~i~~~~~~~~~~~eCV~Cg~~e 40 (61)
T pfam09526 10 VCPKCSAMDTIRMWRENGVEYVECVSCGYTD 40 (61)
T ss_pred CCCCCCCCCEEEEEECCCCEEEEECCCCCCC
T ss_conf 1898756537988723994699977899981
No 254
>pfam08882 Acetone_carb_G Acetone carboxylase gamma subunit. Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO(2) to form acetoacetate.
Probab=46.38 E-value=7.2 Score=20.10 Aligned_cols=14 Identities=14% Similarity=0.235 Sum_probs=10.0
Q ss_pred CCCCCCCEECHHHH
Q ss_conf 27789871532331
Q gi|254780459|r 28 VSPYTQNSWPLAYF 41 (129)
Q Consensus 28 iCP~CG~e~~~~~~ 41 (129)
-||.||+-++.+.+
T Consensus 70 yCP~Cgt~~evE~~ 83 (106)
T pfam08882 70 YCPGCGTLHEVEYL 83 (106)
T ss_pred ECCCCCCCEEECCC
T ss_conf 77986431145336
No 255
>PRK02935 hypothetical protein; Provisional
Probab=46.34 E-value=7.4 Score=20.03 Aligned_cols=25 Identities=16% Similarity=0.151 Sum_probs=14.2
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 11788887442148887227789871
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
-+||+|++.--=|+|.- .|=.|.+-
T Consensus 70 V~CP~C~K~TKmLGrvD-~CM~C~ep 94 (117)
T PRK02935 70 VICPSCDKPTKMLGRVD-ACMHCNQP 94 (117)
T ss_pred EECCCCCCCHHHHHHHH-HHHHCCCC
T ss_conf 78989997113420214-31306997
No 256
>pfam11023 DUF2614 Protein of unknown function (DUF2614). This is a family of proteins conserved in the Bacillaceae family. Some members are annotated as being protein YgzB. The function is not known.
Probab=46.15 E-value=7.5 Score=20.00 Aligned_cols=25 Identities=20% Similarity=0.271 Sum_probs=13.1
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 11788887442148887227789871
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
-+||+|++.--=|+|.- .|=.|++-
T Consensus 70 V~CP~C~K~TKmLGrvD-~CM~C~ep 94 (114)
T pfam11023 70 VVCPNCGKPTKMLGRVD-ACMHCNEP 94 (114)
T ss_pred EECCCCCCCHHHHHHHH-HHHHCCCC
T ss_conf 78989997113420214-31306997
No 257
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=46.11 E-value=9.3 Score=19.41 Aligned_cols=24 Identities=17% Similarity=0.325 Sum_probs=11.7
Q ss_pred CCCCCCCCCCEEEE-CCCCCCCCCC
Q ss_conf 83117888874421-4888722778
Q gi|254780459|r 8 TKRTCPDTGKRFYD-LNKQVIVSPY 31 (129)
Q Consensus 8 ~KR~C~~Cg~KFYD-lnk~PiiCP~ 31 (129)
.=..||+||++.-- -+..-+-||+
T Consensus 403 ~P~~CP~C~s~l~~~~~~~~~~C~N 427 (668)
T PRK07956 403 MPTHCPVCGSELVREEGEAVLRCTN 427 (668)
T ss_pred CCCCCCCCCCEEEEECCCEEEECCC
T ss_conf 6778767798579936963787789
No 258
>PRK08566 DNA-directed RNA polymerase subunit alpha; Validated
Probab=45.81 E-value=3.7 Score=21.88 Aligned_cols=12 Identities=17% Similarity=0.282 Sum_probs=5.7
Q ss_pred CCCCCCCCCCCE
Q ss_conf 887227789871
Q gi|254780459|r 24 KQVIVSPYTQNS 35 (129)
Q Consensus 24 k~PiiCP~CG~e 35 (129)
+.-..||.||+.
T Consensus 143 ~k~~~C~~Cg~~ 154 (881)
T PRK08566 143 AKRMVCPHCGEE 154 (881)
T ss_pred HHCCCCCCCCCC
T ss_conf 524568555885
No 259
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=45.66 E-value=14 Score=18.42 Aligned_cols=31 Identities=19% Similarity=0.243 Sum_probs=23.6
Q ss_pred CCCCCCCCCEEEECCCCC----CCCCCCCCEECHH
Q ss_conf 311788887442148887----2277898715323
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQV----IVSPYTQNSWPLA 39 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~P----iiCP~CG~e~~~~ 39 (129)
.|+-..=|..+|+++..| ++|=.||..++..
T Consensus 72 ~~~~~~~~~~~y~~~~~~~H~HliC~~CG~v~e~~ 106 (145)
T COG0735 72 HRLEFEGGKTRYELNSEPHHHHLICLDCGKVIEFE 106 (145)
T ss_pred EEEEECCCEEEEEECCCCCCCEEEECCCCCEEEEC
T ss_conf 99973797799970799862368967989988854
No 260
>pfam08646 Rep_fac-A_C Replication factor-A C terminal domain. This domain is found at the C terminal of replication factor A. Replication factor A (RPA) binds single-stranded DNA and is involved in replication, repair, and recombination of DNA.
Probab=45.48 E-value=12 Score=18.66 Aligned_cols=28 Identities=18% Similarity=0.416 Sum_probs=21.9
Q ss_pred CCCC--CCCCEEEECCCCCCCCCCCCCEEC
Q ss_conf 1178--888744214888722778987153
Q gi|254780459|r 10 RTCP--DTGKRFYDLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 10 R~C~--~Cg~KFYDlnk~PiiCP~CG~e~~ 37 (129)
..|| .|.+|--+-.-.--.|++|+.+|+
T Consensus 19 ~ACp~~~CnKKv~~~~~g~~~CekC~~~~~ 48 (146)
T pfam08646 19 PACPSEDCNKKVTEQGDGTWRCEKCDKEFP 48 (146)
T ss_pred CCCCCCCCCCCCEECCCCEEECCCCCCCCC
T ss_conf 789952278542857997198212388688
No 261
>PHA00733 hypothetical protein
Probab=45.42 E-value=5.3 Score=20.90 Aligned_cols=28 Identities=18% Similarity=0.271 Sum_probs=18.3
Q ss_pred CCCCCCCCEEEEC---------CCCCCCCCCCCCEEC
Q ss_conf 1178888744214---------888722778987153
Q gi|254780459|r 10 RTCPDTGKRFYDL---------NKQVIVSPYTQNSWP 37 (129)
Q Consensus 10 R~C~~Cg~KFYDl---------nk~PiiCP~CG~e~~ 37 (129)
-+||-|=+-|--. .----+||+||.+|.
T Consensus 93 ~VCPlCLtPFsS~~slkqHiRY~Eh~k~C~~C~K~F~ 129 (147)
T PHA00733 93 YVCPLCLMPFSSSVSLKQHIRYTEHTKVCPVCGKEFR 129 (147)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHC
T ss_conf 0066425731417999999877632750771435642
No 262
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=45.14 E-value=13 Score=18.55 Aligned_cols=26 Identities=15% Similarity=0.074 Sum_probs=19.2
Q ss_pred CCCEEEECCC-CCCCCCCCCCEECHHH
Q ss_conf 8874421488-8722778987153233
Q gi|254780459|r 15 TGKRFYDLNK-QVIVSPYTQNSWPLAY 40 (129)
Q Consensus 15 Cg~KFYDlnk-~PiiCP~CG~e~~~~~ 40 (129)
....++=|.| .|--||.||.-|.+..
T Consensus 67 h~v~W~~l~~g~p~RC~eCG~~fkL~~ 93 (97)
T cd00924 67 HDVIWMWLEKGKPKRCPECGHVFKLVD 93 (97)
T ss_pred CEEEEEEECCCCCCCCCCCCCEEEEEE
T ss_conf 641798861799833787777899887
No 263
>pfam10080 DUF2318 Predicted membrane protein (DUF2318). Members of this family of hypothetical bacterial proteins have no known function.
Probab=44.87 E-value=8.2 Score=19.75 Aligned_cols=32 Identities=13% Similarity=0.174 Sum_probs=26.9
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCEECHHHHH
Q ss_conf 17888874421488872277898715323310
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFE 42 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~ 42 (129)
.|.-||.+=|=-.-.-+||=+||.-|.+..+-
T Consensus 37 AC~iC~~~GY~q~g~~~vC~~C~~~~~~~~IG 68 (102)
T pfam10080 37 ACDICGDKGYYQKGDKLICKNCGVRFFLPSIG 68 (102)
T ss_pred HHHHCCCCCEEEECCEEEEECCCCEEEHHHCC
T ss_conf 03633757606999999885289697532227
No 264
>pfam12387 Peptidase_C74 Pestivirus NS2 peptidase. The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the bovine viral diarrhea virus polyprotein, a cleavage that is correlated with cytopathogenicity. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv.
Probab=44.87 E-value=7.9 Score=19.85 Aligned_cols=25 Identities=16% Similarity=0.085 Sum_probs=16.6
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEECH
Q ss_conf 11788887442148887227789871532
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~~ 38 (129)
.+|.-|..|=+ .--.||+||.-=+|
T Consensus 163 ilCtVCE~r~w----kg~~CPKCGr~G~p 187 (200)
T pfam12387 163 ILCTVCENRDW----KGGNCPKCGRQGPP 187 (200)
T ss_pred EEEEEECCCCC----CCCCCCCCCCCCCC
T ss_conf 99865306645----89999876678998
No 265
>TIGR01384 TFS_arch transcription factor S; InterPro: IPR006288 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 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. These sequences are the archaeal DNA-directed RNA polymerase, subunit M (also known as transcription factor S), a protein related in size and sequence to certain eukaryotic RNA polymerase small subunits, and in sequence and function to the much larger eukaryotic transcription factor IIS (TFIIS). Although originally suggested to be a subunit of the archaeal RNA polymerase, it elutes separately from active polymerase in gel filtration experiments and acts, like TFIIs, as an induction factor for RNA cleavage by RNA polymerase . ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=44.63 E-value=8.2 Score=19.77 Aligned_cols=28 Identities=14% Similarity=0.140 Sum_probs=18.5
Q ss_pred CCCCCCCEEEE---CCCCCCCCCCCCCEECH
Q ss_conf 17888874421---48887227789871532
Q gi|254780459|r 11 TCPDTGKRFYD---LNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 11 ~C~~Cg~KFYD---lnk~PiiCP~CG~e~~~ 38 (129)
-||.||.--.= =+|.--+||.||=|-+.
T Consensus 2 FCPKCgs~M~P~K~~Gkn~~~C~~CGYE~~~ 32 (111)
T TIGR01384 2 FCPKCGSLMVPDKKNGKNKYKCRKCGYEKEI 32 (111)
T ss_pred CCCCCCCCCCCCCCCCCCEEECCCCCCCCCC
T ss_conf 8786697158543069501162888873304
No 266
>pfam06676 DUF1178 Protein of unknown function (DUF1178). This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=44.01 E-value=13 Score=18.57 Aligned_cols=33 Identities=27% Similarity=0.547 Sum_probs=19.9
Q ss_pred CCCCCCCEE---------EE--CCCCCCCCCCCCCEECHHHHHCC
Q ss_conf 178888744---------21--48887227789871532331012
Q gi|254780459|r 11 TCPDTGKRF---------YD--LNKQVIVSPYTQNSWPLAYFEAP 44 (129)
Q Consensus 11 ~C~~Cg~KF---------YD--lnk~PiiCP~CG~e~~~~~~~~~ 44 (129)
.| +||-.| |+ .+|.=|.||.||..-.-..+-.|
T Consensus 7 ~C-~~~H~FEgWF~ss~~fe~Q~~~gli~CP~Cgs~~V~KalMAP 50 (145)
T pfam06676 7 RC-DHGHRFEGWFASSADFDKQQARGLVSCPVCGSTEVEKALMAP 50 (145)
T ss_pred EC-CCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCEEEEECCCC
T ss_conf 67-999956414568899999998699179999998365613688
No 267
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=44.00 E-value=15 Score=18.20 Aligned_cols=26 Identities=12% Similarity=0.245 Sum_probs=13.0
Q ss_pred CCCCCCCEE--EECCCCCCCCCCCCCEE
Q ss_conf 178888744--21488872277898715
Q gi|254780459|r 11 TCPDTGKRF--YDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 11 ~C~~Cg~KF--YDlnk~PiiCP~CG~e~ 36 (129)
.||.|+.-= |---.+++.|..||+.+
T Consensus 37 kCpgC~~it~VFSHAqt~V~C~~C~t~L 64 (85)
T PTZ00083 37 KCPGCLTITTVFSHAQTVVICGGCSSQL 64 (85)
T ss_pred ECCCCCCEEEEEECCCEEEECCCCCCEE
T ss_conf 8999997037873386478826758784
No 268
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=43.97 E-value=9.8 Score=19.27 Aligned_cols=24 Identities=21% Similarity=0.249 Sum_probs=15.5
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 1788887442148887227789871
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
-|..|+ .+|=+..--..||+||..
T Consensus 72 ~C~~C~-~~~~~e~~~~~CP~C~s~ 95 (115)
T COG0375 72 WCLDCG-QEVELEELDYRCPKCGSI 95 (115)
T ss_pred EECCCC-CEECCHHHEEECCCCCCC
T ss_conf 942399-760215531088899998
No 269
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=43.82 E-value=17 Score=17.74 Aligned_cols=26 Identities=19% Similarity=0.281 Sum_probs=13.1
Q ss_pred CCCCCCCEEEECCC-----CCCCCCCCCCEE
Q ss_conf 17888874421488-----872277898715
Q gi|254780459|r 11 TCPDTGKRFYDLNK-----QVIVSPYTQNSW 36 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk-----~PiiCP~CG~e~ 36 (129)
.|++||....-.-+ .+-.||+||..+
T Consensus 322 kc~~c~~e~~~~~~~~~~~~~~~c~~cg~~~ 352 (403)
T TIGR03676 322 KCPNCGYEEEKTVKPEEGDKSEACPKCGSEL 352 (403)
T ss_pred ECCCCCCEEEEECCCCCCCCCCCCCCCCCCE
T ss_conf 7688882588731544344566885568720
No 270
>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=43.79 E-value=12 Score=18.69 Aligned_cols=29 Identities=24% Similarity=0.274 Sum_probs=15.2
Q ss_pred HCCCCCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 278311788887442148887227789871
Q gi|254780459|r 6 LGTKRTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 6 lG~KR~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
.|-.+.=..=||.|-||-.+ =+||-||+.
T Consensus 15 ~Gd~~~gi~pGT~F~dLP~~-W~CP~C~a~ 43 (50)
T cd00730 15 EGDPDEGIPPGTPFEDLPDD-WVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCCCCHHHCCCC-CCCCCCCCC
T ss_conf 78856796988997898898-778799982
No 271
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.72 E-value=10 Score=19.10 Aligned_cols=25 Identities=12% Similarity=0.312 Sum_probs=17.1
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEEC
Q ss_conf 1178888744214888722778987153
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~ 37 (129)
--||-||.+. --+.+.||.|++.+.
T Consensus 7 ~~cPvcg~~~---iVTeL~c~~~etTVr 31 (122)
T COG3877 7 NRCPVCGRKL---IVTELKCSNCETTVR 31 (122)
T ss_pred CCCCCCCCCC---EEEEEECCCCCCEEE
T ss_conf 8998556320---367874288874575
No 272
>pfam11789 zf-Nse Zinc-finger of the MIZ type in Nse subunit. Nse1 and Nse2 are novel non-SMC subunits of the fission yeast Smc5-6 DNA repair complex. This family is the zinc-finger domain similar to the MIZ type of zinc-finger.
Probab=43.69 E-value=12 Score=18.65 Aligned_cols=33 Identities=21% Similarity=0.181 Sum_probs=25.3
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEECHHHHHCCCC
Q ss_conf 1178888744214888722778987153233101234
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFEAPTS 46 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~~~~~ 46 (129)
-+||=+...| ++|+..-+||+.|+-+.+....+
T Consensus 12 l~CPiT~~~~----~~Pv~s~~C~H~yek~aI~~~i~ 44 (57)
T pfam11789 12 LTCPITLLPF----KEPVTSKKCNHVFEKDAILSMLR 44 (57)
T ss_pred EECCCCCCHH----HCCCCCCCCCCEECHHHHHHHHH
T ss_conf 4887822454----37877687798286999999998
No 273
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1; InterPro: IPR004403 These proteins are translation factors that have been characterised in eukaryotes as the non-GTP-binding subunit of a cytosolic heterodimer that acts as a translation release factor for all three stop codons. Members of this orthologous family are found in Eukarya and Archaea. The name used should be eRF1 for the Archaea and aRF1 for the Eukarya. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.; GO: 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=43.38 E-value=13 Score=18.43 Aligned_cols=30 Identities=17% Similarity=0.412 Sum_probs=19.8
Q ss_pred CCCCCCCCCEE----EECC----C---CCCCCCCCCCEECH
Q ss_conf 31178888744----2148----8---87227789871532
Q gi|254780459|r 9 KRTCPDTGKRF----YDLN----K---QVIVSPYTQNSWPL 38 (129)
Q Consensus 9 KR~C~~Cg~KF----YDln----k---~PiiCP~CG~e~~~ 38 (129)
|-.|++||... -++. + ++.+||+||.+...
T Consensus 332 ~~~ca~c~~~~e~t~~~~~~ikl~eel~~~~c~~~g~~m~~ 372 (425)
T TIGR00108 332 TYKCAECGEVIEKTVRELKDIKLKEELKFAICPACGQEMDV 372 (425)
T ss_pred EEECCCCCCEEEEECCCHHHHHHHHHCCCCCCHHHCCEEEE
T ss_conf 44228989577420454122003340685457403872333
No 274
>PRK08620 DNA topoisomerase III; Provisional
Probab=43.34 E-value=17 Score=17.84 Aligned_cols=13 Identities=8% Similarity=0.054 Sum_probs=8.3
Q ss_pred CCCCCCCCCCEEC
Q ss_conf 8722778987153
Q gi|254780459|r 25 QVIVSPYTQNSWP 37 (129)
Q Consensus 25 ~PiiCP~CG~e~~ 37 (129)
+-+-||.||....
T Consensus 647 ~~~~Cp~C~~~~~ 659 (726)
T PRK08620 647 TNARCPNCKKKLE 659 (726)
T ss_pred CCCCCCCCCCEEE
T ss_conf 2894999998568
No 275
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=42.99 E-value=10 Score=19.21 Aligned_cols=10 Identities=20% Similarity=0.202 Sum_probs=5.4
Q ss_pred CCCCCCCCEE
Q ss_conf 2277898715
Q gi|254780459|r 27 IVSPYTQNSW 36 (129)
Q Consensus 27 iiCP~CG~e~ 36 (129)
-+||-||..+
T Consensus 135 ~vC~vCGy~~ 144 (166)
T COG1592 135 WVCPVCGYTH 144 (166)
T ss_pred EECCCCCCCC
T ss_conf 8768788812
No 276
>pfam00684 DnaJ_CXXCXGXG DnaJ central domain (4 repeats). The central cysteine-rich (CR) domain of DnaJ proteins contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DNAJ cysteine rich domain and various hydrophobic peptides has been found.
Probab=42.79 E-value=18 Score=17.62 Aligned_cols=29 Identities=24% Similarity=0.261 Sum_probs=20.6
Q ss_pred HCCCCCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 27831178888744214888722778987
Q gi|254780459|r 6 LGTKRTCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 6 lG~KR~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
+=.++.|+.|.-.=|.=+..+.+||.|+-
T Consensus 8 ~~r~~~C~~C~G~G~~~~~~~~~C~~C~G 36 (79)
T pfam00684 8 LSRKVTCPHCHGTGAKPGKKPKTCPTCNG 36 (79)
T ss_pred EEECCCCCCCCCEEECCCCCCCCCCCCCC
T ss_conf 25456889996604089998868989888
No 277
>pfam10071 DUF2310 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310). Members of this family of proteobacterial zinc ribbon proteins are thought to bind to nucleic acids, however their exact function has not as yet been defined.
Probab=42.39 E-value=9.8 Score=19.27 Aligned_cols=13 Identities=31% Similarity=0.534 Sum_probs=8.7
Q ss_pred CCCCCCCCEECHH
Q ss_conf 2277898715323
Q gi|254780459|r 27 IVSPYTQNSWPLA 39 (129)
Q Consensus 27 iiCP~CG~e~~~~ 39 (129)
=.||+||.+|-+.
