Query 032810
Match_columns 133
No_of_seqs 23 out of 25
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 06:14:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032810.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032810hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08792 A2L_zn_ribbon: A2L zi 97.2 0.00026 5.7E-09 42.8 2.3 31 101-131 2-32 (33)
2 TIGR02642 phage_xxxx uncharact 95.5 0.0078 1.7E-07 48.0 1.8 25 102-128 99-123 (186)
3 PRK12380 hydrogenase nickel in 93.9 0.047 1E-06 39.6 2.4 31 97-129 65-95 (113)
4 PF00684 DnaJ_CXXCXGXG: DnaJ c 93.4 0.069 1.5E-06 35.0 2.3 26 100-128 39-64 (66)
5 PF00684 DnaJ_CXXCXGXG: DnaJ c 93.0 0.078 1.7E-06 34.8 2.1 28 102-129 15-50 (66)
6 PRK00564 hypA hydrogenase nick 91.4 0.11 2.4E-06 37.9 1.5 54 75-130 29-98 (117)
7 PF09297 zf-NADH-PPase: NADH p 91.1 0.12 2.5E-06 30.0 1.1 27 102-128 3-29 (32)
8 TIGR00630 uvra excinuclease AB 90.5 0.15 3.3E-06 48.6 1.9 28 102-129 736-768 (924)
9 TIGR00100 hypA hydrogenase nic 90.5 0.21 4.5E-06 36.3 2.2 54 75-130 29-96 (115)
10 COG0178 UvrA Excinuclease ATPa 90.5 0.16 3.4E-06 49.4 2.0 27 102-128 730-761 (935)
11 PRK03681 hypA hydrogenase nick 89.6 0.29 6.2E-06 35.6 2.3 30 98-129 66-96 (114)
12 PRK03824 hypA hydrogenase nick 89.5 0.31 6.7E-06 36.4 2.5 33 98-130 66-117 (135)
13 PRK00398 rpoP DNA-directed RNA 89.3 0.28 6.2E-06 30.2 1.9 29 102-130 3-31 (46)
14 PRK00349 uvrA excinuclease ABC 89.2 0.21 4.5E-06 47.8 1.7 28 102-129 738-770 (943)
15 PRK00635 excinuclease ABC subu 87.9 0.29 6.3E-06 50.1 1.9 34 95-129 1601-1639(1809)
16 smart00659 RPOLCX RNA polymera 87.2 0.44 9.6E-06 30.2 1.8 26 103-129 3-28 (44)
17 PRK14296 chaperone protein Dna 87.1 0.41 8.8E-06 40.6 2.0 6 123-128 209-214 (372)
18 PF01155 HypA: Hydrogenase exp 87.0 0.32 7E-06 35.0 1.2 54 74-129 28-95 (113)
19 PF07282 OrfB_Zn_ribbon: Putat 86.7 0.38 8.2E-06 30.9 1.3 28 101-128 27-54 (69)
20 TIGR02349 DnaJ_bact chaperone 86.0 0.54 1.2E-05 39.0 2.1 23 102-128 186-208 (354)
21 smart00834 CxxC_CXXC_SSSS Puta 86.0 0.93 2E-05 26.3 2.6 25 104-128 7-34 (41)
22 PRK14295 chaperone protein Dna 85.8 0.69 1.5E-05 39.5 2.8 24 101-128 204-227 (389)
23 PRK14281 chaperone protein Dna 85.8 0.65 1.4E-05 39.6 2.6 24 101-128 204-227 (397)
24 PLN03165 chaperone protein dna 85.7 0.6 1.3E-05 34.8 2.1 12 104-115 54-65 (111)
25 PRK00762 hypA hydrogenase nick 85.5 0.49 1.1E-05 34.8 1.5 55 75-130 29-102 (124)
26 PRK10767 chaperone protein Dna 84.9 0.74 1.6E-05 38.6 2.5 24 101-128 180-203 (371)
27 PRK14285 chaperone protein Dna 84.7 0.73 1.6E-05 38.9 2.4 23 102-128 185-207 (365)
28 COG0675 Transposase and inacti 84.6 0.54 1.2E-05 35.4 1.4 24 101-129 308-331 (364)
29 PRK14284 chaperone protein Dna 84.4 0.73 1.6E-05 39.2 2.3 13 102-114 197-209 (391)
30 PRK14279 chaperone protein Dna 84.4 0.76 1.7E-05 39.2 2.4 24 101-128 211-234 (392)
31 PRK14297 chaperone protein Dna 84.3 0.69 1.5E-05 39.1 2.1 24 101-128 190-213 (380)
32 TIGR03655 anti_R_Lar restricti 84.3 1 2.2E-05 28.6 2.4 30 103-132 2-38 (53)
33 PRK14282 chaperone protein Dna 84.3 0.69 1.5E-05 38.9 2.1 23 102-128 195-217 (369)
34 PF10080 DUF2318: Predicted me 84.1 1.3 2.8E-05 32.5 3.2 40 88-129 22-61 (102)
35 TIGR02349 DnaJ_bact chaperone 83.7 0.88 1.9E-05 37.7 2.4 28 102-129 160-195 (354)
36 PRK14286 chaperone protein Dna 83.7 0.95 2.1E-05 38.3 2.7 25 101-129 188-212 (372)
37 PRK14298 chaperone protein Dna 83.6 0.77 1.7E-05 39.0 2.1 6 123-128 201-206 (377)
38 PF01927 Mut7-C: Mut7-C RNAse 83.5 0.76 1.6E-05 34.1 1.8 27 103-130 92-134 (147)
39 PRK14280 chaperone protein Dna 83.4 0.96 2.1E-05 38.2 2.6 25 101-129 185-209 (376)
40 PF01302 CAP_GLY: CAP-Gly doma 83.0 2.5 5.4E-05 28.2 4.0 55 69-132 10-65 (69)
41 PRK14298 chaperone protein Dna 83.0 0.87 1.9E-05 38.7 2.2 27 103-129 159-193 (377)
42 PRK14289 chaperone protein Dna 82.9 0.87 1.9E-05 38.5 2.1 7 122-128 213-219 (386)
43 PRK14277 chaperone protein Dna 82.8 0.89 1.9E-05 38.6 2.2 22 103-128 199-220 (386)
44 PRK00432 30S ribosomal protein 82.8 0.71 1.5E-05 29.9 1.2 26 102-128 20-45 (50)
45 PRK14282 chaperone protein Dna 82.7 1 2.2E-05 38.0 2.4 27 103-129 170-204 (369)
46 PRK14288 chaperone protein Dna 82.5 1.1 2.3E-05 38.0 2.5 23 102-128 178-200 (369)
47 PF08271 TF_Zn_Ribbon: TFIIB z 82.4 1.1 2.5E-05 27.2 2.0 27 104-130 2-29 (43)
48 PF14354 Lar_restr_allev: Rest 82.4 1.2 2.6E-05 28.0 2.2 26 103-128 4-37 (61)
49 PRK14287 chaperone protein Dna 82.3 0.94 2E-05 38.3 2.1 23 102-128 181-203 (371)
50 COG0484 DnaJ DnaJ-class molecu 82.2 0.91 2E-05 39.9 2.1 37 91-128 131-167 (371)
51 PLN03165 chaperone protein dna 82.2 1.1 2.3E-05 33.5 2.2 21 101-128 74-94 (111)
52 PRK14278 chaperone protein Dna 82.2 1.2 2.6E-05 37.8 2.7 23 102-128 182-204 (378)
53 PRK14280 chaperone protein Dna 82.2 1 2.2E-05 38.2 2.2 27 103-129 161-195 (376)
54 PRK14290 chaperone protein Dna 82.1 1.2 2.7E-05 37.4 2.7 24 101-128 190-213 (365)
55 PRK14296 chaperone protein Dna 82.0 0.94 2E-05 38.4 2.0 27 103-129 167-201 (372)
56 PRK14276 chaperone protein Dna 82.0 1 2.2E-05 38.2 2.2 23 102-128 189-211 (380)
57 PRK14276 chaperone protein Dna 82.0 1 2.2E-05 38.2 2.2 27 103-129 164-198 (380)
58 PRK14289 chaperone protein Dna 81.7 1 2.2E-05 38.1 2.1 26 103-128 172-205 (386)
59 PRK14284 chaperone protein Dna 81.6 1 2.3E-05 38.2 2.1 27 103-129 176-206 (391)
60 PRK14287 chaperone protein Dna 81.5 1.1 2.4E-05 37.9 2.2 27 103-129 156-190 (371)
61 PRK14277 chaperone protein Dna 81.4 1.2 2.7E-05 37.7 2.6 27 103-129 173-207 (386)
62 PRK14297 chaperone protein Dna 81.3 1.2 2.7E-05 37.6 2.5 28 102-129 165-200 (380)
63 COG0484 DnaJ DnaJ-class molecu 81.1 1.2 2.6E-05 39.2 2.4 26 99-128 180-205 (371)
64 PRK14301 chaperone protein Dna 80.9 1.1 2.4E-05 37.9 2.1 24 101-128 182-205 (373)
65 PF07754 DUF1610: Domain of un 80.4 0.96 2.1E-05 26.2 1.1 22 105-127 1-23 (24)
66 PRK14285 chaperone protein Dna 80.4 1.2 2.6E-05 37.6 2.1 27 103-129 164-194 (365)
67 cd00350 rubredoxin_like Rubred 80.3 1.1 2.5E-05 26.2 1.4 22 104-128 3-25 (33)
68 PRK14294 chaperone protein Dna 80.3 1.2 2.7E-05 37.4 2.1 24 101-128 182-205 (366)
69 cd00729 rubredoxin_SM Rubredox 80.2 1.2 2.7E-05 26.6 1.6 24 102-128 2-26 (34)
70 PRK14279 chaperone protein Dna 80.1 1.1 2.5E-05 38.2 1.9 26 103-128 191-220 (392)
71 PRK14290 chaperone protein Dna 80.1 1.1 2.3E-05 37.8 1.7 27 103-129 166-200 (365)
72 PRK10767 chaperone protein Dna 79.9 1.3 2.9E-05 37.1 2.2 26 104-129 161-190 (371)
73 PRK14300 chaperone protein Dna 79.8 1 2.2E-05 38.1 1.5 12 104-115 164-175 (372)
74 PRK14301 chaperone protein Dna 79.4 1.6 3.4E-05 37.0 2.5 27 103-129 162-192 (373)
75 PRK14291 chaperone protein Dna 79.3 1.5 3.3E-05 37.2 2.3 24 100-128 193-216 (382)
76 PRK14293 chaperone protein Dna 79.2 1.7 3.7E-05 36.7 2.6 23 102-128 186-208 (374)
77 PRK14278 chaperone protein Dna 78.8 1.4 3.1E-05 37.3 2.1 26 103-128 157-190 (378)
78 PRK14283 chaperone protein Dna 78.6 1.4 3.1E-05 37.1 2.0 12 104-115 165-176 (378)
79 PRK14295 chaperone protein Dna 78.6 1.4 3E-05 37.7 1.9 26 103-128 184-213 (389)
80 PRK14281 chaperone protein Dna 78.2 1.5 3.3E-05 37.4 2.1 27 103-129 180-214 (397)
81 TIGR02605 CxxC_CxxC_SSSS putat 78.1 2.3 5.1E-05 26.1 2.4 25 104-128 7-34 (52)
82 PTZ00037 DnaJ_C chaperone prot 77.9 1.6 3.4E-05 38.2 2.1 26 101-128 191-216 (421)
83 PF13719 zinc_ribbon_5: zinc-r 77.7 1.4 3E-05 26.5 1.3 27 104-130 4-35 (37)
84 PRK14293 chaperone protein Dna 77.5 1.7 3.8E-05 36.6 2.2 27 103-129 161-195 (374)
85 PRK14291 chaperone protein Dna 77.4 1.7 3.7E-05 36.8 2.2 26 104-129 175-204 (382)
86 PRK14292 chaperone protein Dna 77.3 1.5 3.4E-05 36.7 1.9 13 103-115 158-170 (371)
87 PRK14294 chaperone protein Dna 77.3 1.8 3.9E-05 36.4 2.2 26 104-129 163-192 (366)
88 COG1096 Predicted RNA-binding 76.8 2.4 5.2E-05 34.6 2.7 27 100-128 147-173 (188)
89 PRK14288 chaperone protein Dna 76.2 1.8 4E-05 36.6 2.0 27 103-129 157-187 (369)
90 COG1571 Predicted DNA-binding 76.0 1.1 2.4E-05 40.2 0.7 29 101-130 349-377 (421)
91 PF11781 RRN7: RNA polymerase 76.0 1.8 3.9E-05 26.4 1.4 24 104-128 10-33 (36)
92 PRK14300 chaperone protein Dna 76.0 2.1 4.6E-05 36.2 2.3 24 101-128 183-206 (372)
93 PTZ00037 DnaJ_C chaperone prot 75.9 1.6 3.4E-05 38.2 1.6 10 104-113 168-177 (421)
94 PF09723 Zn-ribbon_8: Zinc rib 75.7 2.5 5.4E-05 25.9 2.0 26 103-128 6-34 (42)
95 PRK14286 chaperone protein Dna 75.4 1.7 3.6E-05 36.9 1.5 26 104-129 169-198 (372)
96 PRK13130 H/ACA RNA-protein com 75.2 2 4.4E-05 28.9 1.6 23 103-131 6-28 (56)
97 PF13453 zf-TFIIB: Transcripti 74.8 1.8 3.9E-05 26.1 1.2 26 104-130 1-29 (41)
98 COG1592 Rubrerythrin [Energy p 74.2 1.6 3.4E-05 34.6 1.1 23 102-127 134-156 (166)
99 TIGR02098 MJ0042_CXXC MJ0042 f 74.0 2.2 4.8E-05 24.9 1.4 28 103-130 3-35 (38)
100 PF13248 zf-ribbon_3: zinc-rib 73.5 1.6 3.4E-05 24.6 0.7 25 102-130 2-26 (26)
101 PHA02942 putative transposase; 72.4 2.1 4.6E-05 36.7 1.5 27 101-128 324-350 (383)
102 PHA00626 hypothetical protein 72.3 2.6 5.7E-05 29.2 1.7 27 104-130 2-33 (59)
103 COG1579 Zn-ribbon protein, pos 72.1 0.86 1.9E-05 37.9 -0.9 31 102-132 197-233 (239)
104 PRK11788 tetratricopeptide rep 71.4 2.2 4.7E-05 33.2 1.2 22 104-129 356-377 (389)
105 PRK12775 putative trifunctiona 71.2 1.8 4E-05 41.3 0.9 30 101-133 820-851 (1006)
106 cd00924 Cyt_c_Oxidase_Vb Cytoc 70.7 4.2 9.1E-05 29.6 2.5 38 86-130 45-89 (97)
107 PRK14283 chaperone protein Dna 70.4 3.6 7.8E-05 34.8 2.4 24 101-128 188-211 (378)
108 COG1656 Uncharacterized conser 69.3 1.8 3.9E-05 34.7 0.4 27 102-129 97-139 (165)
109 COG1107 Archaea-specific RecJ- 69.2 3.1 6.7E-05 39.8 2.0 22 104-128 55-76 (715)
110 PF14319 Zn_Tnp_IS91: Transpos 68.9 3.8 8.2E-05 29.7 2.0 29 101-129 41-69 (111)
111 PF09526 DUF2387: Probable met 68.8 4.6 9.9E-05 28.0 2.3 32 97-128 3-38 (71)
112 PF01096 TFIIS_C: Transcriptio 68.4 3.5 7.6E-05 25.1 1.5 25 104-128 2-36 (39)
113 PF03604 DNA_RNApol_7kD: DNA d 67.8 2.8 6.1E-05 25.3 0.9 25 104-129 2-26 (32)
114 PRK09521 exosome complex RNA-b 67.3 5.9 0.00013 30.4 2.8 34 91-128 141-174 (189)
115 PRK00420 hypothetical protein; 66.9 3.7 8.1E-05 30.8 1.6 28 102-130 23-50 (112)
116 smart00440 ZnF_C2C2 C2C2 Zinc 66.7 4.9 0.00011 24.6 1.9 25 104-128 2-36 (40)
117 PRK14292 chaperone protein Dna 66.4 4.3 9.4E-05 34.1 2.1 24 101-128 182-205 (371)
118 PRK07591 threonine synthase; V 66.0 3.7 8E-05 35.1 1.6 26 102-130 18-43 (421)
119 PF10263 SprT-like: SprT-like 65.9 3.8 8.3E-05 29.3 1.5 32 102-133 123-156 (157)
120 COG0375 HybF Zn finger protein 64.8 4.3 9.2E-05 30.7 1.6 28 99-128 67-94 (115)
121 cd03031 GRX_GRX_like Glutaredo 64.2 4.6 9.9E-05 30.8 1.7 25 103-127 100-140 (147)
122 cd01411 SIR2H SIR2H: Uncharact 64.0 3.4 7.3E-05 32.6 1.0 29 102-130 118-146 (225)
123 PF14803 Nudix_N_2: Nudix N-te 63.8 5.4 0.00012 24.3 1.6 24 103-127 1-29 (34)
124 PRK09263 anaerobic ribonucleos 63.3 3.3 7.3E-05 38.6 1.0 26 103-128 642-667 (711)
125 PF02591 DUF164: Putative zinc 62.8 6.3 0.00014 25.0 1.9 15 116-130 42-56 (56)
126 COG1996 RPC10 DNA-directed RNA 62.2 4.3 9.2E-05 26.9 1.1 26 103-128 7-32 (49)
127 TIGR00373 conserved hypothetic 62.2 3.2 6.9E-05 31.6 0.5 27 104-131 111-139 (158)
128 smart00531 TFIIE Transcription 61.8 2.5 5.3E-05 31.5 -0.1 27 103-130 100-133 (147)
129 TIGR02642 phage_xxxx uncharact 61.1 5.5 0.00012 32.0 1.7 23 96-118 109-131 (186)
130 PRK04023 DNA polymerase II lar 61.1 4 8.8E-05 40.8 1.1 22 101-128 625-646 (1121)
131 PF10058 DUF2296: Predicted in 60.9 5.5 0.00012 26.2 1.4 26 104-129 24-53 (54)
132 PF07295 DUF1451: Protein of u 60.7 5.8 0.00013 30.6 1.7 27 103-129 113-139 (146)
133 TIGR03831 YgiT_finger YgiT-typ 59.4 5.4 0.00012 23.2 1.1 10 120-129 32-41 (46)
134 PRK06266 transcription initiat 59.0 4.4 9.6E-05 31.6 0.8 27 104-131 119-147 (178)
135 TIGR01384 TFS_arch transcripti 58.5 7.6 0.00017 26.8 1.9 27 101-127 61-97 (104)
136 COG5437 Predicted secreted pro 58.1 8.9 0.00019 30.4 2.3 29 70-100 86-117 (138)
137 TIGR02443 conserved hypothetic 57.6 9.9 0.00021 26.2 2.3 32 97-128 4-39 (59)
138 smart00661 RPOL9 RNA polymeras 56.8 7.6 0.00016 23.5 1.5 26 103-129 1-29 (52)
139 PF04606 Ogr_Delta: Ogr/Delta- 56.7 10 0.00022 23.6 2.0 25 104-128 1-35 (47)
140 PLN02294 cytochrome c oxidase 56.4 9.1 0.0002 31.1 2.2 37 87-130 106-151 (174)
141 cd03031 GRX_GRX_like Glutaredo 56.1 9 0.00019 29.2 2.1 11 104-114 135-145 (147)
142 PF12760 Zn_Tnp_IS1595: Transp 55.7 12 0.00027 22.9 2.3 24 104-127 20-44 (46)
143 PRK14714 DNA polymerase II lar 55.0 7.9 0.00017 39.5 2.0 10 102-111 667-676 (1337)
144 TIGR00354 polC DNA polymerase, 53.8 8.5 0.00018 38.5 2.0 24 100-129 623-646 (1095)
145 COG3809 Uncharacterized protei 53.5 9.5 0.00021 28.3 1.8 25 104-129 3-30 (88)
146 PF08274 PhnA_Zn_Ribbon: PhnA 53.4 7.4 0.00016 23.3 1.0 24 104-128 4-27 (30)
147 PRK00635 excinuclease ABC subu 52.9 9.1 0.0002 39.8 2.1 26 103-128 721-748 (1809)
148 PF14599 zinc_ribbon_6: Zinc-r 52.6 9.1 0.0002 26.0 1.4 27 103-129 31-57 (61)
149 PTZ00043 cytochrome c oxidase 52.0 12 0.00027 32.2 2.4 38 86-130 145-191 (268)
150 COG1198 PriA Primosomal protei 52.0 8.8 0.00019 36.4 1.7 13 117-129 472-484 (730)
151 PF15288 zf-CCHC_6: Zinc knuck 50.2 6.4 0.00014 25.2 0.4 9 121-129 2-10 (40)
152 PHA02540 61 DNA primase; Provi 49.2 12 0.00026 32.4 2.0 27 102-128 27-63 (337)
153 PF14446 Prok-RING_1: Prokaryo 48.9 11 0.00023 25.4 1.3 23 103-128 6-29 (54)
154 PRK11032 hypothetical protein; 48.7 12 0.00026 29.5 1.8 28 102-129 124-151 (160)
155 PF02146 SIR2: Sir2 family; I 47.7 12 0.00025 27.9 1.5 30 101-130 104-139 (178)
156 PF13717 zinc_ribbon_4: zinc-r 47.6 12 0.00025 22.6 1.2 27 103-129 3-34 (36)
157 PRK00241 nudC NADH pyrophospha 47.5 12 0.00027 30.3 1.7 27 102-128 99-125 (256)
158 PRK09678 DNA-binding transcrip 46.7 16 0.00036 25.5 2.0 26 104-129 3-38 (72)
159 PRK14704 anaerobic ribonucleos 46.3 9.2 0.0002 35.3 0.9 21 103-128 560-580 (618)
160 TIGR01053 LSD1 zinc finger dom 46.2 15 0.00033 21.9 1.5 27 102-128 1-27 (31)
161 PRK14715 DNA polymerase II lar 45.6 13 0.00027 38.7 1.8 24 100-129 672-695 (1627)
162 cd01675 RNR_III Class III ribo 45.6 10 0.00022 34.2 1.0 21 104-128 520-540 (555)
163 smart00132 LIM Zinc-binding do 44.8 19 0.0004 19.5 1.7 11 121-131 28-38 (39)
164 PF06906 DUF1272: Protein of u 44.5 10 0.00022 26.1 0.7 11 120-130 41-51 (57)
165 PLN02569 threonine synthase 44.2 11 0.00025 33.4 1.1 25 103-130 50-74 (484)
166 PRK05978 hypothetical protein; 43.9 11 0.00024 29.4 0.9 29 102-130 33-62 (148)
167 PF03811 Zn_Tnp_IS1: InsA N-te 43.9 24 0.00053 21.6 2.2 26 101-126 4-35 (36)
168 PF04135 Nop10p: Nucleolar RNA 43.7 22 0.00047 23.8 2.2 21 103-129 6-26 (53)
169 PF03833 PolC_DP2: DNA polymer 42.9 8 0.00017 38.0 0.0 45 79-129 628-676 (900)
170 KOG2907 RNA polymerase I trans 42.9 9.3 0.0002 29.4 0.3 28 100-127 72-109 (116)
171 PRK11827 hypothetical protein; 42.4 13 0.00028 25.3 1.0 35 96-131 2-37 (60)
172 TIGR00595 priA primosomal prot 41.8 14 0.0003 32.6 1.3 24 104-128 224-261 (505)
173 PF12677 DUF3797: Domain of un 41.2 8.7 0.00019 25.8 -0.0 14 115-128 8-21 (49)
174 cd01407 SIR2-fam SIR2 family o 40.8 12 0.00026 29.0 0.7 29 102-130 109-143 (218)
175 TIGR02487 NrdD anaerobic ribon 39.8 13 0.00027 33.8 0.7 22 103-128 525-546 (579)
176 TIGR01206 lysW lysine biosynth 39.2 22 0.00048 23.6 1.7 29 102-130 2-32 (54)
177 PF13465 zf-H2C2_2: Zinc-finge 38.6 13 0.00029 20.4 0.5 15 116-130 10-24 (26)
178 PRK07111 anaerobic ribonucleos 38.5 14 0.00031 34.7 0.9 21 103-128 681-701 (735)
179 PF09082 DUF1922: Domain of un 38.1 21 0.00045 25.2 1.4 25 103-129 4-28 (68)
180 PF01215 COX5B: Cytochrome c o 37.9 15 0.00032 28.5 0.7 40 86-130 77-122 (136)
181 KOG0712 Molecular chaperone (D 37.7 19 0.00041 31.6 1.4 26 101-128 169-194 (337)
182 PF03966 Trm112p: Trm112p-like 37.5 20 0.00043 23.5 1.2 19 114-132 47-65 (68)
183 PHA02998 RNA polymerase subuni 37.3 24 0.00051 29.4 1.9 28 102-129 143-180 (195)
184 smart00731 SprT SprT homologue 36.3 24 0.00053 25.8 1.7 61 73-133 83-146 (146)
185 PF10825 DUF2752: Protein of u 36.0 14 0.00031 23.6 0.4 9 120-128 9-17 (52)
186 PF14952 zf-tcix: Putative tre 35.9 17 0.00037 23.9 0.7 11 119-129 10-20 (44)
187 COG2888 Predicted Zn-ribbon RN 35.7 23 0.00051 24.7 1.4 24 104-128 11-35 (61)
188 PF12172 DUF35_N: Rubredoxin-l 35.7 23 0.00049 20.7 1.2 27 98-129 8-34 (37)
189 PRK08271 anaerobic ribonucleos 35.0 19 0.00041 33.5 1.1 22 103-128 567-588 (623)
190 PF13824 zf-Mss51: Zinc-finger 34.7 22 0.00047 24.1 1.1 21 104-127 1-21 (55)
191 PRK03564 formate dehydrogenase 34.6 24 0.00053 30.3 1.6 45 83-127 154-219 (309)
192 cd01413 SIR2_Af2 SIR2_Af2: Arc 34.5 21 0.00045 28.0 1.1 29 102-130 113-146 (222)
193 PF01396 zf-C4_Topoisom: Topoi 34.5 21 0.00046 21.7 0.9 15 103-118 2-16 (39)
194 PF13597 NRDD: Anaerobic ribon 34.4 20 0.00042 32.3 1.1 21 103-128 492-512 (546)
195 PRK05580 primosome assembly pr 34.3 21 0.00046 32.7 1.3 22 102-128 408-429 (679)
196 cd01410 SIRT7 SIRT7: Eukaryoti 34.2 14 0.0003 28.9 0.1 29 102-130 95-130 (206)
197 PF11331 DUF3133: Protein of u 34.1 28 0.00061 22.7 1.5 8 83-90 1-8 (46)
198 PF10571 UPF0547: Uncharacteri 33.9 21 0.00045 20.6 0.7 10 122-131 2-11 (26)
199 PF13005 zf-IS66: zinc-finger 33.8 38 0.00083 20.2 2.0 8 103-110 3-10 (47)
200 PRK06921 hypothetical protein; 33.7 26 0.00056 28.3 1.5 16 102-117 32-47 (266)
201 PF04216 FdhE: Protein involve 33.5 24 0.00053 28.6 1.4 25 103-127 173-204 (290)
202 PF09865 DUF2092: Predicted pe 33.4 23 0.0005 28.6 1.2 17 70-88 148-164 (214)
203 PRK14890 putative Zn-ribbon RN 33.3 24 0.00051 24.3 1.1 8 120-127 25-32 (59)
204 PRK09710 lar restriction allev 33.2 38 0.00083 23.6 2.1 34 98-131 2-38 (64)
205 PRK14873 primosome assembly pr 33.1 24 0.00052 32.8 1.5 21 102-128 410-430 (665)