T Consensus 222 r~CP~Cg~dW~L~ 234 (259)
T pfam10071 222 RKCPSCGGDWRLA 234 (259)
T ss_pred CCCCCCCCCCCCC
T ss_conf 9998999751669
No 278
>pfam02591 DUF164 Putative zinc ribbon domain.
Probab=42.37 E-value=8.3 Score=19.73 Aligned_cols=28 Identities=14% Similarity=0.328 Sum_probs=19.0
Q ss_pred CCCCCCCCCCE-----EEECCC--CCCCCCCCCCE
Q ss_conf 83117888874-----421488--87227789871
Q gi|254780459|r 8 TKRTCPDTGKR-----FYDLNK--QVIVSPYTQNS 35 (129)
Q Consensus 8 ~KR~C~~Cg~K-----FYDlnk--~PiiCP~CG~e 35 (129)
...+|..|+++ |-.+.+ ..+.||+||..
T Consensus 21 ~~~~C~gC~~~i~~q~~~~l~~~~~i~~Cp~CgRi 55 (56)
T pfam02591 21 EGGACGGCRMKLPPQTLNELRKGDEIVRCPHCGRI 55 (56)
T ss_pred CCCCCCCCCEECCHHHHHHHHCCCCEEECCCCCCC
T ss_conf 59956768747399999999869985799798863
No 279
>PRK11595 gluconate periplasmic binding protein; Provisional
Probab=42.29 E-value=9.2 Score=19.45 Aligned_cols=24 Identities=8% Similarity=0.083 Sum_probs=17.3
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 117888874421488872277898715
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
.+|+.|-.+|- +.|..||.||...
T Consensus 21 ~lC~~C~~~l~---~~~~~C~~Cg~p~ 44 (227)
T PRK11595 21 GICSVCSRALR---TLPTLCPQCGLPA 44 (227)
T ss_pred CCCHHHHCCCC---CCCCCCCCCCCCC
T ss_conf 44666760087---6667575136967
No 280
>pfam06906 DUF1272 Protein of unknown function (DUF1272). 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=42.26 E-value=9.9 Score=19.25 Aligned_cols=11 Identities=18% Similarity=0.057 Sum_probs=8.7
Q ss_pred CCCCCCCCEEC
Q ss_conf 22778987153
Q gi|254780459|r 27 IVSPYTQNSWP 37 (129)
Q Consensus 27 iiCP~CG~e~~ 37 (129)
-+||+||-+|.
T Consensus 42 ~~CPNCgGelv 52 (57)
T pfam06906 42 GVCPNCGGELV 52 (57)
T ss_pred CCCCCCCCCCC
T ss_conf 84849988125
No 281
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'; InterPro: IPR012758 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 kD, 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 the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanococcus jannaschii contains an intein.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0008270 zinc ion binding, 0006350 transcription.
Probab=42.05 E-value=4.6 Score=21.29 Aligned_cols=28 Identities=18% Similarity=0.204 Sum_probs=15.0
Q ss_pred EEEECCCCCCCCCCCCCEECHHHHHCCC
Q ss_conf 4421488872277898715323310123
Q gi|254780459|r 18 RFYDLNKQVIVSPYTQNSWPLAYFEAPT 45 (129)
Q Consensus 18 KFYDlnk~PiiCP~CG~e~~~~~~~~~~ 45 (129)
+.|..-+.--.||+||.+..-..+.+|.
T Consensus 139 ~i~k~A~k~~~CPhCg~~q~~ik~eKP~ 166 (901)
T TIGR02390 139 KIVKEAAKRMKCPHCGEEQKKIKFEKPT 166 (901)
T ss_pred HHHHHHHHCCCCCCCCCCCCCEEEECCE
T ss_conf 9999986178798887412432452771
No 282
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=42.00 E-value=13 Score=18.52 Aligned_cols=33 Identities=18% Similarity=0.395 Sum_probs=24.4
Q ss_pred CHHHCC----CCCCCCCCCEEEECCCC----CCCCCCCCCE
Q ss_conf 522278----31178888744214888----7227789871
Q gi|254780459|r 3 KPELGT----KRTCPDTGKRFYDLNKQ----VIVSPYTQNS 35 (129)
Q Consensus 3 K~elG~----KR~C~~Cg~KFYDlnk~----PiiCP~CG~e 35 (129)
.|.|-+ --.||+||.-|.-|.|. --.|-.||.-
T Consensus 450 npswqkddessdscpscgr~f~slsrplgtRAhhCR~CG~R 490 (1374)
T PTZ00303 450 NPSWQKDDESSDSCPSCGRAFISLSRPLGTRAHHCRSCGIR 490 (1374)
T ss_pred CCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCHHCCCCHHH
T ss_conf 85446566556777541403455046555430012211178
No 283
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=41.77 E-value=11 Score=19.03 Aligned_cols=37 Identities=19% Similarity=0.210 Sum_probs=25.5
Q ss_pred CCCHHHCCCCCCCCCCCEEEEC---------CC---CCCCCCCCCCEEC
Q ss_conf 9752227831178888744214---------88---8722778987153
Q gi|254780459|r 1 MAKPELGTKRTCPDTGKRFYDL---------NK---QVIVSPYTQNSWP 37 (129)
Q Consensus 1 MaK~elG~KR~C~~Cg~KFYDl---------nk---~PiiCP~CG~e~~ 37 (129)
|.+...++.-.||+||.-||=. ++ .-.+|=.||--+.
T Consensus 6 ~~~~~~~~~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 6 FPKEEFETRIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred CCCCEEEEEECCCCCCCEEEEEEEEECCCCCCEEEEEEEECCCCCCCCC
T ss_conf 5510023351488551021688874137855518999998144688432
No 284
>KOG3014 consensus
Probab=41.67 E-value=10 Score=19.21 Aligned_cols=15 Identities=27% Similarity=0.826 Sum_probs=9.4
Q ss_pred HHCCCC----CCCCCCCEE
Q ss_conf 227831----178888744
Q gi|254780459|r 5 ELGTKR----TCPDTGKRF 19 (129)
Q Consensus 5 elG~KR----~C~~Cg~KF 19 (129)
++|.|+ .|..|||+|
T Consensus 29 d~Gqk~fg~~~C~~Cgm~Y 47 (257)
T KOG3014 29 DAGQKDFGAVKCKECGMKY 47 (257)
T ss_pred ECCCCCCCCEEHHHCCCEE
T ss_conf 1576301846521147653
No 285
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=41.65 E-value=25 Score=16.75 Aligned_cols=28 Identities=14% Similarity=0.383 Sum_probs=19.3
Q ss_pred CCCCCCCC---EEEECCCC-CCCCCCCCCEEC
Q ss_conf 11788887---44214888-722778987153
Q gi|254780459|r 10 RTCPDTGK---RFYDLNKQ-VIVSPYTQNSWP 37 (129)
Q Consensus 10 R~C~~Cg~---KFYDlnk~-PiiCP~CG~e~~ 37 (129)
-+|+.||. ++---+|. =+.|=.||+.-+
T Consensus 99 V~C~~C~sPDT~L~ke~r~~~L~C~ACGA~rp 130 (201)
T PRK12336 99 VICSECGRPDTRLVKSDRVLMLKCDACGAHRP 130 (201)
T ss_pred EECCCCCCCCCEEEEECCEEEEEECCCCCCCC
T ss_conf 89789999886899979859999637899986
No 286
>pfam07503 zf-HYPF HypF finger. The HypF family of proteins are involved in the maturation and regulation of hydrogenase. In the N-terminus they appear to have two Zinc finger domains, as modelled by this family.
Probab=40.95 E-value=5.7 Score=20.70 Aligned_cols=28 Identities=25% Similarity=0.444 Sum_probs=20.6
Q ss_pred CCCCCCCEEEECC-C----CCCCCCCCCCEECH
Q ss_conf 1788887442148-8----87227789871532
Q gi|254780459|r 11 TCPDTGKRFYDLN-K----QVIVSPYTQNSWPL 38 (129)
Q Consensus 11 ~C~~Cg~KFYDln-k----~PiiCP~CG~e~~~ 38 (129)
+|+.|-..|.|-+ | -||-|+.||--|.+
T Consensus 1 lC~~C~~Ey~dp~~RR~h~~~isC~~CGPr~~i 33 (35)
T pfam07503 1 LCPECLKEYFDPLNRRFHAQFISCTNCGPRLSL 33 (35)
T ss_pred CCHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEE
T ss_conf 977899997496665545776568787888685
No 287
>KOG3084 consensus
Probab=40.86 E-value=14 Score=18.43 Aligned_cols=29 Identities=21% Similarity=0.338 Sum_probs=17.2
Q ss_pred CCCCCCCCCEEE------ECCCCCCCCCCCCCEEC
Q ss_conf 311788887442------14888722778987153
Q gi|254780459|r 9 KRTCPDTGKRFY------DLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 9 KR~C~~Cg~KFY------Dlnk~PiiCP~CG~e~~ 37 (129)
-|.||.||.+-. -+.=.-.+||.|+..|+
T Consensus 150 ykFCp~CG~~tkp~e~g~k~~Cs~~~C~~~n~~yP 184 (345)
T KOG3084 150 YKFCPGCGSPTKPEEAGTKLQCSDETCPSCNVIYP 184 (345)
T ss_pred HCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEECC
T ss_conf 31075668986435688532300144884875656
No 288
>pfam01215 COX5B Cytochrome c oxidase subunit Vb.
Probab=40.72 E-value=16 Score=18.01 Aligned_cols=25 Identities=12% Similarity=0.081 Sum_probs=19.8
Q ss_pred CCEEEECCC-CCCCCCCCCCEECHHH
Q ss_conf 874421488-8722778987153233
Q gi|254780459|r 16 GKRFYDLNK-QVIVSPYTQNSWPLAY 40 (129)
Q Consensus 16 g~KFYDlnk-~PiiCP~CG~e~~~~~ 40 (129)
...++=|.| .|--||.||..|.+..
T Consensus 70 ~v~W~~l~kg~p~RC~eCG~~fkL~~ 95 (99)
T pfam01215 70 TIIWHTVAKKKPTRCPECGSVYKLKH 95 (99)
T ss_pred EEEEEEECCCCCCCCCCCCCEEEEEE
T ss_conf 46899861799730787887899997
No 289
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=40.52 E-value=12 Score=18.68 Aligned_cols=14 Identities=14% Similarity=-0.014 Sum_probs=10.0
Q ss_pred CCCCCCCCCCCEEC
Q ss_conf 88722778987153
Q gi|254780459|r 24 KQVIVSPYTQNSWP 37 (129)
Q Consensus 24 k~PiiCP~CG~e~~ 37 (129)
+-|=.||.||+...
T Consensus 409 ~~P~~CP~C~s~lv 422 (706)
T TIGR00575 409 KFPTHCPSCGSPLV 422 (706)
T ss_pred ECCCCCCCCCCEEE
T ss_conf 42871888883311
No 290
>pfam11781 RRN7 RNA polymerase I-specific transcription initiation factor Rrn7. 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=40.39 E-value=12 Score=18.73 Aligned_cols=30 Identities=7% Similarity=0.134 Sum_probs=23.3
Q ss_pred CCCCCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 783117888874421488872277898715
Q gi|254780459|r 7 GTKRTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 7 G~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
|....|..|+.+||...-==-.|-.||+..
T Consensus 6 ~~~~~C~~C~~~~~~~~dG~~yC~~Cg~~~ 35 (36)
T pfam11781 6 GPNEACGVCRSVWFRSDDGFYYCTRCGHVA 35 (36)
T ss_pred CCCHHHHHCCCEEEEECCCEEEEEEECCCC
T ss_conf 744144010443567128789885504415
No 291
>PRK10436 hypothetical protein; Provisional
Probab=40.29 E-value=13 Score=18.62 Aligned_cols=31 Identities=10% Similarity=0.162 Sum_probs=18.7
Q ss_pred HCCCCCCCCCCCEEE-------ECC------CCCCCCCCCCCEE
Q ss_conf 278311788887442-------148------8872277898715
Q gi|254780459|r 6 LGTKRTCPDTGKRFY-------DLN------KQVIVSPYTQNSW 36 (129)
Q Consensus 6 lG~KR~C~~Cg~KFY-------Dln------k~PiiCP~CG~e~ 36 (129)
...+|+||.|-..+- .++ ..+.=||.|++=|
T Consensus 349 RLVR~LCp~Ck~~~~~~~~~~~~~~~~~~~~~~~~GC~~C~tGY 392 (461)
T PRK10436 349 RLVRKLCPHCRQQQSEPVHLPANIWPSPLPHWQAVGCEHCYHGF 392 (461)
T ss_pred CCCCCCCHHHCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf 03432373327866754210133043433202578873338998
No 292
>TIGR02109 PQQ_syn_pqqE coenzyme PQQ biosynthesis protein E; InterPro: IPR011843 This entry describes coenzyme PQQ biosynthesis protein E, a gene required for the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ). PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases.; GO: 0051539 4 iron 4 sulfur cluster binding, 0018189 pyrroloquinoline quinone biosynthetic process.
Probab=40.14 E-value=12 Score=18.82 Aligned_cols=14 Identities=21% Similarity=0.430 Sum_probs=10.5
Q ss_pred CCCCCCCCCCCEEC
Q ss_conf 88722778987153
Q gi|254780459|r 24 KQVIVSPYTQNSWP 37 (129)
Q Consensus 24 k~PiiCP~CG~e~~ 37 (129)
|=|+-||||..=..
T Consensus 16 RCPL~CPYCSNPLe 29 (363)
T TIGR02109 16 RCPLQCPYCSNPLE 29 (363)
T ss_pred CCCCCCCCCCCCHH
T ss_conf 58887779897068
No 293
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=39.96 E-value=14 Score=18.43 Aligned_cols=20 Identities=15% Similarity=0.240 Sum_probs=14.4
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 1788887442148887227789871
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
+| -||+- |- .|.-||.||+.
T Consensus 2 ~C-rCG~~---l~-~p~~Cl~Cg~~ 21 (227)
T COG4031 2 IC-RCGAE---LS-SPAFCLNCGRR 21 (227)
T ss_pred CC-CCCCC---CC-CCCHHCCCCCC
T ss_conf 56-46786---56-56110036996
No 294
>pfam11706 zf-CGNR CGNR zinc finger. This family consists of a C-terminal zinc finger domain. It seems likely to be DNA-binding given the conservation of many positively charged residues. The domain is named after a highly conserved motif found in many members of the family.
Probab=39.53 E-value=17 Score=17.78 Aligned_cols=26 Identities=27% Similarity=0.390 Sum_probs=19.2
Q ss_pred CCC--CCCCCEEEECCCC--CCCCC--CCCCE
Q ss_conf 117--8888744214888--72277--89871
Q gi|254780459|r 10 RTC--PDTGKRFYDLNKQ--VIVSP--YTQNS 35 (129)
Q Consensus 10 R~C--~~Cg~KFYDlnk~--PiiCP--~CG~e 35 (129)
|.| |.|+.-|||.-|. =-=|. -||.-
T Consensus 3 r~C~~~~C~~~F~D~Sr~~~RrwCsm~~CGnR 34 (44)
T pfam11706 3 RACAAPDCTWLFLDTSRNGRRRWCSMARCGNR 34 (44)
T ss_pred CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCH
T ss_conf 34399998669885899988635584424388
No 295
>PRK07726 DNA topoisomerase III; Provisional
Probab=39.44 E-value=19 Score=17.47 Aligned_cols=27 Identities=7% Similarity=0.026 Sum_probs=18.6
Q ss_pred CCCCCCCEEEECCCCCCCC-----CCCCCEECH
Q ss_conf 1788887442148887227-----789871532
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVS-----PYTQNSWPL 38 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiC-----P~CG~e~~~ 38 (129)
.||.||..-+.- +.=.-| |.|+..+.-
T Consensus 632 ~CP~Cg~~v~~~-~k~~~Cs~y~~~~C~F~i~k 663 (716)
T PRK07726 632 SCKKCDGDVIDK-GTFYGCSNYNTTQCDFTISK 663 (716)
T ss_pred CCCCCCCEEEEC-CEEEECCCCCCCCCCEEEEC
T ss_conf 599999983776-75897379989999979513
No 296
>pfam07191 DUF1407 Protein of unknown function (DUF1407). This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family have 8 highly conserved cysteine residues, which form two zinc ribbon domains.
Probab=39.34 E-value=16 Score=17.91 Aligned_cols=27 Identities=22% Similarity=0.416 Sum_probs=17.5
Q ss_pred CCCCCCCCCCCEEEECCCCCCCCCCCCCEEC
Q ss_conf 7831178888744214888722778987153
Q gi|254780459|r 7 GTKRTCPDTGKRFYDLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 7 G~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~ 37 (129)
|-...|+.|+..| +.-..||-|+.+..
T Consensus 15 ~~~~~C~~C~~~~----~~~a~CP~C~~~Lq 41 (70)
T pfam07191 15 GGHYHCDQCQKDF----KKQALCPDCHQELE 41 (70)
T ss_pred CCCEECHHHCCEE----EEEEECCCCCCHHH
T ss_conf 9977970330101----47898976243789
No 297
>pfam12230 PRP21_like_P Pre-mRNA splicing factor PRP21 like protein. This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with pfam01805. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form.
Probab=39.08 E-value=13 Score=18.60 Aligned_cols=16 Identities=25% Similarity=0.268 Sum_probs=12.7
Q ss_pred CCCCCCCCCEECHHHH
Q ss_conf 7227789871532331
Q gi|254780459|r 26 VIVSPYTQNSWPLAYF 41 (129)
Q Consensus 26 PiiCP~CG~e~~~~~~ 41 (129)
-++||-||.-++...+
T Consensus 162 ~~~cPitGq~IP~~e~ 177 (223)
T pfam12230 162 MIKCPITGELIPEDEM 177 (223)
T ss_pred EEECCCCCCCCCHHHH
T ss_conf 6577877781777899
No 298
>pfam08792 A2L_zn_ribbon A2L zinc ribbon domain. This zinc ribbon domain is found associated with some viral A2L transcription factors.
Probab=38.80 E-value=9.7 Score=19.30 Aligned_cols=28 Identities=18% Similarity=0.386 Sum_probs=19.0
Q ss_pred CCCCCCCCE-EEECCCCCCCCCCCCCEEC
Q ss_conf 117888874-4214888722778987153
Q gi|254780459|r 10 RTCPDTGKR-FYDLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 10 R~C~~Cg~K-FYDlnk~PiiCP~CG~e~~ 37 (129)
+.|--||.- -|=-++.-.+||.||.+|+
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~~~ 32 (33)
T pfam08792 4 KKCKYCGGNGIVNKEDDYEVCIFCGASFP 32 (33)
T ss_pred CCCEECCCCCEECCCCCEEEEEEECCCCC
T ss_conf 40415178740115687689999667478
No 299
>PRK09919 hypothetical protein; Provisional
Probab=38.80 E-value=12 Score=18.79 Aligned_cols=17 Identities=18% Similarity=0.221 Sum_probs=12.6
Q ss_pred CCCCCCCCCCEECHHHH
Q ss_conf 87227789871532331
Q gi|254780459|r 25 QVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 25 ~PiiCP~CG~e~~~~~~ 41 (129)
+-+|||.||..|....-
T Consensus 7 dtvv~P~tG~~FS~I~~ 23 (114)
T PRK09919 7 DTVIQPSTGISFSAISS 23 (114)
T ss_pred EEEECCCCCCCHHHHHH
T ss_conf 01873888861444445
No 300
>TIGR00280 L37a ribosomal protein L37a; 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 of 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.
Probab=38.54 E-value=12 Score=18.71 Aligned_cols=29 Identities=17% Similarity=0.371 Sum_probs=22.7
Q ss_pred CCCCCCCCCCCEEEECCCC---CCCCCCCCCEEC
Q ss_conf 7831178888744214888---722778987153
Q gi|254780459|r 7 GTKRTCPDTGKRFYDLNKQ---VIVSPYTQNSWP 37 (129)
Q Consensus 7 G~KR~C~~Cg~KFYDlnk~---PiiCP~CG~e~~ 37 (129)
=.|..||+||.|- |.|. -=.|-.||..|.
T Consensus 34 ~~kY~C~~CG~k~--vKR~s~GIW~C~~Cg~~~A 65 (92)
T TIGR00280 34 KKKYVCPVCGKKA--VKRESTGIWKCRKCGAKFA 65 (92)
T ss_pred HCCCCCCCCCCCC--CCCCCCCCCCCCCCCCEEC
T ss_conf 4167888875897--3406653340267897522
No 301
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=38.46 E-value=15 Score=18.11 Aligned_cols=27 Identities=11% Similarity=0.043 Sum_probs=17.1
Q ss_pred CCCCCCCEEEECCC-CCCCCCCCCCEEC
Q ss_conf 17888874421488-8722778987153
Q gi|254780459|r 11 TCPDTGKRFYDLNK-QVIVSPYTQNSWP 37 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk-~PiiCP~CG~e~~ 37 (129)
-|++|++=|-+-.- ++-.||.||+...
T Consensus 127 Yc~~ce~f~~~~~l~d~g~cp~cg~~~e 154 (644)
T PRK12267 127 YCVSCETFFTESQLVDGGKCPDSGHEVE 154 (644)
T ss_pred CCCCCCCCCCHHHCCCCCCCCCCCCCCE
T ss_conf 2587543336244045786877899764
No 302
>KOG0909 consensus
Probab=38.31 E-value=22 Score=17.13 Aligned_cols=45 Identities=9% Similarity=-0.039 Sum_probs=28.5
Q ss_pred HCCCCCCCCCCCEE-EECCCCC---------------CCCCCCCCEE------CHHHHHCCCCCCCC
Q ss_conf 27831178888744-2148887---------------2277898715------32331012344344
Q gi|254780459|r 6 LGTKRTCPDTGKRF-YDLNKQV---------------IVSPYTQNSW------PLAYFEAPTSPEKE 50 (129)
Q Consensus 6 lG~KR~C~~Cg~KF-YDlnk~P---------------iiCP~CG~e~------~~~~~~~~~~~~~~ 50 (129)
|=.+-.|+.||.+- -=|...| -+|-.||++- +|..++.+|++|-+
T Consensus 158 WvN~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~RFPRYNdp~kLLeTRkGRCG 224 (500)
T KOG0909 158 WVNNPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETRFPRYNDPIKLLETRKGRCG 224 (500)
T ss_pred ECCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCEEEEEEECCCCCCCCCCCCCCHHHHHHHCCCCCC
T ss_conf 4478985310241145546889964676368754899983588876657665898999763467620
No 303
>TIGR02676 cas_provis_2 CRISPR-associated large protein (provisional); InterPro: IPR013492 Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognizable features . This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins..
Probab=37.13 E-value=12 Score=18.64 Aligned_cols=10 Identities=30% Similarity=0.491 Sum_probs=7.3
Q ss_pred CCCCCCCCEE
Q ss_conf 2277898715
Q gi|254780459|r 27 IVSPYTQNSW 36 (129)
Q Consensus 27 iiCP~CG~e~ 36 (129)
=||||||+.+
T Consensus 973 gIcpY~Ga~i 982 (1104)
T TIGR02676 973 GICPYSGASI 982 (1104)
T ss_pred CCCCCCCCCC
T ss_conf 8787778887
No 304
>PRK12860 transcriptional activator FlhC; Provisional
Probab=37.11 E-value=23 Score=17.05 Aligned_cols=37 Identities=11% Similarity=0.093 Sum_probs=22.0
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEECHHHHHCCCC
Q ss_conf 1178888744214888722778987153233101234
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFEAPTS 46 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~~~~~ 46 (129)
-.|..||..|-=-+-+|...--||.=-+|...-+.++
T Consensus 135 ~~C~~CgG~FV~ha~d~~~~fvC~lC~pPsRAgK~rk 171 (189)
T PRK12860 135 ARCRRCGGKFVTHAHDLRHNFVCGLCQPPSRAGKTKK 171 (189)
T ss_pred CCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 6777778815522356788877789889521123333
No 305
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=36.98 E-value=21 Score=17.25 Aligned_cols=11 Identities=45% Similarity=0.827 Sum_probs=8.2
Q ss_pred CCCCCCCCCCC
Q ss_conf 78311788887
Q gi|254780459|r 7 GTKRTCPDTGK 17 (129)
Q Consensus 7 G~KR~C~~Cg~ 17 (129)
++...||.||.
T Consensus 58 ~~~~~Cp~C~~ 68 (140)
T COG0551 58 KTGVKCPKCGK 68 (140)
T ss_pred CCCEECCCCCC
T ss_conf 47766776677
No 306
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit; InterPro: IPR012755 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 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=36.88 E-value=15 Score=18.18 Aligned_cols=29 Identities=14% Similarity=0.197 Sum_probs=21.4
Q ss_pred CCCCCCEEEECCCCCCCCCCCCCEECHHHHH
Q ss_conf 7888874421488872277898715323310
Q gi|254780459|r 12 CPDTGKRFYDLNKQVIVSPYTQNSWPLAYFE 42 (129)
Q Consensus 12 C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~ 42 (129)
|. || ||--....-|+|-.||.++......
T Consensus 64 C~-CG-kykrvrhrGivCerCGvevtes~vr 92 (625)
T TIGR02387 64 CY-CG-KYKRVRHRGIVCERCGVEVTESRVR 92 (625)
T ss_pred CC-CC-CEEEEEECCEEEECCCEEEECCEEE
T ss_conf 10-46-4015542212650365023112001
No 307
>pfam04423 Rad50_zn_hook Rad50 zinc hook motif. The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.
Probab=36.81 E-value=13 Score=18.44 Aligned_cols=14 Identities=7% Similarity=-0.104 Sum_probs=11.1
Q ss_pred CCCCCCCEECHHHH
Q ss_conf 27789871532331
Q gi|254780459|r 28 VSPYTQNSWPLAYF 41 (129)
Q Consensus 28 iCP~CG~e~~~~~~ 41 (129)
.||-||..|+.+..
T Consensus 22 ~CPvC~r~l~~e~~ 35 (54)
T pfam04423 22 CCPVCGRPLDEEHE 35 (54)
T ss_pred CCCCCCCCCCHHHH
T ss_conf 77766997667889
No 308
>PRK04173 glycyl-tRNA synthetase; Provisional
Probab=36.45 E-value=15 Score=18.16 Aligned_cols=25 Identities=20% Similarity=0.409 Sum_probs=16.6
Q ss_pred CCCCCCCEEE------EC-----------------CCCCCCCCCCCCE
Q ss_conf 1788887442------14-----------------8887227789871
Q gi|254780459|r 11 TCPDTGKRFY------DL-----------------NKQVIVSPYTQNS 35 (129)
Q Consensus 11 ~C~~Cg~KFY------Dl-----------------nk~PiiCP~CG~e 35 (129)
-|.+||.+|= ++ .+.-|.||.||..
T Consensus 90 ~c~~~~~r~RaD~Lie~~~~~~~~~~~~~~l~~~i~~~~i~cP~cg~~ 137 (460)
T PRK04173 90 ECKKCKKRYRADHLIEEYLGIDAEGLSNEELEELIEENNIKCPECGGE 137 (460)
T ss_pred ECCCCCCEECHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCC
T ss_conf 757678363016776665320123358999999999708879999996
No 309
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=36.32 E-value=19 Score=17.58 Aligned_cols=34 Identities=15% Similarity=0.148 Sum_probs=21.4
Q ss_pred CCCCCCCCCCEE-EECCC-----CCCCCCCCCCEECHHHH
Q ss_conf 831178888744-21488-----87227789871532331
Q gi|254780459|r 8 TKRTCPDTGKRF-YDLNK-----QVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 8 ~KR~C~~Cg~KF-YDlnk-----~PiiCP~CG~e~~~~~~ 41 (129)
+|-.||.|+.=. +=.+. .=-.||.||..|.....
T Consensus 29 ~~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~~~ 68 (129)
T COG3677 29 TKVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVETG 68 (129)
T ss_pred CCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEECC
T ss_conf 6776898885110237774266525356875860011137
No 310
>COG5595 Zn-ribbon-containing, possibly nucleic-acid-binding protein [General function prediction only]
Probab=36.17 E-value=13 Score=18.45 Aligned_cols=12 Identities=25% Similarity=0.589 Sum_probs=7.5
Q ss_pred CCCCCCCCEECH
Q ss_conf 227789871532
Q gi|254780459|r 27 IVSPYTQNSWPL 38 (129)
Q Consensus 27 iiCP~CG~e~~~ 38 (129)
--||+||..|..
T Consensus 219 r~CPsC~k~Wql 230 (256)
T COG5595 219 RCCPSCGKDWQL 230 (256)
T ss_pred CCCCCCCCCCEE
T ss_conf 789755631010
No 311
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=36.11 E-value=22 Score=17.15 Aligned_cols=34 Identities=18% Similarity=0.178 Sum_probs=22.4
Q ss_pred HHCCCCCCCCCCCEEEECCCCCCCCCCCCCEECH
Q ss_conf 2278311788887442148887227789871532
Q gi|254780459|r 5 ELGTKRTCPDTGKRFYDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 5 elG~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~ 38 (129)
-+|.=-.|+.||...--|-.----||.||..|..
T Consensus 236 ~~g~~~~c~~cg~~~~~~~~~~~~c~~Cg~~~~~ 269 (380)
T COG1867 236 NLGYIYHCSRCGEIVGSFREVDEKCPHCGGKVHL 269 (380)
T ss_pred HCCCEEECCCCCCEECCCCCCCCCCCCCCCCCEE
T ss_conf 5470788266410003555444557766652002
No 312
>pfam10605 3HBOH 3HB-oligomer hydrolase (3HBOH). D-(-)-3-hydroxybutyrate oligomer hydrolase (also known as 3HB-oligomer hydrolase) functions in the degradation of poly-3-hydroxybutyrate (PHB). It catalyses the hydrolysis of D(-)-3-hydroxybutyrate oligomers (3HB-oligomers) into 3HB-monomers.
Probab=35.80 E-value=11 Score=18.86 Aligned_cols=22 Identities=41% Similarity=0.552 Sum_probs=13.5
Q ss_pred HHHCCCCCCC------CCCCEEEECCCC
Q ss_conf 2227831178------888744214888
Q gi|254780459|r 4 PELGTKRTCP------DTGKRFYDLNKQ 25 (129)
Q Consensus 4 ~elG~KR~C~------~Cg~KFYDlnk~ 25 (129)
-|||.||-|- -.|.--+||--+
T Consensus 164 GEWGLK~gCAVAYTDKGtG~g~HdL~td 191 (689)
T pfam10605 164 GEWGLKRGCAVAYTDKGTGAGPHDLATD 191 (689)
T ss_pred CHHHCCCCCEEEEECCCCCCCCCCCCCC
T ss_conf 4112124835998348778775414578
No 313
>PRK02244 DNA-directed RNA polymerase subunit P; Provisional
Probab=35.78 E-value=16 Score=18.04 Aligned_cols=12 Identities=17% Similarity=0.279 Sum_probs=9.6
Q ss_pred CCCCCCCCCCEE
Q ss_conf 872277898715
Q gi|254780459|r 25 QVIVSPYTQNSW 36 (129)
Q Consensus 25 ~PiiCP~CG~e~ 36 (129)
.-+-||+||+-+
T Consensus 18 ~gvRCpyCGHRi 29 (44)
T PRK02244 18 GGVRCPYCGHRI 29 (44)
T ss_pred CCCCCCCCCCEE
T ss_conf 667178656388
No 314
>TIGR02865 spore_II_E stage II sporulation protein E; InterPro: IPR014221 This entry contains the stage II sporulation protein E (SpoIIE), which is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation and it has phosphatase activity, located in the C-terminal region, which is required to activate sigma-F. All members of this entry are found in endospore-forming Gram-positive bacteria. A homologous protein, not a member of this entry, is found in the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis..
Probab=35.52 E-value=14 Score=18.37 Aligned_cols=11 Identities=18% Similarity=0.591 Sum_probs=6.8
Q ss_pred CCCCCCCCCCE
Q ss_conf 83117888874
Q gi|254780459|r 8 TKRTCPDTGKR 18 (129)
Q Consensus 8 ~KR~C~~Cg~K 18 (129)
++|+|++|.+|
T Consensus 378 ~~~vCq~C~m~ 388 (794)
T TIGR02865 378 AERVCQSCNMK 388 (794)
T ss_pred CCCCCCCCCCC
T ss_conf 24347864112
No 315
>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=35.38 E-value=24 Score=16.93 Aligned_cols=25 Identities=20% Similarity=0.347 Sum_probs=19.1
Q ss_pred CCCEEEECCC-C---CCCCCCCCCEECHH
Q ss_conf 8874421488-8---72277898715323
Q gi|254780459|r 15 TGKRFYDLNK-Q---VIVSPYTQNSWPLA 39 (129)
Q Consensus 15 Cg~KFYDlnk-~---PiiCP~CG~e~~~~ 39 (129)
=|..+|+++. . =++|=.||..++..
T Consensus 58 ~~~~~y~~~~~~~H~HliC~~Cg~i~~~~ 86 (116)
T cd07153 58 DGKARYELNTDEHHHHLICTKCGKVIDFE 86 (116)
T ss_pred CCEEEEEECCCCCCEEEEECCCCCEEEEC
T ss_conf 98059984499996189999999999955
No 316
>pfam09237 GAGA GAGA factor. Members of this family bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognizes the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognizes the A in the fourth position of the consensus sequence.
Probab=35.37 E-value=5.8 Score=20.68 Aligned_cols=17 Identities=18% Similarity=0.126 Sum_probs=12.7
Q ss_pred ECCCCCCCCCCCCCEEC
Q ss_conf 14888722778987153
Q gi|254780459|r 21 DLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 21 Dlnk~PiiCP~CG~e~~ 37 (129)
-+.-.|.+||-||+.+-
T Consensus 19 s~seqpatcpic~avir 35 (54)
T pfam09237 19 SQSEQPATCPICQAVIR 35 (54)
T ss_pred CCCCCCCCCCHHHHHHH
T ss_conf 21359977704899999
No 317
>PRK05778 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Validated
Probab=35.00 E-value=19 Score=17.47 Aligned_cols=26 Identities=19% Similarity=0.123 Sum_probs=17.8
Q ss_pred CCEEEECCCCC-CCCCCCCCEECHHHH
Q ss_conf 87442148887-227789871532331
Q gi|254780459|r 16 GKRFYDLNKQV-IVSPYTQNSWPLAYF 41 (129)
Q Consensus 16 g~KFYDlnk~P-iiCP~CG~e~~~~~~ 41 (129)
|.+|-+..+-| +-||+||.-.....+
T Consensus 7 ~~~~~~~~~~p~~wCpGCG~~~il~~i 33 (306)
T PRK05778 7 GLTYLRYDGLPTTWCPGCGNFSILNAF 33 (306)
T ss_pred CCEEECCCCCCCCCCCCCCCHHHHHHH
T ss_conf 446661689977658999858999999
No 318
>KOG1597 consensus
Probab=34.90 E-value=23 Score=17.04 Aligned_cols=30 Identities=20% Similarity=0.120 Sum_probs=20.8
Q ss_pred CCCCCCC----EEEECCCCCCCCCCCCCEECHHH
Q ss_conf 1788887----44214888722778987153233
Q gi|254780459|r 11 TCPDTGK----RFYDLNKQVIVSPYTQNSWPLAY 40 (129)
Q Consensus 11 ~C~~Cg~----KFYDlnk~PiiCP~CG~e~~~~~ 40 (129)
+|+.|.. ---|+..--.+|+.||-++.-..
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r~ 35 (308)
T KOG1597 2 TCPDCKRHPENLVEDHSAGDTVCSECGLVLEDRI 35 (308)
T ss_pred CCCCCCCCCCCEEEECCCCCEECCCCCEEECCCC
T ss_conf 8877778998733542688566023772621424
No 319
>pfam09706 Cas_CXXC_CXXC CRISPR-associated protein (Cas_CXXC_CXXC). CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry describes a conserved region of about 65 amino acids from an otherwise highly divergent protein found in a minority of CRISPR-associated protein regions. This region features two motifs of CXXC.
Probab=34.49 E-value=14 Score=18.39 Aligned_cols=18 Identities=11% Similarity=0.270 Sum_probs=11.3
Q ss_pred EEECCCCCCCCCCCCCEE
Q ss_conf 421488872277898715
Q gi|254780459|r 19 FYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 19 FYDlnk~PiiCP~CG~e~ 36 (129)
|+.+|-..-+||-|--.|
T Consensus 44 fwn~~~~~~iCpiC~liy 61 (69)
T pfam09706 44 FWNGKNGADICPICALIY 61 (69)
T ss_pred CCCCCCCCCCCHHHHHHH
T ss_conf 515768974065889888
No 320
>pfam06221 zf-C2HC5 Putative zinc finger motif, C2HC5-type. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4.
Probab=34.42 E-value=12 Score=18.75 Aligned_cols=27 Identities=11% Similarity=0.166 Sum_probs=19.4
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 117888874421488872277898715
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
-.|.+||.-.--+..----|+.||+-+
T Consensus 16 ~NCl~CGrIiC~~eg~~~pC~fCg~~v 42 (54)
T pfam06221 16 PNCLNCGKIICEKEGLEGPCSFCGTPL 42 (54)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf 667654452310037878898778925
No 321
>TIGR00781 ccoO cytochrome c oxidase, cbb3-type, subunit II; InterPro: IPR003468 Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO) . Cytochrome cbb3 oxidases are required both to support symbiotic nitrogen fixation, whilst ensuring that the oxygen-labile nitrogenase is not compromised. Cytochrome cbb3 oxidases consist of four subunits: FixN (or CcoN), FixO (or CcoO), FixP (or CcoP) and FixQ (or CcoQ). The catalytic core is comprised of subunits FixN, FixO and FixP, where FixN acts as the catalytic subunit, and Fix O and FixP are membrane-bound mono- and di-haem cytochromes c, respectively. The FixQ subunit protects the core complex in the presence of oxygen from proteolytic degradation . This entry represents the mono-haem FixO subunit.; GO: 0004129 cytochrome-c oxidase activity, 0006118 electron transport.
Probab=34.26 E-value=14 Score=18.31 Aligned_cols=13 Identities=54% Similarity=0.928 Sum_probs=10.2
Q ss_pred HHCCCCCCCCCCCEEEECCC
Q ss_conf 22783117888874421488
Q gi|254780459|r 5 ELGTKRTCPDTGKRFYDLNK 24 (129)
Q Consensus 5 elG~KR~C~~Cg~KFYDlnk 24 (129)
-||-|||-| ||-|
T Consensus 96 qWGSKRtGP-------DLaR 108 (234)
T TIGR00781 96 QWGSKRTGP-------DLAR 108 (234)
T ss_pred CCCCCCCCC-------CHHH
T ss_conf 688766576-------5010
No 322
>KOG1812 consensus
Probab=34.12 E-value=20 Score=17.33 Aligned_cols=26 Identities=15% Similarity=0.364 Sum_probs=16.5
Q ss_pred CCCCCCCCEEEECCC--CCCCCCCCCCEEC
Q ss_conf 117888874421488--8722778987153
Q gi|254780459|r 10 RTCPDTGKRFYDLNK--QVIVSPYTQNSWP 37 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk--~PiiCP~CG~e~~ 37 (129)
|.||.|+... .|++ ..++|. ||+.|-
T Consensus 307 r~CpkC~~~i-e~~~GCnhm~Cr-C~~~fc 334 (384)
T KOG1812 307 RQCPKCKFMI-ELSEGCNHMTCR-CGHQFC 334 (384)
T ss_pred CCCCCCCEEE-EECCCEEEEEEE-CCCEEE
T ss_conf 7573162243-403770068861-457252
No 323
>TIGR00595 priA primosomal protein N'; InterPro: IPR005259 All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.; GO: 0003677 DNA binding, 0006260 DNA replication.
Probab=33.97 E-value=20 Score=17.38 Aligned_cols=24 Identities=17% Similarity=0.123 Sum_probs=17.0
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 3117888874421488872277898715
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
+-.|.-||.+ ...|.+||.|+...
T Consensus 253 ~l~ch~c~~~----~~~p~~cp~c~~~~ 276 (524)
T TIGR00595 253 KLRCHYCGYQ----EPVPKTCPACGSED 276 (524)
T ss_pred EEEEECCCCC----CCCCCCCCCCCCCC
T ss_conf 0122105766----77754364446643
No 324
>PRK08173 DNA topoisomerase III; Validated
Probab=33.87 E-value=28 Score=16.50 Aligned_cols=27 Identities=15% Similarity=0.250 Sum_probs=19.1
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCEECH
Q ss_conf 1788887442148887227789871532
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e~~~ 38 (129)
.||.||..-+.-.|. .-|-.|+..+..