206 COG5349 Uncharacterized protei 33.1 13 0.00027 29.1 -0.3 27 103-130 22-50 (126)
207 PF13901 DUF4206: Domain of un 33.0 22 0.00049 27.9 1.1 26 104-129 144-181 (202)
208 TIGR00311 aIF-2beta translatio 32.9 42 0.0009 25.5 2.5 29 103-131 98-129 (133)
209 PF07649 C1_3: C1-like domain; 32.5 22 0.00049 20.0 0.8 22 103-127 1-22 (30)
210 COG0846 SIR2 NAD-dependent pro 32.1 30 0.00065 28.7 1.7 28 101-128 121-154 (250)
211 PRK08270 anaerobic ribonucleos 32.0 23 0.00049 33.0 1.1 22 103-129 627-648 (656)
212 COG2816 NPY1 NTP pyrophosphohy 31.9 27 0.00058 30.0 1.4 27 102-128 111-137 (279)
213 PRK14714 DNA polymerase II lar 31.5 26 0.00056 36.0 1.4 24 102-130 679-702 (1337)
214 PF06677 Auto_anti-p27: Sjogre 31.4 42 0.00091 21.1 1.9 25 102-127 17-41 (41)
215 PRK00183 hypothetical protein; 31.3 11 0.00025 29.4 -0.8 12 118-131 146-157 (157)
216 COG3357 Predicted transcriptio 30.8 28 0.0006 26.3 1.2 29 96-127 51-83 (97)
217 PF09538 FYDLN_acid: Protein o 30.6 29 0.00063 25.6 1.3 29 102-131 9-37 (108)
218 PRK04023 DNA polymerase II lar 30.5 25 0.00054 35.5 1.1 11 101-111 637-647 (1121)
219 PRK08579 anaerobic ribonucleos 30.1 25 0.00055 32.6 1.1 23 102-128 568-590 (625)
220 TIGR01385 TFSII transcription 30.0 35 0.00075 29.0 1.8 30 100-129 256-295 (299)
221 PF09332 Mcm10: Mcm10 replicat 29.9 31 0.00068 30.2 1.5 13 117-129 299-312 (344)
222 COG3813 Uncharacterized protei 29.5 24 0.00051 26.0 0.6 13 118-130 39-51 (84)
223 PF07092 DUF1356: Protein of u 29.3 21 0.00046 30.0 0.4 15 104-118 40-54 (238)
224 PF05180 zf-DNL: DNL zinc fing 29.2 47 0.001 23.0 2.1 29 100-128 2-37 (66)
225 PLN03123 poly [ADP-ribose] pol 29.2 26 0.00056 34.4 1.0 31 91-130 292-322 (981)
226 PF13878 zf-C2H2_3: zinc-finge 29.2 24 0.00052 21.7 0.5 16 94-109 5-20 (41)
227 PF01873 eIF-5_eIF-2B: Domain 29.2 36 0.00078 25.5 1.6 26 103-128 94-122 (125)
228 PTZ00408 NAD-dependent deacety 29.1 26 0.00057 28.3 0.9 29 102-130 117-149 (242)
229 PF11635 Med16: Mediator compl 29.1 23 0.00049 32.9 0.6 30 100-130 711-751 (753)
230 smart00653 eIF2B_5 domain pres 28.8 43 0.00094 24.6 1.9 26 103-128 81-109 (110)
231 PF12773 DZR: Double zinc ribb 28.6 29 0.00063 20.9 0.8 28 102-130 12-39 (50)
232 PF03110 SBP: SBP domain; Int 28.6 26 0.00056 24.9 0.7 31 102-132 21-52 (79)
233 PF00628 PHD: PHD-finger; Int 28.3 36 0.00077 20.3 1.2 23 104-129 1-23 (51)
234 PF11023 DUF2614: Protein of u 28.3 28 0.00061 26.7 0.9 10 121-130 86-95 (114)
235 smart00238 BIR Baculoviral inh 28.0 42 0.00091 21.3 1.5 19 112-130 27-46 (71)
236 PRK00415 rps27e 30S ribosomal 27.5 62 0.0013 22.2 2.3 29 102-130 11-40 (59)
237 PRK08351 DNA-directed RNA poly 27.4 24 0.00053 24.1 0.4 7 122-128 17-23 (61)
238 KOG2593 Transcription initiati 27.3 27 0.00058 31.9 0.7 28 103-130 129-163 (436)
239 COG2260 Predicted Zn-ribbon RN 27.2 28 0.00062 24.1 0.7 21 103-129 6-26 (59)
240 PF05191 ADK_lid: Adenylate ki 27.1 34 0.00073 20.8 0.9 16 102-118 21-36 (36)
241 cd01412 SIRT5_Af1_CobB SIRT5_A 26.4 34 0.00073 26.4 1.0 29 102-130 109-140 (224)
242 PF04438 zf-HIT: HIT zinc fing 26.1 40 0.00087 19.8 1.1 19 103-128 3-21 (30)
243 PRK12722 transcriptional activ 26.0 47 0.001 26.9 1.8 30 99-128 131-162 (187)
244 PRK08665 ribonucleotide-diphos 25.8 39 0.00084 31.9 1.5 23 103-127 725-747 (752)
245 cd04476 RPA1_DBD_C RPA1_DBD_C: 25.5 48 0.0011 24.3 1.7 47 73-130 15-61 (166)
246 TIGR02827 RNR_anaer_Bdell anae 25.5 35 0.00077 31.6 1.2 22 103-128 533-554 (586)
247 KOG3507 DNA-directed RNA polym 25.2 34 0.00073 24.0 0.8 24 104-128 22-45 (62)
248 TIGR01056 topB DNA topoisomera 25.0 37 0.00081 31.3 1.2 26 102-129 611-636 (660)
249 COG1675 TFA1 Transcription ini 24.9 30 0.00065 27.7 0.5 12 119-130 131-142 (176)
250 PF08273 Prim_Zn_Ribbon: Zinc- 24.9 46 0.00099 20.9 1.2 26 103-128 4-34 (40)
251 PF08209 Sgf11: Sgf11 (transcr 24.3 45 0.00098 20.3 1.1 12 118-129 2-13 (33)
252 COG2835 Uncharacterized conser 24.2 65 0.0014 22.3 2.0 36 97-132 3-38 (60)
253 PF10071 DUF2310: Zn-ribbon-co 23.9 37 0.0008 28.8 0.9 27 101-127 219-248 (258)
254 PRK08332 ribonucleotide-diphos 23.9 38 0.00082 35.5 1.1 26 101-127 1703-1733(1740)
255 PF00096 zf-C2H2: Zinc finger, 23.9 26 0.00056 17.8 -0.0 10 121-130 1-10 (23)
256 PF05515 Viral_NABP: Viral nuc 23.4 20 0.00043 27.7 -0.7 13 118-130 60-72 (124)
257 PRK06393 rpoE DNA-directed RNA 23.4 32 0.00069 23.9 0.3 15 97-111 12-26 (64)
258 COG2051 RPS27A Ribosomal prote 23.1 66 0.0014 22.8 1.9 28 103-130 20-48 (67)
259 PRK14892 putative transcriptio 22.8 66 0.0014 23.6 1.9 26 103-129 22-51 (99)
260 smart00778 Prim_Zn_Ribbon Zinc 22.8 40 0.00086 20.9 0.7 9 120-128 3-11 (37)
261 COG4049 Uncharacterized protei 22.7 33 0.00071 24.2 0.3 12 119-130 16-27 (65)
262 COG2103 Predicted sugar phosph 22.5 22 0.00047 31.2 -0.7 23 77-99 132-155 (298)
263 KOG0712 Molecular chaperone (D 22.4 46 0.00099 29.2 1.2 25 104-128 145-178 (337)
264 PF08063 PADR1: PADR1 (NUC008) 22.4 58 0.0013 21.3 1.4 18 101-118 13-30 (55)
265 PRK00481 NAD-dependent deacety 22.4 41 0.00088 26.5 0.8 27 102-130 122-152 (242)
266 PF01807 zf-CHC2: CHC2 zinc fi 22.1 54 0.0012 22.8 1.3 25 104-128 35-62 (97)
267 PF05876 Terminase_GpA: Phage 21.8 44 0.00096 30.1 1.0 17 50-66 131-147 (557)
268 COG4734 ArdA Antirestriction p 21.7 32 0.0007 28.5 0.1 12 119-130 46-57 (193)
269 PRK07218 replication factor A; 21.7 44 0.00096 29.8 1.0 20 103-128 298-317 (423)
270 cd02345 ZZ_dah Zinc finger, ZZ 21.7 66 0.0014 20.3 1.5 23 104-129 2-24 (49)
271 COG5257 GCD11 Translation init 21.2 52 0.0011 30.0 1.3 26 102-130 57-82 (415)
272 PF14690 zf-ISL3: zinc-finger 20.9 62 0.0013 19.1 1.2 15 103-117 3-17 (47)
273 KOG2824 Glutaredoxin-related p 20.6 71 0.0015 27.8 2.0 13 103-115 230-242 (281)
274 PF14205 Cys_rich_KTR: Cystein 20.6 70 0.0015 21.9 1.5 24 104-127 6-35 (55)
275 PF06827 zf-FPG_IleRS: Zinc fi 20.5 78 0.0017 17.7 1.5 25 103-127 2-28 (30)
276 TIGR01562 FdhE formate dehydro 20.4 51 0.0011 28.2 1.1 45 83-127 151-217 (305)
277 PF01485 IBR: IBR domain; Int 20.4 45 0.00098 20.1 0.6 27 103-129 19-49 (64)
278 PF10609 ParA: ParA/MinD ATPas 20.4 68 0.0015 22.7 1.5 15 116-130 61-75 (81)
279 TIGR00595 priA primosomal prot 20.2 71 0.0015 28.3 2.0 19 104-131 215-233 (505)
280 PRK03988 translation initiatio 20.1 88 0.0019 23.9 2.2 29 103-131 103-134 (138)
281 cd00296 SIR2 SIR2 superfamily 20.0 48 0.001 24.9 0.8 27 102-130 113-144 (222)
No 1
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=97.22 E-value=0.00026 Score=42.84 Aligned_cols=31 Identities=42% Similarity=0.967 Sum_probs=27.3
Q ss_pred eeeeccccccceeEeecCeeecCCCCCCCcc
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGMSYG 131 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGGFl~ 131 (133)
.+++|+.|++.||+.+++.+.-|+.||--.|
T Consensus 2 ~~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 2 NLKKCSKCGGNGIVNKEDDYEVCIFCGSSFP 32 (33)
T ss_pred CceEcCCCCCCeEEEecCCeEEcccCCcEee
Confidence 4689999999999999999999999996554
No 2
>TIGR02642 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q.
Probab=95.49 E-value=0.0078 Score=48.02 Aligned_cols=25 Identities=32% Similarity=0.856 Sum_probs=23.0
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
|+.|+.|+|+|.+.++. .+|+.|+|
T Consensus 99 ~~~C~~C~G~G~~i~~~--~~C~~C~G 123 (186)
T TIGR02642 99 SCKCPRCRGTGLIQRRQ--RECDTCAG 123 (186)
T ss_pred CCcCCCCCCeeEEecCC--CCCCCCCC
Confidence 89999999999998865 78999998
No 3
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=93.88 E-value=0.047 Score=39.63 Aligned_cols=31 Identities=26% Similarity=0.347 Sum_probs=22.9
Q ss_pred eeeeeeeeccccccceeEeecCeeecCCCCCCC
Q 032810 97 KRIIAQRRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 97 KRIi~Q~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
.++-.+-+|..|+.. ...+.+++.||.||++
T Consensus 65 ~~vp~~~~C~~Cg~~--~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 65 VYKPAQAWCWDCSQV--VEIHQHDAQCPHCHGE 95 (113)
T ss_pred EeeCcEEEcccCCCE--EecCCcCccCcCCCCC
Confidence 456678899999943 3344566779999986
No 4
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and 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 [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=93.37 E-value=0.069 Score=35.04 Aligned_cols=26 Identities=31% Similarity=0.775 Sum_probs=12.4
Q ss_pred eeeeeccccccceeEeecCeeecCCCCCC
Q 032810 100 IAQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 100 i~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
..|..|+.|+|+|-+. ...+|+.|.|
T Consensus 39 ~~~~~C~~C~G~G~~i---~~~~C~~C~G 64 (66)
T PF00684_consen 39 QMQQTCPKCGGTGKII---EKDPCKTCKG 64 (66)
T ss_dssp EEEEE-TTTSSSSEE----TSSB-SSSTT
T ss_pred EEEEECCCCcceeeEE---CCCCCCCCCC
Confidence 4455566666666554 2235666655
No 5
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and 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 [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=93.02 E-value=0.078 Score=34.80 Aligned_cols=28 Identities=39% Similarity=0.897 Sum_probs=21.3
Q ss_pred eeeccccccceeEeecC--------eeecCCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREK--------DYFKCPECGMS 129 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~--------~~~kC~~CGGF 129 (133)
.+.|+.|+|+|.|.... ....|+.|+|.
T Consensus 15 ~~~C~~C~G~G~~~~~~~~~~~~~~~~~~C~~C~G~ 50 (66)
T PF00684_consen 15 PKTCPQCNGSGQVTRRQQTPGGVFQMQQTCPKCGGT 50 (66)
T ss_dssp -EE-TTSSSSSEEEEEEESSSTTEEEEEE-TTTSSS
T ss_pred CcCCcCCCCeeEEEEEEeCCCeEEEEEEECCCCcce
Confidence 45899999999998764 57889999984
No 6
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=91.37 E-value=0.11 Score=37.87 Aligned_cols=54 Identities=17% Similarity=0.280 Sum_probs=32.2
Q ss_pred eEEEEeeeecccee--------------EEeeeeec-eeeeeeeeccccccceeEeecC-eeecCCCCCCCc
Q 032810 75 WQIIVGAIAGVTPF--------------VVAGIEFS-KRIIAQRRCEVCGGSGLVLREK-DYFKCPECGMSY 130 (133)
Q Consensus 75 Wqi~vG~iAGv~PF--------------vvAg~EF~-KRIi~Q~rCe~C~GsGLV~r~~-~~~kC~~CGGFl 130 (133)
=.+-||-++||.|= +.+|-|+- .++-++-+|..|+-. ...+. .+++||.||++-
T Consensus 29 V~l~IG~ls~V~pe~L~faf~~~~~~T~~~ega~L~Ie~vp~~~~C~~Cg~~--~~~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 29 VVVGIGERSGMDKSLFVSAFETFREESLVCKDAILDIVDEKVELECKDCSHV--FKPNALDYGVCEKCHSKN 98 (117)
T ss_pred EEEEEccccCcCHHHHHHHHHHHhcCCcccCCCEEEEEecCCEEEhhhCCCc--cccCCccCCcCcCCCCCc
Confidence 34567777777661 11222221 345567899999933 22323 456799999974
No 7
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=91.13 E-value=0.12 Score=30.04 Aligned_cols=27 Identities=30% Similarity=0.613 Sum_probs=18.7
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.+-|+.||+.=....+...++||.||-
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CcccCcCCccccCCCCcCEeECCCCcC
Confidence 477999999988888889999999984
No 8
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.53 E-value=0.15 Score=48.57 Aligned_cols=28 Identities=36% Similarity=0.776 Sum_probs=24.4
Q ss_pred eeeccccccceeEeecC-----eeecCCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREK-----DYFKCPECGMS 129 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~-----~~~kC~~CGGF 129 (133)
+-||+.|+|.|.+..+- -+..|+.|+|.
T Consensus 736 ~G~C~~C~G~G~~~~~~~f~~~~~~~C~~C~G~ 768 (924)
T TIGR00630 736 GGRCEACQGDGVIKIEMHFLPDVYVPCEVCKGK 768 (924)
T ss_pred CCCCCCCccceEEEEEccCCCCcccCCCCcCCc
Confidence 68999999999999763 47899999995
No 9
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=90.53 E-value=0.21 Score=36.29 Aligned_cols=54 Identities=24% Similarity=0.499 Sum_probs=33.7
Q ss_pred eEEEEeeeeccceeEE-------------eeeee-ceeeeeeeeccccccceeEeecCeeecCCCCCCCc
Q 032810 75 WQIIVGAIAGVTPFVV-------------AGIEF-SKRIIAQRRCEVCGGSGLVLREKDYFKCPECGMSY 130 (133)
Q Consensus 75 Wqi~vG~iAGv~PFvv-------------Ag~EF-~KRIi~Q~rCe~C~GsGLV~r~~~~~kC~~CGGFl 130 (133)
=.+.||-++||.|=.+ .|-|. =+.+-+.-+|..|+- -+..+.+++.||.||+.-
T Consensus 29 V~l~iG~ls~V~p~~L~faf~~~~~~t~~ega~L~I~~~p~~~~C~~Cg~--~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 29 VTLEIGELSCVNPSQLQFAFEVVREGTVAEGAKLNIEDEPVECECEDCSE--EVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred EEEEEccccccCHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcccCCC--EEecCCcCccCcCCcCCC
Confidence 3456787877776221 11111 134556789999993 333445678999999864
No 10
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=90.50 E-value=0.16 Score=49.36 Aligned_cols=27 Identities=37% Similarity=0.823 Sum_probs=24.1
Q ss_pred eeeccccccceeEeec-----CeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLRE-----KDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~-----~~~~kC~~CGG 128 (133)
.-|||.|+|.|.++-+ +-|..|+.|.|
T Consensus 730 GGRCe~C~GdG~ikIeM~FLpdVyv~CevC~G 761 (935)
T COG0178 730 GGRCEACQGDGVIKIEMHFLPDVYVPCEVCHG 761 (935)
T ss_pred CcCCccccCCceEEEEeccCCCceeeCCCcCC
Confidence 4699999999999977 45899999998
No 11
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=89.62 E-value=0.29 Score=35.62 Aligned_cols=30 Identities=27% Similarity=0.502 Sum_probs=21.3
Q ss_pred eeeeeeeccccccceeEeecCe-eecCCCCCCC
Q 032810 98 RIIAQRRCEVCGGSGLVLREKD-YFKCPECGMS 129 (133)
Q Consensus 98 RIi~Q~rCe~C~GsGLV~r~~~-~~kC~~CGGF 129 (133)
++=++-+|..|+- .+....+ +++||.||++
T Consensus 66 ~~p~~~~C~~Cg~--~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 66 EQEAECWCETCQQ--YVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred eeCcEEEcccCCC--eeecCCccCCcCcCcCCC
Confidence 4556789999994 3434333 4889999986
No 12
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=89.52 E-value=0.31 Score=36.40 Aligned_cols=33 Identities=27% Similarity=0.622 Sum_probs=22.9
Q ss_pred eeeeeeeccccccceeEee-------------------cCeeecCCCCCCCc
Q 032810 98 RIIAQRRCEVCGGSGLVLR-------------------EKDYFKCPECGMSY 130 (133)
Q Consensus 98 RIi~Q~rCe~C~GsGLV~r-------------------~~~~~kC~~CGGFl 130 (133)
++-..-+|..||-.--+.. ...+++||.||+.-
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 4446679999996544431 04678899999863
No 13
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=89.35 E-value=0.28 Score=30.16 Aligned_cols=29 Identities=24% Similarity=0.574 Sum_probs=19.8
Q ss_pred eeeccccccceeEeecCeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGGFl 130 (133)
.-+|+.|+..=-+..+....+||.||.-+
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeE
Confidence 45899998843333333389999999854
No 14
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=89.16 E-value=0.21 Score=47.80 Aligned_cols=28 Identities=36% Similarity=0.796 Sum_probs=24.2
Q ss_pred eeeccccccceeEeec-----CeeecCCCCCCC
Q 032810 102 QRRCEVCGGSGLVLRE-----KDYFKCPECGMS 129 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~-----~~~~kC~~CGGF 129 (133)
+-||+.|+|.|.|..+ +-+..|+.|+|.
T Consensus 738 ~G~C~~C~G~G~~~~~~~f~~~~~~~C~~C~G~ 770 (943)
T PRK00349 738 GGRCEACQGDGVIKIEMHFLPDVYVPCDVCKGK 770 (943)
T ss_pred CCCCCcccccceEEEEeccCCCccccCccccCc
Confidence 6789999999999976 347899999995
No 15
>PRK00635 excinuclease ABC subunit A; Provisional
Probab=87.89 E-value=0.29 Score=50.07 Aligned_cols=34 Identities=29% Similarity=0.556 Sum_probs=27.3
Q ss_pred eceeeeeeeeccccccceeEeec-----CeeecCCCCCCC
Q 032810 95 FSKRIIAQRRCEVCGGSGLVLRE-----KDYFKCPECGMS 129 (133)
Q Consensus 95 F~KRIi~Q~rCe~C~GsGLV~r~-----~~~~kC~~CGGF 129 (133)
||=. ..+-|||.|+|.|.+.-+ +-+..|+.|+|.
T Consensus 1601 FSfN-~~~GrC~~C~G~G~i~i~m~fl~dv~~~C~~C~G~ 1639 (1809)
T PRK00635 1601 FSTN-TKQGQCSDCWGLGYQWIDRAFYALEKRPCPTCSGF 1639 (1809)
T ss_pred cccc-CCCCCCCCCccCceEEEecccCCCcccCCCCCCCc
Confidence 4444 347899999999999876 458899999994
No 16
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=87.24 E-value=0.44 Score=30.18 Aligned_cols=26 Identities=35% Similarity=0.866 Sum_probs=18.6
Q ss_pred eeccccccceeEeecCeeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
-+|..|+..= -..+....+||+||.-
T Consensus 3 Y~C~~Cg~~~-~~~~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGREN-EIKSKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEe-ecCCCCceECCCCCce
Confidence 3688998752 2235688999999963
No 17
>PRK14296 chaperone protein DnaJ; Provisional
Probab=87.05 E-value=0.41 Score=40.60 Aligned_cols=6 Identities=33% Similarity=1.038 Sum_probs=3.1
Q ss_pred CCCCCC
Q 032810 123 CPECGM 128 (133)
Q Consensus 123 C~~CGG 128 (133)
|+.|.|
T Consensus 209 C~~C~G 214 (372)
T PRK14296 209 CKNCKG 214 (372)
T ss_pred ccCCCC
Confidence 555554
No 18
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=87.02 E-value=0.32 Score=35.04 Aligned_cols=54 Identities=30% Similarity=0.622 Sum_probs=29.3
Q ss_pred eeEEEEeeeeccceeEE-------------eeeee-ceeeeeeeeccccccceeEeecCeeecCCCCCCC
Q 032810 74 TWQIIVGAIAGVTPFVV-------------AGIEF-SKRIIAQRRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 74 ~Wqi~vG~iAGv~PFvv-------------Ag~EF-~KRIi~Q~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
.=.+.||-++||.|=.+ .|.|+ -.++=++-+|..|+-..-+.... +.||.||+.
T Consensus 28 ~V~l~iG~ls~V~pe~L~f~f~~~~~~T~~e~a~L~Ie~~p~~~~C~~Cg~~~~~~~~~--~~CP~Cgs~ 95 (113)
T PF01155_consen 28 KVRLEIGELSGVEPEALRFAFEVLAEGTILEGAELEIEEVPARARCRDCGHEFEPDEFD--FSCPRCGSP 95 (113)
T ss_dssp EEEEEEETTS---HHHHHHHHHHHHCCSTTTT-EEEEEEE--EEEETTTS-EEECHHCC--HH-SSSSSS
T ss_pred EEEEEECCcccCCHHHHHHHHHHHhCCCCccCCEEEEEecCCcEECCCCCCEEecCCCC--CCCcCCcCC
Confidence 34566777777777322 11111 13455678999999877665444 789999986
No 19
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=86.67 E-value=0.38 Score=30.94 Aligned_cols=28 Identities=32% Similarity=0.847 Sum_probs=22.7
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.-+.|+.|+...--.+....+.|+.||-
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGF 54 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCC
Confidence 4678999998765556778999999985
No 20
>TIGR02349 DnaJ_bact chaperone protein DnaJ. This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.
Probab=86.01 E-value=0.54 Score=38.99 Aligned_cols=23 Identities=39% Similarity=1.081 Sum_probs=10.1
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
|..|..|+|.|-+.++ +|+.|.|
T Consensus 186 ~~~C~~C~G~G~~~~~----~C~~C~G 208 (354)
T TIGR02349 186 QQTCPTCGGEGKIIKE----PCSTCKG 208 (354)
T ss_pred EEecCCCCCcceecCC----CCCCCCC
Confidence 3344444444444322 3555554
No 21
>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=86.00 E-value=0.93 Score=26.28 Aligned_cols=25 Identities=48% Similarity=0.980 Sum_probs=18.0
Q ss_pred eccccccceeEee---cCeeecCCCCCC
Q 032810 104 RCEVCGGSGLVLR---EKDYFKCPECGM 128 (133)
Q Consensus 104 rCe~C~GsGLV~r---~~~~~kC~~CGG 128 (133)
+|..|+-.=-+.. +.....||+||+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 8999987433332 256888999998
No 22
>PRK14295 chaperone protein DnaJ; Provisional
Probab=85.84 E-value=0.69 Score=39.45 Aligned_cols=24 Identities=29% Similarity=0.721 Sum_probs=19.2
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|..|..|+|.|.+.++ +|+.|.|
T Consensus 204 ~~~~C~~C~G~G~~~~~----~C~~C~G 227 (389)
T PRK14295 204 LSEPCPDCKGRGLIADD----PCLVCKG 227 (389)
T ss_pred EEEecCCCcceeEEecc----CCCCCCC
Confidence 57789999999988643 5999987
No 23
>PRK14281 chaperone protein DnaJ; Provisional
Probab=85.77 E-value=0.65 Score=39.61 Aligned_cols=24 Identities=38% Similarity=1.023 Sum_probs=17.1
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|..|..|+|.|-+.++ +|+.|.|
T Consensus 204 ~~~~C~~C~G~G~~~~~----~C~~C~G 227 (397)
T PRK14281 204 NITACPTCGGEGRVVKD----RCPACYG 227 (397)
T ss_pred EEEecCCCcceeeeeCC----CCCCCCC
Confidence 36678888888877543 4888887
No 24
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=85.67 E-value=0.6 Score=34.82 Aligned_cols=12 Identities=50% Similarity=0.908 Sum_probs=5.6
Q ss_pred eccccccceeEe
Q 032810 104 RCEVCGGSGLVL 115 (133)
Q Consensus 104 rCe~C~GsGLV~ 115 (133)
.|..|+|+|.+.
T Consensus 54 ~C~~C~G~G~v~ 65 (111)
T PLN03165 54 VCRFCVGSGNVT 65 (111)
T ss_pred CCCCCcCcCeEE
Confidence 444444444443
No 25
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=85.52 E-value=0.49 Score=34.85 Aligned_cols=55 Identities=22% Similarity=0.506 Sum_probs=32.1
Q ss_pred eEEEEeeeeccceeEE-------------eeeeec-eeeeeeeeccccccceeEeec---C--eeecCCCCCCCc
Q 032810 75 WQIIVGAIAGVTPFVV-------------AGIEFS-KRIIAQRRCEVCGGSGLVLRE---K--DYFKCPECGMSY 130 (133)
Q Consensus 75 Wqi~vG~iAGv~PFvv-------------Ag~EF~-KRIi~Q~rCe~C~GsGLV~r~---~--~~~kC~~CGGFl 130 (133)
=.+.||-++||.|=++ +|-|+- .++=++-+| .|+-..-+... . .++.||.||++-
T Consensus 29 V~l~IG~ls~V~pe~L~faf~~~~~gT~~egA~L~I~~vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~ 102 (124)
T PRK00762 29 VTLEIGRLTMLNPEQLRFMLDVLAEGTIAEDADLIVEMIPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKR 102 (124)
T ss_pred EEEEECCccccCHHHHHHHHHHHhCCCCcCCCEEEEEecCeeEEe-eCcCcccccccchhccccCCcCcCCCCCC
Confidence 3456777777776221 222221 345577899 99955333211 1 247899999864
No 26
>PRK10767 chaperone protein DnaJ; Provisional
Probab=84.89 E-value=0.74 Score=38.60 Aligned_cols=24 Identities=29% Similarity=0.809 Sum_probs=15.0
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|..|..|+|.|.+.+ .+|+.|.|
T Consensus 180 ~~~~C~~C~G~G~~~~----~~C~~C~G 203 (371)
T PRK10767 180 VQQTCPTCHGRGKIIK----DPCKKCHG 203 (371)
T ss_pred EEEeCCCCCCceeECC----CCCCCCCC
Confidence 4556777777776543 34777776
No 27
>PRK14285 chaperone protein DnaJ; Provisional
Probab=84.72 E-value=0.73 Score=38.91 Aligned_cols=23 Identities=26% Similarity=0.759 Sum_probs=10.7
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
|..|..|+|.|-+.++ +|+.|.|
T Consensus 185 ~~~C~~C~G~G~~~~~----~C~~C~G 207 (365)
T PRK14285 185 TTTCPKCYGNGKIISN----PCKSCKG 207 (365)
T ss_pred eeecCCCCCcccccCC----CCCCCCC
Confidence 4445555555544322 3555554
No 28
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=84.59 E-value=0.54 Score=35.43 Aligned_cols=24 Identities=38% Similarity=1.054 Sum_probs=19.6
Q ss_pred eeeeccccccceeEeecCeeecCCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
..+.|+.||. .....++||.||-.
T Consensus 308 tS~~C~~cg~-----~~~r~~~C~~cg~~ 331 (364)
T COG0675 308 TSKTCPCCGH-----LSGRLFKCPRCGFV 331 (364)
T ss_pred CcccccccCC-----ccceeEECCCCCCe
Confidence 3478999999 55778999999965
No 29
>PRK14284 chaperone protein DnaJ; Provisional
Probab=84.44 E-value=0.73 Score=39.17 Aligned_cols=13 Identities=46% Similarity=1.055 Sum_probs=5.6
Q ss_pred eeeccccccceeE
Q 032810 102 QRRCEVCGGSGLV 114 (133)
Q Consensus 102 Q~rCe~C~GsGLV 114 (133)
|..|..|+|.|-+
T Consensus 197 ~~~C~~C~G~G~~ 209 (391)
T PRK14284 197 ASTCPECGGEGRV 209 (391)
T ss_pred EEECCCCCCCCcc
Confidence 3344444444433
No 30
>PRK14279 chaperone protein DnaJ; Provisional
Probab=84.37 E-value=0.76 Score=39.23 Aligned_cols=24 Identities=29% Similarity=0.818 Sum_probs=17.9
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|..|..|+|.|-+-++ +|+.|.|
T Consensus 211 ~~~~C~~C~G~G~~i~~----~C~~C~G 234 (392)
T PRK14279 211 FSEPCTDCRGTGSIIED----PCEECKG 234 (392)
T ss_pred EEEecCCCCceeEEeCC----cCCCCCC
Confidence 56788888888877543 4888887
No 31
>PRK14297 chaperone protein DnaJ; Provisional
Probab=84.34 E-value=0.69 Score=39.07 Aligned_cols=24 Identities=38% Similarity=0.895 Sum_probs=12.8
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|..|..|+|.|.+.+ .+|+.|.|
T Consensus 190 ~~~~C~~C~G~G~~~~----~~C~~C~G 213 (380)
T PRK14297 190 STTTCDKCGGSGKVIE----DPCNKCHG 213 (380)
T ss_pred EEEeCCCCCCCceEcC----CCCCCCCC
Confidence 3555555555555533 23666655
No 32
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=84.33 E-value=1 Score=28.58 Aligned_cols=30 Identities=40% Similarity=0.994 Sum_probs=22.2
Q ss_pred eeccccccceeEee-------cCeeecCCCCCCCccc
Q 032810 103 RRCEVCGGSGLVLR-------EKDYFKCPECGMSYGL 132 (133)
Q Consensus 103 ~rCe~C~GsGLV~r-------~~~~~kC~~CGGFl~~ 132 (133)
+.|+-|||.....+ +..+++|..||--.|.
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 57999999988444 1247799999976653
No 33
>PRK14282 chaperone protein DnaJ; Provisional
Probab=84.32 E-value=0.69 Score=38.92 Aligned_cols=23 Identities=48% Similarity=1.048 Sum_probs=10.7
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
|..|..|+|.|-+.+ -+|+.|.|
T Consensus 195 ~~~C~~C~G~G~~~~----~~C~~C~G 217 (369)
T PRK14282 195 ERTCERCGGTGKIPG----EYCHECGG 217 (369)
T ss_pred EEECCCCCCcceeCC----CCCCCCCC
Confidence 344555555554432 23556655
No 34
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=84.14 E-value=1.3 Score=32.48 Aligned_cols=40 Identities=25% Similarity=0.632 Sum_probs=30.5
Q ss_pred eEEeeeeeceeeeeeeeccccccceeEeecCeeecCCCCCCC
Q 032810 88 FVVAGIEFSKRIIAQRRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 88 FvvAg~EF~KRIi~Q~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
|++..-+ |+=.++--.|+.|++.|..+++. ..-|..||--
T Consensus 22 f~i~~~d-g~~~va~daCeiC~~~GY~q~g~-~lvC~~C~~~ 61 (102)
T PF10080_consen 22 FAIKKPD-GSYRVAFDACEICGPKGYYQEGD-QLVCKNCGVR 61 (102)
T ss_pred EEEECCC-CCEEEEEEeccccCCCceEEECC-EEEEecCCCE
Confidence 4445555 77777888999999999997665 4569999853
No 35
>TIGR02349 DnaJ_bact chaperone protein DnaJ. This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.
Probab=83.72 E-value=0.88 Score=37.72 Aligned_cols=28 Identities=39% Similarity=0.991 Sum_probs=21.4
Q ss_pred eeeccccccceeEeecCe--------eecCCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKD--------YFKCPECGMS 129 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~--------~~kC~~CGGF 129 (133)
...|..|+|+|.|..... ...|+.|+|.
T Consensus 160 ~~~C~~C~G~G~~~~~~~~~~g~~~~~~~C~~C~G~ 195 (354)
T TIGR02349 160 PKTCPTCGGTGQVRRQQGTPFGFFQQQQTCPTCGGE 195 (354)
T ss_pred CccCCCCCCeeEEEEEEeccCCceEEEEecCCCCCc
Confidence 357999999998775542 4689999884
No 36
>PRK14286 chaperone protein DnaJ; Provisional
Probab=83.67 E-value=0.95 Score=38.31 Aligned_cols=25 Identities=32% Similarity=0.865 Sum_probs=18.4
Q ss_pred eeeeccccccceeEeecCeeecCCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
.|..|..|+|.|-+.++ +|+.|.|.
T Consensus 188 ~~~~C~~C~G~G~~~~~----~C~~C~G~ 212 (372)
T PRK14286 188 VATTCPTCRGKGTVISN----PCKTCGGQ 212 (372)
T ss_pred EEEeCCCCCceeeEecc----cCCCCCCC
Confidence 56688888888877643 48888873
No 37
>PRK14298 chaperone protein DnaJ; Provisional
Probab=83.57 E-value=0.77 Score=39.02 Aligned_cols=6 Identities=50% Similarity=1.420 Sum_probs=3.2
Q ss_pred CCCCCC
Q 032810 123 CPECGM 128 (133)
Q Consensus 123 C~~CGG 128 (133)
|+.|.|
T Consensus 201 C~~C~G 206 (377)
T PRK14298 201 CPVCSG 206 (377)
T ss_pred CCCCCC
Confidence 555554
No 38
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=83.50 E-value=0.76 Score=34.08 Aligned_cols=27 Identities=41% Similarity=1.072 Sum_probs=19.6
Q ss_pred eeccccccceeEeecC----------------eeecCCCCCCCc
Q 032810 103 RRCEVCGGSGLVLREK----------------DYFKCPECGMSY 130 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~----------------~~~kC~~CGGFl 130 (133)
.||..|+| =|+.-++ .+.+|+.||-.+
T Consensus 92 sRC~~CN~-~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 92 SRCPKCNG-PLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CccCCCCc-EeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 59999999 4544332 388999999653
No 39
>PRK14280 chaperone protein DnaJ; Provisional
Probab=83.40 E-value=0.96 Score=38.25 Aligned_cols=25 Identities=32% Similarity=0.868 Sum_probs=15.5
Q ss_pred eeeeccccccceeEeecCeeecCCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
.|..|..|+|.|-+.+ -+|+.|.|.
T Consensus 185 ~~~~C~~C~G~G~~~~----~~C~~C~G~ 209 (376)
T PRK14280 185 NRQTCPHCNGTGQEIK----EKCPTCHGK 209 (376)
T ss_pred EEEEcCCCCCCCceec----CCCCCCCCc
Confidence 3556777777776543 337777763
No 40
>PF01302 CAP_GLY: CAP-Gly domain; InterPro: IPR000938 Cytoskeleton-associated proteins (CAP) are made of three distinct parts, an N-terminal section that is most probably globular and contains the CAP-Gly domain, a large central region predicted to be in an alpha-helical coiled-coil conformation and, finally, a short C-terminal globular domain. The CAP-Gly domain is a conserved, glycine-rich domain of about 42 residues found in some CAPs []. Proteins known to contain this domain include restin (also known as cytoplasmic linker protein-170 or CLIP-170), a 160 kDa protein associated with intermediate filaments and that links endocytic vesicles to microtubules; vertebrate dynactin (150 kDa dynein-associated polypeptide; DAP) and Drosophila glued, a major component of activator I; yeast protein BIK1, which seems to be required for the formation or stabilisation of microtubules during mitosis and for spindle pole body fusion during conjugation; yeast protein NIP100 (NIP80); human protein CKAP1/TFCB; Schizosaccharomyces pombe protein alp11 and Caenorhabditis elegans hypothetical protein F53F4.3. The latter proteins contain a N-terminal ubiquitin domain and a C-terminal CAP-Gly domain. The crystal structure of the CAP-Gly domain of C. elegans F53F4.3 protein, solved by single wavelength sulphur-anomalous phasing, revealed a novel protein fold containing three beta-sheets. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove. Residues in the groove are highly conserved as measured from the information content of the aligned sequences. The C-terminal tail of another molecule in the crystal is bound in this groove []. ; PDB: 2CP6_A 2E4H_A 2E3H_A 3E2U_B 2HL3_B 3TQ7_Q 2HKQ_B 2HQH_A 2HKN_B 2HL5_C ....
Probab=83.03 E-value=2.5 Score=28.25 Aligned_cols=55 Identities=20% Similarity=0.388 Sum_probs=36.8
Q ss_pred CCcceeeEEEEeeeeccceeEEeeeeeceeeeeeeeccccccceeEeecCeeecC-CCCCCCccc
Q 032810 69 VTAEVTWQIIVGAIAGVTPFVVAGIEFSKRIIAQRRCEVCGGSGLVLREKDYFKC-PECGMSYGL 132 (133)
Q Consensus 69 ~~~e~~Wqi~vG~iAGv~PFvvAg~EF~KRIi~Q~rCe~C~GsGLV~r~~~~~kC-~~CGGFl~~ 132 (133)
+......--|+|-+.+..+=.|+|+|+-.. -..+.|+ ..+++||.| |.+|-|++.
T Consensus 10 ~~~~~G~vryiG~~~~~~~g~~vGVEld~~------~G~~dGt---~~G~rYF~c~~~~G~Fv~~ 65 (69)
T PF01302_consen 10 PGGRRGTVRYIGPVPGFKSGIWVGVELDEP------RGKNDGT---VKGKRYFECPPNHGIFVRP 65 (69)
T ss_dssp TTTEEEEEEEEEE-SSSSSSEEEEEEESSS------TSSBSSE---ETTEESS-SSTTTEEEEEG
T ss_pred CCCCEEEEEEEeeCCCCCCCEEEEEEEcCC------CCCCCcE---ECCEEEeeeCCCCEEEecH
Confidence 333445666789888777778999999443 2334444 478899999 788888763
No 41
>PRK14298 chaperone protein DnaJ; Provisional
Probab=82.96 E-value=0.87 Score=38.69 Aligned_cols=27 Identities=33% Similarity=0.843 Sum_probs=20.4
Q ss_pred eeccccccceeEeecC--------eeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK--------DYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~--------~~~kC~~CGGF 129 (133)
+.|..|.|+|.|.... ....|+.|+|.
T Consensus 159 ~~C~~C~G~G~~~~~~~~~~g~~~~~~~C~~C~G~ 193 (377)
T PRK14298 159 KRCPTCGGTGQVTTTRSTPLGQFVTTTTCSTCHGR 193 (377)
T ss_pred CcCCCCCCccEEEEEEecCceeEEEEEeCCCCCCC
Confidence 5699999999876543 35689999884
No 42
>PRK14289 chaperone protein DnaJ; Provisional
Probab=82.86 E-value=0.87 Score=38.47 Aligned_cols=7 Identities=57% Similarity=1.421 Sum_probs=3.7
Q ss_pred cCCCCCC
Q 032810 122 KCPECGM 128 (133)
Q Consensus 122 kC~~CGG 128 (133)
+|+.|+|
T Consensus 213 ~C~~C~G 219 (386)
T PRK14289 213 KCKKCGG 219 (386)
T ss_pred CCCCCCC
Confidence 3555555
No 43
>PRK14277 chaperone protein DnaJ; Provisional
Probab=82.81 E-value=0.89 Score=38.57 Aligned_cols=22 Identities=36% Similarity=1.094 Sum_probs=11.1
Q ss_pred eeccccccceeEeecCeeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
..|..|+|+|.+.++ +|..|.|
T Consensus 199 ~~C~~C~G~G~~~~~----~C~~C~G 220 (386)
T PRK14277 199 RTCDRCHGEGKIITD----PCNKCGG 220 (386)
T ss_pred EECCCCCcceeeccC----CCCCCCC
Confidence 355555555554322 3666655
No 44
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=82.81 E-value=0.71 Score=29.89 Aligned_cols=26 Identities=27% Similarity=0.837 Sum_probs=20.6
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
-+-|+.|+.. +.......+.|..||=
T Consensus 20 ~~fCP~Cg~~-~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 20 NKFCPRCGSG-FMAEHLDRWHCGKCGY 45 (50)
T ss_pred cCcCcCCCcc-hheccCCcEECCCcCC
Confidence 3479999876 6667778899999983
No 45
>PRK14282 chaperone protein DnaJ; Provisional
Probab=82.67 E-value=1 Score=37.98 Aligned_cols=27 Identities=30% Similarity=0.735 Sum_probs=21.4
Q ss_pred eeccccccceeEeecC--------eeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK--------DYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~--------~~~kC~~CGGF 129 (133)
+.|..|+|+|.|.... ....|+.|+|.
T Consensus 170 ~~C~~C~G~G~~~~~~~~~~G~~~~~~~C~~C~G~ 204 (369)
T PRK14282 170 VTCPKCHGTGRIREERRSFFGVFVSERTCERCGGT 204 (369)
T ss_pred cCCCCCCCcCEEEEEEEccCcceEEEEECCCCCCc
Confidence 5799999999887543 35689999984
No 46
>PRK14288 chaperone protein DnaJ; Provisional
Probab=82.47 E-value=1.1 Score=38.00 Aligned_cols=23 Identities=26% Similarity=0.834 Sum_probs=11.8
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
|..|..|+|.|.+.+ .+|+.|.|
T Consensus 178 ~~~C~~C~G~G~~~~----~~C~~C~G 200 (369)
T PRK14288 178 AQTCGACQGKGKIIK----TPCQACKG 200 (369)
T ss_pred EEecCCCCCCceEcc----ccCccCCC
Confidence 345555555555432 23666665
No 47
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=82.37 E-value=1.1 Score=27.19 Aligned_cols=27 Identities=30% Similarity=0.950 Sum_probs=19.5
Q ss_pred eccccccceeEeec-CeeecCCCCCCCc
Q 032810 104 RCEVCGGSGLVLRE-KDYFKCPECGMSY 130 (133)
Q Consensus 104 rCe~C~GsGLV~r~-~~~~kC~~CGGFl 130 (133)
+|+.|+.+-++.-. ...+-|+.||--|
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-BBE
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCCEe
Confidence 69999999966543 4567999998543
No 48
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=82.36 E-value=1.2 Score=28.02 Aligned_cols=26 Identities=31% Similarity=1.075 Sum_probs=18.8
Q ss_pred eeccccccceeEeecC--------eeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK--------DYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~--------~~~kC~~CGG 128 (133)
+.|+-||..-+..+.. ++..|..||.
T Consensus 4 kPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 5799995555555432 6789999986
No 49
>PRK14287 chaperone protein DnaJ; Provisional
Probab=82.35 E-value=0.94 Score=38.32 Aligned_cols=23 Identities=39% Similarity=1.055 Sum_probs=12.7
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
|..|..|.|+|-+.+ .+|+.|+|
T Consensus 181 ~~~C~~C~G~G~~~~----~~C~~C~G 203 (371)
T PRK14287 181 RRVCHHCEGTGKIIK----QKCATCGG 203 (371)
T ss_pred EEeCCCCCCCCcccc----ccCCCCCC
Confidence 445666666655533 23666666
No 50
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=82.25 E-value=0.91 Score=39.93 Aligned_cols=37 Identities=30% Similarity=0.600 Sum_probs=16.3
Q ss_pred eeeeeceeeeeeeeccccccceeEeecCeeecCCCCCC
Q 032810 91 AGIEFSKRIIAQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 91 Ag~EF~KRIi~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|.|--=++-.+.-|+.|.|+|.= .+..+..|+.|+|
T Consensus 131 ~G~~~~i~~~~~~~C~~C~GsGak-~gt~~~tC~tC~G 167 (371)
T COG0484 131 FGVKKEIRVTRSVTCSTCHGSGAK-PGTDPKTCPTCNG 167 (371)
T ss_pred cCceeeEecceeeECCcCCCCCCC-CCCCCCcCCCCCC
Confidence 344433344445555555555431 1123444444444
No 51
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=82.24 E-value=1.1 Score=33.49 Aligned_cols=21 Identities=29% Similarity=0.822 Sum_probs=17.6
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|..|..|.|+|-+ .|+.|.|
T Consensus 74 ~~~~C~~C~G~Gk~-------~C~~C~G 94 (111)
T PLN03165 74 EVSKCINCDGAGSL-------TCTTCQG 94 (111)
T ss_pred EEEECCCCCCccee-------eCCCCCC
Confidence 58899999999953 3999987
No 52
>PRK14278 chaperone protein DnaJ; Provisional
Probab=82.21 E-value=1.2 Score=37.81 Aligned_cols=23 Identities=39% Similarity=0.834 Sum_probs=13.0
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
|..|..|+|.|-+.+ .+|+.|.|
T Consensus 182 ~~~C~~C~G~G~~~~----~~C~~C~G 204 (378)
T PRK14278 182 SRPCPTCRGVGEVIP----DPCHECAG 204 (378)
T ss_pred EEECCCCCccceeeC----CCCCCCCC
Confidence 445666666665543 23777666
No 53
>PRK14280 chaperone protein DnaJ; Provisional
Probab=82.20 E-value=1 Score=38.15 Aligned_cols=27 Identities=41% Similarity=0.907 Sum_probs=16.7
Q ss_pred eeccccccceeEeecC--------eeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK--------DYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~--------~~~kC~~CGGF 129 (133)
..|..|.|+|.|.... ....|+.|+|.
T Consensus 161 ~~C~~C~G~G~~~~~~~~~~g~~~~~~~C~~C~G~ 195 (376)
T PRK14280 161 ETCSHCGGSGQVSVEQNTPFGRVVNRQTCPHCNGT 195 (376)
T ss_pred ccCCCCCCEEEEEEEeecCCceEEEEEEcCCCCCC
Confidence 3477777777665432 24578888773
No 54
>PRK14290 chaperone protein DnaJ; Provisional
Probab=82.09 E-value=1.2 Score=37.37 Aligned_cols=24 Identities=38% Similarity=0.942 Sum_probs=14.0
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|..|..|+|.|-+.+ .+|+.|.|
T Consensus 190 ~~~~C~~C~G~G~~~~----~~C~~C~G 213 (365)
T PRK14290 190 TVTTCRTCGGRGRIPE----EKCPRCNG 213 (365)
T ss_pred EEEeCCCCCCceeEcc----CCCCCCCC
Confidence 3456666666665532 24777765
No 55
>PRK14296 chaperone protein DnaJ; Provisional
Probab=82.03 E-value=0.94 Score=38.42 Aligned_cols=27 Identities=37% Similarity=0.726 Sum_probs=19.5
Q ss_pred eeccccccceeEeecC--------eeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK--------DYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~--------~~~kC~~CGGF 129 (133)
..|..|+|+|.|.... ....|+.|+|-
T Consensus 167 ~~C~~C~G~G~~~~~~~~g~~~~q~~~~C~~C~G~ 201 (372)
T PRK14296 167 HICNNCHGTGEVLVQKNMGFFQFQQSAKCNVCNGA 201 (372)
T ss_pred ccCCCCCCCceEEEEEeccceEEEEEecCCCcCCc
Confidence 4688888888877553 23578888873
No 56
>PRK14276 chaperone protein DnaJ; Provisional
Probab=82.02 E-value=1 Score=38.19 Aligned_cols=23 Identities=35% Similarity=0.836 Sum_probs=12.9
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
|..|..|+|.|-+.+ -+|+.|.|
T Consensus 189 ~~~C~~C~G~G~~~~----~~C~~C~G 211 (380)
T PRK14276 189 QVTCDVCHGTGKEIK----EPCQTCHG 211 (380)
T ss_pred EEECCCCCCCCcccc----CCCCCCCC
Confidence 455666666665543 23666665
No 57
>PRK14276 chaperone protein DnaJ; Provisional
Probab=81.97 E-value=1 Score=38.21 Aligned_cols=27 Identities=26% Similarity=0.641 Sum_probs=17.3
Q ss_pred eeccccccceeEeecC--------eeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK--------DYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~--------~~~kC~~CGGF 129 (133)
..|..|.|+|.|.... ....|+.|+|.
T Consensus 164 ~~C~~C~G~G~~~~~~~~~~G~~~~~~~C~~C~G~ 198 (380)
T PRK14276 164 VTCGKCHGSGVITVDTQTPLGMMRRQVTCDVCHGT 198 (380)
T ss_pred ccCCCCCCeeEEEEEEecCCceEEEEEECCCCCCC
Confidence 3577777777765442 24578888773
No 58
>PRK14289 chaperone protein DnaJ; Provisional
Probab=81.75 E-value=1 Score=38.06 Aligned_cols=26 Identities=38% Similarity=0.824 Sum_probs=17.8
Q ss_pred eeccccccceeEeecC--------eeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK--------DYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~--------~~~kC~~CGG 128 (133)
+.|..|.|+|.+.... ....|+.|+|
T Consensus 172 ~~C~~C~G~G~~~~~~~~~~G~~~~~~~C~~C~G 205 (386)
T PRK14289 172 ETCPTCKGSGSVTRVQNTILGTMQTQSTCPTCNG 205 (386)
T ss_pred CcCCCCcCeEEEEEEEecccceEEEEEecCCCCc
Confidence 5688888888776432 2567888876
No 59
>PRK14284 chaperone protein DnaJ; Provisional
Probab=81.56 E-value=1 Score=38.23 Aligned_cols=27 Identities=41% Similarity=0.941 Sum_probs=18.6
Q ss_pred eeccccccceeEeecC----eeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK----DYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~----~~~kC~~CGGF 129 (133)
+.|..|+|+|.|.... ....|+.|+|.