T Consensus 626 ~CP~Cg~~i~~~~k~-y~C~~C~f~i~k 652 (857)
T PRK08173 626 PCPNCGGVVKENYRR-FACTKCDFSISK 652 (857)
T ss_pred CCCCCCCEEEECCCE-EECCCCCEEEEE
T ss_conf 888889516755618-977999778763
No 325
>PRK00635 excinuclease ABC subunit A; Provisional
Probab=33.75 E-value=26 Score=16.68 Aligned_cols=27 Identities=22% Similarity=0.316 Sum_probs=16.4
Q ss_pred CCCCCCCCCCCEE-------EECCCCCCCCCCCC
Q ss_conf 7831178888744-------21488872277898
Q gi|254780459|r 7 GTKRTCPDTGKRF-------YDLNKQVIVSPYTQ 33 (129)
Q Consensus 7 G~KR~C~~Cg~KF-------YDlnk~PiiCP~CG 33 (129)
-.+..||.||..| |=||-.-=-||.|.
T Consensus 242 s~~~~cp~~~~~~~~l~p~~FSFNsP~GaCp~C~ 275 (1809)
T PRK00635 242 STQVTIPETQQTYTPLTPQLFSPHSLEDRCPQCQ 275 (1809)
T ss_pred EECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 1045689878746888836568899998898998
No 326
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=33.48 E-value=18 Score=17.62 Aligned_cols=24 Identities=8% Similarity=0.252 Sum_probs=17.1
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 311788887442148887227789871
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
-+.|..|. |=++.+-=+||.||..
T Consensus 4 ~kAC~~Ck---~l~~~d~e~CP~Cgs~ 27 (64)
T COG2093 4 EKACKNCK---RLTPEDTEICPVCGST 27 (64)
T ss_pred HHHHHHCC---CCCCCCCCCCCCCCCC
T ss_conf 67876346---2378877408788994
No 327
>cd02037 MRP-like MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter.
Probab=33.09 E-value=22 Score=17.11 Aligned_cols=16 Identities=19% Similarity=0.067 Sum_probs=10.7
Q ss_pred CCCCCCCCCCCCCEEC
Q ss_conf 4888722778987153
Q gi|254780459|r 22 LNKQVIVSPYTQNSWP 37 (129)
Q Consensus 22 lnk~PiiCP~CG~e~~ 37 (129)
.|+.-.+||.||+...
T Consensus 128 eNMs~~~c~~c~~~~~ 143 (169)
T cd02037 128 ENMSYFVCPHCGKKIY 143 (169)
T ss_pred ECCCCCCCCCCCCEEE
T ss_conf 8796660799997352
No 328
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.88 E-value=13 Score=18.48 Aligned_cols=15 Identities=13% Similarity=0.071 Sum_probs=10.8
Q ss_pred CCCCCCCCCCCCEEC
Q ss_conf 888722778987153
Q gi|254780459|r 23 NKQVIVSPYTQNSWP 37 (129)
Q Consensus 23 nk~PiiCP~CG~e~~ 37 (129)
||--=.||.||.++.
T Consensus 38 ~~l~g~CPnCGGelv 52 (84)
T COG3813 38 NRLHGLCPNCGGELV 52 (84)
T ss_pred HHHCCCCCCCCCHHH
T ss_conf 764584889875132
No 329
>PRK10391 oriC-binding nucleoid-associated protein; Provisional
Probab=32.79 E-value=16 Score=18.03 Aligned_cols=18 Identities=28% Similarity=0.392 Sum_probs=13.2
Q ss_pred CCCCCCCCEEEECCCCCC
Q ss_conf 117888874421488872
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVI 27 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~Pi 27 (129)
|.=..+|.|+|||+|-|.
T Consensus 47 rAEL~~g~KLyD~gkVP~ 64 (71)
T PRK10391 47 RAELVSGGRLFDLGQVPK 64 (71)
T ss_pred HHHHHHCCCCCCCCCCCH
T ss_conf 999982466455364889
No 330
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=32.77 E-value=26 Score=16.67 Aligned_cols=26 Identities=12% Similarity=0.247 Sum_probs=19.7
Q ss_pred CCCCCCCC----EE-EECCCCCCCCCCCCCE
Q ss_conf 11788887----44-2148887227789871
Q gi|254780459|r 10 RTCPDTGK----RF-YDLNKQVIVSPYTQNS 35 (129)
Q Consensus 10 R~C~~Cg~----KF-YDlnk~PiiCP~CG~e 35 (129)
..|..||. .| |....--++|+.|+..
T Consensus 151 ~~C~~cg~~~~~~y~fs~~~Gg~~c~~~~~~ 181 (235)
T PRK00085 151 DHCAVCGADPDLTYRFSPKSGGAVCRECRAD 181 (235)
T ss_pred HHHHCCCCCCCCCEEEEECCCCEECCCCCHH
T ss_conf 2341689988864899816797887654676
No 331
>KOG3608 consensus
Probab=32.62 E-value=2.8 Score=22.58 Aligned_cols=34 Identities=18% Similarity=0.430 Sum_probs=22.6
Q ss_pred CCCCCC------CEEEE-------CCCCCCCCCCCCCEECHHHHHCC
Q ss_conf 178888------74421-------48887227789871532331012
Q gi|254780459|r 11 TCPDTG------KRFYD-------LNKQVIVSPYTQNSWPLAYFEAP 44 (129)
Q Consensus 11 ~C~~Cg------~KFYD-------lnk~PiiCP~CG~e~~~~~~~~~ 44 (129)
.||.|| +|||| ||+.|-.|--|..-|..+.+++.
T Consensus 209 ACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~ 255 (467)
T KOG3608 209 ACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKS 255 (467)
T ss_pred ECCHHHHHHCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 66437878624338999987534414772378999988758999999
No 332
>KOG0119 consensus
Probab=32.59 E-value=21 Score=17.23 Aligned_cols=34 Identities=18% Similarity=0.185 Sum_probs=19.9
Q ss_pred CCCCCCCCCE---EEEC----CCCCCCCCCCCCEECHHHHH
Q ss_conf 3117888874---4214----88872277898715323310
Q gi|254780459|r 9 KRTCPDTGKR---FYDL----NKQVIVSPYTQNSWPLAYFE 42 (129)
Q Consensus 9 KR~C~~Cg~K---FYDl----nk~PiiCP~CG~e~~~~~~~ 42 (129)
-|.|.+||.. -|+- +-.-=+|++||.-+....=.
T Consensus 261 ~~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc 301 (554)
T KOG0119 261 NRACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDC 301 (554)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 33465457776511027765444014344257755512347
No 333
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=32.58 E-value=3.1 Score=22.34 Aligned_cols=38 Identities=11% Similarity=0.131 Sum_probs=26.3
Q ss_pred CHHHCC------CCCCCCCCCEEEECCCCC-CCCCCCCCEECHHH
Q ss_conf 522278------311788887442148887-22778987153233
Q gi|254780459|r 3 KPELGT------KRTCPDTGKRFYDLNKQV-IVSPYTQNSWPLAY 40 (129)
Q Consensus 3 K~elG~------KR~C~~Cg~KFYDlnk~P-iiCP~CG~e~~~~~ 40 (129)
+..|+. +-+|++||+-|-.|-+.- .=|-.|=..|....
T Consensus 62 ~t~~~~~~~~~e~l~C~~C~~Tfk~f~~~g~fGCaeCY~tf~~~i 106 (176)
T COG3880 62 KTKWQIEQEDEELLGCHNCGMTFKEFIQSGLFGCAECYKTFESQI 106 (176)
T ss_pred CCCCCHHHHHHHHHCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 310112466799825750135299999834324088899888875
No 334
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=32.39 E-value=22 Score=17.16 Aligned_cols=32 Identities=13% Similarity=0.216 Sum_probs=16.1
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEECHHHH
Q ss_conf 11788887442148887227789871532331
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~ 41 (129)
|.|+.||.+|.-|.=+|.-=|--+..++.+.+
T Consensus 27 ~~c~~cg~~~~~l~LTpPaD~R~~fp~die~I 58 (202)
T COG5270 27 RRCSVCGSKVEELRLTPPADVRPAFPYDIEVI 58 (202)
T ss_pred CCCCCCCCCCEEEEECCCCCCCCCCCHHHHHH
T ss_conf 52456677600788679987462680579999
No 335
>KOG2684 consensus
Probab=32.30 E-value=17 Score=17.75 Aligned_cols=27 Identities=26% Similarity=0.479 Sum_probs=18.4
Q ss_pred CCCCCCCCCEEE------EC-CCCCCCCCCCCCE
Q ss_conf 311788887442------14-8887227789871
Q gi|254780459|r 9 KRTCPDTGKRFY------DL-NKQVIVSPYTQNS 35 (129)
Q Consensus 9 KR~C~~Cg~KFY------Dl-nk~PiiCP~CG~e 35 (129)
+-.|..||-||= ++ |-.-++||.|+..
T Consensus 203 t~sCt~C~~k~~~~~~~~~~~~~~vp~CP~C~~~ 236 (412)
T KOG2684 203 TASCTKCGYKKPFEELREDIRNQEVPVCPDCEGK 236 (412)
T ss_pred EEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCCC
T ss_conf 2433113532674788899862767648433455
No 336
>KOG3576 consensus
Probab=32.27 E-value=5.6 Score=20.78 Aligned_cols=26 Identities=23% Similarity=0.551 Sum_probs=14.6
Q ss_pred CCCCCCCEE---EECCC--------CCCCCCCCCCEE
Q ss_conf 178888744---21488--------872277898715
Q gi|254780459|r 11 TCPDTGKRF---YDLNK--------QVIVSPYTQNSW 36 (129)
Q Consensus 11 ~C~~Cg~KF---YDlnk--------~PiiCP~CG~e~ 36 (129)
.|.-||+-| |||.| .|--|--|+..|
T Consensus 147 lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaf 183 (267)
T KOG3576 147 LCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAF 183 (267)
T ss_pred HHHHCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHH
T ss_conf 9854267653135455541033676651002466778
No 337
>KOG1734 consensus
Probab=31.89 E-value=11 Score=19.06 Aligned_cols=15 Identities=20% Similarity=0.306 Sum_probs=9.1
Q ss_pred CCCCCCCEECHHHHH
Q ss_conf 277898715323310
Q gi|254780459|r 28 VSPYTQNSWPLAYFE 42 (129)
Q Consensus 28 iCP~CG~e~~~~~~~ 42 (129)
+||+|-.-++...+.
T Consensus 272 tCPYCKekVdl~rmf 286 (328)
T KOG1734 272 TCPYCKEKVDLKRMF 286 (328)
T ss_pred CCCHHHHHHHHHHHC
T ss_conf 895288784486640
No 338
>PRK00912 ribonuclease P protein component 3; Provisional
Probab=31.78 E-value=16 Score=17.96 Aligned_cols=12 Identities=42% Similarity=0.808 Sum_probs=9.2
Q ss_pred CCEEEECCCCCC
Q ss_conf 874421488872
Q gi|254780459|r 16 GKRFYDLNKQVI 27 (129)
Q Consensus 16 g~KFYDlnk~Pi 27 (129)
-.||||||=-++
T Consensus 3 ~~~fyDl~vh~~ 14 (237)
T PRK00912 3 KPKFYDLNVHPV 14 (237)
T ss_pred CCCCEECCCCCC
T ss_conf 775144256777
No 339
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=31.48 E-value=16 Score=17.98 Aligned_cols=29 Identities=17% Similarity=0.154 Sum_probs=16.7
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCC-EECHHHH
Q ss_conf 178888744214888722778987-1532331
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQN-SWPLAYF 41 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~-e~~~~~~ 41 (129)
+=.++|.|.+ +=.-|-||.||. +|+...+
T Consensus 254 IL~slglR~~--g~~iISCPtCGRt~~dl~~~ 283 (367)
T PRK00366 254 ILQSLGLRSR--GPNVISCPTCGRTEFDVIQT 283 (367)
T ss_pred HHHHCCCCCC--CCEEEECCCCCCCCCCHHHH
T ss_conf 9997286636--85176588755533629999
No 340
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=31.39 E-value=42 Score=15.44 Aligned_cols=30 Identities=20% Similarity=0.244 Sum_probs=19.2
Q ss_pred CCCCCCCE------EEECCCCCCCC-CCCCCEECHHH
Q ss_conf 17888874------42148887227-78987153233
Q gi|254780459|r 11 TCPDTGKR------FYDLNKQVIVS-PYTQNSWPLAY 40 (129)
Q Consensus 11 ~C~~Cg~K------FYDlnk~PiiC-P~CG~e~~~~~ 40 (129)
+|++||+- =||....-|.+ ..||.+.....
T Consensus 184 iC~~cGkv~~t~v~~~d~~~~~v~y~~~cG~~~~~~~ 220 (513)
T PRK00750 184 ICPKCGKVLQVPVISVDADAGTITYDDECGHEGEVPV 220 (513)
T ss_pred ECCCCCCEEEEEEEEEECCCCEEEEECCCCCEEEECC
T ss_conf 6188895520468999779988999849998787636
No 341
>pfam01428 zf-AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues.
Probab=31.30 E-value=21 Score=17.27 Aligned_cols=20 Identities=10% Similarity=0.169 Sum_probs=14.8
Q ss_pred CCCEEEECCCCCCCCCCCCCEECH
Q ss_conf 887442148887227789871532
Q gi|254780459|r 15 TGKRFYDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 15 Cg~KFYDlnk~PiiCP~CG~e~~~ 38 (129)
|+.+=+ -|++|+.||..|=+
T Consensus 6 C~~~~~----l~~~C~~C~~~fC~ 25 (43)
T pfam01428 6 CKKKDF----LPFKCRFCGGTFCL 25 (43)
T ss_pred CCCCEE----ECCCCHHHCCHHHH
T ss_conf 788442----46371121842457
No 342
>COG1029 FwdB Formylmethanofuran dehydrogenase subunit B [Energy production and conversion]
Probab=31.02 E-value=17 Score=17.75 Aligned_cols=12 Identities=17% Similarity=0.404 Sum_probs=8.0
Q ss_pred CCCCCCCCCCEE
Q ss_conf 872277898715
Q gi|254780459|r 25 QVIVSPYTQNSW 36 (129)
Q Consensus 25 ~PiiCP~CG~e~ 36 (129)
.-+|||.||+--
T Consensus 4 k~~vCp~CG~lC 15 (429)
T COG1029 4 KNVVCPFCGTLC 15 (429)
T ss_pred EEEECCCCCCCC
T ss_conf 247767655410
No 343
>pfam06827 zf-FPG_IleRS Zinc finger found in FPG and IleRS. This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:3.2.2.23.
Probab=30.99 E-value=26 Score=16.69 Aligned_cols=24 Identities=17% Similarity=0.378 Sum_probs=18.4
Q ss_pred CCCCCCCEEEECCC---CCCCCCCCCC
Q ss_conf 17888874421488---8722778987
Q gi|254780459|r 11 TCPDTGKRFYDLNK---QVIVSPYTQN 34 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk---~PiiCP~CG~ 34 (129)
-|+-|++.+=++.. .+-+||-|..
T Consensus 3 kC~RCw~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T pfam06827 3 KCPRCWTYIEKVGQGGRSTFLCPRCQK 29 (30)
T ss_pred CCCCCCCEEEEEEECCCCCCCCCCCCC
T ss_conf 277479971576855888811805324
No 344
>TIGR03031 cas_csx12 CRISPR-associated protein, Csx12 family. Members of this family of CRISPR-associated (cas) protein are found, so far, in CRISPR/cas loci in Wolinella succinogenes DSM 1740, Legionella pneumophila str. Paris, and Francisella tularensis, where the last probably is an example of a degenerate CRISPR locus, having neither repeats nor a functional Cas1. The characteristic repeat length is 37 base pairs and period is about 72. One region of this large protein shows sequence similarity to pfam01844, HNH endonuclease.
Probab=30.96 E-value=18 Score=17.63 Aligned_cols=10 Identities=30% Similarity=0.444 Sum_probs=6.0
Q ss_pred CCCCCCCCEE
Q ss_conf 2277898715
Q gi|254780459|r 27 IVSPYTQNSW 36 (129)
Q Consensus 27 iiCP~CG~e~ 36 (129)
=||||||+.+
T Consensus 761 gIcpY~Ga~i 770 (802)
T TIGR03031 761 GICPYKGASI 770 (802)
T ss_pred CCCCCCCCCC
T ss_conf 6787879987
No 345
>pfam01753 zf-MYND MYND finger.
Probab=30.74 E-value=35 Score=15.94 Aligned_cols=21 Identities=14% Similarity=0.444 Sum_probs=13.2
Q ss_pred CCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 7888874421488872277898715
Q gi|254780459|r 12 CPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 12 C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
|..||.+ ...++.|+.|+..+
T Consensus 1 C~~C~~~----~~~~~~C~~C~~~~ 21 (39)
T pfam01753 1 CANCGKE----ALKLLRCSRCKAVY 21 (39)
T ss_pred CCCCCCC----CCCCCCCCCCCCEE
T ss_conf 9988997----87668087999980
No 346
>pfam08421 Methyltransf_13 Hypothetical methyltransferase. This domain is found at the N-terminus of bacterial methyltransferases.
Probab=30.72 E-value=28 Score=16.46 Aligned_cols=17 Identities=29% Similarity=0.436 Sum_probs=10.5
Q ss_pred CCCCC----CEEEECCCCCCC
Q ss_conf 78888----744214888722
Q gi|254780459|r 12 CPDTG----KRFYDLNKQVIV 28 (129)
Q Consensus 12 C~~Cg----~KFYDlnk~Pii 28 (129)
|..|| .+|.+|++.|+.
T Consensus 1 CriC~s~~l~~~l~lG~~Pl~ 21 (78)
T pfam08421 1 CRLCGSTDLLPVLDLGAQPLC 21 (78)
T ss_pred CCCCCCCCCEEEEECCCCCCC
T ss_conf 978879875188877888623
No 347
>pfam04551 GcpE GcpE protein. In a variety of organisms, including plants and several eubacteria, isoprenoids are synthesized by the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Although different enzymes of this pathway have been described, the terminal biosynthetic steps of the MEP pathway have not been fully elucidated. GcpE gene of Escherichia coli is involved in this pathway.
Probab=30.71 E-value=17 Score=17.81 Aligned_cols=27 Identities=19% Similarity=0.197 Sum_probs=15.5
Q ss_pred CCCCCEEEECCCCCCCCCCCCC-EECHHHH
Q ss_conf 8888744214888722778987-1532331
Q gi|254780459|r 13 PDTGKRFYDLNKQVIVSPYTQN-SWPLAYF 41 (129)
Q Consensus 13 ~~Cg~KFYDlnk~PiiCP~CG~-e~~~~~~ 41 (129)
+++|.|. +.=.-|-||.||. +|+...+
T Consensus 245 ~sl~lR~--~g~~iISCPtCGR~~~dl~~~ 272 (345)
T pfam04551 245 QSLGLRK--RGVEIISCPTCGRTLFDLIKV 272 (345)
T ss_pred HHCCCCC--CCCEEEECCCCCCCCCCHHHH
T ss_conf 9728775--786487588746611559999
No 348
>pfam04035 consensus
Probab=30.65 E-value=21 Score=17.27 Aligned_cols=22 Identities=9% Similarity=0.241 Sum_probs=14.3
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 11788887442148887227789871
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
+.|..|..-+-+ +-+||.||..
T Consensus 2 kAC~~C~~i~~~----~~~Cp~Cgs~ 23 (60)
T pfam04035 2 KACKNCKRLTEE----DTTCPVCGSE 23 (60)
T ss_pred CCHHHCCCCCCC----CCCCCCCCCC
T ss_conf 144239727899----9818898398
No 349
>pfam08772 NOB1_Zn_bind Nin one binding (NOB1) Zn-ribbon like. This domain corresponds to a zinc ribbon and is found on the RNA binding protein NOB1.
Probab=30.39 E-value=21 Score=17.29 Aligned_cols=23 Identities=26% Similarity=0.296 Sum_probs=16.4
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 1788887442148887227789871
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
.|..|-+-..|+.| .-||+||.-
T Consensus 11 rC~aCf~~t~~~~k--~FCpkCGn~ 33 (73)
T pfam08772 11 RCHACFKTTPDMTK--QFCPKCGNA 33 (73)
T ss_pred EEEECCCCCCCCCC--CCCCCCCCC
T ss_conf 54232348489766--127536999
No 350
>pfam10058 DUF2296 Predicted integral membrane metal-binding protein (DUF2296). This domain, found in various hypothetical bacterial and eukaryotic metal-binding proteins, has no known function.