T Consensus 176 ~~C~~C~G~G~v~~~~G~~~~~~~C~~C~G~ 206 (391)
T PRK14284 176 KVCDRCKGSGQVVQSRGFFSMASTCPECGGE 206 (391)
T ss_pred eecCccCCeeEEEEEeceEEEEEECCCCCCC
Confidence 5688888888876431 34577777763
No 60
>PRK14287 chaperone protein DnaJ; Provisional
Probab=81.46 E-value=1.1 Score=37.90 Aligned_cols=27 Identities=33% Similarity=0.725 Sum_probs=17.3
Q ss_pred eeccccccceeEeecC--------eeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK--------DYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~--------~~~kC~~CGGF 129 (133)
..|..|.|+|.|.... ....|+.|+|.
T Consensus 156 ~~C~~C~G~G~~~~~~~~~~G~~~~~~~C~~C~G~ 190 (371)
T PRK14287 156 ETCSHCGGSGQLNVEQNTPFGRVVNRRVCHHCEGT 190 (371)
T ss_pred cccCCCCCEEEEEEEEecCCceEEEEEeCCCCCCC
Confidence 3577777777665432 24578888774
No 61
>PRK14277 chaperone protein DnaJ; Provisional
Probab=81.44 E-value=1.2 Score=37.70 Aligned_cols=27 Identities=30% Similarity=0.675 Sum_probs=20.6
Q ss_pred eeccccccceeEeecC--------eeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK--------DYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~--------~~~kC~~CGGF 129 (133)
..|..|.|+|.|.... ....|+.|+|-
T Consensus 173 ~~C~~C~G~G~~~~~~~~~~G~~~~~~~C~~C~G~ 207 (386)
T PRK14277 173 VTCPVCHGTGQVRTRQNTPFGRIVNIRTCDRCHGE 207 (386)
T ss_pred ccCCCCCCEEEEEEEEeccCceEEEEEECCCCCcc
Confidence 5799999999876543 34689999884
No 62
>PRK14297 chaperone protein DnaJ; Provisional
Probab=81.32 E-value=1.2 Score=37.56 Aligned_cols=28 Identities=32% Similarity=0.888 Sum_probs=22.0
Q ss_pred eeeccccccceeEeecC--------eeecCCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREK--------DYFKCPECGMS 129 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~--------~~~kC~~CGGF 129 (133)
...|..|.|+|.+.... ....|+.|+|-
T Consensus 165 ~~~C~~C~G~G~~~~~~~~~~G~~~~~~~C~~C~G~ 200 (380)
T PRK14297 165 PKTCDKCGGTGQIRVQRNTPLGSFVSTTTCDKCGGS 200 (380)
T ss_pred CccCCCccCeEEEEEEEEcCCceeEEEEeCCCCCCC
Confidence 46799999999886442 46799999984
No 63
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=81.14 E-value=1.2 Score=39.22 Aligned_cols=26 Identities=27% Similarity=0.681 Sum_probs=15.8
Q ss_pred eeeeeeccccccceeEeecCeeecCCCCCC
Q 032810 99 IIAQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 99 Ii~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
...|+.|..|+|+|-+- .-+|+.|.|
T Consensus 180 ~~~~~~C~~C~G~G~~i----~~pC~~C~G 205 (371)
T COG0484 180 FSFQQTCPTCNGTGKII----KDPCGKCKG 205 (371)
T ss_pred EEEEEECCCCccceeEC----CCCCCCCCC
Confidence 34566666666666655 235666665
No 64
>PRK14301 chaperone protein DnaJ; Provisional
Probab=80.93 E-value=1.1 Score=37.93 Aligned_cols=24 Identities=38% Similarity=0.898 Sum_probs=15.4
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|..|..|+|+|-+.+ .+|+.|.|
T Consensus 182 ~~~~C~~C~G~G~~~~----~~C~~C~G 205 (373)
T PRK14301 182 IAVPCPVCRGEGRVIT----HPCPKCKG 205 (373)
T ss_pred EEEeCCCCCceeeecC----CCCCCCCC
Confidence 3666777777776643 24777776
No 65
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=80.42 E-value=0.96 Score=26.20 Aligned_cols=22 Identities=45% Similarity=1.115 Sum_probs=15.6
Q ss_pred ccccccceeEeec-CeeecCCCCC
Q 032810 105 CEVCGGSGLVLRE-KDYFKCPECG 127 (133)
Q Consensus 105 Ce~C~GsGLV~r~-~~~~kC~~CG 127 (133)
|..|+ ..|..++ .-.|+||+||
T Consensus 1 C~sC~-~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCG-RPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCC-CcccCcccCceEeCCCCC
Confidence 45553 4566677 5689999998
No 66
>PRK14285 chaperone protein DnaJ; Provisional
Probab=80.37 E-value=1.2 Score=37.62 Aligned_cols=27 Identities=33% Similarity=0.748 Sum_probs=19.6
Q ss_pred eeccccccceeEeecC----eeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK----DYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~----~~~kC~~CGGF 129 (133)
..|..|.|+|.|.... ....|+.|+|-
T Consensus 164 ~~C~~C~G~G~~~~~~G~~~~~~~C~~C~G~ 194 (365)
T PRK14285 164 SICNMCNGSGRVMQGGGFFRVTTTCPKCYGN 194 (365)
T ss_pred ccCCCccCceeEEecCceeEEeeecCCCCCc
Confidence 4688888888776542 45689999873
No 67
>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=80.34 E-value=1.1 Score=26.23 Aligned_cols=22 Identities=36% Similarity=1.011 Sum_probs=16.2
Q ss_pred eccccccceeEeecC-eeecCCCCCC
Q 032810 104 RCEVCGGSGLVLREK-DYFKCPECGM 128 (133)
Q Consensus 104 rCe~C~GsGLV~r~~-~~~kC~~CGG 128 (133)
+|.+|| .+..++ ...+||.||.
T Consensus 3 ~C~~CG---y~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCG---YIYDGEEAPWVCPVCGA 25 (33)
T ss_pred ECCCCC---CEECCCcCCCcCcCCCC
Confidence 577775 665554 7889999985
No 68
>PRK14294 chaperone protein DnaJ; Provisional
Probab=80.33 E-value=1.2 Score=37.41 Aligned_cols=24 Identities=29% Similarity=0.663 Sum_probs=17.7
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|..|..|+|.|-+.+ .+|+.|.|
T Consensus 182 ~~~~C~~C~G~G~~~~----~~C~~C~G 205 (366)
T PRK14294 182 IRTTCPRCRGMGKVIV----SPCKTCHG 205 (366)
T ss_pred EEeeCCCCCCcCeecC----cCCCCCCC
Confidence 4778888888887643 34888887
No 69
>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=80.24 E-value=1.2 Score=26.59 Aligned_cols=24 Identities=38% Similarity=0.821 Sum_probs=17.9
Q ss_pred eeeccccccceeEeecC-eeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREK-DYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~-~~~kC~~CGG 128 (133)
.-+|.+|| .+..++ -+.+||.||-
T Consensus 2 ~~~C~~CG---~i~~g~~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCG---YIHEGEEAPEKCPICGA 26 (34)
T ss_pred eEECCCCC---CEeECCcCCCcCcCCCC
Confidence 34788885 666665 5789999985
No 70
>PRK14279 chaperone protein DnaJ; Provisional
Probab=80.14 E-value=1.1 Score=38.18 Aligned_cols=26 Identities=31% Similarity=0.760 Sum_probs=14.4
Q ss_pred eeccccccceeEeecC----eeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK----DYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~----~~~kC~~CGG 128 (133)
..|..|.|+|.|.... ....|+.|+|
T Consensus 191 ~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G 220 (392)
T PRK14279 191 KVCPTCNGSGVISRNQGAFGFSEPCTDCRG 220 (392)
T ss_pred CCCCCCcceEEEEEEecceEEEEecCCCCc
Confidence 3466666666554432 2356777766
No 71
>PRK14290 chaperone protein DnaJ; Provisional
Probab=80.05 E-value=1.1 Score=37.75 Aligned_cols=27 Identities=26% Similarity=0.593 Sum_probs=16.0
Q ss_pred eeccccccceeEeecC--------eeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK--------DYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~--------~~~kC~~CGGF 129 (133)
+.|..|+|+|.+.... ....|+.|+|.
T Consensus 166 ~~C~~C~G~G~~~~~~~~g~~~~~~~~~C~~C~G~ 200 (365)
T PRK14290 166 ITCPTCHGTGQQRIVRGQGFFRMVTVTTCRTCGGR 200 (365)
T ss_pred ccCCCCCCcCEEEEEeccCeEEEEEEEeCCCCCCc
Confidence 3566777777554332 24577777763
No 72
>PRK10767 chaperone protein DnaJ; Provisional
Probab=79.86 E-value=1.3 Score=37.10 Aligned_cols=26 Identities=31% Similarity=0.700 Sum_probs=16.2
Q ss_pred eccccccceeEeecC----eeecCCCCCCC
Q 032810 104 RCEVCGGSGLVLREK----DYFKCPECGMS 129 (133)
Q Consensus 104 rCe~C~GsGLV~r~~----~~~kC~~CGGF 129 (133)
.|..|+|+|.|.... ....|+.|+|.
T Consensus 161 ~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~ 190 (371)
T PRK10767 161 TCPTCHGAGQVRMQQGFFTVQQTCPTCHGR 190 (371)
T ss_pred cCCCCCCeeEEEEeeceEEEEEeCCCCCCc
Confidence 577777777665331 34478888773
No 73
>PRK14300 chaperone protein DnaJ; Provisional
Probab=79.83 E-value=1 Score=38.06 Aligned_cols=12 Identities=33% Similarity=0.966 Sum_probs=6.0
Q ss_pred eccccccceeEe
Q 032810 104 RCEVCGGSGLVL 115 (133)
Q Consensus 104 rCe~C~GsGLV~ 115 (133)
.|..|.|+|.+.
T Consensus 164 ~C~~C~G~G~~~ 175 (372)
T PRK14300 164 TCDACSGVGATR 175 (372)
T ss_pred cCCCccCeEEEE
Confidence 455555555443
No 74
>PRK14301 chaperone protein DnaJ; Provisional
Probab=79.40 E-value=1.6 Score=37.04 Aligned_cols=27 Identities=37% Similarity=0.794 Sum_probs=18.6
Q ss_pred eeccccccceeEeecC----eeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK----DYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~----~~~kC~~CGGF 129 (133)
..|..|+|+|.|.... ....|+.|+|.
T Consensus 162 ~~C~~C~G~G~v~~~~G~~~~~~~C~~C~G~ 192 (373)
T PRK14301 162 ETCRHCGGSGQVRQSQGFFQIAVPCPVCRGE 192 (373)
T ss_pred cccCCccCeeEEEEEeeeEEEEEeCCCCCce
Confidence 4588888888776442 35678888873
No 75
>PRK14291 chaperone protein DnaJ; Provisional
Probab=79.29 E-value=1.5 Score=37.18 Aligned_cols=24 Identities=33% Similarity=0.917 Sum_probs=17.1
Q ss_pred eeeeeccccccceeEeecCeeecCCCCCC
Q 032810 100 IAQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 100 i~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
..|..|..|+|.|.+ + .+|..|.|
T Consensus 193 ~~~~~C~~C~G~G~~-~----~~C~~C~G 216 (382)
T PRK14291 193 RISQTCPTCGGEGVL-R----EPCSKCNG 216 (382)
T ss_pred EEEecCCCCCCceEE-c----cCCCCCCC
Confidence 357788888888843 2 35888887
No 76
>PRK14293 chaperone protein DnaJ; Provisional
Probab=79.20 E-value=1.7 Score=36.68 Aligned_cols=23 Identities=35% Similarity=0.996 Sum_probs=12.7
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
|..|..|.|.|-+.++ .|..|.|
T Consensus 186 ~~~C~~C~G~G~~~~~----~C~~C~G 208 (374)
T PRK14293 186 VSECPTCNGTGQVIED----PCDACGG 208 (374)
T ss_pred EeeCCCCCcceeEecc----CCCCCCC
Confidence 4456666666655322 3666665
No 77
>PRK14278 chaperone protein DnaJ; Provisional
Probab=78.84 E-value=1.4 Score=37.31 Aligned_cols=26 Identities=35% Similarity=0.792 Sum_probs=16.2
Q ss_pred eeccccccceeEeecC--------eeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK--------DYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~--------~~~kC~~CGG 128 (133)
+.|..|.|+|.|.... ....|+.|+|
T Consensus 157 ~~C~~C~G~G~~~~~~~~~~g~~~~~~~C~~C~G 190 (378)
T PRK14278 157 VTCDTCGGRGEVQTVQRSFLGQVMTSRPCPTCRG 190 (378)
T ss_pred eecCCccCceEEEEEEeccceeEEEEEECCCCCc
Confidence 3577777777665432 2456777776
No 78
>PRK14283 chaperone protein DnaJ; Provisional
Probab=78.64 E-value=1.4 Score=37.15 Aligned_cols=12 Identities=50% Similarity=1.201 Sum_probs=6.3
Q ss_pred eccccccceeEe
Q 032810 104 RCEVCGGSGLVL 115 (133)
Q Consensus 104 rCe~C~GsGLV~ 115 (133)
.|..|.|+|.+.
T Consensus 165 ~C~~C~G~G~~~ 176 (378)
T PRK14283 165 TCPTCGGTGQVK 176 (378)
T ss_pred cCCCcCCccEEE
Confidence 355555555554
No 79
>PRK14295 chaperone protein DnaJ; Provisional
Probab=78.60 E-value=1.4 Score=37.66 Aligned_cols=26 Identities=38% Similarity=0.820 Sum_probs=15.0
Q ss_pred eeccccccceeEeecC----eeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK----DYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~----~~~kC~~CGG 128 (133)
+.|..|.|+|.|.... ....|+.|+|
T Consensus 184 ~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G 213 (389)
T PRK14295 184 RVCPTCSGTGQVSRNSGGFSLSEPCPDCKG 213 (389)
T ss_pred cCCCCCCCEeEEEEEecceEEEEecCCCcc
Confidence 3466666666555432 2446777776
No 80
>PRK14281 chaperone protein DnaJ; Provisional
Probab=78.23 E-value=1.5 Score=37.43 Aligned_cols=27 Identities=37% Similarity=0.856 Sum_probs=15.6
Q ss_pred eeccccccceeEeecC--------eeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK--------DYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~--------~~~kC~~CGGF 129 (133)
..|..|+|+|.+.... ....|+.|+|.
T Consensus 180 ~~C~~C~G~G~~~~~~~~~~g~~~~~~~C~~C~G~ 214 (397)
T PRK14281 180 ETCPTCHGSGEVRQASKTMFGQFVNITACPTCGGE 214 (397)
T ss_pred ccCCCCCCCcEEEEEEecccceEEEEEecCCCcce
Confidence 3466666666654432 24467777763
No 81
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=78.06 E-value=2.3 Score=26.08 Aligned_cols=25 Identities=40% Similarity=0.870 Sum_probs=16.6
Q ss_pred eccccccce--eEe-ecCeeecCCCCCC
Q 032810 104 RCEVCGGSG--LVL-REKDYFKCPECGM 128 (133)
Q Consensus 104 rCe~C~GsG--LV~-r~~~~~kC~~CGG 128 (133)
+|..|+-.= +.. .+.....||.||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 899998732 222 2235678999997
No 82
>PTZ00037 DnaJ_C chaperone protein; Provisional
Probab=77.88 E-value=1.6 Score=38.16 Aligned_cols=26 Identities=35% Similarity=0.850 Sum_probs=15.8
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|..|..|+|+|-+.+.+ -+|+.|.|
T Consensus 191 ~~~~C~~C~G~G~~i~~~--~~C~~C~G 216 (421)
T PTZ00037 191 TQSTCNSCNGQGKIIPES--KKCKNCSG 216 (421)
T ss_pred EEEeCCCCCCcceecccc--ccCCcCCC
Confidence 355677777776554322 34888877
No 83
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=77.65 E-value=1.4 Score=26.52 Aligned_cols=27 Identities=26% Similarity=0.672 Sum_probs=21.9
Q ss_pred eccccccceeEeec-----CeeecCCCCCCCc
Q 032810 104 RCEVCGGSGLVLRE-----KDYFKCPECGMSY 130 (133)
Q Consensus 104 rCe~C~GsGLV~r~-----~~~~kC~~CGGFl 130 (133)
+|+.|+..--|..+ +..+||+.|+-.+
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 69999998887755 5699999998644
No 84
>PRK14293 chaperone protein DnaJ; Provisional
Probab=77.53 E-value=1.7 Score=36.63 Aligned_cols=27 Identities=37% Similarity=0.928 Sum_probs=16.6
Q ss_pred eeccccccceeEeecC--------eeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK--------DYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~--------~~~kC~~CGGF 129 (133)
.+|..|.|+|.|.... ....|+.|+|.
T Consensus 161 ~~C~~C~G~G~~~~~~~~~~g~~~~~~~C~~C~G~ 195 (374)
T PRK14293 161 TTCSTCGGAGQVRRATRTPFGSFTQVSECPTCNGT 195 (374)
T ss_pred eeCCCCCCcceEEEEEecCcceEEEEeeCCCCCcc
Confidence 3567777777665332 24578888763
No 85
>PRK14291 chaperone protein DnaJ; Provisional
Probab=77.38 E-value=1.7 Score=36.81 Aligned_cols=26 Identities=38% Similarity=0.887 Sum_probs=15.5
Q ss_pred eccccccceeEeecC----eeecCCCCCCC
Q 032810 104 RCEVCGGSGLVLREK----DYFKCPECGMS 129 (133)
Q Consensus 104 rCe~C~GsGLV~r~~----~~~kC~~CGGF 129 (133)
.|..|+|+|.+.... ....|+.|+|-
T Consensus 175 ~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~ 204 (382)
T PRK14291 175 VCPTCGGSGEIYQRGGFFRISQTCPTCGGE 204 (382)
T ss_pred cCCCCCCceEEEEecceEEEEecCCCCCCc
Confidence 466666666655432 34567777763
No 86
>PRK14292 chaperone protein DnaJ; Provisional
Probab=77.33 E-value=1.5 Score=36.70 Aligned_cols=13 Identities=38% Similarity=0.981 Sum_probs=6.9
Q ss_pred eeccccccceeEe
Q 032810 103 RRCEVCGGSGLVL 115 (133)
Q Consensus 103 ~rCe~C~GsGLV~ 115 (133)
..|..|+|+|.+.
T Consensus 158 ~~C~~C~G~G~~~ 170 (371)
T PRK14292 158 KTCPTCRGAGAVR 170 (371)
T ss_pred ccCCCCCCccEEE
Confidence 3455556655443
No 87
>PRK14294 chaperone protein DnaJ; Provisional
Probab=77.28 E-value=1.8 Score=36.43 Aligned_cols=26 Identities=38% Similarity=0.819 Sum_probs=16.4
Q ss_pred eccccccceeEeecC----eeecCCCCCCC
Q 032810 104 RCEVCGGSGLVLREK----DYFKCPECGMS 129 (133)
Q Consensus 104 rCe~C~GsGLV~r~~----~~~kC~~CGGF 129 (133)
.|..|+|+|.+.... ....|+.|+|-
T Consensus 163 ~C~~C~G~G~~~~~~G~~~~~~~C~~C~G~ 192 (366)
T PRK14294 163 TCPQCGGSGQVTQSQGFFSIRTTCPRCRGM 192 (366)
T ss_pred cCCCcCCeEEEEEEeeeEEEEeeCCCCCCc
Confidence 477777777665321 35678888873
No 88
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=76.77 E-value=2.4 Score=34.65 Aligned_cols=27 Identities=37% Similarity=0.892 Sum_probs=21.6
Q ss_pred eeeeeccccccceeEeecCeeecCCCCCC
Q 032810 100 IAQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 100 i~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
++--+|+.|++ .|+. +.+-.+||.||-
T Consensus 147 VI~A~CsrC~~-~L~~-~~~~l~Cp~Cg~ 173 (188)
T COG1096 147 VIYARCSRCRA-PLVK-KGNMLKCPNCGN 173 (188)
T ss_pred EEEEEccCCCc-ceEE-cCcEEECCCCCC
Confidence 45568999975 5776 888899999994
No 89
>PRK14288 chaperone protein DnaJ; Provisional
Probab=76.21 E-value=1.8 Score=36.59 Aligned_cols=27 Identities=26% Similarity=0.599 Sum_probs=15.4
Q ss_pred eeccccccceeEeecC----eeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK----DYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~----~~~kC~~CGGF 129 (133)
+.|..|+|+|.|.... ....|+.|+|.
T Consensus 157 ~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~ 187 (369)
T PRK14288 157 ETCKQCNGQGQVFMRQGFMSFAQTCGACQGK 187 (369)
T ss_pred cCCCCCCCCcEEEEEeceEEEEEecCCCCCC
Confidence 4566666666554332 23467777763
No 90
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=76.02 E-value=1.1 Score=40.20 Aligned_cols=29 Identities=28% Similarity=0.768 Sum_probs=21.7
Q ss_pred eeeeccccccceeEeecCeeecCCCCCCCc
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGMSY 130 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGGFl 130 (133)
..-+|..|||+ +-+.++..|||+.||--+
T Consensus 349 ~~p~Cp~Cg~~-m~S~G~~g~rC~kCg~~~ 377 (421)
T COG1571 349 VNPVCPRCGGR-MKSAGRNGFRCKKCGTRA 377 (421)
T ss_pred cCCCCCccCCc-hhhcCCCCcccccccccC
Confidence 34589999997 344555699999999644
No 91
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=75.98 E-value=1.8 Score=26.42 Aligned_cols=24 Identities=29% Similarity=0.977 Sum_probs=20.6
Q ss_pred eccccccceeEeecCeeecCCCCCC
Q 032810 104 RCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 104 rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
+|++|+.. +...+.-++-|..||-
T Consensus 10 ~C~~C~~~-~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSR-WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCCCCe-EeEccCCEEEhhhCce
Confidence 59999999 8888888888999983
No 92
>PRK14300 chaperone protein DnaJ; Provisional
Probab=75.97 E-value=2.1 Score=36.16 Aligned_cols=24 Identities=25% Similarity=0.814 Sum_probs=18.5
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|..|..|.|.|-+-+ .+|+.|.|
T Consensus 183 ~~~~C~~C~G~G~~~~----~~C~~C~G 206 (372)
T PRK14300 183 IEQACHKCQGNGQIIK----NPCKKCHG 206 (372)
T ss_pred EEEeCCCCCccceEeC----CCCCCCCC
Confidence 5678888888887754 34888887
No 93
>PTZ00037 DnaJ_C chaperone protein; Provisional
Probab=75.94 E-value=1.6 Score=38.18 Aligned_cols=10 Identities=40% Similarity=1.408 Sum_probs=5.2
Q ss_pred ecccccccee
Q 032810 104 RCEVCGGSGL 113 (133)
Q Consensus 104 rCe~C~GsGL 113 (133)
.|..|+|+|.
T Consensus 168 ~C~~C~G~G~ 177 (421)
T PTZ00037 168 DCKLCNGQGI 177 (421)
T ss_pred cCCCCCCCCe
Confidence 3555555554
No 94
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=75.75 E-value=2.5 Score=25.93 Aligned_cols=26 Identities=50% Similarity=0.962 Sum_probs=19.1
Q ss_pred eeccccccceeEeec---CeeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLRE---KDYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~---~~~~kC~~CGG 128 (133)
-+|+.|+..==+... .....||+||+
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 489999866544432 46889999998
No 95
>PRK14286 chaperone protein DnaJ; Provisional
Probab=75.38 E-value=1.7 Score=36.88 Aligned_cols=26 Identities=38% Similarity=0.842 Sum_probs=14.6
Q ss_pred eccccccceeEeecC----eeecCCCCCCC
Q 032810 104 RCEVCGGSGLVLREK----DYFKCPECGMS 129 (133)
Q Consensus 104 rCe~C~GsGLV~r~~----~~~kC~~CGGF 129 (133)
.|..|.|+|.|.... ....|+.|+|.
T Consensus 169 ~C~~C~G~G~v~~~~G~~~~~~~C~~C~G~ 198 (372)
T PRK14286 169 TCPDCGGSGQIRRTQGFFSVATTCPTCRGK 198 (372)
T ss_pred cCCCCcCeEEEEEEeceEEEEEeCCCCCce
Confidence 466666666554332 23467777763
No 96
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=75.24 E-value=2 Score=28.89 Aligned_cols=23 Identities=39% Similarity=0.772 Sum_probs=18.5
Q ss_pred eeccccccceeEeecCeeecCCCCCCCcc
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGMSYG 131 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGGFl~ 131 (133)
++|+.|+--.| .-.||.||+-+.
T Consensus 6 r~C~~CgvYTL------k~~CP~CG~~t~ 28 (56)
T PRK13130 6 RKCPKCGVYTL------KEICPVCGGKTK 28 (56)
T ss_pred eECCCCCCEEc------cccCcCCCCCCC
Confidence 68999998888 347999998653
No 97
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=74.82 E-value=1.8 Score=26.11 Aligned_cols=26 Identities=31% Similarity=0.718 Sum_probs=17.7
Q ss_pred eccccccceeEeecC---eeecCCCCCCCc
Q 032810 104 RCEVCGGSGLVLREK---DYFKCPECGMSY 130 (133)
Q Consensus 104 rCe~C~GsGLV~r~~---~~~kC~~CGGFl 130 (133)
.|+.|+. -|....- ....|++|||..