Probab=30.25 E-value=15 Score=18.21 Aligned_cols=14 Identities=7% Similarity=0.169 Sum_probs=9.9
Q ss_pred CCCCCCCCCCCCEE
Q ss_conf 88872277898715
Q gi|254780459|r 23 NKQVIVSPYTQNSW 36 (129)
Q Consensus 23 nk~PiiCP~CG~e~ 36 (129)
||.++||++|....
T Consensus 16 ~r~aLIC~~C~~hN 29 (51)
T pfam10058 16 NRYALICSKCHSHN 29 (51)
T ss_pred CCEEEECHHHHHHC
T ss_conf 85214852345328
No 351
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=30.13 E-value=27 Score=16.57 Aligned_cols=13 Identities=0% Similarity=-0.207 Sum_probs=8.0
Q ss_pred CCCCCCCCCCEEC
Q ss_conf 8722778987153
Q gi|254780459|r 25 QVIVSPYTQNSWP 37 (129)
Q Consensus 25 ~PiiCP~CG~e~~ 37 (129)
.-++|..||.++.
T Consensus 70 ~g~~C~tCG~~~~ 82 (1284)
T PRK00566 70 RGKICERCGVEIT 82 (1284)
T ss_pred CCCCCCCCCCCCC
T ss_conf 9858999998745
No 352
>KOG1859 consensus
Probab=30.10 E-value=29 Score=16.44 Aligned_cols=24 Identities=21% Similarity=0.325 Sum_probs=16.9
Q ss_pred CCCCCCCEEEE----------------CCC--CCCCCCCCCC
Q ss_conf 17888874421----------------488--8722778987
Q gi|254780459|r 11 TCPDTGKRFYD----------------LNK--QVIVSPYTQN 34 (129)
Q Consensus 11 ~C~~Cg~KFYD----------------lnk--~PiiCP~CG~ 34 (129)
.|.+||+.|-. +-| +|-+||.||.
T Consensus 675 ~C~~cgt~F~~eqp~kg~~~kelr~pd~~k~~t~~v~~~~~s 716 (1096)
T KOG1859 675 RCVNCGTQFLIEQPEKGSKIKELRCPDSRKVYTTNVTSGLHS 716 (1096)
T ss_pred EECCCCCCCCCCCCCCCCCHHHHCCCCHHHCCCCCCCCCCCC
T ss_conf 311465503434755464313314753110013444665456
No 353
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=30.00 E-value=31 Score=16.24 Aligned_cols=34 Identities=12% Similarity=0.072 Sum_probs=17.3
Q ss_pred CCCCCCCEEEECCCCCCCCCCCC-------------CEECHHHHHCCC
Q ss_conf 17888874421488872277898-------------715323310123
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQ-------------NSWPLAYFEAPT 45 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG-------------~e~~~~~~~~~~ 45 (129)
-|++|++=|+| ..--=+||+|| ..+.|..+..++
T Consensus 128 Yc~~~e~fl~d-r~v~g~cp~cg~~~a~GD~Ce~Cg~~~~P~~l~~p~ 174 (558)
T COG0143 128 YCVSCERFLPD-RYVEGTCPKCGGEDARGDQCENCGRTLDPTELINPV 174 (558)
T ss_pred ECCCCCCCCCC-HHEECCCCCCCCCCCCCCHHHHCCCCCCCHHCCCCE
T ss_conf 73543564562-102055898675345764343226757921217981
No 354
>KOG3053 consensus
Probab=29.97 E-value=14 Score=18.30 Aligned_cols=38 Identities=21% Similarity=0.246 Sum_probs=24.0
Q ss_pred CCCCCCCCCCEEEE----CCC-CCCCCCCCCCEECHHHHHCCC
Q ss_conf 83117888874421----488-872277898715323310123
Q gi|254780459|r 8 TKRTCPDTGKRFYD----LNK-QVIVSPYTQNSWPLAYFEAPT 45 (129)
Q Consensus 8 ~KR~C~~Cg~KFYD----lnk-~PiiCP~CG~e~~~~~~~~~~ 45 (129)
+|-+-++|=.+..| .|. .++.||-|.|||.........
T Consensus 48 ~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~l~~ 90 (293)
T KOG3053 48 TKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQLGP 90 (293)
T ss_pred CHHHHHHHHHHHHHHHHCCCCCCEEECHHHCCHHEEECCCCCH
T ss_conf 2789999999987387528987636640011202032366573
No 355
>pfam04959 ARS2 Arsenite-resistance protein 2. Arsenite is a carcinogenic compound which can act as a co-mutagen by inhibiting DNA repair. Arsenite-resistance protein 2 is thought to play a role in arsenite resistance.
Probab=29.95 E-value=19 Score=17.47 Aligned_cols=11 Identities=55% Similarity=1.102 Sum_probs=6.0
Q ss_pred CCCCCCCCCEE
Q ss_conf 31178888744
Q gi|254780459|r 9 KRTCPDTGKRF 19 (129)
Q Consensus 9 KR~C~~Cg~KF 19 (129)
|-.||-||+||
T Consensus 77 KWLCPLSGKKF 87 (211)
T pfam04959 77 KWLCPLSGKKF 87 (211)
T ss_pred CEECCCCCCCC
T ss_conf 45246767755
No 356
>COG1013 PorB Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit [Energy production and conversion]
Probab=29.89 E-value=19 Score=17.59 Aligned_cols=19 Identities=11% Similarity=-0.067 Sum_probs=12.9
Q ss_pred CCCCCCCCCCEECHHHHHC
Q ss_conf 8722778987153233101
Q gi|254780459|r 25 QVIVSPYTQNSWPLAYFEA 43 (129)
Q Consensus 25 ~PiiCP~CG~e~~~~~~~~ 43 (129)
-+.-||+||.-.....+.+
T Consensus 14 ~~~~CpGCG~~~~l~~i~~ 32 (294)
T COG1013 14 PTRWCPGCGEFIILKLLTQ 32 (294)
T ss_pred CCCCCCCCCCHHHHHHHHH
T ss_conf 8763889983499999998
No 357
>pfam12523 DUF3725 Protein of unknown function (DUF3725). This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with pfam01577. There is a conserved FLE sequence motif.
Probab=29.61 E-value=15 Score=18.12 Aligned_cols=22 Identities=18% Similarity=0.297 Sum_probs=20.0
Q ss_pred CCCCEEEECCCCCCCCCCCCCE
Q ss_conf 8887442148887227789871
Q gi|254780459|r 14 DTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 14 ~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
.||.-+|||+-.--.|-+||..
T Consensus 47 mvg~LgYdf~~Elw~Ch~C~nt 68 (74)
T pfam12523 47 MVGRLGYDFESELWFCHNCDNT 68 (74)
T ss_pred HHHHCCCCCCCCEEEEECCCCC
T ss_conf 8755067765325888326643
No 358
>PRK00595 rpmG 50S ribosomal protein L33; Validated
Probab=29.53 E-value=30 Score=16.31 Aligned_cols=28 Identities=21% Similarity=0.277 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCEEEECCCCCCC----------CCCCCC
Q ss_conf 7831178888744214888722----------778987
Q gi|254780459|r 7 GTKRTCPDTGKRFYDLNKQVIV----------SPYTQN 34 (129)
Q Consensus 7 G~KR~C~~Cg~KFYDlnk~Pii----------CP~CG~ 34 (129)
.++-.|..|+.+||=-.|.+-. ||.|..
T Consensus 8 ~I~L~ct~~~~~~Y~T~KNkrn~perlelkKycp~~rk 45 (53)
T PRK00595 8 KIKLESTEGTGRFYTTTKNKRNTPEKLELKKYDPVLRK 45 (53)
T ss_pred EEEEEEECCCCEEEEECCCCCCCCCEEEEECCCCCCCC
T ss_conf 89999807887788872657889520689822877740
No 359
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=29.39 E-value=4.3 Score=21.50 Aligned_cols=24 Identities=17% Similarity=0.275 Sum_probs=14.7
Q ss_pred CCCCCCCCEEEECCCCCCCCC--CCCCE
Q ss_conf 117888874421488872277--89871
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSP--YTQNS 35 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP--~CG~e 35 (129)
|.|-||--|. |.+-|+-|| +||+.
T Consensus 37 rmCESCvdRI--Fs~GpAqCP~~gC~kI 62 (314)
T COG5220 37 RMCESCVDRI--FSRGPAQCPYKGCGKI 62 (314)
T ss_pred HHHHHHHHHH--HCCCCCCCCCCCHHHH
T ss_conf 9999999998--6279888998437899
No 360
>pfam09855 DUF2082 Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082). This domain, found in various hypothetical prokaryotic proteins, as well as some Zn-ribbon nucleic-acid-binding proteins has no known function.
Probab=28.90 E-value=21 Score=17.24 Aligned_cols=26 Identities=27% Similarity=0.696 Sum_probs=18.0
Q ss_pred CCCCCCC----------------EEEEC-CCC--CCCCCCCCC-EE
Q ss_conf 1788887----------------44214-888--722778987-15
Q gi|254780459|r 11 TCPDTGK----------------RFYDL-NKQ--VIVSPYTQN-SW 36 (129)
Q Consensus 11 ~C~~Cg~----------------KFYDl-nk~--PiiCP~CG~-e~ 36 (129)
+||.||- ||+|. ||. -|.|-.||- ||
T Consensus 2 ~C~KCg~~~~e~~ei~~TG~~~Sk~fdvQn~kF~~vtC~~CgYTEf 47 (64)
T pfam09855 2 GCPKCGNTEYEVGQIRTTGGGLSKIFDVQNKKFTVVTCKRCGYTEF 47 (64)
T ss_pred CCCCCCCCCEEEEEEEECCCCHHHHEEECCCEEEEEEECCCCCEEE
T ss_conf 1687799312302688507566783510575799999167787777
No 361
>PRK07220 DNA topoisomerase I; Validated
Probab=28.75 E-value=49 Score=15.00 Aligned_cols=11 Identities=9% Similarity=-0.260 Sum_probs=5.2
Q ss_pred CCCCCCCCCCE
Q ss_conf 87227789871
Q gi|254780459|r 25 QVIVSPYTQNS 35 (129)
Q Consensus 25 ~PiiCP~CG~e 35 (129)
+..+||.||..
T Consensus 634 ~~~~C~~~~~~ 644 (740)
T PRK07220 634 TDKVCEAHGLH 644 (740)
T ss_pred CCCCCCCCCCE
T ss_conf 78868779983
No 362
>KOG2906 consensus
Probab=28.75 E-value=33 Score=16.02 Aligned_cols=40 Identities=13% Similarity=0.140 Sum_probs=24.5
Q ss_pred CCCCCCCEEE---ECCCCCCCCCCCCCEECHHHHHCCCCCCCC
Q ss_conf 1788887442---148887227789871532331012344344
Q gi|254780459|r 11 TCPDTGKRFY---DLNKQVIVSPYTQNSWPLAYFEAPTSPEKE 50 (129)
Q Consensus 11 ~C~~Cg~KFY---Dlnk~PiiCP~CG~e~~~~~~~~~~~~~~~ 50 (129)
.||+||--.- +=+..-.-|+.|+-.|++.....++...+.
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~~ei~~r~~~~~ 45 (105)
T KOG2906 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFPISREISSRKYPKL 45 (105)
T ss_pred CCCCCCCEEEEECCCEEEEEECCCCCCEEEEEEEEECCCCCCC
T ss_conf 4688788899942874767773789734014565430346660
No 363
>COG5017 Uncharacterized conserved protein [Function unknown]
Probab=28.66 E-value=11 Score=18.91 Aligned_cols=12 Identities=33% Similarity=0.764 Sum_probs=8.2
Q ss_pred CCCCEEEECCCC
Q ss_conf 888744214888
Q gi|254780459|r 14 DTGKRFYDLNKQ 25 (129)
Q Consensus 14 ~Cg~KFYDlnk~ 25 (129)
+||+-||+|||-
T Consensus 5 TvGstf~~f~rl 16 (161)
T COG5017 5 TVGSTFYPFNRL 16 (161)
T ss_pred EECCCCCHHHHH
T ss_conf 945755528889
No 364
>KOG2071 consensus
Probab=28.56 E-value=20 Score=17.45 Aligned_cols=12 Identities=42% Similarity=0.814 Sum_probs=7.8
Q ss_pred CCCCCCCCEEEE
Q ss_conf 117888874421
Q gi|254780459|r 10 RTCPDTGKRFYD 21 (129)
Q Consensus 10 R~C~~Cg~KFYD 21 (129)
+.|-+||.||=+
T Consensus 419 nqC~~CG~R~~~ 430 (579)
T KOG2071 419 NQCKSCGLRFDD 430 (579)
T ss_pred CHHCCCCCCCCC
T ss_conf 210266532366
No 365
>pfam11709 Mit_ribos_Mrp51 Mitochondrial ribosomal protein subunit. This family is the mitochondrial ribosomal small-subunit protein Mrp51. Its function is not entirely clear, but deletion of the MRP51 gene completely blocked mitochondrial gene expression.
Probab=28.51 E-value=29 Score=16.41 Aligned_cols=17 Identities=29% Similarity=0.565 Sum_probs=12.6
Q ss_pred CCCHHHCCCCCCCCCCC
Q ss_conf 97522278311788887
Q gi|254780459|r 1 MAKPELGTKRTCPDTGK 17 (129)
Q Consensus 1 MaK~elG~KR~C~~Cg~ 17 (129)
+++-+||.||.=|+=.+
T Consensus 46 ~~R~dWGLKr~lP~k~~ 62 (302)
T pfam11709 46 LARGDWGLKRPLPSKST 62 (302)
T ss_pred HHCCCCCCCCCCCCCCC
T ss_conf 43155555665765578
No 366
>TIGR01054 rgy reverse gyrase; InterPro: IPR005736 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. Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage . 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, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=28.47 E-value=25 Score=16.83 Aligned_cols=27 Identities=22% Similarity=0.332 Sum_probs=18.6
Q ss_pred CCCCCCCEEEECCC----CCCCCCCCCCEEC
Q ss_conf 17888874421488----8722778987153
Q gi|254780459|r 11 TCPDTGKRFYDLNK----QVIVSPYTQNSWP 37 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk----~PiiCP~CG~e~~ 37 (129)
.|..||..|=|=.- --=.||+||.+-.
T Consensus 756 rC~dcG~QfTd~~~leeli~e~cpkcgs~~~ 786 (1843)
T TIGR01054 756 RCRDCGEQFTDEEDLEELIKELCPKCGSENI 786 (1843)
T ss_pred EECCCCCCCCCHHHHHHHHHHHHCCCCCCCC
T ss_conf 1335887436715589999986025787555
No 367
>KOG4537 consensus
Probab=28.45 E-value=9.7 Score=19.31 Aligned_cols=27 Identities=15% Similarity=0.203 Sum_probs=23.1
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 117888874421488872277898715
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
-+||.||+-..-..-.|+-|-.|....
T Consensus 41 e~Cp~C~~Ilm~dr~~~~~CVsC~~~~ 67 (178)
T KOG4537 41 EICPKCEKILMRDRDNPMFCVSCINDL 67 (178)
T ss_pred HHCCHHHHHHHHHCCCCEEEEEEECCC
T ss_conf 224208778876145754777510013
No 368
>KOG2989 consensus
Probab=28.43 E-value=17 Score=17.84 Aligned_cols=14 Identities=7% Similarity=-0.050 Sum_probs=10.9
Q ss_pred CCCCCCCCCCCEEC
Q ss_conf 88722778987153
Q gi|254780459|r 24 KQVIVSPYTQNSWP 37 (129)
Q Consensus 24 k~PiiCP~CG~e~~ 37 (129)
|.-|.||.|+++..
T Consensus 75 Rf~i~Ct~cl~el~ 88 (253)
T KOG2989 75 RFYIKCTRCLRELS 88 (253)
T ss_pred EEEEECCCHHHHHH
T ss_conf 65221340576663
No 369
>TIGR02026 BchE magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase; InterPro: IPR011772 This entry respresents the cobalamin-dependent oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under anaerobic conditions . This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under anaerobic conditions (a separate enzyme, AcsF, acts under aerobic conditions). This entry identifies two clades of sequences, one from photosynthetic, non-cyanobacterial bacteria and another including Synechocystis and several non-photosynthetic bacteria. The function of the Synechocystis gene is supported by gene clustering with other photosynthetic genes, so the purpose of the gene in the non-photosynthetic bacteria is uncertain. Note that homologues of this gene are not found in plants which rely solely on the aerobic cyclase.; GO: 0016709 oxidoreductase activity acting on paired donors with incorporation or reduction of molecular oxygen NADH or NADPH as one donor and incorporation of one atom of oxygen, 0050661 NADP binding, 0015995 chlorophyll biosynthetic process.
Probab=28.12 E-value=31 Score=16.23 Aligned_cols=25 Identities=32% Similarity=0.717 Sum_probs=20.4
Q ss_pred CCCCEEEECCCCCCCCCCCCCEECH
Q ss_conf 8887442148887227789871532
Q gi|254780459|r 14 DTGKRFYDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 14 ~Cg~KFYDlnk~PiiCP~CG~e~~~ 38 (129)
.-|.+||||+|.-+.-|.....++.
T Consensus 466 ~V~R~FydlGr~~~~gPq~~~~idf 490 (506)
T TIGR02026 466 TVTRRFYDLGRRVLVGPQSKEKIDF 490 (506)
T ss_pred CCCEEEEECCCEEEECCCCCCEEEE
T ss_conf 7731565527325526874000320
No 370
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit; InterPro: IPR011883 Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation , . Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA . .
Probab=28.12 E-value=27 Score=16.60 Aligned_cols=19 Identities=11% Similarity=0.078 Sum_probs=14.0
Q ss_pred EEEECCCCCCCCCCCCCEE
Q ss_conf 4421488872277898715
Q gi|254780459|r 18 RFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 18 KFYDlnk~PiiCP~CG~e~ 36 (129)
.---|-+..+-||+||...
T Consensus 103 ~~l~~~~~~v~CPRCgS~~ 121 (152)
T TIGR02159 103 LVLSLEPPSVQCPRCGSAD 121 (152)
T ss_pred EECCCCCCCCCCCCCCCCC
T ss_conf 0012468777888877521
No 371
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=27.70 E-value=37 Score=15.78 Aligned_cols=28 Identities=21% Similarity=0.373 Sum_probs=18.7
Q ss_pred CCCCCCCCE---EE----------EC---------CCCCCCCCCCCCEEC
Q ss_conf 117888874---42----------14---------888722778987153
Q gi|254780459|r 10 RTCPDTGKR---FY----------DL---------NKQVIVSPYTQNSWP 37 (129)
Q Consensus 10 R~C~~Cg~K---FY----------Dl---------nk~PiiCP~CG~e~~ 37 (129)
..||.||.| .+ .+ ++.=..|..||..|.
T Consensus 39 ~~CP~Cg~~~~~~~~~~~~~I~~L~~~~~~~~L~~r~rR~~c~~c~~~~~ 88 (402)
T COG3464 39 HRCPECGQRTIRRHGWRIRKIQDLPLFEVPVYLFLRKRRYKCCRCGKRFA 88 (402)
T ss_pred CCCCCCCCCCEECCCCCCCEEEECCCCCEEEEEEECCCEEEEEECCCCCC
T ss_conf 89999986402213454202121155771688750244266420588654
No 372
>pfam04997 RNA_pol_Rpb1_1 RNA polymerase Rpb1, domain 1. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.
Probab=27.63 E-value=30 Score=16.33 Aligned_cols=12 Identities=25% Similarity=0.457 Sum_probs=7.5
Q ss_pred CCCCCCCCCEEE
Q ss_conf 311788887442
Q gi|254780459|r 9 KRTCPDTGKRFY 20 (129)
Q Consensus 9 KR~C~~Cg~KFY 20 (129)
+.+|++||..+.
T Consensus 54 ~~~C~TCg~~~~ 65 (330)
T pfam04997 54 KSICETCGVEVT 65 (330)
T ss_pred CCCCCCCCCCCC
T ss_conf 986889999877
No 373
>PRK11295 hypothetical protein; Provisional
Probab=27.26 E-value=15 Score=18.20 Aligned_cols=22 Identities=9% Similarity=0.027 Sum_probs=16.5
Q ss_pred CCCCCCCCCCCCCEECHHHHHC
Q ss_conf 4888722778987153233101
Q gi|254780459|r 22 LNKQVIVSPYTQNSWPLAYFEA 43 (129)
Q Consensus 22 lnk~PiiCP~CG~e~~~~~~~~ 43 (129)
|.-.|-||-.||.+|.-..+..