T Consensus 1 ~CP~C~~-~l~~~~~~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGT-ELEPVRLGDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCc-ccceEEECCEEEEECCCCCeEE
Confidence 4888877 3554332 467899999963
No 98
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=74.18 E-value=1.6 Score=34.65 Aligned_cols=23 Identities=35% Similarity=0.751 Sum_probs=19.5
Q ss_pred eeeccccccceeEeecCeeecCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECG 127 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CG 127 (133)
--+|.+| |-...+.-+-+||-||
T Consensus 134 ~~vC~vC---Gy~~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVC---GYTHEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCC---CCcccCCCCCcCCCCC
Confidence 3579999 6777778899999999
No 99
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=73.97 E-value=2.2 Score=24.88 Aligned_cols=28 Identities=25% Similarity=0.570 Sum_probs=21.1
Q ss_pred eeccccccceeEeec-----CeeecCCCCCCCc
Q 032810 103 RRCEVCGGSGLVLRE-----KDYFKCPECGMSY 130 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~-----~~~~kC~~CGGFl 130 (133)
-.|+.|+..=-|..+ +..++|+.||.-|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 479999987666643 4579999999754
No 100
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=73.53 E-value=1.6 Score=24.55 Aligned_cols=25 Identities=32% Similarity=0.727 Sum_probs=17.7
Q ss_pred eeeccccccceeEeecCeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGGFl 130 (133)
++.|..|+- ..+.....|+.||--|
T Consensus 2 ~~~Cp~Cg~----~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGA----EIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCC----cCCcccccChhhCCCC
Confidence 467888987 2355677899999643
No 101
>PHA02942 putative transposase; Provisional
Probab=72.42 E-value=2.1 Score=36.70 Aligned_cols=27 Identities=33% Similarity=0.878 Sum_probs=19.4
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.-+.|+.||.-.- ..+...++|+.||=
T Consensus 324 TSq~Cs~CG~~~~-~l~~r~f~C~~CG~ 350 (383)
T PHA02942 324 SSVSCPKCGHKMV-EIAHRYFHCPSCGY 350 (383)
T ss_pred CCccCCCCCCccC-cCCCCEEECCCCCC
Confidence 4478999997542 22356899999984
No 102
>PHA00626 hypothetical protein
Probab=72.25 E-value=2.6 Score=29.24 Aligned_cols=27 Identities=26% Similarity=0.697 Sum_probs=18.9
Q ss_pred eccccccceeEe-----ecCeeecCCCCCCCc
Q 032810 104 RCEVCGGSGLVL-----REKDYFKCPECGMSY 130 (133)
Q Consensus 104 rCe~C~GsGLV~-----r~~~~~kC~~CGGFl 130 (133)
.|+.|+..-++. .-...++|+.||=++
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 488887654553 225788999999654
No 103
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=72.14 E-value=0.86 Score=37.88 Aligned_cols=31 Identities=26% Similarity=0.492 Sum_probs=21.3
Q ss_pred eeeccccc------cceeEeecCeeecCCCCCCCccc
Q 032810 102 QRRCEVCG------GSGLVLREKDYFKCPECGMSYGL 132 (133)
Q Consensus 102 Q~rCe~C~------GsGLV~r~~~~~kC~~CGGFl~~ 132 (133)
-++|..|. ..-.|.+++..++||.||-||=|
T Consensus 197 g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRILy~ 233 (239)
T COG1579 197 GRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRILYY 233 (239)
T ss_pred CCcccCCeeeecHHHHHHHhcCCCCccCCccchHHHh
Confidence 35666664 12234457889999999999865
No 104
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=71.42 E-value=2.2 Score=33.22 Aligned_cols=22 Identities=36% Similarity=1.022 Sum_probs=16.1
Q ss_pred eccccccceeEeecCeeecCCCCCCC
Q 032810 104 RCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 104 rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
.|..|| +++ ...+..||.||+|
T Consensus 356 ~c~~cg---~~~-~~~~~~c~~c~~~ 377 (389)
T PRK11788 356 RCRNCG---FTA-RTLYWHCPSCKAW 377 (389)
T ss_pred ECCCCC---CCC-ccceeECcCCCCc
Confidence 466664 544 4678899999998
No 105
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=71.18 E-value=1.8 Score=41.27 Aligned_cols=30 Identities=37% Similarity=0.727 Sum_probs=21.6
Q ss_pred eeeeccccccceeEeec--CeeecCCCCCCCcccC
Q 032810 101 AQRRCEVCGGSGLVLRE--KDYFKCPECGMSYGLI 133 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~--~~~~kC~~CGGFl~~i 133 (133)
-|-||..|+- |+.+ --|-+||.|||-|-|+
T Consensus 820 ~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~ 851 (1006)
T PRK12775 820 LQWRCDDCGK---VSEGFAFPYGMCPACGGKLQAL 851 (1006)
T ss_pred eeeehhhhcc---ccccccCCcCcCcccccchhhh
Confidence 4778888853 4443 2478999999998874
No 106
>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=70.74 E-value=4.2 Score=29.65 Aligned_cols=38 Identities=34% Similarity=0.730 Sum_probs=27.0
Q ss_pred ceeEEeeeeeceeeeeeeecccccc-ce------eEeecCeeecCCCCCCCc
Q 032810 86 TPFVVAGIEFSKRIIAQRRCEVCGG-SG------LVLREKDYFKCPECGMSY 130 (133)
Q Consensus 86 ~PFvvAg~EF~KRIi~Q~rCe~C~G-sG------LV~r~~~~~kC~~CGGFl 130 (133)
.|.+|-++ |.+||+- |-| .+ +..+++.+.||++||-.+
T Consensus 45 ~P~lVpS~-~~~RiVG------C~g~~~~h~v~W~~l~~g~~~rC~eCG~~f 89 (97)
T cd00924 45 DPNLVPSA-FDKRIVG------CICEPDSHDVIWMWLEKGKPKRCPECGHVF 89 (97)
T ss_pred CCeEecCC-CCCeEEe------eeCCCCCceEEEEEEeCCCceeCCCCCcEE
Confidence 68888888 7899884 422 23 233556799999999765
No 107
>PRK14283 chaperone protein DnaJ; Provisional
Probab=70.35 E-value=3.6 Score=34.80 Aligned_cols=24 Identities=25% Similarity=0.674 Sum_probs=18.7
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|..|..|.|.|...+ ..|..|.|
T Consensus 188 ~~~~C~~C~G~G~~~~----~~C~~C~G 211 (378)
T PRK14283 188 NVTTCPDCQGEGKIVE----KPCSNCHG 211 (378)
T ss_pred EEEECCCCCccceecC----CCCCCCCC
Confidence 4678999999997743 44999987
No 108
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=69.34 E-value=1.8 Score=34.66 Aligned_cols=27 Identities=33% Similarity=1.004 Sum_probs=18.2
Q ss_pred eeeccccccceeEeecC----------------eeecCCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREK----------------DYFKCPECGMS 129 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~----------------~~~kC~~CGGF 129 (133)
-.||+.|+|. |+...+ ..-+|+.||-.
T Consensus 97 ~~RCp~CN~~-L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 97 FSRCPECNGE-LEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKI 139 (165)
T ss_pred cccCcccCCE-eccCcHHHHhhccchhhhhcccceeECCCCccc
Confidence 3599999997 444332 24459999854
No 109
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=69.24 E-value=3.1 Score=39.76 Aligned_cols=22 Identities=50% Similarity=1.085 Sum_probs=12.1
Q ss_pred eccccccceeEeecCeeecCCCCCC
Q 032810 104 RCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 104 rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
-|+.|.|.|-|.- |..|+.|||
T Consensus 55 pc~~c~gkG~V~v---~~~c~~c~G 76 (715)
T COG1107 55 PCPKCRGKGTVTV---YDTCPECGG 76 (715)
T ss_pred CCCeeccceeEEE---EeecccCCC
Confidence 3555666555542 455666655
No 110
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=68.89 E-value=3.8 Score=29.74 Aligned_cols=29 Identities=31% Similarity=0.704 Sum_probs=25.0
Q ss_pred eeeeccccccceeEeecCeeecCCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
.+-+|+.|+-..++.-.=.-+-||.||+.
T Consensus 41 ~~~~C~~Cg~~~~~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 41 HRYRCEDCGHEKIVYNSCKNRHCPSCQAK 69 (111)
T ss_pred ceeecCCCCceEEecCcccCcCCCCCCCh
Confidence 35689999999999988777899999974
No 111
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=68.78 E-value=4.6 Score=27.97 Aligned_cols=32 Identities=34% Similarity=0.793 Sum_probs=25.9
Q ss_pred eeeeeeeeccccccceeEe----ecCeeecCCCCCC
Q 032810 97 KRIIAQRRCEVCGGSGLVL----REKDYFKCPECGM 128 (133)
Q Consensus 97 KRIi~Q~rCe~C~GsGLV~----r~~~~~kC~~CGG 128 (133)
||.|+--.|+.|+.---++ .+..++-|-+||=
T Consensus 3 krFIAGa~CP~C~~~D~i~~~~e~~ve~vECV~CGy 38 (71)
T PF09526_consen 3 KRFIAGAVCPKCQAMDTIMMWRENGVEYVECVECGY 38 (71)
T ss_pred ceEecCccCCCCcCccEEEEEEeCCceEEEecCCCC
Confidence 8999999999999876444 3357999999983
No 112
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=68.41 E-value=3.5 Score=25.10 Aligned_cols=25 Identities=28% Similarity=0.800 Sum_probs=17.4
Q ss_pred eccccccceeEeecC----------eeecCCCCCC
Q 032810 104 RCEVCGGSGLVLREK----------DYFKCPECGM 128 (133)
Q Consensus 104 rCe~C~GsGLV~r~~----------~~~kC~~CGG 128 (133)
.|+.|+....+.... .+++|.+||-
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~ 36 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGH 36 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCC
Confidence 599999999988532 3788999984
No 113
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=67.82 E-value=2.8 Score=25.26 Aligned_cols=25 Identities=40% Similarity=0.917 Sum_probs=15.5
Q ss_pred eccccccceeEeecCeeecCCCCCCC
Q 032810 104 RCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 104 rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
.|..|+-.=- .......||++||.-
T Consensus 2 ~C~~Cg~~~~-~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVE-LKPGDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE--BSTSSTSSBSSSS-S
T ss_pred CCCcCCCeeE-cCCCCcEECCcCCCe
Confidence 3677765433 344568899999963
No 114
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=67.32 E-value=5.9 Score=30.35 Aligned_cols=34 Identities=29% Similarity=0.679 Sum_probs=24.7
Q ss_pred eeeeeceeeeeeeeccccccceeEeecCeeecCCCCCC
Q 032810 91 AGIEFSKRIIAQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 91 Ag~EF~KRIi~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.+-|||+ .+-+|+.|++ -|+..+....+|+.||-
T Consensus 141 k~~~lGv---v~a~~~~~g~-~~~~~~~~~~~c~~~~~ 174 (189)
T PRK09521 141 KGKDLGV---IYAMCSRCRT-PLVKKGENELKCPNCGN 174 (189)
T ss_pred ecCCceE---EEEEccccCC-ceEECCCCEEECCCCCC
Confidence 3445554 2348999865 47888888999999994
No 115
>PRK00420 hypothetical protein; Validated
Probab=66.95 E-value=3.7 Score=30.77 Aligned_cols=28 Identities=32% Similarity=0.676 Sum_probs=20.5
Q ss_pred eeeccccccceeEeecCeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGGFl 130 (133)
...|++|+ +=|..-.+....||.||-++
T Consensus 23 ~~~CP~Cg-~pLf~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 23 SKHCPVCG-LPLFELKDGEVVCPVHGKVY 50 (112)
T ss_pred cCCCCCCC-CcceecCCCceECCCCCCee
Confidence 47899998 44555355577899999764
No 116
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=66.74 E-value=4.9 Score=24.64 Aligned_cols=25 Identities=24% Similarity=0.806 Sum_probs=19.9
Q ss_pred eccccccceeEeec----------CeeecCCCCCC
Q 032810 104 RCEVCGGSGLVLRE----------KDYFKCPECGM 128 (133)
Q Consensus 104 rCe~C~GsGLV~r~----------~~~~kC~~CGG 128 (133)
.|+.|++...|... -.++.|.+||-
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~ 36 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGH 36 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCC
Confidence 69999999999632 14889999984
No 117
>PRK14292 chaperone protein DnaJ; Provisional
Probab=66.39 E-value=4.3 Score=34.08 Aligned_cols=24 Identities=29% Similarity=0.757 Sum_probs=19.0
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|..|..|.|.|...+ ..|+.|.|
T Consensus 182 ~~~~C~~C~G~G~~~~----~~C~~C~G 205 (371)
T PRK14292 182 TQQPCPTCRGEGQIIT----DPCTVCRG 205 (371)
T ss_pred EeeecCCCcccceecC----CCCCCCCC
Confidence 3678999999998753 56999977
No 118
>PRK07591 threonine synthase; Validated
Probab=66.04 E-value=3.7 Score=35.15 Aligned_cols=26 Identities=23% Similarity=0.479 Sum_probs=18.1
Q ss_pred eeeccccccceeEeecCeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGGFl 130 (133)
..+|..|+-. ..-+ ...+||+|||.|
T Consensus 18 ~l~C~~Cg~~--~~~~-~~~~C~~cg~~l 43 (421)
T PRK07591 18 ALKCRECGAE--YPLG-PIHVCEECFGPL 43 (421)
T ss_pred EEEeCCCCCc--CCCC-CCccCCCCCCeE
Confidence 4689999865 1122 338999999876
No 119
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=65.94 E-value=3.8 Score=29.30 Aligned_cols=32 Identities=25% Similarity=0.562 Sum_probs=20.9
Q ss_pred eeeccccccceeEeecC--eeecCCCCCCCcccC
Q 032810 102 QRRCEVCGGSGLVLREK--DYFKCPECGMSYGLI 133 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~--~~~kC~~CGGFl~~i 133 (133)
.-+|..|+..=-..+.. ...+|+.|||.|-+|
T Consensus 123 ~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~l~~~ 156 (157)
T PF10263_consen 123 VYRCPSCGREYKRHRRSKRKRYRCGRCGGPLVQV 156 (157)
T ss_pred EEEcCCCCCEeeeecccchhhEECCCCCCEEEEc
Confidence 45799998764322221 245799999988653
No 120
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=64.85 E-value=4.3 Score=30.75 Aligned_cols=28 Identities=36% Similarity=0.671 Sum_probs=19.7
Q ss_pred eeeeeeccccccceeEeecCeeecCCCCCC
Q 032810 99 IIAQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 99 Ii~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
+=.+-+|..|+ +-+..+...++||.||+
T Consensus 67 ~p~~~~C~~C~--~~~~~e~~~~~CP~C~s 94 (115)
T COG0375 67 EPAECWCLDCG--QEVELEELDYRCPKCGS 94 (115)
T ss_pred eccEEEeccCC--CeecchhheeECCCCCC
Confidence 34678999994 44555555555999995
No 121
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=64.16 E-value=4.6 Score=30.77 Aligned_cols=25 Identities=40% Similarity=1.084 Sum_probs=17.9
Q ss_pred eeccccccceeEe------------ec----CeeecCCCCC
Q 032810 103 RRCEVCGGSGLVL------------RE----KDYFKCPECG 127 (133)
Q Consensus 103 ~rCe~C~GsGLV~------------r~----~~~~kC~~CG 127 (133)
..|+.|+|.++|. .+ ....||++|.
T Consensus 100 ~~C~~Cgg~rfv~C~~C~Gs~k~~~~~~~~~~~~~rC~~Cn 140 (147)
T cd03031 100 GVCEGCGGARFVPCSECNGSCKVFAENATAAGGFLRCPECN 140 (147)
T ss_pred CCCCCCCCcCeEECCCCCCcceEEeccCcccccEEECCCCC
Confidence 3599999998886 11 2367888884
No 122
>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=63.97 E-value=3.4 Score=32.55 Aligned_cols=29 Identities=21% Similarity=0.224 Sum_probs=17.4
Q ss_pred eeeccccccceeEeecCeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGGFl 130 (133)
.-+|..|+..--........+|+.|||.|
T Consensus 118 ~~~C~~C~~~~~~~~~~~~p~C~~Cgg~l 146 (225)
T cd01411 118 RIYCTVCGKTVDWEEYLKSPYHAKCGGVI 146 (225)
T ss_pred eeEeCCCCCccchhhcCCCCCCCCCCCEe
Confidence 45799995432111112246899999964
No 123
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=63.78 E-value=5.4 Score=24.29 Aligned_cols=24 Identities=42% Similarity=1.144 Sum_probs=13.2
Q ss_pred eeccccccceeEee-----cCeeecCCCCC
Q 032810 103 RRCEVCGGSGLVLR-----EKDYFKCPECG 127 (133)
Q Consensus 103 ~rCe~C~GsGLV~r-----~~~~~kC~~CG 127 (133)
|-|..||+. |..+ ++.-..|++||
T Consensus 1 kfC~~CG~~-l~~~ip~gd~r~R~vC~~Cg 29 (34)
T PF14803_consen 1 KFCPQCGGP-LERRIPEGDDRERLVCPACG 29 (34)
T ss_dssp -B-TTT--B--EEE--TT-SS-EEEETTTT
T ss_pred CccccccCh-hhhhcCCCCCccceECCCCC
Confidence 469999988 5553 24567899998
No 124
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=63.31 E-value=3.3 Score=38.59 Aligned_cols=26 Identities=35% Similarity=0.784 Sum_probs=20.1
Q ss_pred eeccccccceeEeecCeeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
-+|..||-.|-..-......||.||.
T Consensus 642 ~~C~~CG~~Ge~~~~~~~~~CP~CG~ 667 (711)
T PRK09263 642 DECYECGFTGEFECTEKGFTCPKCGN 667 (711)
T ss_pred cccCCCCCCccccCCCCCCcCcCCCC
Confidence 57999998887744444589999994
No 125
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=62.83 E-value=6.3 Score=24.96 Aligned_cols=15 Identities=27% Similarity=0.795 Sum_probs=11.8
Q ss_pred ecCeeecCCCCCCCc
Q 032810 116 REKDYFKCPECGMSY 130 (133)
Q Consensus 116 r~~~~~kC~~CGGFl 130 (133)
+++....||+||-+|
T Consensus 42 ~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 42 KGDEIVFCPNCGRIL 56 (56)
T ss_pred cCCCeEECcCCCccC
Confidence 445789999999765
No 126
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=62.24 E-value=4.3 Score=26.91 Aligned_cols=26 Identities=31% Similarity=0.732 Sum_probs=17.1
Q ss_pred eeccccccceeEeecCeeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
-+|..|+-.=-........+||.||.
T Consensus 7 Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 7 YKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEhhhcCCeeehhhccCceeCCCCCc
Confidence 46888875432233456888999985
No 127
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=62.22 E-value=3.2 Score=31.60 Aligned_cols=27 Identities=26% Similarity=0.573 Sum_probs=16.9
Q ss_pred eccccccceeEeec--CeeecCCCCCCCcc
Q 032810 104 RCEVCGGSGLVLRE--KDYFKCPECGMSYG 131 (133)
Q Consensus 104 rCe~C~GsGLV~r~--~~~~kC~~CGGFl~ 131 (133)
.|+.|+-. .-.-+ .+.|.||.|||.|-
T Consensus 111 ~Cp~c~~r-~tf~eA~~~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 111 ICPNMCVR-FTFNEAMELNFTCPRCGAMLD 139 (158)
T ss_pred ECCCCCcE-eeHHHHHHcCCcCCCCCCEee
Confidence 48888721 11111 24799999999773
No 128
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=61.82 E-value=2.5 Score=31.46 Aligned_cols=27 Identities=30% Similarity=0.811 Sum_probs=16.6
Q ss_pred eeccccccceeEeec-------CeeecCCCCCCCc
Q 032810 103 RRCEVCGGSGLVLRE-------KDYFKCPECGMSY 130 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~-------~~~~kC~~CGGFl 130 (133)
-.|+.|+-. .-..+ ...|.||.||+-|
T Consensus 100 Y~Cp~C~~~-y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 100 YKCPNCQSK-YTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred EECcCCCCE-eeHHHHHHhcCCCCcEECCCCCCEE
Confidence 369999632 11111 1229999999976
No 129
>TIGR02642 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q.
Probab=61.10 E-value=5.5 Score=31.98 Aligned_cols=23 Identities=26% Similarity=0.475 Sum_probs=17.6
Q ss_pred ceeeeeeeeccccccceeEeecC
Q 032810 96 SKRIIAQRRCEVCGGSGLVLREK 118 (133)
Q Consensus 96 ~KRIi~Q~rCe~C~GsGLV~r~~ 118 (133)
||.|..+..|..|+|+|-|....
T Consensus 109 G~~i~~~~~C~~C~G~G~v~~~~ 131 (186)
T TIGR02642 109 GLIQRRQRECDTCAGTGRFRPTV 131 (186)
T ss_pred eEEecCCCCCCCCCCccEEeeeE
Confidence 34444468999999999998664
No 130
>PRK04023 DNA polymerase II large subunit; Validated
Probab=61.09 E-value=4 Score=40.77 Aligned_cols=22 Identities=41% Similarity=1.075 Sum_probs=13.9
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
..++|..||-.+ ..++||.||.
T Consensus 625 g~RfCpsCG~~t------~~frCP~CG~ 646 (1121)
T PRK04023 625 GRRKCPSCGKET------FYRRCPFCGT 646 (1121)
T ss_pred cCccCCCCCCcC------CcccCCCCCC
Confidence 346777777664 4566766664
No 131
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=60.92 E-value=5.5 Score=26.16 Aligned_cols=26 Identities=35% Similarity=0.834 Sum_probs=18.9
Q ss_pred ecccccc-ceeEeecC---eeecCCCCCCC
Q 032810 104 RCEVCGG-SGLVLREK---DYFKCPECGMS 129 (133)
Q Consensus 104 rCe~C~G-sGLV~r~~---~~~kC~~CGGF 129 (133)
-|+.|.. .||+.++. -.++|+.||-+
T Consensus 24 IC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 24 ICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred ECcccchhhcccccccCCceEEEcCCCCCc
Confidence 3888865 68985443 37899999854
No 132
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=60.72 E-value=5.8 Score=30.58 Aligned_cols=27 Identities=30% Similarity=0.682 Sum_probs=22.4
Q ss_pred eeccccccceeEeecCeeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
.+|..|+-.=-+..-...-.||.||+-
T Consensus 113 l~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 113 LVCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred EecccCCCEEEecCCCcCCCCCCCCCC
Confidence 579999987777766778999999983
No 133
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=59.42 E-value=5.4 Score=23.21 Aligned_cols=10 Identities=40% Similarity=1.172 Sum_probs=7.2
Q ss_pred eecCCCCCCC
Q 032810 120 YFKCPECGMS 129 (133)
Q Consensus 120 ~~kC~~CGGF 129 (133)
...|++||-.
T Consensus 32 ~~~C~~CGE~ 41 (46)
T TIGR03831 32 ALVCPQCGEE 41 (46)
T ss_pred ccccccCCCE
Confidence 4579999854
No 134
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=59.04 E-value=4.4 Score=31.59 Aligned_cols=27 Identities=30% Similarity=0.705 Sum_probs=16.8
Q ss_pred eccccccceeEeec--CeeecCCCCCCCcc
Q 032810 104 RCEVCGGSGLVLRE--KDYFKCPECGMSYG 131 (133)
Q Consensus 104 rCe~C~GsGLV~r~--~~~~kC~~CGGFl~ 131 (133)
.|+.|+-. .-.-+ .+.|+||.|||-|-
T Consensus 119 ~Cp~C~~r-ytf~eA~~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 119 FCPNCHIR-FTFDEAMEYGFRCPQCGEMLE 147 (178)
T ss_pred ECCCCCcE-EeHHHHhhcCCcCCCCCCCCe
Confidence 48887621 11111 25799999999873
No 135
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=58.53 E-value=7.6 Score=26.79 Aligned_cols=27 Identities=26% Similarity=0.780 Sum_probs=21.4
Q ss_pred eeeeccccccceeEeec----------CeeecCCCCC
Q 032810 101 AQRRCEVCGGSGLVLRE----------KDYFKCPECG 127 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~----------~~~~kC~~CG 127 (133)
++.+|+.|+....+.-. -..+.|..||
T Consensus 61 ~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~ 97 (104)
T TIGR01384 61 TRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCG 97 (104)
T ss_pred ccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCC
Confidence 36899999999977632 2489999998
No 136
>COG5437 Predicted secreted protein [Function unknown]
Probab=58.06 E-value=8.9 Score=30.37 Aligned_cols=29 Identities=31% Similarity=0.715 Sum_probs=22.6
Q ss_pred CcceeeEEEE---eeeeccceeEEeeeeeceeee
Q 032810 70 TAEVTWQIIV---GAIAGVTPFVVAGIEFSKRII 100 (133)
Q Consensus 70 ~~e~~Wqi~v---G~iAGv~PFvvAg~EF~KRIi 100 (133)
..-+.||++. |.++| ||.|+.|||+-+-.
T Consensus 86 ~s~~~wkvv~pdfg~~~G--~fiv~aley~g~hD 117 (138)
T COG5437 86 DSIVCWKVVNPDFGLFGG--PFIVAALEYEGPHD 117 (138)
T ss_pred CCceEEEEEccCcccccC--cEEEEEeeecCCCC
Confidence 3446899995 77777 89999999986643
No 137
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=57.59 E-value=9.9 Score=26.18 Aligned_cols=32 Identities=31% Similarity=0.720 Sum_probs=24.9
Q ss_pred eeeeeeeeccccccceeEe----ecCeeecCCCCCC
Q 032810 97 KRIIAQRRCEVCGGSGLVL----REKDYFKCPECGM 128 (133)
Q Consensus 97 KRIi~Q~rCe~C~GsGLV~----r~~~~~kC~~CGG 128 (133)
||.|+--.|+.|+----++ -+..++-|-+||=
T Consensus 4 KRFIAGA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~ 39 (59)
T TIGR02443 4 KRFIAGAVCPACSAQDTLAMWKENNIELVECVECGY 39 (59)
T ss_pred ceEeccccCCCCcCccEEEEEEeCCceEEEeccCCC
Confidence 8999999999999765433 2246899999983
No 138
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=56.83 E-value=7.6 Score=23.46 Aligned_cols=26 Identities=35% Similarity=0.857 Sum_probs=16.7
Q ss_pred eeccccccceeEeecC---eeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREK---DYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~---~~~kC~~CGGF 129 (133)
+-|+.||. =|..++. ..+.|+.||--
T Consensus 1 ~FCp~Cg~-~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 1 KFCPKCGN-MLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCC-ccccccCCCCCEEECCcCCCe
Confidence 35899966 3333332 37789999943
No 139
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=56.68 E-value=10 Score=23.63 Aligned_cols=25 Identities=32% Similarity=0.906 Sum_probs=20.0
Q ss_pred eccccccceeEeecC--------eeecCCC--CCC
Q 032810 104 RCEVCGGSGLVLREK--------DYFKCPE--CGM 128 (133)
Q Consensus 104 rCe~C~GsGLV~r~~--------~~~kC~~--CGG 128 (133)
+|+.|+....+.+.. .|..|.+ ||=
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~ 35 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGH 35 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCC
Confidence 699999999888653 5888987 873
No 140
>PLN02294 cytochrome c oxidase subunit Vb
Probab=56.43 E-value=9.1 Score=31.14 Aligned_cols=37 Identities=38% Similarity=0.833 Sum_probs=24.1
Q ss_pred eeEEeeeeeceeeeeeeecccccc-ce--------eEeecCeeecCCCCCCCc
Q 032810 87 PFVVAGIEFSKRIIAQRRCEVCGG-SG--------LVLREKDYFKCPECGMSY 130 (133)
Q Consensus 87 PFvvAg~EF~KRIi~Q~rCe~C~G-sG--------LV~r~~~~~kC~~CGGFl 130 (133)
|.+|=+| |-+||+ -|-| .| +-..++.+.+||+||-.+
T Consensus 106 P~lVpS~-~d~RiV------GCtg~~~eDsh~v~Wf~L~kGkp~RCpeCG~~f 151 (174)
T PLN02294 106 PAVVKSY-YDKRIV------GCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYF 151 (174)
T ss_pred CcEeccC-CCceEE------eeCCCCCCCCceeEEEEecCCCceeCCCCCCEE
Confidence 5566665 777877 3555 22 223556788899999754
No 141
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=56.10 E-value=9 Score=29.18 Aligned_cols=11 Identities=55% Similarity=1.204 Sum_probs=5.3
Q ss_pred eccccccceeE
Q 032810 104 RCEVCGGSGLV 114 (133)
Q Consensus 104 rCe~C~GsGLV 114 (133)
||..|.--|||
T Consensus 135 rC~~Cnengl~ 145 (147)
T cd03031 135 RCPECNENGLV 145 (147)
T ss_pred ECCCCCccccc
Confidence 45555444444
No 142
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=55.71 E-value=12 Score=22.95 Aligned_cols=24 Identities=21% Similarity=0.743 Sum_probs=17.9
Q ss_pred eccccccceeEe-ecCeeecCCCCC
Q 032810 104 RCEVCGGSGLVL-REKDYFKCPECG 127 (133)
Q Consensus 104 rCe~C~GsGLV~-r~~~~~kC~~CG 127 (133)
.|+.|+..-... ++...++|.+|+
T Consensus 20 ~CP~Cg~~~~~~~~~~~~~~C~~C~ 44 (46)
T PF12760_consen 20 VCPHCGSTKHYRLKTRGRYRCKACR 44 (46)
T ss_pred CCCCCCCeeeEEeCCCCeEECCCCC
Confidence 499999874443 335899999997
No 143
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=55.02 E-value=7.9 Score=39.46 Aligned_cols=10 Identities=50% Similarity=1.268 Sum_probs=6.9
Q ss_pred eeeccccccc
Q 032810 102 QRRCEVCGGS 111 (133)
Q Consensus 102 Q~rCe~C~Gs 111 (133)
+++|+.|+..