T Consensus 20 lk~~pwvcgrc~ref~~~nl~e 41 (115)
T PRK11295 20 LKLYPWVCGRCSREFVYSNLRE 41 (115)
T ss_pred HHHCCHHHHHHHHHHCCCCHHH
T ss_conf 7634324413320312012245
No 374
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=27.15 E-value=30 Score=16.32 Aligned_cols=28 Identities=7% Similarity=0.042 Sum_probs=18.2
Q ss_pred CCCCCCCCCEE-E--------ECCCCCCCCCCCCCEE
Q ss_conf 31178888744-2--------1488872277898715
Q gi|254780459|r 9 KRTCPDTGKRF-Y--------DLNKQVIVSPYTQNSW 36 (129)
Q Consensus 9 KR~C~~Cg~KF-Y--------Dlnk~PiiCP~CG~e~ 36 (129)
-++|..|.+-. . .=++--++|..||+..
T Consensus 56 R~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~ 92 (105)
T COG2023 56 RTICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIR 92 (105)
T ss_pred HHHCCCCCCCCCCCCCEEEEECCCEEEEEECCCCCEE
T ss_conf 7762053764436863599970775899944788688
No 375
>COG2993 CcoO Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]
Probab=27.12 E-value=22 Score=17.13 Aligned_cols=17 Identities=53% Similarity=0.851 Sum_probs=11.6
Q ss_pred HHCCCCCCCC---CCCEEEE
Q ss_conf 2278311788---8874421
Q gi|254780459|r 5 ELGTKRTCPD---TGKRFYD 21 (129)
Q Consensus 5 elG~KR~C~~---Cg~KFYD 21 (129)
-||.||+-|- -|.||-|
T Consensus 98 lWGSKRTGPDLaRVG~ryS~ 117 (227)
T COG2993 98 LWGSKRTGPDLARVGGRYSD 117 (227)
T ss_pred HHCCCCCCCCHHHHCCCCCC
T ss_conf 20477668316663564362
No 376
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=26.78 E-value=16 Score=18.05 Aligned_cols=11 Identities=9% Similarity=0.145 Sum_probs=8.1
Q ss_pred CCCCCCCCEEC
Q ss_conf 22778987153
Q gi|254780459|r 27 IVSPYTQNSWP 37 (129)
Q Consensus 27 iiCP~CG~e~~ 37 (129)
.-||-||..|-
T Consensus 18 lrCPRC~~~FR 28 (65)
T COG4049 18 LRCPRCGMVFR 28 (65)
T ss_pred EECCCHHHHHH
T ss_conf 50775017887
No 377
>KOG3352 consensus
Probab=26.64 E-value=38 Score=15.72 Aligned_cols=25 Identities=16% Similarity=0.106 Sum_probs=16.4
Q ss_pred CCCEEEECCCC-CCCCCCCCCEECHH
Q ss_conf 88744214888-72277898715323
Q gi|254780459|r 15 TGKRFYDLNKQ-VIVSPYTQNSWPLA 39 (129)
Q Consensus 15 Cg~KFYDlnk~-PiiCP~CG~e~~~~ 39 (129)
+-..|+=|-|. +--||.||+-|.+.
T Consensus 121 ~~V~Wmwl~Kge~~rc~eCG~~fkL~ 146 (153)
T KOG3352 121 HAVVWMWLEKGETQRCPECGHYFKLV 146 (153)
T ss_pred CCEEEEEEECCCCCCCCCCCCEEEEE
T ss_conf 63489988768745587665668854
No 378
>TIGR02986 restrict_Alw26I type II restriction endonuclease, Alw26I/Eco31I/Esp3I family; InterPro: IPR014328 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 . 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. This entry represents type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family , whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I)..
Probab=26.54 E-value=26 Score=16.72 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=4.8
Q ss_pred CCCCCCCCEEE
Q ss_conf 11788887442
Q gi|254780459|r 10 RTCPDTGKRFY 20 (129)
Q Consensus 10 R~C~~Cg~KFY 20 (129)
|.|..||..|+
T Consensus 86 kpC~~CG~~m~ 96 (461)
T TIGR02986 86 KPCKKCGKEMS 96 (461)
T ss_pred CCHHHCCCEEE
T ss_conf 62102684466
No 379
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.11 E-value=20 Score=17.38 Aligned_cols=31 Identities=19% Similarity=0.399 Sum_probs=21.6
Q ss_pred CCCCCCCCCCE----EE-----ECC---CCCCCCCCCCCEECH
Q ss_conf 83117888874----42-----148---887227789871532
Q gi|254780459|r 8 TKRTCPDTGKR----FY-----DLN---KQVIVSPYTQNSWPL 38 (129)
Q Consensus 8 ~KR~C~~Cg~K----FY-----Dln---k~PiiCP~CG~e~~~ 38 (129)
|--.||.|.+- || -|+ +-|--|-+||.-|+-
T Consensus 38 ti~qcp~csasirgd~~vegvlglg~dye~psfchncgs~fpw 80 (160)
T COG4306 38 TITQCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPW 80 (160)
T ss_pred HHHCCCCCCCCCCCCCEEEEEECCCCCCCCCCHHHCCCCCCCC
T ss_conf 8853875677545640012221158787894065417998870
No 380
>TIGR00411 redox_disulf_1 redox-active disulfide protein 1; InterPro: IPR004502 This group of proteins includes thioredoxins, glutaredoxins, protein-disulphide isomerases, and others, some of which have several such domains. The sequence of proteins in this group at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although overall the sequence seems closer to thioredoxins. Proteins may be involved in a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis.
Probab=26.07 E-value=25 Score=16.74 Aligned_cols=11 Identities=18% Similarity=0.398 Sum_probs=7.8
Q ss_pred CCCCCCCCCCE
Q ss_conf 87227789871
Q gi|254780459|r 25 QVIVSPYTQNS 35 (129)
Q Consensus 25 ~PiiCP~CG~e 35 (129)
+-.+||||=.-
T Consensus 7 TSPtCPyCP~A 17 (82)
T TIGR00411 7 TSPTCPYCPKA 17 (82)
T ss_pred CCCCCCCCCCH
T ss_conf 18876888543
No 381
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=25.97 E-value=42 Score=15.43 Aligned_cols=36 Identities=14% Similarity=0.189 Sum_probs=24.7
Q ss_pred CCCCCCCCCCCEE-------EECCCCCCCCCCCC-----CEECHHHHH
Q ss_conf 7831178888744-------21488872277898-----715323310
Q gi|254780459|r 7 GTKRTCPDTGKRF-------YDLNKQVIVSPYTQ-----NSWPLAYFE 42 (129)
Q Consensus 7 G~KR~C~~Cg~KF-------YDlnk~PiiCP~CG-----~e~~~~~~~ 42 (129)
-.+..||.||..| |=||..-=-||.|- .+|++..+.
T Consensus 243 S~~~acp~~g~~~~eleprlFSFNsP~GaCp~C~GlG~~~~~D~~~vi 290 (935)
T COG0178 243 SENFACPVCGFSIPELEPRLFSFNSPFGACPTCDGLGVKLEVDPDLVI 290 (935)
T ss_pred ECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECHHHCC
T ss_conf 104678866722477775520579999879767876504651765507
No 382
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=25.94 E-value=34 Score=16.01 Aligned_cols=19 Identities=11% Similarity=0.177 Sum_probs=15.1
Q ss_pred EEECCC-CCCCCCCCCCEEC
Q ss_conf 421488-8722778987153
Q gi|254780459|r 19 FYDLNK-QVIVSPYTQNSWP 37 (129)
Q Consensus 19 FYDlnk-~PiiCP~CG~e~~ 37 (129)
||=.++ +-+.|.+||.++.
T Consensus 26 Fyytg~~D~v~C~~C~~~l~ 45 (69)
T cd00022 26 FYYTGRGDEVKCFFCGLELK 45 (69)
T ss_pred CEECCCCCEEEECCCCCEEC
T ss_conf 88759998899686896943
No 383
>KOG3475 consensus
Probab=25.92 E-value=13 Score=18.49 Aligned_cols=29 Identities=21% Similarity=0.496 Sum_probs=23.5
Q ss_pred HHHCCCC-----CCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 2227831-----178888744214888722778987
Q gi|254780459|r 4 PELGTKR-----TCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 4 ~elG~KR-----~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
..+|+++ +|--||.+-|-+.|+ .|-+||-
T Consensus 6 ~sFGKr~nkshtlC~RCG~~syH~QKs--tC~~CGY 39 (92)
T KOG3475 6 SSFGKRHNKSHTLCRRCGRRSYHIQKS--TCSSCGY 39 (92)
T ss_pred CHHHHCCCCCHHHHHHHCCHHHHHHCC--CCCCCCC
T ss_conf 014311365108998747266654104--2443589
No 384
>pfam05280 FlhC Flagellar transcriptional activator (FlhC). This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in E. coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator.
Probab=25.91 E-value=55 Score=14.71 Aligned_cols=32 Identities=13% Similarity=0.071 Sum_probs=18.9
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCEECHHHHH
Q ss_conf 17888874421488872277898715323310
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFE 42 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~ 42 (129)
.|..||-.|-=-...|....-||-=-+|...-
T Consensus 136 ~C~~CgG~FV~ha~~~~~~fvC~lC~pPsRAg 167 (176)
T pfam05280 136 RCKCCGGHFVTHAHDLQHNFVCGLCQPPSRAG 167 (176)
T ss_pred CCCCCCCCEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf 66777881550013578885567988941000
No 385
>pfam06750 DiS_P_DiS Bacterial Peptidase A24 N-terminal domain. This family is found at the N-terminus of the pre-pilin peptidases (pfam01478). It's function has not been specifically determined; however some of the family have been characterized as bifunctional. and this domain may contain the N-methylation activity (EC:2.1.1.-). It consists of an intracellular region between a pair of transmembrane. This region contains an invariant proline and two almost fully conserved disulphide bridges - hence the name DiS-P-DiS. The cysteines have been shown to be essential to the overall function of the enzyme in, but their role was incorrectly ascribed.
Probab=25.89 E-value=24 Score=16.95 Aligned_cols=33 Identities=18% Similarity=0.421 Sum_probs=18.7
Q ss_pred CCCCCCCCCEEEECCCCCCC--------CCCCCCEECHHHH
Q ss_conf 31178888744214888722--------7789871532331
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIV--------SPYTQNSWPLAYF 41 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~Pii--------CP~CG~e~~~~~~ 41 (129)
.=.|++||++-==+..=||+ |.+|++.+++...
T Consensus 27 rS~C~~C~~~L~~~~lIPi~s~l~~rGkCr~C~~~I~~~y~ 67 (86)
T pfam06750 27 RSHCPHCGHKLRWYDNIPILSYLLLRGRCRYCGAPISIRYP 67 (86)
T ss_pred CCCCCCCCCCCHHHHHCHHHHHHHCCCCCCCCCCCCCHHHH
T ss_conf 98093569967547837899999708782689994070899
No 386
>pfam10367 Vps39_2 Vacuolar sorting protein 39 domain 2. This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange. This domain is involved in localisation and in mediating the interactions of Vps39 with Vps11.
Probab=25.87 E-value=20 Score=17.43 Aligned_cols=14 Identities=21% Similarity=0.442 Sum_probs=9.8
Q ss_pred HCCCCCCCCCCCEE
Q ss_conf 27831178888744
Q gi|254780459|r 6 LGTKRTCPDTGKRF 19 (129)
Q Consensus 6 lG~KR~C~~Cg~KF 19 (129)
.+-.|+|+-|++||
T Consensus 75 i~e~~~C~vC~k~i 88 (109)
T pfam10367 75 VTEESVCAVCHKRL 88 (109)
T ss_pred ECCCCCCHHHCCCC
T ss_conf 77997436548837
No 387
>pfam09889 DUF2116 Uncharacterized protein containing a Zn-ribbon (DUF2116). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=25.83 E-value=25 Score=16.81 Aligned_cols=14 Identities=7% Similarity=-0.183 Sum_probs=8.2
Q ss_pred CCCCCCCEECHHHH
Q ss_conf 27789871532331
Q gi|254780459|r 28 VSPYTQNSWPLAYF 41 (129)
Q Consensus 28 iCP~CG~e~~~~~~ 41 (129)
.||.||+.++|+..
T Consensus 5 HC~vCG~~Ipp~e~ 18 (59)
T pfam09889 5 HCIVCGTAIPPDES 18 (59)
T ss_pred CCCCCCCCCCCCCC
T ss_conf 35657997894322
No 388
>KOG3507 consensus
Probab=25.78 E-value=31 Score=16.25 Aligned_cols=28 Identities=18% Similarity=0.051 Sum_probs=23.0
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 3117888874421488872277898715
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
+-+|-.||.+--=--+++|-|-.||.-+
T Consensus 20 iYiCgdC~~en~lk~~D~irCReCG~RI 47 (62)
T KOG3507 20 IYICGDCGQENTLKRGDVIRCRECGYRI 47 (62)
T ss_pred EEEECCCCCCCCCCCCCCEEHHHCCHHH
T ss_conf 9880235662311678838622253689
No 389
>TIGR00201 comF comF family protein; InterPro: IPR005222 Proteins in this family are found in bacterial species which posses systems for natural transformation with exogenous DNA (eg Bacillus subtilis, Haemophilus influenzae), and also species without these systems (eg Escherichia coli). Competence protein F has been shown to be important for the uptake of exogenous DNA in naturally competent bacteria, though the precise role of this protein is not yet known , . GntX is a periplasmic gluconate binding protein thought to be part of a high-affinity gluconate transport system ..
Probab=25.74 E-value=34 Score=15.94 Aligned_cols=21 Identities=24% Similarity=0.340 Sum_probs=15.8
Q ss_pred CCCCCCEEEECCCC-CCCCCCCCCEE
Q ss_conf 78888744214888-72277898715
Q gi|254780459|r 12 CPDTGKRFYDLNKQ-VIVSPYTQNSW 36 (129)
Q Consensus 12 C~~Cg~KFYDlnk~-PiiCP~CG~e~ 36 (129)
|+-||.++ ++ -.+|+-||...
T Consensus 1 C~~C~k~~----~S~~a~C~~C~~~~ 22 (207)
T TIGR00201 1 CSLCGKRI----KSSKALCDQCGSER 22 (207)
T ss_pred CCCCCCCC----CCCCCCCCCCCCHH
T ss_conf 98888873----00776246666246
No 390
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=25.67 E-value=37 Score=15.76 Aligned_cols=27 Identities=19% Similarity=0.407 Sum_probs=20.8
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCEECHH
Q ss_conf 17888874421488872277898715323
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~ 39 (129)
.||.|+..+= +.-.-..|++ |+.|+..
T Consensus 4 ~CPvC~~~L~-~~~~sl~C~~-~H~FD~A 30 (272)
T PRK11088 4 QCPLCHQPLT-LEENSWICPQ-NHQFDCA 30 (272)
T ss_pred ECCCCCCCCE-ECCCEEECCC-CCCCCCC
T ss_conf 0899991201-0796888589-9887456
No 391
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=25.23 E-value=12 Score=18.65 Aligned_cols=15 Identities=33% Similarity=0.762 Sum_probs=11.0
Q ss_pred CCCCCCCCEEEECCC
Q ss_conf 117888874421488
Q gi|254780459|r 10 RTCPDTGKRFYDLNK 24 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk 24 (129)
.||+.||+||--|.|
T Consensus 77 IicLEDGkkfKSLKR 91 (148)
T COG4957 77 IICLEDGKKFKSLKR 91 (148)
T ss_pred EEEECCCCCHHHHHH
T ss_conf 877026852278999
No 392
>cd03038 GST_N_etherase_LigE GST_N family, Beta etherase LigE subfamily; composed of proteins similar to Sphingomonas paucimobilis beta etherase, LigE, a GST-like protein that catalyzes the cleavage of the beta-aryl ether linkages present in low-moleculer weight lignins using GSH as the hydrogen donor. This reaction is an essential step in the degradation of lignin, a complex phenolic polymer that is the most abundant aromatic material in the biosphere. The beta etherase activity of LigE is enantioselective and it complements the activity of the other GST family beta etherase, LigF.
Probab=24.93 E-value=37 Score=15.72 Aligned_cols=18 Identities=33% Similarity=0.479 Sum_probs=12.8
Q ss_pred CEEEECC-CCCCC--CCCCCC
Q ss_conf 7442148-88722--778987
Q gi|254780459|r 17 KRFYDLN-KQVIV--SPYTQN 34 (129)
Q Consensus 17 ~KFYDln-k~Pii--CP~CG~ 34 (129)
.+||||- +.|.. ||+|-.
T Consensus 1 i~lyDl~~~~~~~~~SP~~wk 21 (84)
T cd03038 1 ITLYDLAGKDPVRAFSPNVWK 21 (84)
T ss_pred CEEEECCCCCCCCEECCCHHH
T ss_conf 988856899999703862699
No 393
>pfam04780 DUF629 Protein of unknown function (DUF629). This family represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=24.69 E-value=19 Score=17.58 Aligned_cols=10 Identities=30% Similarity=0.806 Sum_probs=3.8
Q ss_pred CCCCCCEEEE
Q ss_conf 7888874421
Q gi|254780459|r 12 CPDTGKRFYD 21 (129)
Q Consensus 12 C~~Cg~KFYD 21 (129)
|.+|+.|||+
T Consensus 60 C~~Cs~kF~~ 69 (466)
T pfam04780 60 CRTCSEKFSD 69 (466)
T ss_pred ECCHHHHCCC
T ss_conf 0234513287
No 394
>PRK11670 putative ATPase; Provisional
Probab=24.65 E-value=35 Score=15.91 Aligned_cols=15 Identities=13% Similarity=0.293 Sum_probs=9.7
Q ss_pred CCCCCCCCEEEECCC
Q ss_conf 117888874421488
Q gi|254780459|r 10 RTCPDTGKRFYDLNK 24 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk 24 (129)
++||.||.+.|-|++
T Consensus 281 ~~c~~c~~~~~iFg~ 295 (369)
T PRK11670 281 HICSNCGHHEPIFGT 295 (369)
T ss_pred CCCCCCCCCCEECCC
T ss_conf 336899971001366
No 395
>PRK07758 hypothetical protein; Provisional
Probab=24.33 E-value=23 Score=16.98 Aligned_cols=30 Identities=20% Similarity=0.387 Sum_probs=20.5
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCEECHHH
Q ss_conf 31178888744214888722778987153233
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNSWPLAY 40 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~ 40 (129)
=|+|- =|-+||--. +=..||.|..+--|..
T Consensus 7 l~~c~-~gh~~yks~-~cp~cp~c~ke~~~~~ 36 (95)
T PRK07758 7 LRTCE-KGHEYYKSS-DCPTCPTCEKERKPKE 36 (95)
T ss_pred HHHHH-CCCCEECCC-CCCCCCCCCCCCCCCH
T ss_conf 88875-656211268-9999975111358742
No 396
>TIGR03318 YdfZ_fam putative selenium-binding protein YdfZ. This small protein has a very limited distribution, being found so far only among some gamma-Proteobacteria. The member from Escherichia coli was shown to bind selenium in the absence of a working SelD-dependent selenium incorporation system. Note that while the E. coli member contains a single Cys residue, a likely selenium binding site, some other members of this protein family contain two Cys residues or none.
Probab=24.15 E-value=29 Score=16.43 Aligned_cols=12 Identities=33% Similarity=0.575 Sum_probs=10.5
Q ss_pred CEEEECCCCCCC
Q ss_conf 744214888722
Q gi|254780459|r 17 KRFYDLNKQVIV 28 (129)
Q Consensus 17 ~KFYDlnk~Pii 28 (129)
+|-||-||.+|+
T Consensus 1 mk~YDRnRNait 12 (65)
T TIGR03318 1 MKTYDRNRNAIT 12 (65)
T ss_pred CCCCCCCCCCCC
T ss_conf 952004656567
No 397
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=24.14 E-value=46 Score=15.18 Aligned_cols=30 Identities=20% Similarity=0.447 Sum_probs=20.8
Q ss_pred CCCCCCCCCCE--EEECCCCCCC---CCCCCCEEC
Q ss_conf 83117888874--4214888722---778987153
Q gi|254780459|r 8 TKRTCPDTGKR--FYDLNKQVIV---SPYTQNSWP 37 (129)
Q Consensus 8 ~KR~C~~Cg~K--FYDlnk~Pii---CP~CG~e~~ 37 (129)
.+-|||.|--+ .|-+.-.|++ ||.|.+--.
T Consensus 191 ~alIC~~C~hhngl~~~~ek~~~efiC~~Cn~~n~ 225 (251)
T COG5415 191 KALICPQCHHHNGLYRLAEKPIIEFICPHCNHKND 225 (251)
T ss_pred HHHCCCCCCCCCCCCCCCCCCCHHEECCCCHHHCC
T ss_conf 65445502354665564434530016356421058
No 398
>pfam10013 DUF2256 Uncharacterized protein conserved in bacteria (DUF2256). Members of this family of hypothetical bacterial proteins have no known function.
Probab=24.14 E-value=35 Score=15.92 Aligned_cols=11 Identities=9% Similarity=0.320 Sum_probs=6.3
Q ss_pred CCCCCCCCEEC
Q ss_conf 22778987153
Q gi|254780459|r 27 IVSPYTQNSWP 37 (129)
Q Consensus 27 iiCP~CG~e~~ 37 (129)
=+||.||..|.
T Consensus 9 K~C~~C~rpf~ 19 (42)
T pfam10013 9 KICPVCGRPFT 19 (42)
T ss_pred CCCCCCCCCCH
T ss_conf 64654699528
No 399
>KOG0478 consensus
Probab=23.99 E-value=43 Score=15.35 Aligned_cols=27 Identities=15% Similarity=0.238 Sum_probs=19.0
Q ss_pred CCCCCCCEEE---ECC--CCCCCCCCCCCEEC
Q ss_conf 1788887442---148--88722778987153
Q gi|254780459|r 11 TCPDTGKRFY---DLN--KQVIVSPYTQNSWP 37 (129)
Q Consensus 11 ~C~~Cg~KFY---Dln--k~PiiCP~CG~e~~ 37 (129)
.|.-||..-| |=+ +.|+.|+.||+...
T Consensus 266 rC~vC~~~~~ve~drg~i~eP~~C~~C~~~~~ 297 (804)
T KOG0478 266 RCSVCGHEIAVESDRGRIKEPMLCKECGTTNS 297 (804)
T ss_pred HHHHCCCEEEEEEECCCCCCCCCCCCCCCCCC
T ss_conf 03315755789740673588850300167664
No 400
>pfam06090 Ins_P5_2-kin Inositol-pentakisphosphate 2-kinase. This is a family of inositol-pentakisphosphate 2-kinases (EC 2.7.1.158) (also known as inositol 1,3,4,5,6-pentakisphosphate 2-kinase, Ins(1,3,4,5,6)P5 2-kinase) and InsP5 2-kinase). This enzyme phosphorylates Ins(1,3,4,5,6)P5 to form Ins(1,2,3,4,5,6)P6 (also known as InsP6 or phytate). InsP6 is involved in many processes such as mRNA export, nonhomologous end-joining, endocytosis and ion channel regulation.
Probab=23.97 E-value=13 Score=18.61 Aligned_cols=32 Identities=25% Similarity=0.327 Sum_probs=23.5
Q ss_pred CHHHCC--------CCCCCCCCCEEEECCCCCC--CCCCCCC
Q ss_conf 522278--------3117888874421488872--2778987
Q gi|254780459|r 3 KPELGT--------KRTCPDTGKRFYDLNKQVI--VSPYTQN 34 (129)
Q Consensus 3 K~elG~--------KR~C~~Cg~KFYDlnk~Pi--iCP~CG~ 34 (129)
||.||. .|+|-.|-...|=+.+..+ ...||=-
T Consensus 125 KPKwl~~s~s~~~~~~~CR~C~~q~lK~~~~~~~~~s~yCPL 166 (301)
T pfam06090 125 KPKWLFLSPSAPIKARVCRFCAHQALKLARGGISEISSYCPL 166 (301)
T ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf 544005577765455404588999988632577767888973
No 401
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=23.86 E-value=32 Score=16.13 Aligned_cols=13 Identities=15% Similarity=0.371 Sum_probs=5.7
Q ss_pred CCCCCCCCCCCEE
Q ss_conf 7831178888744
Q gi|254780459|r 7 GTKRTCPDTGKRF 19 (129)
Q Consensus 7 G~KR~C~~Cg~KF 19 (129)
+.+-+|.-||--|
T Consensus 423 ~~~~~c~vc~~~~ 435 (479)
T PRK05452 423 GPRMQCSVCQWIY 435 (479)
T ss_pred CCEEEEEEEEEEE
T ss_conf 5448997720461
No 402
>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=23.68 E-value=24 Score=16.88 Aligned_cols=15 Identities=40% Similarity=0.747 Sum_probs=12.5
Q ss_pred CHHHCCCCCCCCCCC
Q ss_conf 522278311788887
Q gi|254780459|r 3 KPELGTKRTCPDTGK 17 (129)
Q Consensus 3 K~elG~KR~C~~Cg~ 17 (129)
.|+||+|.+|.+-|-
T Consensus 237 ~pdW~~~l~~h~wgG 251 (660)
T COG3972 237 QPDWGTKLFCHNWGG 251 (660)
T ss_pred CCCCCCEEEEECCCC
T ss_conf 887242688843578
No 403
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=23.55 E-value=23 Score=17.02 Aligned_cols=28 Identities=14% Similarity=0.150 Sum_probs=15.9
Q ss_pred CCCCCCCEEE----------ECCCCCC-----CCCCCCCEECH
Q ss_conf 1788887442----------1488872-----27789871532
Q gi|254780459|r 11 TCPDTGKRFY----------DLNKQVI-----VSPYTQNSWPL 38 (129)
Q Consensus 11 ~C~~Cg~KFY----------Dlnk~Pi-----iCP~CG~e~~~ 38 (129)
-||.||..|| .+.-.|. +||.|+..+.+
T Consensus 229 pCPHCGe~q~l~~~e~~~~~g~~~~~~~~~~~~c~h~~~~i~~ 271 (611)
T COG5525 229 PCPHCGEEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVIRP 271 (611)
T ss_pred ECCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHCCCCCCEEEE
T ss_conf 6788871430122344777676454022243212456723345
No 404
>PRK13796 GTP-binding protein YqeH; Provisional
Probab=23.52 E-value=37 Score=15.77 Aligned_cols=10 Identities=0% Similarity=-0.283 Sum_probs=4.7
Q ss_pred CCCCCCCCEE
Q ss_conf 2277898715
Q gi|254780459|r 27 IVSPYTQNSW 36 (129)
Q Consensus 27 iiCP~CG~e~ 36 (129)
+.|++||+.+
T Consensus 5 ~kC~GCGa~l 14 (367)
T PRK13796 5 LKCIGCGAPI 14 (367)
T ss_pred CEECCCCCEE
T ss_conf 8828987834
No 405
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=23.45 E-value=34 Score=15.99 Aligned_cols=24 Identities=17% Similarity=0.245 Sum_probs=17.5
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCEECH
Q ss_conf 1788887442148887227789871532
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQNSWPL 38 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~e~~~ 38 (129)
.|+-|..+| ..|++-+.||+.|=-
T Consensus 1 ~C~iC~~~~----~~~~~~~~CgH~fC~ 24 (45)
T cd00162 1 ECPICLEEF----REPVVLLPCGHVFCR 24 (45)
T ss_pred CCCCCCHHH----CCEEEEECCCCCCCH
T ss_conf 984088032----781188189991068
No 406
>pfam05207 zf-CSL CSL zinc finger. This is a zinc binding motif which contains four cysteine residues which chelate zinc. This domain is often found associated with a pfam00226 domain. This domain is named after the conserved motif of the final cysteine.
Probab=23.43 E-value=47 Score=15.14 Aligned_cols=27 Identities=26% Similarity=0.375 Sum_probs=16.7
Q ss_pred CCCCCCCCCEEE----ECCCC--CCCCCCCCCEE
Q ss_conf 311788887442----14888--72277898715
Q gi|254780459|r 9 KRTCPDTGKRFY----DLNKQ--VIVSPYTQNSW 36 (129)
Q Consensus 9 KR~C~~Cg~KFY----Dlnk~--PiiCP~CG~e~ 36 (129)
-+-|+ ||-+|. +|..- -+.||+|.--+
T Consensus 18 ~y~Cr-CGd~f~i~~~~l~~~e~iv~C~sCSL~i 50 (55)
T pfam05207 18 YYPCR-CGDEFEITEEDLEEGEVVVQCPSCSLWI 50 (55)
T ss_pred EECCC-CCCEEEECHHHHHCCCEEEECCCCCEEE
T ss_conf 86789-9997998899984899599799994099
No 407
>TIGR02474 pec_lyase pectate lyase; InterPro: IPR012669 Members of this family are isozymes of pectate lyase (4.2.2.2 from EC), also called polygalacturonic transeliminase and alpha-1,4-D-endopolygalacturonic acid lyase..
Probab=23.31 E-value=24 Score=16.90 Aligned_cols=22 Identities=41% Similarity=0.757 Sum_probs=13.7
Q ss_pred CCCCC---CEEEECCC---------CCCCCCCCC
Q ss_conf 78888---74421488---------872277898
Q gi|254780459|r 12 CPDTG---KRFYDLNK---------QVIVSPYTQ 33 (129)
Q Consensus 12 C~~Cg---~KFYDlnk---------~PiiCP~CG 33 (129)
|+-|. .|||+|+- .|||--+-.
T Consensus 284 ~~ga~vLWaRFY~Ld~sfDvvsGarkPivGtyPs 317 (356)
T TIGR02474 284 EPGAKVLWARFYDLDTSFDVVSGARKPIVGTYPS 317 (356)
T ss_pred CCCCCHHHHHHHHCCCCEEEEECCCCCEECCCCC
T ss_conf 7727523344230178343520576760016753
No 408
>pfam02433 FixO Cytochrome C oxidase, mono-heme subunit/FixO. The bacterial oxidase complex, fixNOPQ or cytochrome cbb3, is thought to be required for respiration in endosymbiosis. FixO is a membrane bound mono-heme constituent of the fixNOPQ complex.
Probab=22.96 E-value=29 Score=16.35 Aligned_cols=17 Identities=47% Similarity=0.900 Sum_probs=11.7
Q ss_pred HHCCCCCCCC---CCCEEEE
Q ss_conf 2278311788---8874421
Q gi|254780459|r 5 ELGTKRTCPD---TGKRFYD 21 (129)
Q Consensus 5 elG~KR~C~~---Cg~KFYD 21 (129)
-||+||+-|- -|.||=|
T Consensus 96 lwGskRtGPDL~rvGgr~sd 115 (226)
T pfam02433 96 QWGSKRTGPDLARVGGKYSD 115 (226)
T ss_pred HCCCCCCCCCHHHHCCCCCH
T ss_conf 20587668446552375784
No 409
>pfam05443 ROS_MUCR ROS/MUCR transcriptional regulator protein. This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti. This gene encodes a 15.5-kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid and is necessary for succinoglycan production. Sinorhizobium meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of alfalfa nodules. MucR from Sinorhizobium meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan.
Probab=22.73 E-value=17 Score=17.89 Aligned_cols=14 Identities=36% Similarity=0.672 Sum_probs=7.7
Q ss_pred CCCCCCCCCEEEEC
Q ss_conf 31178888744214
Q gi|254780459|r 9 KRTCPDTGKRFYDL 22 (129)
Q Consensus 9 KR~C~~Cg~KFYDl 22 (129)
.-+|..||++|==|
T Consensus 70 ~iicledGK~~K~L 83 (130)
T pfam05443 70 YIICLEDGKKFKTL 83 (130)
T ss_pred EEEEEECCCCCCHH
T ss_conf 47871078532079
No 410
>KOG4317 consensus
Probab=22.66 E-value=45 Score=15.23 Aligned_cols=25 Identities=12% Similarity=0.149 Sum_probs=14.9
Q ss_pred CCCCCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 783117888874421488872277898715
Q gi|254780459|r 7 GTKRTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 7 G~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
|.--+|+-||..|-- -+||-|..-|
T Consensus 5 s~~~~C~ic~vq~~~-----YtCPRCn~~Y 29 (383)
T KOG4317 5 SSFLACGICGVQKRE-----YTCPRCNLLY 29 (383)
T ss_pred CCEEECCCCCCCCCC-----CCCCCCCCCC
T ss_conf 750342345544200-----5587777642
No 411
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=22.57 E-value=31 Score=16.26 Aligned_cols=26 Identities=31% Similarity=0.676 Sum_probs=16.7
Q ss_pred CCCCCCC----------------EEEEC--CCC-CCCCCCCCC-EE
Q ss_conf 1788887----------------44214--888-722778987-15
Q gi|254780459|r 11 TCPDTGK----------------RFYDL--NKQ-VIVSPYTQN-SW 36 (129)
Q Consensus 11 ~C~~Cg~----------------KFYDl--nk~-PiiCP~CG~-e~ 36 (129)
.||.||- ||+|. ||. -|.|-.||- ||
T Consensus 6 kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYtEf 51 (68)
T COG3478 6 KCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYTEF 51 (68)
T ss_pred CCCCCCCCCHHHCEEECCCCCCCEEEEECCCEEEEEEECCCCCHHH
T ss_conf 3877688622121345247772114886066799998034885532
No 412
>pfam05290 Baculo_IE-1 Baculovirus immediate-early protein (IE-0). The Autographa californica multinucleocapsid nuclear polyhedrosis virus (AcMNPV) ie-1 gene product (IE-1) is thought to play a central role in stimulating early viral transcription. IE-1 has been demonstrated to activate several early viral gene promoters and to negatively regulate the promoters of two other AcMNPV regulatory genes, ie-0 and ie-2. It is thought that that IE-1 negatively regulates the expression of certain genes by binding directly, or as part of a complex, to promoter regions containing a specific IE-1-binding motif (5'-ACBYGTAA-3') near their mRNA start sites.
Probab=22.34 E-value=8.9 Score=19.55 Aligned_cols=30 Identities=13% Similarity=0.241 Sum_probs=22.8
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEECHH
Q ss_conf 117888874421488872277898715323
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWPLA 39 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~ 39 (129)
|+|-.|=+..+-+-..=++||-|-|+|--.
T Consensus 105 ~iCn~Cya~LWK~~~~ypvCPvCkTSFKss 134 (141)
T pfam05290 105 KICNLCYANLWKFCTVYPVCPVCKTSFKSS 134 (141)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf 599999999998745587788666765677
No 413
>pfam10825 DUF2752 Protein of unknown function (DUF2752). This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=22.34 E-value=30 Score=16.35 Aligned_cols=10 Identities=20% Similarity=-0.011 Sum_probs=7.5
Q ss_pred CCCCCCCCCE
Q ss_conf 7227789871
Q gi|254780459|r 26 VIVSPYTQNS 35 (129)
Q Consensus 26 PiiCP~CG~e 35 (129)
=+-||+||..
T Consensus 9 G~~CPgCG~t 18 (52)
T pfam10825 9 GIPCPGCGLT 18 (52)
T ss_pred CCCCCCCHHH
T ss_conf 7889864589
No 414
>PRK04351 hypothetical protein; Provisional
Probab=22.17 E-value=65 Score=14.25 Aligned_cols=30 Identities=20% Similarity=0.277 Sum_probs=12.0
Q ss_pred HCCCCCCCCCCCEEEECCCCCCCCCCCCCEE
Q ss_conf 2783117888874421488872277898715
Q gi|254780459|r 6 LGTKRTCPDTGKRFYDLNKQVIVSPYTQNSW 36 (129)
Q Consensus 6 lG~KR~C~~Cg~KFYDlnk~PiiCP~CG~e~ 36 (129)
.|.=|-||.-.... --.|---.|-+||..|
T Consensus 95 Vgg~Ry~p~~~~~~-~~~~y~Y~C~~Cg~~y 124 (151)
T PRK04351 95 VGGPRYCPPLEKSK-KNKKYLYECQSCGQVY 124 (151)
T ss_pred HCCCCCCCCCCCCC-CCCEEEEECCCCCCEE
T ss_conf 19966578765456-6742999889998765
No 415
>TIGR02443 TIGR02443 conserved hypothetical protein; 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=21.82 E-value=36 Score=15.86 Aligned_cols=25 Identities=12% Similarity=0.341 Sum_probs=13.1
Q ss_pred CCCCCCCE----EEECCC-CCCCCCCCCCE
Q ss_conf 17888874----421488-87227789871
Q gi|254780459|r 11 TCPDTGKR----FYDLNK-QVIVSPYTQNS 35 (129)
Q Consensus 11 ~C~~Cg~K----FYDlnk-~PiiCP~CG~e 35 (129)
+||.|+++ .|-=|. .-+-|=.||..
T Consensus 11 ~CP~C~~~D~l~~W~EN~i~~VECV~Cgy~ 40 (63)
T TIGR02443 11 KCPACSAQDTLAMWKENNIELVECVECGYQ 40 (63)
T ss_pred CCCCCCCCCCEEEECCCCCCEEEEECCCCC
T ss_conf 288888745400020189772663158851
No 416
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=21.82 E-value=46 Score=15.19 Aligned_cols=26 Identities=15% Similarity=0.381 Sum_probs=20.8
Q ss_pred CCEEEECCCCC--CCCCCCCCEECHHHH
Q ss_conf 87442148887--227789871532331
Q gi|254780459|r 16 GKRFYDLNKQV--IVSPYTQNSWPLAYF 41 (129)
Q Consensus 16 g~KFYDlnk~P--iiCP~CG~e~~~~~~ 41 (129)
..|||=.-+.| +.|-||+..|....+
T Consensus 123 ~s~F~~~~~~~~~lrC~YCe~~~~~~~v 150 (153)
T COG1781 123 ESKFYVVSKEPLALRCKYCEKTFSEDEV 150 (153)
T ss_pred CCCEEEEECCCCEEEEEECCCEECHHHH
T ss_conf 8646996068858898823759241013
No 417
>pfam04438 zf-HIT HIT zinc finger. This presumed zinc finger contains up to 6 cysteine residues that could coordinate zinc. The domain is named after the HIT protein. This domain is also found in the Thyroid receptor interacting protein 3 (TRIP-3) that specifically interact with the ligand binding domain of the thyroid receptor.
Probab=21.81 E-value=38 Score=15.70 Aligned_cols=10 Identities=10% Similarity=-0.077 Sum_probs=5.0
Q ss_pred CCCCCCCCCE
Q ss_conf 7227789871
Q gi|254780459|r 26 VIVSPYTQNS 35 (129)
Q Consensus 26 PiiCP~CG~e 35 (129)
--.||.|+.-
T Consensus 13 kY~Cp~C~~~ 22 (30)
T pfam04438 13 KYRCPRCGVR 22 (30)
T ss_pred CCCCCCCCCC
T ss_conf 3238898985
No 418
>pfam05605 Di19 Drought induced 19 protein (Di19). This family consists of several drought induced 19 (Di19) like proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought. The precise function of Di19 is unknown.
Probab=21.72 E-value=36 Score=15.86 Aligned_cols=12 Identities=17% Similarity=0.099 Sum_probs=6.1
Q ss_pred CCCCCCCCCCEE
Q ss_conf 872277898715
Q gi|254780459|r 25 QVIVSPYTQNSW 36 (129)
Q Consensus 25 ~PiiCP~CG~e~ 36 (129)
...|||-|.+-+
T Consensus 62 kngVCPVCa~~V 73 (210)
T pfam05605 62 KNGVCPVCADRV 73 (210)
T ss_pred CCCCCCCHHHHC
T ss_conf 376474067650
No 419
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=21.63 E-value=35 Score=15.88 Aligned_cols=24 Identities=8% Similarity=0.115 Sum_probs=16.2
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCC-EEC
Q ss_conf 31178888744214888722778987-153
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQN-SWP 37 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~-e~~ 37 (129)
.+.|-.|..-+-+ =.||.||. .|.