T Consensus 667 ~rkCPkCG~~ 676 (1337)
T PRK14714 667 RRRCPSCGTE 676 (1337)
T ss_pred EEECCCCCCc
Confidence 6677777764
No 144
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=53.80 E-value=8.5 Score=38.54 Aligned_cols=24 Identities=46% Similarity=1.041 Sum_probs=19.7
Q ss_pred eeeeeccccccceeEeecCeeecCCCCCCC
Q 032810 100 IAQRRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 100 i~Q~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
+..++|..|+-.. .+.+||.||+-
T Consensus 623 v~~RKCPkCG~yT------lk~rCP~CG~~ 646 (1095)
T TIGR00354 623 IAIRKCPQCGKES------FWLKCPVCGEL 646 (1095)
T ss_pred EEEEECCCCCccc------ccccCCCCCCc
Confidence 5678999998654 57899999985
No 145
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.54 E-value=9.5 Score=28.27 Aligned_cols=25 Identities=32% Similarity=0.739 Sum_probs=18.9
Q ss_pred eccccccceeEeecCe---eecCCCCCCC
Q 032810 104 RCEVCGGSGLVLREKD---YFKCPECGMS 129 (133)
Q Consensus 104 rCe~C~GsGLV~r~~~---~~kC~~CGGF 129 (133)
-|++|+- -||+..++ .--||.|+|.
T Consensus 3 lCP~C~v-~l~~~~rs~vEiD~CPrCrGV 30 (88)
T COG3809 3 LCPICGV-ELVMSVRSGVEIDYCPRCRGV 30 (88)
T ss_pred ccCcCCc-eeeeeeecCceeeeCCccccE
Confidence 5888865 48887765 5679999984
No 146
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=53.38 E-value=7.4 Score=23.29 Aligned_cols=24 Identities=33% Similarity=1.092 Sum_probs=13.7
Q ss_pred eccccccceeEeecCeeecCCCCCC
Q 032810 104 RCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 104 rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
+|+.|+.. -...|+..+-||+||.
T Consensus 4 ~Cp~C~se-~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSE-YTYEDGELLVCPECGH 27 (30)
T ss_dssp --TTT------EE-SSSEEETTTTE
T ss_pred CCCCCCCc-ceeccCCEEeCCcccc
Confidence 68999754 4457888899999985
No 147
>PRK00635 excinuclease ABC subunit A; Provisional
Probab=52.91 E-value=9.1 Score=39.79 Aligned_cols=26 Identities=27% Similarity=0.694 Sum_probs=21.9
Q ss_pred eeccccccceeEee--cCeeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLR--EKDYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r--~~~~~kC~~CGG 128 (133)
-||+.|+|.|.+.- +..+..|+.|+|
T Consensus 721 G~C~~c~g~g~i~v~m~~~~v~c~~C~G 748 (1809)
T PRK00635 721 GACAECQGLGSITTTDNRTSIPCPSCLG 748 (1809)
T ss_pred CCCCcceeeEEEEEecCCceEECCccCC
Confidence 49999999998555 456889999999
No 148
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=52.58 E-value=9.1 Score=25.97 Aligned_cols=27 Identities=26% Similarity=0.399 Sum_probs=15.0
Q ss_pred eeccccccceeEeecCeeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
-.|-.|+..+-|.---.+-||+.||.+
T Consensus 31 IlCNDC~~~s~v~fH~lg~KC~~C~SY 57 (61)
T PF14599_consen 31 ILCNDCNAKSEVPFHFLGHKCSHCGSY 57 (61)
T ss_dssp EEESSS--EEEEE--TT----TTTS--
T ss_pred EECCCCCCccceeeeHhhhcCCCCCCc
Confidence 359999999999888889999999975
No 149
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=52.02 E-value=12 Score=32.24 Aligned_cols=38 Identities=26% Similarity=0.687 Sum_probs=29.0
Q ss_pred ceeEEeeeeeceeeeeeeecccccc---ce------eEeecCeeecCCCCCCCc
Q 032810 86 TPFVVAGIEFSKRIIAQRRCEVCGG---SG------LVLREKDYFKCPECGMSY 130 (133)
Q Consensus 86 ~PFvvAg~EF~KRIi~Q~rCe~C~G---sG------LV~r~~~~~kC~~CGGFl 130 (133)
-|.+|-++ +.+||+- |-| .. +..+++...||++||-.+
T Consensus 145 dPiLVpSy-~deRyVG------CTGg~~EDeH~VvWFwLrEGkpqRCpECGqVF 191 (268)
T PTZ00043 145 NPVLVPSV-GTERVVG------CTGGTGEHEHVPLWFRCREGFLYRCGECDQIF 191 (268)
T ss_pred CCeEeccC-CCceEEe------ccCCCccCCceeEEEEecCCCCccCCCCCcEE
Confidence 58888777 8899984 555 22 556888999999999755
No 150
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=52.01 E-value=8.8 Score=36.43 Aligned_cols=13 Identities=46% Similarity=0.851 Sum_probs=10.7
Q ss_pred cCeeecCCCCCCC
Q 032810 117 EKDYFKCPECGMS 129 (133)
Q Consensus 117 ~~~~~kC~~CGGF 129 (133)
++.+..||+||++
T Consensus 472 ~~~p~~Cp~Cgs~ 484 (730)
T COG1198 472 EPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCC
Confidence 3568899999987
No 151
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=50.23 E-value=6.4 Score=25.23 Aligned_cols=9 Identities=44% Similarity=1.099 Sum_probs=7.6
Q ss_pred ecCCCCCCC
Q 032810 121 FKCPECGMS 129 (133)
Q Consensus 121 ~kC~~CGGF 129 (133)
+||..||+|
T Consensus 2 ~kC~~CG~~ 10 (40)
T PF15288_consen 2 VKCKNCGAF 10 (40)
T ss_pred ccccccccc
Confidence 589999987
No 152
>PHA02540 61 DNA primase; Provisional
Probab=49.17 E-value=12 Score=32.39 Aligned_cols=27 Identities=44% Similarity=1.123 Sum_probs=23.5
Q ss_pred eeecccccc--------ceeEeecCe--eecCCCCCC
Q 032810 102 QRRCEVCGG--------SGLVLREKD--YFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~G--------sGLV~r~~~--~~kC~~CGG 128 (133)
.-+|+-|+- |+-|..++. .++|-+||-
T Consensus 27 ~~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa 63 (337)
T PHA02540 27 NFRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGY 63 (337)
T ss_pred EecCCCCCCccccCcCCcEEEeccCCceEEEecCCCC
Confidence 468999998 799998887 999999983
No 153
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=48.85 E-value=11 Score=25.45 Aligned_cols=23 Identities=43% Similarity=1.116 Sum_probs=17.2
Q ss_pred eeccccccceeEee-cCeeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLR-EKDYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r-~~~~~kC~~CGG 128 (133)
.+|.+|+. ..+ +..-+.||+||-
T Consensus 6 ~~C~~Cg~---~~~~~dDiVvCp~Cga 29 (54)
T PF14446_consen 6 CKCPVCGK---KFKDGDDIVVCPECGA 29 (54)
T ss_pred ccChhhCC---cccCCCCEEECCCCCC
Confidence 47888864 444 678999999984
No 154
>PRK11032 hypothetical protein; Provisional
Probab=48.66 E-value=12 Score=29.52 Aligned_cols=28 Identities=25% Similarity=0.503 Sum_probs=23.2
Q ss_pred eeeccccccceeEeecCeeecCCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
..+|+.|+-.=-+..-...-.||.||+-
T Consensus 124 ~LvC~~Cg~~~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 124 NLVCEKCHHHLAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred eEEecCCCCEEEecCCCcCCCCCCCCCC
Confidence 4689999988777777788899999973
No 155
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=47.69 E-value=12 Score=27.91 Aligned_cols=30 Identities=30% Similarity=0.577 Sum_probs=19.7
Q ss_pred eeeeccccccceeEe------ecCeeecCCCCCCCc
Q 032810 101 AQRRCEVCGGSGLVL------REKDYFKCPECGMSY 130 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~------r~~~~~kC~~CGGFl 130 (133)
.+-+|..|+-.=-.. ..+...+|+.|||.|
T Consensus 104 ~~~~C~~C~~~~~~~~~~~~~~~~~~~~C~~C~~~l 139 (178)
T PF02146_consen 104 FRLRCSKCGKEYDREDIVDSIDEEEPPRCPKCGGLL 139 (178)
T ss_dssp EEEEETTTSBEEEGHHHHHHHHTTSSCBCTTTSCBE
T ss_pred ceeeecCCCccccchhhcccccccccccccccCccC
Confidence 456899998732211 224456999999965
No 156
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=47.59 E-value=12 Score=22.55 Aligned_cols=27 Identities=22% Similarity=0.508 Sum_probs=20.3
Q ss_pred eeccccccceeEeec-----CeeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLRE-----KDYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~-----~~~~kC~~CGGF 129 (133)
-.|+.|+..=-|..+ ...++|+.||--
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence 368999887766644 468999999853
No 157
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=47.50 E-value=12 Score=30.34 Aligned_cols=27 Identities=26% Similarity=0.544 Sum_probs=20.9
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.+-|..||..=-+..+..-+.|++||-
T Consensus 99 ~~fC~~CG~~~~~~~~~~~~~C~~c~~ 125 (256)
T PRK00241 99 HRFCGYCGHPMHPSKTEWAMLCPHCRE 125 (256)
T ss_pred CccccccCCCCeecCCceeEECCCCCC
Confidence 568999999744445667888999984
No 158
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=46.74 E-value=16 Score=25.46 Aligned_cols=26 Identities=19% Similarity=0.726 Sum_probs=20.9
Q ss_pred eccccccceeEeecC--------eeecCC--CCCCC
Q 032810 104 RCEVCGGSGLVLREK--------DYFKCP--ECGMS 129 (133)
Q Consensus 104 rCe~C~GsGLV~r~~--------~~~kC~--~CGGF 129 (133)
+|..|+..-.|.+.+ .|..|. +||--
T Consensus 3 ~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~t 38 (72)
T PRK09678 3 HCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSAT 38 (72)
T ss_pred cCCCCCCccEEEEChhcChhhheeeeecCCCCCCCE
Confidence 799999999777553 599998 99853
No 159
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=46.34 E-value=9.2 Score=35.33 Aligned_cols=21 Identities=38% Similarity=0.931 Sum_probs=16.0
Q ss_pred eeccccccceeEeecCeeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
-+|..||-.|- ....||.||.
T Consensus 560 ~~C~~CGy~g~-----~~~~CP~CG~ 580 (618)
T PRK14704 560 DRCKCCSYHGV-----IGNECPSCGN 580 (618)
T ss_pred eecCCCCCCCC-----cCccCcCCCC
Confidence 47999986653 2489999994
No 160
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=46.20 E-value=15 Score=21.95 Aligned_cols=27 Identities=22% Similarity=0.399 Sum_probs=22.3
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
|-.|.-|+-.=...++...+||.-|..
T Consensus 1 q~~C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 1 QVVCGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred CcCcCCCCcEeecCCCCCeEECCCCCe
Confidence 567888887777778999999999974
No 161
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=45.64 E-value=13 Score=38.71 Aligned_cols=24 Identities=46% Similarity=0.967 Sum_probs=19.5
Q ss_pred eeeeeccccccceeEeecCeeecCCCCCCC
Q 032810 100 IAQRRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 100 i~Q~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
+..++|..|+-.| ++.+||.||.-
T Consensus 672 i~~~~Cp~Cg~~~------~~~~Cp~CG~~ 695 (1627)
T PRK14715 672 IAFFKCPKCGKVG------LYHVCPFCGTR 695 (1627)
T ss_pred EEeeeCCCCCCcc------ccccCcccCCc
Confidence 5678999998765 58899999974
No 162
>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=45.58 E-value=10 Score=34.16 Aligned_cols=21 Identities=48% Similarity=1.078 Sum_probs=16.0
Q ss_pred eccccccceeEeecCeeecCCCCCC
Q 032810 104 RCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 104 rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|..||-.|- +...+||.||-
T Consensus 520 ~C~~CG~~~~----~~~~~CP~CGs 540 (555)
T cd01675 520 ICNDCGYIGE----GEGFKCPKCGS 540 (555)
T ss_pred cCCCCCCCCc----CCCCCCcCCCC
Confidence 7999986442 45689999984
No 163
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=44.76 E-value=19 Score=19.50 Aligned_cols=11 Identities=55% Similarity=1.422 Sum_probs=8.5
Q ss_pred ecCCCCCCCcc
Q 032810 121 FKCPECGMSYG 131 (133)
Q Consensus 121 ~kC~~CGGFl~ 131 (133)
|+|..|+--|.
T Consensus 28 f~C~~C~~~L~ 38 (39)
T smart00132 28 FKCSKCGKPLG 38 (39)
T ss_pred CCCcccCCcCc
Confidence 88999987653
No 164
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=44.53 E-value=10 Score=26.12 Aligned_cols=11 Identities=36% Similarity=0.803 Sum_probs=9.2
Q ss_pred eecCCCCCCCc
Q 032810 120 YFKCPECGMSY 130 (133)
Q Consensus 120 ~~kC~~CGGFl 130 (133)
.-.||+|||-|
T Consensus 41 ~~~CPNCgGel 51 (57)
T PF06906_consen 41 NGVCPNCGGEL 51 (57)
T ss_pred cCcCcCCCCcc
Confidence 56899999976
No 165
>PLN02569 threonine synthase
Probab=44.17 E-value=11 Score=33.41 Aligned_cols=25 Identities=12% Similarity=0.283 Sum_probs=17.6
Q ss_pred eeccccccceeEeecCeeecCCCCCCCc
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGMSY 130 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGGFl 130 (133)
.+|..|+-. ..-+....+| .|||-|
T Consensus 50 l~C~~Cg~~--y~~~~~~~~C-~cgg~l 74 (484)
T PLN02569 50 LECPLTGEK--YSLDEVVYRS-KSGGLL 74 (484)
T ss_pred cEeCCCCCc--CCCccccccC-CCCCeE
Confidence 689999754 2334556799 799876
No 166
>PRK05978 hypothetical protein; Provisional
Probab=43.93 E-value=11 Score=29.36 Aligned_cols=29 Identities=31% Similarity=0.705 Sum_probs=20.0
Q ss_pred eeeccccccceeEeec-CeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVLRE-KDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~-~~~~kC~~CGGFl 130 (133)
..||+.|+--.|...= +-.-+|+.||--|
T Consensus 33 ~grCP~CG~G~LF~g~Lkv~~~C~~CG~~~ 62 (148)
T PRK05978 33 RGRCPACGEGKLFRAFLKPVDHCAACGEDF 62 (148)
T ss_pred cCcCCCCCCCcccccccccCCCccccCCcc
Confidence 4699999876665421 3466899999543
No 167
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=43.87 E-value=24 Score=21.59 Aligned_cols=26 Identities=19% Similarity=0.672 Sum_probs=19.2
Q ss_pred eeeeccccccceeEeec------CeeecCCCC
Q 032810 101 AQRRCEVCGGSGLVLRE------KDYFKCPEC 126 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~------~~~~kC~~C 126 (133)
+.-.|+.|+..-.|.+. .+-++|.+|
T Consensus 4 i~v~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 4 IDVHCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred EeeeCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 35679999998845443 368899998
No 168
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 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). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=43.69 E-value=22 Score=23.76 Aligned_cols=21 Identities=48% Similarity=0.975 Sum_probs=12.5
Q ss_pred eeccccccceeEeecCeeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
++|..|+ |..=+ .+||.||+-
T Consensus 6 r~c~~~~----~YTLk--~~cp~cG~~ 26 (53)
T PF04135_consen 6 RKCPGCR----VYTLK--DKCPPCGGP 26 (53)
T ss_dssp EECTTTC----EEESS--SBBTTTSSB
T ss_pred ccCCCCC----cEeCC--CccCCCCCC
Confidence 4566665 22222 479999874
No 169
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=42.95 E-value=8 Score=37.98 Aligned_cols=45 Identities=36% Similarity=0.739 Sum_probs=0.0
Q ss_pred EeeeeccceeEEeeeeece-ee---eeeeeccccccceeEeecCeeecCCCCCCC
Q 032810 79 VGAIAGVTPFVVAGIEFSK-RI---IAQRRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 79 vG~iAGv~PFvvAg~EF~K-RI---i~Q~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
||-..|-+=-+.-+.+.++ -| +..++|..|+-. .++.+||.||..
T Consensus 628 IG~~GG~~R~i~~A~~~~~g~i~vei~~r~Cp~Cg~~------t~~~~Cp~CG~~ 676 (900)
T PF03833_consen 628 IGEAGGSRRDIQKAAKKGKGTIEVEIGRRRCPKCGKE------TFYNRCPECGSH 676 (900)
T ss_dssp -------------------------------------------------------
T ss_pred ccccCcccccHHHHHhcCCCeeEEeeecccCcccCCc------chhhcCcccCCc
Confidence 4545555556666666665 22 456788888754 356677777754
No 170
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=42.89 E-value=9.3 Score=29.45 Aligned_cols=28 Identities=21% Similarity=0.863 Sum_probs=22.2
Q ss_pred eeeeeccccccceeEeec-----C-----eeecCCCCC
Q 032810 100 IAQRRCEVCGGSGLVLRE-----K-----DYFKCPECG 127 (133)
Q Consensus 100 i~Q~rCe~C~GsGLV~r~-----~-----~~~kC~~CG 127 (133)
.+.++|+.||-.++...- . -++-|+.|+
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~ 109 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCK 109 (116)
T ss_pred chhccCcccCCchhhhhhhhcccccCCceEEEEcCccc
Confidence 467899999999998732 2 278899997
No 171
>PRK11827 hypothetical protein; Provisional
Probab=42.44 E-value=13 Score=25.29 Aligned_cols=35 Identities=26% Similarity=0.572 Sum_probs=26.1
Q ss_pred ceeeeeeeeccccccceeEe-ecCeeecCCCCCCCcc
Q 032810 96 SKRIIAQRRCEVCGGSGLVL-REKDYFKCPECGMSYG 131 (133)
Q Consensus 96 ~KRIi~Q~rCe~C~GsGLV~-r~~~~~kC~~CGGFl~ 131 (133)
-|+++.-..|+.|+|. |.. .++.-..|..||=-+|
T Consensus 2 d~~LLeILaCP~ckg~-L~~~~~~~~Lic~~~~laYP 37 (60)
T PRK11827 2 DHRLLEIIACPVCNGK-LWYNQEKQELICKLDNLAFP 37 (60)
T ss_pred ChHHHhheECCCCCCc-CeEcCCCCeEECCccCeecc
Confidence 4566677789999996 444 4566788999997766
No 172
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.79 E-value=14 Score=32.65 Aligned_cols=24 Identities=33% Similarity=0.744 Sum_probs=14.2
Q ss_pred eccccccceeEe-ecC-------------eeecCCCCCC
Q 032810 104 RCEVCGGSGLVL-REK-------------DYFKCPECGM 128 (133)
Q Consensus 104 rCe~C~GsGLV~-r~~-------------~~~kC~~CGG 128 (133)
+|+.|.++ |+. ++. .+.+||+||+
T Consensus 224 ~C~~C~~~-l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s 261 (505)
T TIGR00595 224 CCPNCDVS-LTYHKKEGKLRCHYCGYQEPIPKTCPQCGS 261 (505)
T ss_pred CCCCCCCc-eEEecCCCeEEcCCCcCcCCCCCCCCCCCC
Confidence 47777664 554 332 2557777776
No 173
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=41.24 E-value=8.7 Score=25.78 Aligned_cols=14 Identities=43% Similarity=1.037 Sum_probs=10.9
Q ss_pred eecCeeecCCCCCC
Q 032810 115 LREKDYFKCPECGM 128 (133)
Q Consensus 115 ~r~~~~~kC~~CGG 128 (133)
...+.|-+||.||.
T Consensus 8 ~L~~kY~~Cp~CGN 21 (49)
T PF12677_consen 8 KLSNKYCKCPKCGN 21 (49)
T ss_pred chhhhhccCcccCC
Confidence 34567999999985
No 174
>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=40.76 E-value=12 Score=28.95 Aligned_cols=29 Identities=28% Similarity=0.614 Sum_probs=18.3
Q ss_pred eeeccccccceeEe------ecCeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVL------REKDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~------r~~~~~kC~~CGGFl 130 (133)
.-+|..|+-.=... .+....+||.|||.|
T Consensus 109 ~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~l 143 (218)
T cd01407 109 RVRCTKCGKEYPRDELQADIDREEVPRCPKCGGLL 143 (218)
T ss_pred cceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCcc
Confidence 35699997542211 123457899999975
No 175
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=39.81 E-value=13 Score=33.78 Aligned_cols=22 Identities=45% Similarity=0.853 Sum_probs=14.6
Q ss_pred eeccccccceeEeecCeeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
-+|..||=.|-. ...+||.||.
T Consensus 525 ~~C~~CG~~g~~----~~~~CP~Cgs 546 (579)
T TIGR02487 525 DVCEDCGYTGEG----LNDKCPKCGS 546 (579)
T ss_pred ccCCCCCCCCCC----CCCcCcCCCC
Confidence 469999743322 1378999984
No 176
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=39.17 E-value=22 Score=23.57 Aligned_cols=29 Identities=28% Similarity=0.574 Sum_probs=19.4
Q ss_pred eeeccccccceeEeec--CeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVLRE--KDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~--~~~~kC~~CGGFl 130 (133)
+..|..|+.+=-|..+ .....||.||--|
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence 3479999885333221 4578999999654
No 177
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=38.59 E-value=13 Score=20.43 Aligned_cols=15 Identities=40% Similarity=1.028 Sum_probs=11.0
Q ss_pred ecCeeecCCCCCCCc
Q 032810 116 REKDYFKCPECGMSY 130 (133)
Q Consensus 116 r~~~~~kC~~CGGFl 130 (133)
.+..+++|+.|+--+
T Consensus 10 ~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 10 TGEKPYKCPYCGKSF 24 (26)
T ss_dssp SSSSSEEESSSSEEE
T ss_pred CCCCCCCCCCCcCee
Confidence 356789999998543
No 178
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=38.52 E-value=14 Score=34.68 Aligned_cols=21 Identities=52% Similarity=1.085 Sum_probs=15.2
Q ss_pred eeccccccceeEeecCeeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
-+|..||-.|- ....||.||.