T Consensus 3 ekACr~C~~i~~~-----~~CP~Cgs~~~s 27 (61)
T PRK08351 3 EKACRHCHYITTE-----DRCPVCGSRDLS 27 (61)
T ss_pred HHHHHHCCCCCCC-----CCCCCCCCCCCC
T ss_conf 2546557762689-----958999798688
No 420
>PRK09628 oorB 2-oxoglutarate-acceptor oxidoreductase subunit OorB; Reviewed
Probab=21.62 E-value=27 Score=16.57 Aligned_cols=24 Identities=8% Similarity=0.020 Sum_probs=15.4
Q ss_pred EEEECCCC-CCCCCCCCCEECHHHH
Q ss_conf 44214888-7227789871532331
Q gi|254780459|r 18 RFYDLNKQ-VIVSPYTQNSWPLAYF 41 (129)
Q Consensus 18 KFYDlnk~-PiiCP~CG~e~~~~~~ 41 (129)
||.=.+|- .+-||+||.-.....+
T Consensus 7 ~ylr~~~~P~~wCpGCG~g~Il~~l 31 (281)
T PRK09628 7 EYLRVDKMPTLWCWGCGDGVILKSI 31 (281)
T ss_pred HHHCCCCCCCCCCCCCCCHHHHHHH
T ss_conf 8833568998878899768999999
No 421
>pfam03811 Ins_element1 Insertion element protein.
Probab=21.54 E-value=49 Score=15.00 Aligned_cols=33 Identities=15% Similarity=0.314 Sum_probs=23.9
Q ss_pred CCCCCCCC--EEEECCCCC-----CCCCCCCCEECHHHHH
Q ss_conf 11788887--442148887-----2277898715323310
Q gi|254780459|r 10 RTCPDTGK--RFYDLNKQV-----IVSPYTQNSWPLAYFE 42 (129)
Q Consensus 10 R~C~~Cg~--KFYDlnk~P-----iiCP~CG~e~~~~~~~ 42 (129)
-.||.|+. .-|==++.| --|..|+..|.....-
T Consensus 6 v~Cp~C~s~~~V~KnG~~~~G~QRYrC~~C~r~Fql~ytY 45 (88)
T pfam03811 6 IHCPRCSSTEGVYRHGQSTAGHQRYRCRHCRRTFQLTYTY 45 (88)
T ss_pred EECCCCCCCCCEEECCCCCCCCCCEEECCCCCEEEEEECC
T ss_conf 4797888987677189689998577727789556663011
No 422
>COG4694 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.36 E-value=32 Score=16.18 Aligned_cols=15 Identities=20% Similarity=0.350 Sum_probs=11.7
Q ss_pred CCCCCCCCCCCCCEE
Q ss_conf 488872277898715
Q gi|254780459|r 22 LNKQVIVSPYTQNSW 36 (129)
Q Consensus 22 lnk~PiiCP~CG~e~ 36 (129)
+||+--+||.||.+.
T Consensus 274 ~~k~~q~CpFCg~et 288 (758)
T COG4694 274 YNKDNQICPFCGKET 288 (758)
T ss_pred HCCCCCCCCCCCHHH
T ss_conf 304677798645078
No 423
>pfam06478 Corona_RPol_N Coronavirus RPol N-terminus. This family covers the N-terminal region of the coronavirus RNA-directed RNA Polymerase.
Probab=21.36 E-value=38 Score=15.69 Aligned_cols=22 Identities=23% Similarity=0.282 Sum_probs=18.5
Q ss_pred CCEEEECCCCCCCCCCCCCEEC
Q ss_conf 8744214888722778987153
Q gi|254780459|r 16 GKRFYDLNKQVIVSPYTQNSWP 37 (129)
Q Consensus 16 g~KFYDlnk~PiiCP~CG~e~~ 37 (129)
.-+||||+-.-++-|+||.-+-
T Consensus 201 nG~~YDFGDFv~t~pG~Gv~~~ 222 (355)
T pfam06478 201 NGNFYDFGDFVQTAPGAGVPIC 222 (355)
T ss_pred CCCCCCCCCEEECCCCCCCEEE
T ss_conf 6861003541323899974233
No 424
>TIGR02187 GlrX_arch Glutaredoxin-like domain protein; InterPro: IPR011903 Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system . Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry of archaeal proteins contains a C-terminal domain with homology to bacterial and eukaryotic glutaredoxins, including a CPYC motif. There is an N-terminal domain which has even more distant homology to glutaredoxins. The name "glutaredoxin" may be inappropriate in the sense of working in tandem with glutathione and glutathione reductase which may not be present in the archaea. The overall domain structure appears to be related to bacterial alkylhydroperoxide reductases, but the homology may be distant enough that the function of this family is wholly different..
Probab=21.18 E-value=32 Score=16.12 Aligned_cols=10 Identities=20% Similarity=0.368 Sum_probs=5.8
Q ss_pred CCCCCCCCEE
Q ss_conf 2277898715
Q gi|254780459|r 27 IVSPYTQNSW 36 (129)
Q Consensus 27 iiCP~CG~e~ 36 (129)
.+||||=.-+
T Consensus 157 PtCPYCP~AV 166 (237)
T TIGR02187 157 PTCPYCPRAV 166 (237)
T ss_pred CCCCCHHHHH
T ss_conf 6899725799
No 425
>TIGR00398 metG methionyl-tRNA synthetase; InterPro: IPR002304 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; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Methionyl-tRNA synthetase (6.1.1.10 from EC) is an alpha 2 dimer that belongs to class Ia. In some species (archaea, eubacteria and eukaryota) a coding sequence, similar to the C-term end of MetRS, is present as an independent gene which is a tRNA binding domain as a dimer. In eubacteria, MetRS can also be splitted in two sub-classes corresponding to the presence of one or two CXXC domain specific to zinc binding. The crystal structures of a number of methionyl-tRNA synthases are known , , .; GO: 0000166 nucleotide binding, 0004825 methionine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006431 methionyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=21.17 E-value=65 Score=14.27 Aligned_cols=33 Identities=15% Similarity=0.185 Sum_probs=18.7
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCEECHHHHHCCC
Q ss_conf 3117888874421488872277898715323310123
Q gi|254780459|r 9 KRTCPDTGKRFYDLNKQVIVSPYTQNSWPLAYFEAPT 45 (129)
Q Consensus 9 KR~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~~~~~~ 45 (129)
+-+||.|+.. .+.==.|=.||..+.|..+..||
T Consensus 143 ~g~CP~c~~~----~~~gd~c~~Cg~~leP~~Li~P~ 175 (573)
T TIGR00398 143 EGTCPKCGSE----DARGDHCEVCGRHLEPFELINPR 175 (573)
T ss_pred CCCCCCCCCC----CCCCCCCCCCCCCCCCCHHCCCC
T ss_conf 6748868877----77787755465536850011870
No 426
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.08 E-value=39 Score=15.64 Aligned_cols=11 Identities=9% Similarity=0.129 Sum_probs=5.3
Q ss_pred CCCCCCCCCEE
Q ss_conf 72277898715
Q gi|254780459|r 26 VIVSPYTQNSW 36 (129)
Q Consensus 26 PiiCP~CG~e~ 36 (129)
-+-||-||+-+
T Consensus 7 ~v~CP~Cgkpv 17 (65)
T COG3024 7 TVPCPTCGKPV 17 (65)
T ss_pred CCCCCCCCCCC
T ss_conf 15388778833
No 427
>pfam06170 DUF983 Protein of unknown function (DUF983). This family consists of several bacterial proteins of unknown function.
Probab=20.83 E-value=36 Score=15.83 Aligned_cols=13 Identities=8% Similarity=-0.133 Sum_probs=6.8
Q ss_pred CCCCCCCCCCCEE
Q ss_conf 8872277898715
Q gi|254780459|r 24 KQVIVSPYTQNSW 36 (129)
Q Consensus 24 k~PiiCP~CG~e~ 36 (129)
|---.|+.||..|
T Consensus 6 kv~~~C~~CG~d~ 18 (86)
T pfam06170 6 KVRPACEACGLDY 18 (86)
T ss_pred CCCCCCCCCCCCC
T ss_conf 1467530127835
No 428
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=20.70 E-value=42 Score=15.44 Aligned_cols=21 Identities=19% Similarity=0.267 Sum_probs=17.1
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 178888744214888722778987
Q gi|254780459|r 11 TCPDTGKRFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 11 ~C~~Cg~KFYDlnk~PiiCP~CG~ 34 (129)
.|.+||-+-+=|- -.||+|..
T Consensus 356 RC~~CGF~a~~l~---W~CPsC~~ 376 (389)
T COG2956 356 RCQNCGFTAHTLY---WHCPSCRA 376 (389)
T ss_pred EECCCCCCHHEEE---EECCCCCC
T ss_conf 1001686310135---41887565
No 429
>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=20.67 E-value=35 Score=15.89 Aligned_cols=25 Identities=16% Similarity=0.357 Sum_probs=16.5
Q ss_pred CCCCCCCCCEE-------EECC-----CCCCCCCCCC
Q ss_conf 31178888744-------2148-----8872277898
Q gi|254780459|r 9 KRTCPDTGKRF-------YDLN-----KQVIVSPYTQ 33 (129)
Q Consensus 9 KR~C~~Cg~KF-------YDln-----k~PiiCP~CG 33 (129)
-|.||.|..++ +-+. ..+.=||.|.
T Consensus 395 r~lC~~C~~~~~~~~~~~~~~~~~~~~~~~~GC~~C~ 431 (500)
T COG2804 395 RRLCPHCKEECEPEELARLGLSESLPLYRAVGCEACN 431 (500)
T ss_pred HHHCCHHCCCCCCHHHHHHCCCCCCCCCCCCCCHHHC
T ss_conf 6418231055550355441135432212467865544
No 430
>pfam10609 ParA ParA/MinD ATPase like. This family contains ATPases involved in plasmid partitioning. It also contains the cytosolic Fe-S cluster assembling factor NBP35 which is required for biogenesis and export of both ribosomal subunits.
Probab=20.64 E-value=55 Score=14.72 Aligned_cols=16 Identities=19% Similarity=0.173 Sum_probs=11.4
Q ss_pred CCCCCCCCCCCCEECH
Q ss_conf 8887227789871532
Q gi|254780459|r 23 NKQVIVSPYTQNSWPL 38 (129)
Q Consensus 23 nk~PiiCP~CG~e~~~ 38 (129)
|-+=.+||.||..+.+
T Consensus 62 NMs~~~c~~c~~~~~i 77 (81)
T pfam10609 62 NMSYFVCPDCGEKIYI 77 (81)
T ss_pred CCCCCCCCCCCCEECC
T ss_conf 7975368999987569
No 431
>cd03530 Rieske_NirD_small_Bacillus Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium.
Probab=20.58 E-value=70 Score=14.04 Aligned_cols=33 Identities=15% Similarity=0.323 Sum_probs=25.7
Q ss_pred CCCCCCCCCEEEE--CCCCCCCCCCCCCEECHHHH
Q ss_conf 3117888874421--48887227789871532331
Q gi|254780459|r 9 KRTCPDTGKRFYD--LNKQVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 9 KR~C~~Cg~KFYD--lnk~PiiCP~CG~e~~~~~~ 41 (129)
-..||..|+.... +...-|+||.=|..|++..-
T Consensus 39 ~~~CpH~g~~L~~G~v~~~~i~CP~H~~~Fdl~tG 73 (98)
T cd03530 39 ENRCPHKGGPLSEGIVHGEYVTCPLHNWVIDLETG 73 (98)
T ss_pred ECCCCCCCCEEECCEEECCEEECCCCCCEEECCCC
T ss_conf 68198899787071895999985898999999997
No 432
>COG0267 RpmG Ribosomal protein L33 [Translation, ribosomal structure and biogenesis]
Probab=20.52 E-value=34 Score=15.98 Aligned_cols=29 Identities=21% Similarity=0.291 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCEEEECCCCCC----------CCCCCCCE
Q ss_conf 783117888874421488872----------27789871
Q gi|254780459|r 7 GTKRTCPDTGKRFYDLNKQVI----------VSPYTQNS 35 (129)
Q Consensus 7 G~KR~C~~Cg~KFYDlnk~Pi----------iCP~CG~e 35 (129)
.++-.|..|+.+||=-.|..- -||.|+.-
T Consensus 5 ki~L~ct~c~g~nY~t~kN~r~~~~rLelkKycp~~~kh 43 (50)
T COG0267 5 KIKLACTACTSRNYTTTKNKRNKPERLELKKYCPVCRKH 43 (50)
T ss_pred EEEEEEECCCCEEEEEEECCCCCCCEEEEEECCCCCCCE
T ss_conf 699997446871289865267895317797018545637
No 433
>pfam04641 Rtf2 Replication termination factor 2. It is vital for effective cell-replication that replication is not stalled at any point by, for instance, damaged bases. Rtf2 stabilizes the replication fork stalled at the site-specific replication barrier RTS1 by preventing replication restart until completion of DNA synthesis by a converging replication fork initiated at a flanking origin. The RTS1 element terminates replication forks that are moving in the cen2-distal direction while allowing forks moving in the cen2-proximal direction to pass through the region. Rtf2 contains a C2HC2 motif related to the C3HC4 RING-finger motif, and would appear to fold up, creating a RING finger-like structure but forming only one functional Zn2+ ion-binding site.
Probab=20.47 E-value=53 Score=14.81 Aligned_cols=11 Identities=18% Similarity=0.347 Sum_probs=6.0
Q ss_pred CCCCCCCEECH
Q ss_conf 27789871532
Q gi|254780459|r 28 VSPYTQNSWPL 38 (129)
Q Consensus 28 iCP~CG~e~~~ 38 (129)
.||.||..|..
T Consensus 146 ~C~~C~~~f~~ 156 (254)
T pfam04641 146 VCPVCGKPYSE 156 (254)
T ss_pred CCHHCCCCCCC
T ss_conf 34010782660
No 434
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=20.43 E-value=64 Score=14.28 Aligned_cols=30 Identities=20% Similarity=0.303 Sum_probs=15.9
Q ss_pred HCCCCCCCCCCCEEE--ECCC-CCCCCCCCCCE
Q ss_conf 278311788887442--1488-87227789871
Q gi|254780459|r 6 LGTKRTCPDTGKRFY--DLNK-QVIVSPYTQNS 35 (129)
Q Consensus 6 lG~KR~C~~Cg~KFY--Dlnk-~PiiCP~CG~e 35 (129)
-|.-+-||.|++.|- =|+- .-..||-||+.
T Consensus 15 ~~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~~ 47 (418)
T COG2995 15 PGHLILCPECDMLVSLPRLDSGQSAYCPRCGHT 47 (418)
T ss_pred CCCEECCCCCCCEECCCCCCCCCCCCCCCCCCE
T ss_conf 614405777785531466787770069987886
No 435
>KOG3816 consensus
Probab=20.37 E-value=23 Score=17.01 Aligned_cols=24 Identities=13% Similarity=0.182 Sum_probs=13.3
Q ss_pred CCCCCCC---------EEEECCCCCCCCCCCCC
Q ss_conf 1788887---------44214888722778987
Q gi|254780459|r 11 TCPDTGK---------RFYDLNKQVIVSPYTQN 34 (129)
Q Consensus 11 ~C~~Cg~---------KFYDlnk~PiiCP~CG~ 34 (129)
+|.+|++ .||-=.+.-.+||+|++
T Consensus 476 ~C~~C~k~l~~~~q~~t~~s~ys~~~~cP~c~~ 508 (526)
T KOG3816 476 VCQSCRKSLGVRDQLATQLSNYSALRICPSCKL 508 (526)
T ss_pred HHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 565414523548888899865211111677675
No 436
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=20.32 E-value=35 Score=15.88 Aligned_cols=27 Identities=15% Similarity=0.218 Sum_probs=18.5
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCEECHHH
Q ss_conf 1178888744214888722778987153233
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNSWPLAY 40 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e~~~~~ 40 (129)
-.||.|+. |-|.|.--|.||..|--+-
T Consensus 275 LkCplc~~----Llrnp~kT~cC~~~fc~ec 301 (427)
T COG5222 275 LKCPLCHC----LLRNPMKTPCCGHTFCDEC 301 (427)
T ss_pred CCCCCHHH----HHHCCCCCCCCCCHHHHHH
T ss_conf 13752103----6538545765662579998
No 437
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=20.26 E-value=40 Score=15.58 Aligned_cols=21 Identities=14% Similarity=0.297 Sum_probs=14.4
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCCCE
Q ss_conf 11788887442148887227789871
Q gi|254780459|r 10 RTCPDTGKRFYDLNKQVIVSPYTQNS 35 (129)
Q Consensus 10 R~C~~Cg~KFYDlnk~PiiCP~CG~e 35 (129)
+.|-.|..-.-+ -+||.||.+
T Consensus 6 kACr~C~~i~~~-----~~CP~Cgs~ 26 (64)
T PRK06393 6 RACKKCKRLTPE-----KTCPVHGDE 26 (64)
T ss_pred HHHHHCCCCCCC-----CCCCCCCCC
T ss_conf 436547751788-----878999898
No 438
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=20.21 E-value=60 Score=14.48 Aligned_cols=12 Identities=25% Similarity=0.326 Sum_probs=7.5
Q ss_pred CCCCCCCCCEEC
Q ss_conf 722778987153
Q gi|254780459|r 26 VIVSPYTQNSWP 37 (129)
Q Consensus 26 PiiCP~CG~e~~ 37 (129)
.+.||+|+....
T Consensus 3 ~~~CP~C~~~v~ 14 (67)
T smart00714 3 QLFCPRCQNNVT 14 (67)
T ss_pred EEECCCCCCEEE
T ss_conf 279988999899
No 439
>KOG3854 consensus
Probab=20.11 E-value=30 Score=16.32 Aligned_cols=38 Identities=21% Similarity=0.168 Sum_probs=27.5
Q ss_pred HHHCCCCCCCCCCCEEEECCC----CCCCCCCCCCEECHHHH
Q ss_conf 222783117888874421488----87227789871532331
Q gi|254780459|r 4 PELGTKRTCPDTGKRFYDLNK----QVIVSPYTQNSWPLAYF 41 (129)
Q Consensus 4 ~elG~KR~C~~Cg~KFYDlnk----~PiiCP~CG~e~~~~~~ 41 (129)
.+.--|-+|..|++.+|=.-| .-++|=+|-.+|..-.+
T Consensus 403 Ie~Kf~Y~C~~C~~~~~~~skSl~t~~~~C~~Ckg~i~l~~~ 444 (505)
T KOG3854 403 IEFKFKYTCTKCNKLSGGHSKSLDTSRLRCRYCKGEISLKPV 444 (505)
T ss_pred CCCEEEEEECCCCCCCCCCCCCCCHHHHHHHHCCCCEEEEEE
T ss_conf 221489985346741100103434767778760562689740
No 440
>KOG2231 consensus
Probab=20.05 E-value=48 Score=15.07 Aligned_cols=30 Identities=20% Similarity=0.178 Sum_probs=11.5
Q ss_pred CCCCCCCCCCCEEEEC-C--CCCCCCCCCCCEE
Q ss_conf 7831178888744214-8--8872277898715
Q gi|254780459|r 7 GTKRTCPDTGKRFYDL-N--KQVIVSPYTQNSW 36 (129)
Q Consensus 7 G~KR~C~~Cg~KFYDl-n--k~PiiCP~CG~e~ 36 (129)
|.-+||..|-+|+-=+ | |.-+.||-|-.+|
T Consensus 19 ~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~ 51 (669)
T KOG2231 19 GHNEVCATCVVRLRFELNNRKCSNECPVCRREV 51 (669)
T ss_pred CCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCE
T ss_conf 535300345444333103665444575450000
No 441
>TIGR00155 pqiA_fam integral membrane protein, PqiA family; InterPro: IPR005219 This family consists of uncharacterised predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in Escherichia coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A. .
Probab=20.05 E-value=35 Score=15.88 Aligned_cols=29 Identities=14% Similarity=0.085 Sum_probs=21.6
Q ss_pred CCCCCCCCCEEEEC-----CCCCCCCCCCCCEEC
Q ss_conf 31178888744214-----888722778987153
Q gi|254780459|r 9 KRTCPDTGKRFYDL-----NKQVIVSPYTQNSWP 37 (129)
Q Consensus 9 KR~C~~Cg~KFYDl-----nk~PiiCP~CG~e~~ 37 (129)
-|.|+.|-..||-- .+....||.|.....
T Consensus 226 ~~~c~~c~~~~~~~~~~~~~~~~~~cp~c~~~~~ 259 (421)
T TIGR00155 226 LRLCPGCHFTGLPDSIHYDHQDKPCCPRCSTPLY 259 (421)
T ss_pred HHHHHHHHHHCCCHHHCCCCCCCCCCCCCCCCCH
T ss_conf 7765323221131021023211356753345311
Done!