T Consensus 681 ~~C~~CG~~~~-----~~~~CP~CG~ 701 (735)
T PRK07111 681 DRCPVCGYLGV-----IEDKCPKCGS 701 (735)
T ss_pred eecCCCCCCCC-----cCccCcCCCC
Confidence 47999985432 2489999994
No 179
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=38.06 E-value=21 Score=25.20 Aligned_cols=25 Identities=32% Similarity=0.592 Sum_probs=15.5
Q ss_pred eeccccccceeEeecCeeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
-|| .||--=....+....+| -||--
T Consensus 4 frC-~Cgr~lya~e~~kTkkC-~CG~~ 28 (68)
T PF09082_consen 4 FRC-DCGRYLYAKEGAKTKKC-VCGKT 28 (68)
T ss_dssp EEE-TTS--EEEETT-SEEEE-TTTEE
T ss_pred EEe-cCCCEEEecCCcceeEe-cCCCe
Confidence 378 68665555555679999 89853
No 180
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=37.86 E-value=15 Score=28.52 Aligned_cols=40 Identities=30% Similarity=0.749 Sum_probs=25.6
Q ss_pred ceeEEeeeeeceeeeeeeeccccc-cce-----eEeecCeeecCCCCCCCc
Q 032810 86 TPFVVAGIEFSKRIIAQRRCEVCG-GSG-----LVLREKDYFKCPECGMSY 130 (133)
Q Consensus 86 ~PFvvAg~EF~KRIi~Q~rCe~C~-GsG-----LV~r~~~~~kC~~CGGFl 130 (133)
-|.+|-++ |.+||+- |. |. +.- +...++.+.||++||-++
T Consensus 77 ~P~lVpS~-~~~RiVG---C~-g~~~~sH~v~W~~l~~g~~~RCpeCG~~f 122 (136)
T PF01215_consen 77 DPILVPSY-FDERIVG---CT-GEPDDSHDVIWFWLHKGKPQRCPECGQVF 122 (136)
T ss_dssp S-CEEEES-SSCEEEE---ES-SSTT-SSS-EEEEEETTSEEEETTTEEEE
T ss_pred CCeEccCC-CCceEEe---ec-cCCCCcceeEEEEEeCCCccCCCCCCeEE
Confidence 58888777 8999984 21 22 222 223556689999999765
No 181
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=37.69 E-value=19 Score=31.57 Aligned_cols=26 Identities=31% Similarity=0.650 Sum_probs=14.8
Q ss_pred eeeeccccccceeEeecCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
.|.+|..|.|+|-.. ..+-+|+.|-|
T Consensus 169 ~q~~C~~C~G~G~~~--~~kd~C~~C~G 194 (337)
T KOG0712|consen 169 PQLVCDSCNGSGETI--SLKDRCKTCSG 194 (337)
T ss_pred ceeEeccCCCccccc--cccccCccccc
Confidence 466677777766552 22345666654
No 182
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=37.46 E-value=20 Score=23.49 Aligned_cols=19 Identities=37% Similarity=0.756 Sum_probs=14.0
Q ss_pred EeecCeeecCCCCCCCccc
Q 032810 114 VLREKDYFKCPECGMSYGL 132 (133)
Q Consensus 114 V~r~~~~~kC~~CGGFl~~ 132 (133)
+........||+||--+|-
T Consensus 47 ~~i~eg~L~Cp~c~r~YPI 65 (68)
T PF03966_consen 47 VEIVEGELICPECGREYPI 65 (68)
T ss_dssp EETTTTEEEETTTTEEEEE
T ss_pred ccccCCEEEcCCCCCEEeC
Confidence 3455668899999987763
No 183
>PHA02998 RNA polymerase subunit; Provisional
Probab=37.27 E-value=24 Score=29.37 Aligned_cols=28 Identities=14% Similarity=0.345 Sum_probs=21.3
Q ss_pred eeeccccccceeEeec-----C-----eeecCCCCCCC
Q 032810 102 QRRCEVCGGSGLVLRE-----K-----DYFKCPECGMS 129 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~-----~-----~~~kC~~CGGF 129 (133)
...|+.|++....... . .+++|..||.-
T Consensus 143 ~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~ 180 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKH 180 (195)
T ss_pred CCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCc
Confidence 4589999999887532 2 47899999963
No 184
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=36.28 E-value=24 Score=25.83 Aligned_cols=61 Identities=25% Similarity=0.434 Sum_probs=37.3
Q ss_pred eeeEEEEeeeeccceeEEeeeeeceeeeeeeecccccccee-EeecC--eeecCCCCCCCcccC
Q 032810 73 VTWQIIVGAIAGVTPFVVAGIEFSKRIIAQRRCEVCGGSGL-VLREK--DYFKCPECGMSYGLI 133 (133)
Q Consensus 73 ~~Wqi~vG~iAGv~PFvvAg~EF~KRIi~Q~rCe~C~GsGL-V~r~~--~~~kC~~CGGFl~~i 133 (133)
..|+-|+--+-+..|=.-..++....---.-+|..|+-.=+ +.|.. ...+|..|||-|-+|
T Consensus 83 ~~f~~~~~~~~~~~~~~~h~~~~~~~~~~~y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l~~~ 146 (146)
T smart00731 83 DEWKRWMRQVNGLFPERCHTFLIESVKKYPYRCTGCGQRYLRVRRSNNVSRYRCGKCGGKLILI 146 (146)
T ss_pred HHHHHHHHHHcCCCcceEcCCcccccceEEEECCCCCCCCceEccccCcceEEcCCCCCEEEeC
Confidence 57888888777776632223322221123568988986544 33321 457899999988654
No 185
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=36.03 E-value=14 Score=23.65 Aligned_cols=9 Identities=56% Similarity=1.372 Sum_probs=7.1
Q ss_pred eecCCCCCC
Q 032810 120 YFKCPECGM 128 (133)
Q Consensus 120 ~~kC~~CGG 128 (133)
-..||+||+
T Consensus 9 G~~CPgCG~ 17 (52)
T PF10825_consen 9 GIPCPGCGM 17 (52)
T ss_pred CCCCCCCcH
Confidence 357999997
No 186
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=35.90 E-value=17 Score=23.91 Aligned_cols=11 Identities=45% Similarity=1.068 Sum_probs=8.7
Q ss_pred eeecCCCCCCC
Q 032810 119 DYFKCPECGMS 129 (133)
Q Consensus 119 ~~~kC~~CGGF 129 (133)
-.+|||.||-+
T Consensus 10 GirkCp~CGt~ 20 (44)
T PF14952_consen 10 GIRKCPKCGTY 20 (44)
T ss_pred ccccCCcCcCc
Confidence 46899999965
No 187
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=35.74 E-value=23 Score=24.70 Aligned_cols=24 Identities=33% Similarity=0.815 Sum_probs=12.8
Q ss_pred ecccccccee-EeecCeeecCCCCCC
Q 032810 104 RCEVCGGSGL-VLREKDYFKCPECGM 128 (133)
Q Consensus 104 rCe~C~GsGL-V~r~~~~~kC~~CGG 128 (133)
.|..|+. .| +....-.|.||+||-
T Consensus 11 ~CtSCg~-~i~p~e~~v~F~CPnCGe 35 (61)
T COG2888 11 VCTSCGR-EIAPGETAVKFPCPNCGE 35 (61)
T ss_pred eeccCCC-EeccCCceeEeeCCCCCc
Confidence 5666643 34 223334677777773
No 188
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=35.72 E-value=23 Score=20.68 Aligned_cols=27 Identities=37% Similarity=0.924 Sum_probs=11.6
Q ss_pred eeeeeeeccccccceeEeecCeeecCCCCCCC
Q 032810 98 RIIAQRRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 98 RIi~Q~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
|+++ +||..|+..=.-.+ ..||.||+.
T Consensus 8 ~l~~-~rC~~Cg~~~~pPr----~~Cp~C~s~ 34 (37)
T PF12172_consen 8 RLLG-QRCRDCGRVQFPPR----PVCPHCGSD 34 (37)
T ss_dssp -EEE-EE-TTT--EEES------SEETTTT--
T ss_pred EEEE-EEcCCCCCEecCCC----cCCCCcCcc
Confidence 3444 46777765422222 578999863
No 189
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=35.03 E-value=19 Score=33.51 Aligned_cols=22 Identities=27% Similarity=0.702 Sum_probs=16.1
Q ss_pred eeccccccceeEeecCeeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
-.|..||-.+ ......||.||.
T Consensus 567 ~iC~~CG~~~----~g~~~~CP~CGs 588 (623)
T PRK08271 567 TICNDCHHID----KRTGKRCPICGS 588 (623)
T ss_pred ccCCCCCCcC----CCCCcCCcCCCC
Confidence 4799998642 335689999984
No 190
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=34.73 E-value=22 Score=24.06 Aligned_cols=21 Identities=38% Similarity=0.969 Sum_probs=15.6
Q ss_pred eccccccceeEeecCeeecCCCCC
Q 032810 104 RCEVCGGSGLVLREKDYFKCPECG 127 (133)
Q Consensus 104 rCe~C~GsGLV~r~~~~~kC~~CG 127 (133)
.|.+|+... +....+-||.||
T Consensus 1 ~Cpv~~~~~---~~~v~~~Cp~cG 21 (55)
T PF13824_consen 1 LCPVCKKDL---PAHVNFECPDCG 21 (55)
T ss_pred CCCCCcccc---ccccCCcCCCCC
Confidence 377776653 666788999998
No 191
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=34.63 E-value=24 Score=30.32 Aligned_cols=45 Identities=27% Similarity=0.586 Sum_probs=26.4
Q ss_pred eccceeEEeeee-----------eceeee---eeeeccccccc---eeEe----ecCeeecCCCCC
Q 032810 83 AGVTPFVVAGIE-----------FSKRII---AQRRCEVCGGS---GLVL----REKDYFKCPECG 127 (133)
Q Consensus 83 AGv~PFvvAg~E-----------F~KRIi---~Q~rCe~C~Gs---GLV~----r~~~~~kC~~CG 127 (133)
+...||+||+.- ...+.- ....|++||+. ++|. .+.+|-.|.-|+
T Consensus 154 ~~~a~Fi~AALqv~wa~~a~~l~~~~~~~~~~~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~ 219 (309)
T PRK03564 154 SDKAPFIWAALSLYWAQMAQQIPGKARAEYGEQRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCE 219 (309)
T ss_pred hhHHHHHHHHHHHHHHHHHhhCCcccccccccCCCCCCCCCCcchhheeeccCCCCceEEEcCCCC
Confidence 455688886654 111111 24789999997 5553 234566665555
No 192
>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=34.54 E-value=21 Score=28.01 Aligned_cols=29 Identities=24% Similarity=0.598 Sum_probs=16.8
Q ss_pred eeeccccccceeEe-----ecCeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVL-----REKDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~-----r~~~~~kC~~CGGFl 130 (133)
.-+|..|+-.=-.. ......+|+.|||.|
T Consensus 113 ~~~C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg~l 146 (222)
T cd01413 113 TAYCVNCGSKYDLEEVKYAKKHEVPRCPKCGGII 146 (222)
T ss_pred cceECCCCCCcchhHHHHhccCCCCcCCCCCCcc
Confidence 35688886531100 112356899999865
No 193
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=34.45 E-value=21 Score=21.69 Aligned_cols=15 Identities=47% Similarity=0.992 Sum_probs=11.0
Q ss_pred eeccccccceeEeecC
Q 032810 103 RRCEVCGGSGLVLREK 118 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~ 118 (133)
+.|+.|+ +-||.|..
T Consensus 2 ~~CP~Cg-~~lv~r~~ 16 (39)
T PF01396_consen 2 EKCPKCG-GPLVLRRG 16 (39)
T ss_pred cCCCCCC-ceeEEEEC
Confidence 4799999 66777653
No 194
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=34.35 E-value=20 Score=32.33 Aligned_cols=21 Identities=43% Similarity=0.895 Sum_probs=10.5
Q ss_pred eeccccccceeEeecCeeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
-.|..||-.+ +. ..+||.||-
T Consensus 492 ~~C~~CG~~~----~~-~~~CP~CGs 512 (546)
T PF13597_consen 492 DICPDCGYIG----GE-GDKCPKCGS 512 (546)
T ss_dssp EEETTT---S-------EEE-CCC--
T ss_pred ccccCCCcCC----CC-CCCCCCCCC
Confidence 3699998644 22 888999985
No 195
>PRK05580 primosome assembly protein PriA; Validated
Probab=34.33 E-value=21 Score=32.67 Aligned_cols=22 Identities=45% Similarity=0.988 Sum_probs=0.0
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
+.+|..|| .+...+.+||.||+
T Consensus 408 ~l~Ch~Cg-----~~~~~~~~Cp~Cg~ 429 (679)
T PRK05580 408 RLRCHHCG-----YQEPIPKACPECGS 429 (679)
T ss_pred eEECCCCc-----CCCCCCCCCCCCcC
No 196
>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=34.19 E-value=14 Score=28.94 Aligned_cols=29 Identities=21% Similarity=0.432 Sum_probs=17.7
Q ss_pred eeeccccccceeEe-------ecCeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVL-------REKDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~-------r~~~~~kC~~CGGFl 130 (133)
.-+|..|+-.=-.. .+....+|+.|||.|
T Consensus 95 ~~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~l 130 (206)
T cd01410 95 IEVCKSCGPEYVRDDVVETRGDKETGRRCHACGGIL 130 (206)
T ss_pred cccCCCCCCccchHHHHHHhhcCCCCCcCCCCcCcc
Confidence 56799998431110 112347899999865
No 197
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=34.12 E-value=28 Score=22.71 Aligned_cols=8 Identities=75% Similarity=1.153 Sum_probs=6.0
Q ss_pred eccceeEE
Q 032810 83 AGVTPFVV 90 (133)
Q Consensus 83 AGv~PFvv 90 (133)
||=+||++
T Consensus 1 aGGAPFv~ 8 (46)
T PF11331_consen 1 AGGAPFVV 8 (46)
T ss_pred CCCCCEeE
Confidence 56788886
No 198
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=33.85 E-value=21 Score=20.55 Aligned_cols=10 Identities=50% Similarity=1.255 Sum_probs=5.8
Q ss_pred cCCCCCCCcc
Q 032810 122 KCPECGMSYG 131 (133)
Q Consensus 122 kC~~CGGFl~ 131 (133)
+||+|+...|
T Consensus 2 ~CP~C~~~V~ 11 (26)
T PF10571_consen 2 TCPECGAEVP 11 (26)
T ss_pred cCCCCcCCch
Confidence 5666665544
No 199
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=33.78 E-value=38 Score=20.20 Aligned_cols=8 Identities=63% Similarity=1.535 Sum_probs=5.0
Q ss_pred eecccccc
Q 032810 103 RRCEVCGG 110 (133)
Q Consensus 103 ~rCe~C~G 110 (133)
+.|+.||+
T Consensus 3 ~~C~~Cg~ 10 (47)
T PF13005_consen 3 RACPDCGG 10 (47)
T ss_pred CcCCCCCc
Confidence 45666666
No 200
>PRK06921 hypothetical protein; Provisional
Probab=33.67 E-value=26 Score=28.33 Aligned_cols=16 Identities=19% Similarity=0.686 Sum_probs=12.9
Q ss_pred eeeccccccceeEeec
Q 032810 102 QRRCEVCGGSGLVLRE 117 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~ 117 (133)
+-.|+.|++.|.+..+
T Consensus 32 ~~~Cp~C~dtG~i~~~ 47 (266)
T PRK06921 32 RYDCPKCKDRGIIIYR 47 (266)
T ss_pred CCCCCCCCCCEEEEee
Confidence 3469999999999643
No 201
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=33.48 E-value=24 Score=28.58 Aligned_cols=25 Identities=36% Similarity=0.946 Sum_probs=10.2
Q ss_pred eeccccccc---eeEeec----CeeecCCCCC
Q 032810 103 RRCEVCGGS---GLVLRE----KDYFKCPECG 127 (133)
Q Consensus 103 ~rCe~C~Gs---GLV~r~----~~~~kC~~CG 127 (133)
..|++||+. +.+..+ ++|..|.-||
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~ 204 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCG 204 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT-
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCC
Confidence 578888875 333332 3555555555
No 202
>PF09865 DUF2092: Predicted periplasmic protein (DUF2092); InterPro: IPR019207 This entry represents various hypothetical prokaryotic proteins of unknown function.
Probab=33.38 E-value=23 Score=28.59 Aligned_cols=17 Identities=35% Similarity=0.825 Sum_probs=11.8
Q ss_pred CcceeeEEEEeeeecccee
Q 032810 70 TAEVTWQIIVGAIAGVTPF 88 (133)
Q Consensus 70 ~~e~~Wqi~vG~iAGv~PF 88 (133)
.-++.|||||+ +|--|.
T Consensus 148 ~~~~DwQiWI~--~g~~PL 164 (214)
T PF09865_consen 148 NDDVDWQIWIA--DGDKPL 164 (214)
T ss_pred cCCceEEEEEc--CCCcce
Confidence 34678999998 455553
No 203
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=33.32 E-value=24 Score=24.34 Aligned_cols=8 Identities=63% Similarity=1.701 Sum_probs=3.8
Q ss_pred eecCCCCC
Q 032810 120 YFKCPECG 127 (133)
Q Consensus 120 ~~kC~~CG 127 (133)
.|.||+||
T Consensus 25 ~F~CPnCG 32 (59)
T PRK14890 25 KFLCPNCG 32 (59)
T ss_pred EeeCCCCC
Confidence 44444444
No 204
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=33.15 E-value=38 Score=23.64 Aligned_cols=34 Identities=24% Similarity=0.514 Sum_probs=25.5
Q ss_pred eeeeeeeccccccceeEeecC---eeecCCCCCCCcc
Q 032810 98 RIIAQRRCEVCGGSGLVLREK---DYFKCPECGMSYG 131 (133)
Q Consensus 98 RIi~Q~rCe~C~GsGLV~r~~---~~~kC~~CGGFl~ 131 (133)
|...-|-|+-|+..=+..+.. +++.|..||---|
T Consensus 2 ~~d~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~~~ 38 (64)
T PRK09710 2 RYDNVKPCPFCGCPSVTVKAISGYYRAKCNGCESRTG 38 (64)
T ss_pred CcccccCCCCCCCceeEEEecCceEEEEcCCCCcCcc
Confidence 345568899999988887653 4699999986433
No 205
>PRK14873 primosome assembly protein PriA; Provisional
Probab=33.14 E-value=24 Score=32.78 Aligned_cols=21 Identities=43% Similarity=1.181 Sum_probs=0.0
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
+.+|.-|| ....+.+||+||+
T Consensus 410 ~l~Ch~CG------~~~~p~~Cp~Cgs 430 (665)
T PRK14873 410 TPRCRWCG------RAAPDWRCPRCGS 430 (665)
T ss_pred eeECCCCc------CCCcCccCCCCcC
No 206
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.07 E-value=13 Score=29.10 Aligned_cols=27 Identities=41% Similarity=0.966 Sum_probs=17.9
Q ss_pred eeccccccceeEeec--CeeecCCCCCCCc
Q 032810 103 RRCEVCGGSGLVLRE--KDYFKCPECGMSY 130 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~--~~~~kC~~CGGFl 130 (133)
-||+.|+ .|-..++ |--.+|.+||=-+
T Consensus 22 grCP~CG-eGrLF~gFLK~~p~C~aCG~dy 50 (126)
T COG5349 22 GRCPRCG-EGRLFRGFLKVVPACEACGLDY 50 (126)
T ss_pred CCCCCCC-CchhhhhhcccCchhhhccccc
Confidence 5899995 4544444 4566899998443
No 207
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=33.03 E-value=22 Score=27.88 Aligned_cols=26 Identities=27% Similarity=0.833 Sum_probs=15.9
Q ss_pred eccccccceeEe------------ecCeeecCCCCCCC
Q 032810 104 RCEVCGGSGLVL------------REKDYFKCPECGMS 129 (133)
Q Consensus 104 rCe~C~GsGLV~------------r~~~~~kC~~CGGF 129 (133)
.|+.|.+.|.+= -...-.+|+.|+-.
T Consensus 144 ~C~lC~~kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v 181 (202)
T PF13901_consen 144 SCELCQQKGFICEICNSDDIIFPFQIDTTVRCPKCKSV 181 (202)
T ss_pred HhHHHHhCCCCCccCCCCCCCCCCCCCCeeeCCcCccc
Confidence 566666666542 11357789988754
No 208
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=32.86 E-value=42 Score=25.54 Aligned_cols=29 Identities=21% Similarity=0.576 Sum_probs=20.5
Q ss_pred eeccccccce--eEeecCe-eecCCCCCCCcc
Q 032810 103 RRCEVCGGSG--LVLREKD-YFKCPECGMSYG 131 (133)
Q Consensus 103 ~rCe~C~GsG--LV~r~~~-~~kC~~CGGFl~ 131 (133)
--|..|+..- |+..++- ..+|-+||..-|
T Consensus 98 VlC~~C~sPdT~l~k~~r~~~l~C~ACGa~~~ 129 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVSLLKCEACGAKAP 129 (133)
T ss_pred EECCCCCCCCcEEEEeCCeEEEecccCCCCCc
Confidence 4699999865 4444454 469999997644
No 209
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=32.46 E-value=22 Score=20.00 Aligned_cols=22 Identities=32% Similarity=0.835 Sum_probs=8.6
Q ss_pred eeccccccceeEeecCeeecCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECG 127 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CG 127 (133)
++|..|+.++-- .....|..|.
T Consensus 1 ~~C~~C~~~~~~---~~~Y~C~~Cd 22 (30)
T PF07649_consen 1 FRCDACGKPIDG---GWFYRCSECD 22 (30)
T ss_dssp ---TTTS----S-----EEE-TTT-
T ss_pred CcCCcCCCcCCC---CceEECccCC
Confidence 468888876532 4677899885
No 210
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=32.08 E-value=30 Score=28.69 Aligned_cols=28 Identities=32% Similarity=0.810 Sum_probs=17.8
Q ss_pred eeeecccccccee---Eee---cCeeecCCCCCC
Q 032810 101 AQRRCEVCGGSGL---VLR---EKDYFKCPECGM 128 (133)
Q Consensus 101 ~Q~rCe~C~GsGL---V~r---~~~~~kC~~CGG 128 (133)
..-+|..|+..=. +.+ +...-+|+.|||
T Consensus 121 ~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~ 154 (250)
T COG0846 121 KRVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGG 154 (250)
T ss_pred eeeEeCCCcCccchhhhhhhcccCCCCcCccCCC
Confidence 3468999976533 111 123568999999
No 211
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=31.96 E-value=23 Score=32.96 Aligned_cols=22 Identities=27% Similarity=0.529 Sum_probs=16.1
Q ss_pred eeccccccceeEeecCeeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
-.|..||-. .+..+.||.||.-
T Consensus 627 ~~C~~CG~~-----~g~~~~CP~CG~~ 648 (656)
T PRK08270 627 SICPKHGYL-----SGEHEFCPKCGEE 648 (656)
T ss_pred cccCCCCCc-----CCCCCCCcCCcCc
Confidence 479999852 2446999999964
No 212
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=31.86 E-value=27 Score=30.00 Aligned_cols=27 Identities=30% Similarity=0.577 Sum_probs=23.4
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
-|-|..||+.=-...+...+.|+.||-
T Consensus 111 ~RFCg~CG~~~~~~~~g~~~~C~~cg~ 137 (279)
T COG2816 111 HRFCGRCGTKTYPREGGWARVCPKCGH 137 (279)
T ss_pred CcCCCCCCCcCccccCceeeeCCCCCC
Confidence 578999999887778889999999985
No 213
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=31.49 E-value=26 Score=35.99 Aligned_cols=24 Identities=38% Similarity=1.027 Sum_probs=15.1
Q ss_pred eeeccccccceeEeecCeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGGFl 130 (133)
+.+|+.||.+= + -...||.||.-+
T Consensus 679 ~~fCP~CGs~t----e-~vy~CPsCGaev 702 (1337)
T PRK14714 679 ENRCPDCGTHT----E-PVYVCPDCGAEV 702 (1337)
T ss_pred cccCcccCCcC----C-CceeCccCCCcc
Confidence 45899999873 1 123677776543
No 214
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=31.39 E-value=42 Score=21.12 Aligned_cols=25 Identities=28% Similarity=0.769 Sum_probs=17.3
Q ss_pred eeeccccccceeEeecCeeecCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECG 127 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CG 127 (133)
...|+.| |.=|+...+...-|+.|+
T Consensus 17 ~~~Cp~C-~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDC-GTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred cCccCCC-CCeeEEecCCCEECCCCC
Confidence 4679999 555666233457799996
No 215
>PRK00183 hypothetical protein; Provisional
Probab=31.27 E-value=11 Score=29.40 Aligned_cols=12 Identities=33% Similarity=0.910 Sum_probs=8.9
Q ss_pred CeeecCCCCCCCcc
Q 032810 118 KDYFKCPECGMSYG 131 (133)
Q Consensus 118 ~~~~kC~~CGGFl~ 131 (133)
++|.|| ||+||+
T Consensus 146 kKyKkC--Cg~~~~ 157 (157)
T PRK00183 146 QKFKKC--CAPYLG 157 (157)
T ss_pred HHHHHh--cccccC
Confidence 467777 888875
No 216
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=30.85 E-value=28 Score=26.26 Aligned_cols=29 Identities=38% Similarity=1.023 Sum_probs=19.4
Q ss_pred ceeeeeee-eccccccceeEeec---CeeecCCCCC
Q 032810 96 SKRIIAQR-RCEVCGGSGLVLRE---KDYFKCPECG 127 (133)
Q Consensus 96 ~KRIi~Q~-rCe~C~GsGLV~r~---~~~~kC~~CG 127 (133)
|||++.|- +|-.| |.+.++ +.+-|||.|-
T Consensus 51 g~~Llv~Pa~CkkC---Gfef~~~~ik~pSRCP~CK 83 (97)
T COG3357 51 GKRLLVRPARCKKC---GFEFRDDKIKKPSRCPKCK 83 (97)
T ss_pred CceEEecChhhccc---CccccccccCCcccCCcch
Confidence 56666553 45555 678877 3578999995
No 217
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=30.58 E-value=29 Score=25.57 Aligned_cols=29 Identities=34% Similarity=0.872 Sum_probs=21.3
Q ss_pred eeeccccccceeEeecCeeecCCCCCCCcc
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGMSYG 131 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGGFl~ 131 (133)
.|.|..||-. ..-.++.+..||.||--++
T Consensus 9 KR~Cp~CG~k-FYDLnk~PivCP~CG~~~~ 37 (108)
T PF09538_consen 9 KRTCPSCGAK-FYDLNKDPIVCPKCGTEFP 37 (108)
T ss_pred cccCCCCcch-hccCCCCCccCCCCCCccC
Confidence 3569999754 4445678899999997665
No 218
>PRK04023 DNA polymerase II large subunit; Validated
Probab=30.47 E-value=25 Score=35.51 Aligned_cols=11 Identities=45% Similarity=1.008 Sum_probs=8.4
Q ss_pred eeeeccccccc
Q 032810 101 AQRRCEVCGGS 111 (133)
Q Consensus 101 ~Q~rCe~C~Gs 111 (133)
.+.+|+.||..
T Consensus 637 ~~frCP~CG~~ 647 (1121)
T PRK04023 637 FYRRCPFCGTH 647 (1121)
T ss_pred CcccCCCCCCC
Confidence 56788888876
No 219
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=30.07 E-value=25 Score=32.62 Aligned_cols=23 Identities=39% Similarity=0.928 Sum_probs=16.1
Q ss_pred eeeccccccceeEeecCeeecCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
--+|+.||-.- ......||.||.
T Consensus 568 ~~~C~~CG~~~----~g~~~~CP~CGs 590 (625)
T PRK08579 568 ITVCNKCGRST----TGLYTRCPRCGS 590 (625)
T ss_pred CccCCCCCCcc----CCCCCcCcCCCC
Confidence 45799998621 233689999984
No 220
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=29.98 E-value=35 Score=29.00 Aligned_cols=30 Identities=20% Similarity=0.507 Sum_probs=22.7
Q ss_pred eeeeeccccccceeEeec----------CeeecCCCCCCC
Q 032810 100 IAQRRCEVCGGSGLVLRE----------KDYFKCPECGMS 129 (133)
Q Consensus 100 i~Q~rCe~C~GsGLV~r~----------~~~~kC~~CGGF 129 (133)
-.+..|..|+...-++.. -.++.|..||.-
T Consensus 256 t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~ 295 (299)
T TIGR01385 256 TDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNR 295 (299)
T ss_pred cccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCe
Confidence 346799999999887643 137899999953
No 221
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=29.90 E-value=31 Score=30.16 Aligned_cols=13 Identities=38% Similarity=0.723 Sum_probs=3.9
Q ss_pred cCee-ecCCCCCCC
Q 032810 117 EKDY-FKCPECGMS 129 (133)
Q Consensus 117 ~~~~-~kC~~CGGF 129 (133)
++++ ..|..||++
T Consensus 299 ~r~P~~~C~~Cg~~ 312 (344)
T PF09332_consen 299 ERLPKKHCSNCGSS 312 (344)
T ss_dssp SSS--S--TTT-S-
T ss_pred ccCCCCCCCcCCcC
Confidence 4443 455555544
No 222
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.50 E-value=24 Score=25.99 Aligned_cols=13 Identities=31% Similarity=0.616 Sum_probs=9.8
Q ss_pred CeeecCCCCCCCc
Q 032810 118 KDYFKCPECGMSY 130 (133)
Q Consensus 118 ~~~~kC~~CGGFl 130 (133)
+.---||+|||-|
T Consensus 39 ~l~g~CPnCGGel 51 (84)
T COG3813 39 RLHGLCPNCGGEL 51 (84)
T ss_pred hhcCcCCCCCchh
Confidence 3445799999976
No 223
>PF07092 DUF1356: Protein of unknown function (DUF1356); InterPro: IPR009790 This family consists of several hypothetical mammalian proteins of around 250 residues in length. The function of this family is unknown.
Probab=29.31 E-value=21 Score=30.02 Aligned_cols=15 Identities=40% Similarity=0.986 Sum_probs=13.7
Q ss_pred eccccccceeEeecC
Q 032810 104 RCEVCGGSGLVLREK 118 (133)
Q Consensus 104 rCe~C~GsGLV~r~~ 118 (133)
-|+.|+|+|-+.||.
T Consensus 40 tCPTCqGtGrIP~eq 54 (238)
T PF07092_consen 40 TCPTCQGTGRIPREQ 54 (238)
T ss_pred cCCCCcCCccCCccc
Confidence 799999999999885
No 224
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=29.24 E-value=47 Score=23.00 Aligned_cols=29 Identities=24% Similarity=0.529 Sum_probs=17.9
Q ss_pred eeeeeccccccceeEeecC-------eeecCCCCCC
Q 032810 100 IAQRRCEVCGGSGLVLREK-------DYFKCPECGM 128 (133)
Q Consensus 100 i~Q~rCe~C~GsGLV~r~~-------~~~kC~~CGG 128 (133)
..+-.|..|+.+---+-.+ -..+||+|.-
T Consensus 2 ~l~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~ 37 (66)
T PF05180_consen 2 QLTFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKN 37 (66)
T ss_dssp EEEEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--
T ss_pred eEEEEcCCCCCccceeeCHHHHhCCeEEEECCCCcc
Confidence 3566799998876544322 3789999974
No 225
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=29.22 E-value=26 Score=34.44 Aligned_cols=31 Identities=26% Similarity=0.517 Sum_probs=22.4
Q ss_pred eeeeeceeeeeeeeccccccceeEeecCeeecCCCCCCCc
Q 032810 91 AGIEFSKRIIAQRRCEVCGGSGLVLREKDYFKCPECGMSY 130 (133)
Q Consensus 91 Ag~EF~KRIi~Q~rCe~C~GsGLV~r~~~~~kC~~CGGFl 130 (133)
=|.-|| +..+|+.|+| +|+..+ ..+.|.|++
T Consensus 292 D~m~FG----al~~CP~C~g-~l~~~~----~~Y~C~G~~ 322 (981)
T PLN03123 292 DGMMFG----ALGPCPLCSG-PLLYSG----GMYRCQGYL 322 (981)
T ss_pred HHHHhC----CCCCCCCCCC-eeEEcC----CceEECccc
Confidence 344555 5679999998 888775 455677877
No 226
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=29.21 E-value=24 Score=21.74 Aligned_cols=16 Identities=19% Similarity=0.781 Sum_probs=9.0
Q ss_pred eeceeeeeeeeccccc
Q 032810 94 EFSKRIIAQRRCEVCG 109 (133)
Q Consensus 94 EF~KRIi~Q~rCe~C~ 109 (133)
+||.+......|..|+
T Consensus 5 d~gq~~~~~~~C~~Cg 20 (41)
T PF13878_consen 5 DLGQKSFGATTCPTCG 20 (41)
T ss_pred eCCCCccCCcCCCCCC
Confidence 4555555555666664
No 227
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=29.16 E-value=36 Score=25.52 Aligned_cols=26 Identities=31% Similarity=0.731 Sum_probs=19.0
Q ss_pred eeccccccceeEe--ec-CeeecCCCCCC
Q 032810 103 RRCEVCGGSGLVL--RE-KDYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~--r~-~~~~kC~~CGG 128 (133)
-.|..|+..-... .+ ....+|.+||-
T Consensus 94 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCCEEEETTTSC
T ss_pred EEcCCCCCCccEEEEcCCEEEEEecccCC
Confidence 3699999876544 33 36889999985
No 228
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=29.14 E-value=26 Score=28.30 Aligned_cols=29 Identities=21% Similarity=0.318 Sum_probs=17.0
Q ss_pred eeeccccccceeEee--cCeeecCCCCC--CCc
Q 032810 102 QRRCEVCGGSGLVLR--EKDYFKCPECG--MSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r--~~~~~kC~~CG--GFl 130 (133)
+-+|..|+-.=-... .....+|+.|| |.|
T Consensus 117 ~~~C~~C~~~~~~~~~~~~~~p~C~~Cg~~g~l 149 (242)
T PTZ00408 117 KVRCTATGHVFDWTEDVVHGSSRCKCCGCVGTL 149 (242)
T ss_pred eEEECCCCcccCchhhhhcCCCccccCCCCCCC
Confidence 467999975311110 11246899998 754
No 229
>PF11635 Med16: Mediator complex subunit 16; InterPro: IPR021665 Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression []. Several members including the human protein, Q9Y2X0 from SWISSPROT, have one or more WD40 domains on them, PF00400 from PFAM.
Probab=29.12 E-value=23 Score=32.93 Aligned_cols=30 Identities=27% Similarity=0.402 Sum_probs=18.0
Q ss_pred eeeeeccccccceeEe-----------ecCeeecCCCCCCCc
Q 032810 100 IAQRRCEVCGGSGLVL-----------REKDYFKCPECGMSY 130 (133)
Q Consensus 100 i~Q~rCe~C~GsGLV~-----------r~~~~~kC~~CGGFl 130 (133)
..-|||-+|++--.+. .-.+.++| -|||+.
T Consensus 711 ~~~RrC~RC~~vs~~~~~~~s~~~~~w~~~~~R~C-~CGG~W 751 (753)
T PF11635_consen 711 GKWRRCVRCGSVSEDEDPFTSRATKRWTMRWQRNC-ICGGMW 751 (753)
T ss_pred CceEEeccCCCcccccCCCCcchhhhhhhheeeee-ccCCee
Confidence 3458999998322211 12356677 599974
No 230
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=28.77 E-value=43 Score=24.62 Aligned_cols=26 Identities=31% Similarity=0.806 Sum_probs=18.7
Q ss_pred eeccccccceeEe--ecC-eeecCCCCCC
Q 032810 103 RRCEVCGGSGLVL--REK-DYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~--r~~-~~~kC~~CGG 128 (133)
-.|..|+..--.. .++ +..+|-+||.
T Consensus 81 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 4699999876443 333 5788999995
No 231
>PF12773 DZR: Double zinc ribbon
Probab=28.65 E-value=29 Score=20.93 Aligned_cols=28 Identities=25% Similarity=0.586 Sum_probs=14.7
Q ss_pred eeeccccccceeEeecCeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGGFl 130 (133)
++.|..||-.=. ..+.....|+.||-.+
T Consensus 12 ~~fC~~CG~~l~-~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 12 AKFCPHCGTPLP-PPDQSKKICPNCGAEN 39 (50)
T ss_pred ccCChhhcCChh-hccCCCCCCcCCcCCC
Confidence 455666654321 2344556677776544
No 232
>PF03110 SBP: SBP domain; InterPro: IPR004333 The SBP plant protein domain is a sequence specific DNA-binding domain []. Proteins with this domain probably function as transcription factors involved in the control of early flower development. The domain contains 10 conserved cysteine and histidine residues that probably are zinc ligands.; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 1UL4_A 1WJ0_A 1UL5_A.
Probab=28.60 E-value=26 Score=24.90 Aligned_cols=31 Identities=26% Similarity=0.424 Sum_probs=22.3
Q ss_pred eeeccccccceeEeecC-eeecCCCCCCCccc
Q 032810 102 QRRCEVCGGSGLVLREK-DYFKCPECGMSYGL 132 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~-~~~kC~~CGGFl~~ 132 (133)
.+-||.+..+.-|+.++ ..+-|+.||-|=|+
T Consensus 21 ~rICe~H~ka~~V~~~G~~~RFCQQC~rfh~l 52 (79)
T PF03110_consen 21 YRICEEHAKAPVVVVDGVEQRFCQQCGRFHPL 52 (79)
T ss_dssp TT--HHHHTHSEEEETTEEEEE-TTTSSEEET
T ss_pred cCcchhhcCCCeEEECChhHHHHHHHHcCCCH
Confidence 45789888888888775 57889999998764
No 233
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=28.34 E-value=36 Score=20.30 Aligned_cols=23 Identities=30% Similarity=0.738 Sum_probs=17.2
Q ss_pred eccccccceeEeecCeeecCCCCCCC
Q 032810 104 RCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 104 rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
+|.+|+. ...++....|-.|+-.
T Consensus 1 ~C~vC~~---~~~~~~~i~C~~C~~~ 23 (51)
T PF00628_consen 1 YCPVCGQ---SDDDGDMIQCDSCNRW 23 (51)
T ss_dssp EBTTTTS---SCTTSSEEEBSTTSCE
T ss_pred eCcCCCC---cCCCCCeEEcCCCChh
Confidence 5888888 5566778888888743
No 234
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=28.26 E-value=28 Score=26.72 Aligned_cols=10 Identities=20% Similarity=0.447 Sum_probs=5.1
Q ss_pred ecCCCCCCCc
Q 032810 121 FKCPECGMSY 130 (133)
Q Consensus 121 ~kC~~CGGFl 130 (133)
-.|..|+--|
T Consensus 86 D~CM~C~~pL 95 (114)
T PF11023_consen 86 DACMHCKEPL 95 (114)
T ss_pred hccCcCCCcC
Confidence 3566665433
No 235
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=28.04 E-value=42 Score=21.34 Aligned_cols=19 Identities=32% Similarity=0.515 Sum_probs=10.0
Q ss_pred eeEeec-CeeecCCCCCCCc
Q 032810 112 GLVLRE-KDYFKCPECGMSY 130 (133)
Q Consensus 112 GLV~r~-~~~~kC~~CGGFl 130 (133)
|+...+ +...+|..||.-|
T Consensus 27 Gfyy~~~~d~v~C~~C~~~l 46 (71)
T smart00238 27 GFYYTGVGDEVKCFFCGGEL 46 (71)
T ss_pred CCeECCCCCEEEeCCCCCCc
Confidence 444444 4456666666544
No 236
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=27.53 E-value=62 Score=22.20 Aligned_cols=29 Identities=24% Similarity=0.721 Sum_probs=23.2
Q ss_pred eeeccccccceeEeec-CeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVLRE-KDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~-~~~~kC~~CGGFl 130 (133)
.-+|..|+.-=.|.-. ...++|..||--|
T Consensus 11 ~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred EEECCCCCCeEEEEecCCcEEECcccCCCc
Confidence 3579999988877754 5689999999766
No 237
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=27.38 E-value=24 Score=24.15 Aligned_cols=7 Identities=57% Similarity=1.739 Sum_probs=3.4
Q ss_pred cCCCCCC
Q 032810 122 KCPECGM 128 (133)
Q Consensus 122 kC~~CGG 128 (133)
+||.||+
T Consensus 17 ~CP~Cgs 23 (61)
T PRK08351 17 RCPVCGS 23 (61)
T ss_pred cCCCCcC
Confidence 3555554
No 238
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=27.32 E-value=27 Score=31.94 Aligned_cols=28 Identities=29% Similarity=0.608 Sum_probs=22.1
Q ss_pred eeccccccc-------eeEeecCeeecCCCCCCCc
Q 032810 103 RRCEVCGGS-------GLVLREKDYFKCPECGMSY 130 (133)
Q Consensus 103 ~rCe~C~Gs-------GLV~r~~~~~kC~~CGGFl 130 (133)
-+|+.|+-. =|+.-+..-|+|..|||-|
T Consensus 129 Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 129 YVCPNCQKKYTSLEALQLLDNETGEFHCENCGGEL 163 (436)
T ss_pred ccCCccccchhhhHHHHhhcccCceEEEecCCCch
Confidence 369999876 5666667899999999965
No 239
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=27.15 E-value=28 Score=24.09 Aligned_cols=21 Identities=48% Similarity=1.020 Sum_probs=13.7
Q ss_pred eeccccccceeEeecCeeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
++|..|+-=-| .-+||.|||-
T Consensus 6 rkC~~cg~YTL------ke~Cp~CG~~ 26 (59)
T COG2260 6 RKCPKCGRYTL------KEKCPVCGGD 26 (59)
T ss_pred hcCcCCCceee------cccCCCCCCc
Confidence 57877753221 1489999985
No 240
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=27.05 E-value=34 Score=20.81 Aligned_cols=16 Identities=44% Similarity=0.974 Sum_probs=11.7
Q ss_pred eeeccccccceeEeecC
Q 032810 102 QRRCEVCGGSGLVLREK 118 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~ 118 (133)
...|..||| -||+|++
T Consensus 21 ~~~Cd~cg~-~L~qR~D 36 (36)
T PF05191_consen 21 EGVCDNCGG-ELVQRKD 36 (36)
T ss_dssp TTBCTTTTE-BEBEEGG
T ss_pred CCccCCCCC-eeEeCCC
Confidence 356888888 7888753
No 241
>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=26.36 E-value=34 Score=26.44 Aligned_cols=29 Identities=34% Similarity=0.746 Sum_probs=17.7
Q ss_pred eeeccccccceeEe---ecCeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVL---REKDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~---r~~~~~kC~~CGGFl 130 (133)
.-+|..|+-.=-.. .+....+||.|||-|
T Consensus 109 ~~~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~l 140 (224)
T cd01412 109 RVRCSSCGYVGENNEEIPEEELPRCPKCGGLL 140 (224)
T ss_pred ccccCCCCCCCCcchhhhccCCCCCCCCCCcc
Confidence 45699996532110 122357899999965
No 242
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=26.05 E-value=40 Score=19.77 Aligned_cols=19 Identities=42% Similarity=1.345 Sum_probs=11.0
Q ss_pred eeccccccceeEeecCeeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
..|++|+.. ...+||.||-
T Consensus 3 ~~C~vC~~~-------~kY~Cp~C~~ 21 (30)
T PF04438_consen 3 KLCSVCGNP-------AKYRCPRCGA 21 (30)
T ss_dssp EEETSSSSE-------ESEE-TTT--
T ss_pred CCCccCcCC-------CEEECCCcCC
Confidence 568888762 2348999973
No 243
>PRK12722 transcriptional activator FlhC; Provisional
Probab=26.01 E-value=47 Score=26.92 Aligned_cols=30 Identities=23% Similarity=0.597 Sum_probs=25.4
Q ss_pred eeeeeeccccccceeEeecC--eeecCCCCCC
Q 032810 99 IIAQRRCEVCGGSGLVLREK--DYFKCPECGM 128 (133)
Q Consensus 99 Ii~Q~rCe~C~GsGLV~r~~--~~~kC~~CGG 128 (133)
.+...+|..|+|.=++..+. ..++||-|.+
T Consensus 131 ~L~l~~C~~Cgg~fv~~~~e~~~~f~CplC~~ 162 (187)
T PRK12722 131 MLQLSSCNCCGGHFVTHAHDPVGSFVCGLCQP 162 (187)
T ss_pred cEeeccCCCCCCCeeccccccCCCCcCCCCCC
Confidence 48889999999998877664 4899999976
No 244
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=25.82 E-value=39 Score=31.94 Aligned_cols=23 Identities=39% Similarity=0.729 Sum_probs=17.6
Q ss_pred eeccccccceeEeecCeeecCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECG 127 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CG 127 (133)
..|+.|+ +-|+..++= ..|..||
T Consensus 725 ~~Cp~Cg-~~l~~~~GC-~~C~~CG 747 (752)
T PRK08665 725 GACPECG-SILEHEEGC-VVCHSCG 747 (752)
T ss_pred CCCCCCC-cccEECCCC-CcCCCCC
Confidence 4699996 568877754 4899998
No 245
>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=25.50 E-value=48 Score=24.32 Aligned_cols=47 Identities=17% Similarity=0.367 Sum_probs=33.1
Q ss_pred eeeEEEEeeeeccceeEEeeeeeceeeeeeeeccccccceeEeecCeeecCCCCCCCc
Q 032810 73 VTWQIIVGAIAGVTPFVVAGIEFSKRIIAQRRCEVCGGSGLVLREKDYFKCPECGMSY 130 (133)
Q Consensus 73 ~~Wqi~vG~iAGv~PFvvAg~EF~KRIi~Q~rCe~C~GsGLV~r~~~~~kC~~CGGFl 130 (133)
..|-.+.|.|..+-+ . =.--..|..|+.. ++..+....+|+.|+...
T Consensus 15 ~~~~~v~a~I~~I~~--------~--~~~Y~aC~~C~kk-v~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 15 PDYFTVKATIVFIKP--------D--NWWYPACPGCNKK-VVEEGNGTYRCEKCNKSV 61 (166)
T ss_pred CCEEEEEEEEEEEcC--------C--CeEEccccccCcc-cEeCCCCcEECCCCCCcC
Confidence 467788888776654 1 2446789999876 554444778999999863
No 246
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=25.47 E-value=35 Score=31.62 Aligned_cols=22 Identities=27% Similarity=0.816 Sum_probs=14.8
Q ss_pred eeccccccceeEeecCeeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
-.|..||-. .+.....||.||.
T Consensus 533 siC~~CGy~----~g~~~~~CP~CGs 554 (586)
T TIGR02827 533 TICNDCHHI----DKRTLHRCPVCGS 554 (586)
T ss_pred eecCCCCCc----CCCcCCcCcCCCC
Confidence 368888861 2234589999983
No 247
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=25.16 E-value=34 Score=24.04 Aligned_cols=24 Identities=33% Similarity=0.902 Sum_probs=17.1
Q ss_pred eccccccceeEeecCeeecCCCCCC
Q 032810 104 RCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 104 rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
-|..|+..--+ +.+..++|-+||-
T Consensus 22 iCgdC~~en~l-k~~D~irCReCG~ 45 (62)
T KOG3507|consen 22 ICGDCGQENTL-KRGDVIRCRECGY 45 (62)
T ss_pred Eeccccccccc-cCCCcEehhhcch
Confidence 48888765444 4567899999983
No 248
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=25.04 E-value=37 Score=31.32 Aligned_cols=26 Identities=23% Similarity=0.321 Sum_probs=14.7
Q ss_pred eeeccccccceeEeecCeeecCCCCCCC
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
...|+ |++ .||.+...+-++.+|.+|
T Consensus 611 ~~~cp-cg~-~l~~~~~~~g~f~~c~~~ 636 (660)
T TIGR01056 611 KEPVS-CGG-IAKCPAKDNGRLIDCKKF 636 (660)
T ss_pred CccCC-CCC-ceeeeecCCCeeecCCCC
Confidence 45699 976 555544333445555554
No 249
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=24.91 E-value=30 Score=27.68 Aligned_cols=12 Identities=42% Similarity=0.999 Sum_probs=9.7
Q ss_pred eeecCCCCCCCc
Q 032810 119 DYFKCPECGMSY 130 (133)
Q Consensus 119 ~~~kC~~CGGFl 130 (133)
+-|.||.||.-|
T Consensus 131 ~~F~Cp~Cg~~L 142 (176)
T COG1675 131 LGFTCPKCGEDL 142 (176)
T ss_pred hCCCCCCCCchh
Confidence 459999999876
No 250
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=24.88 E-value=46 Score=20.91 Aligned_cols=26 Identities=27% Similarity=0.761 Sum_probs=13.8
Q ss_pred eeccccccceeEe-ecC----eeecCCCCCC
Q 032810 103 RRCEVCGGSGLVL-REK----DYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~-r~~----~~~kC~~CGG 128 (133)
.-|+.|+|+.-.. -++ --.-|-.|+|
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICRQCGG 34 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEETTTTB
T ss_pred CCCCCCcCccccccCcCcccCCCEECCCCCC
Confidence 3599999976554 222 3556888854
No 251
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=24.28 E-value=45 Score=20.29 Aligned_cols=12 Identities=42% Similarity=1.257 Sum_probs=7.8
Q ss_pred CeeecCCCCCCC
Q 032810 118 KDYFKCPECGMS 129 (133)
Q Consensus 118 ~~~~kC~~CGGF 129 (133)
..++.|+.|+--
T Consensus 2 ~~~~~C~nC~R~ 13 (33)
T PF08209_consen 2 SPYVECPNCGRP 13 (33)
T ss_dssp S-EEE-TTTSSE
T ss_pred CCeEECCCCcCC
Confidence 468999999853
No 252
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=24.16 E-value=65 Score=22.26 Aligned_cols=36 Identities=31% Similarity=0.701 Sum_probs=28.1
Q ss_pred eeeeeeeeccccccceeEeecCeeecCCCCCCCccc
Q 032810 97 KRIIAQRRCEVCGGSGLVLREKDYFKCPECGMSYGL 132 (133)
Q Consensus 97 KRIi~Q~rCe~C~GsGLV~r~~~~~kC~~CGGFl~~ 132 (133)
+|.+.-..|+.|+|.=.+.++++-.-|+.|+--+|.
T Consensus 3 ~~LLeiLaCP~~kg~L~~~~~~~~L~c~~~~~aYpI 38 (60)
T COG2835 3 YRLLEILACPVCKGPLVYDEEKQELICPRCKLAYPI 38 (60)
T ss_pred hhhheeeeccCcCCcceEeccCCEEEecccCceeec
Confidence 356667789999999555577889999999876663
No 253
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=23.89 E-value=37 Score=28.83 Aligned_cols=27 Identities=33% Similarity=0.706 Sum_probs=19.2
Q ss_pred eeeeccccccceeEeec---CeeecCCCCC
Q 032810 101 AQRRCEVCGGSGLVLRE---KDYFKCPECG 127 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~---~~~~kC~~CG 127 (133)
.+|.|+.|||.=.+... -..|||-.|-
T Consensus 219 ~~r~CP~Cg~~W~L~~plh~iFdFKCD~CR 248 (258)
T PF10071_consen 219 QARKCPSCGGDWRLKEPLHDIFDFKCDPCR 248 (258)
T ss_pred hCCCCCCCCCccccCCchhhceeccCCcce
Confidence 46788888886655533 4688888884
No 254
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=23.88 E-value=38 Score=35.52 Aligned_cols=26 Identities=31% Similarity=0.639 Sum_probs=18.7
Q ss_pred eeeeccccccce-----eEeecCeeecCCCCC
Q 032810 101 AQRRCEVCGGSG-----LVLREKDYFKCPECG 127 (133)
Q Consensus 101 ~Q~rCe~C~GsG-----LV~r~~~~~kC~~CG 127 (133)
.+..|++|++.- |++.++- ..||.||
T Consensus 1703 ~~~~cp~c~~~~~~~~~~~~~~gc-~~c~~cg 1733 (1740)
T PRK08332 1703 GVVYCPVCYEKEGKLVELRMESGC-ATCPVCG 1733 (1740)
T ss_pred ccCCCCCCCCCCCcceeeEecCCc-eeCCCCC
Confidence 444599999983 5555554 4899998
No 255
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=23.87 E-value=26 Score=17.84 Aligned_cols=10 Identities=60% Similarity=1.620 Sum_probs=6.6
Q ss_pred ecCCCCCCCc
Q 032810 121 FKCPECGMSY 130 (133)
Q Consensus 121 ~kC~~CGGFl 130 (133)
++|+.||-.+
T Consensus 1 y~C~~C~~~f 10 (23)
T PF00096_consen 1 YKCPICGKSF 10 (23)
T ss_dssp EEETTTTEEE
T ss_pred CCCCCCCCcc
Confidence 4678887544
No 256
>PF05515 Viral_NABP: Viral nucleic acid binding ; InterPro: IPR008891 This family is common to ssRNA positive-strand viruses and are commonly described as nucleic acid binding proteins (NABP).
Probab=23.38 E-value=20 Score=27.75 Aligned_cols=13 Identities=38% Similarity=0.864 Sum_probs=11.2
Q ss_pred CeeecCCCCCCCc
Q 032810 118 KDYFKCPECGMSY 130 (133)
Q Consensus 118 ~~~~kC~~CGGFl 130 (133)
++|-+|+.||.+|
T Consensus 60 kR~~~C~~CG~~l 72 (124)
T PF05515_consen 60 KRYNRCFKCGRYL 72 (124)
T ss_pred HHhCcccccccee
Confidence 5799999999876
No 257
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=23.36 E-value=32 Score=23.91 Aligned_cols=15 Identities=33% Similarity=0.769 Sum_probs=8.3
Q ss_pred eeeeeeeeccccccc
Q 032810 97 KRIIAQRRCEVCGGS 111 (133)
Q Consensus 97 KRIi~Q~rCe~C~Gs 111 (133)
|+|..-..|++||++
T Consensus 12 ~~i~~~~~Cp~Cgs~ 26 (64)
T PRK06393 12 KRLTPEKTCPVHGDE 26 (64)
T ss_pred CcccCCCcCCCCCCC
Confidence 344445566666664
No 258
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=23.08 E-value=66 Score=22.76 Aligned_cols=28 Identities=25% Similarity=0.698 Sum_probs=20.6
Q ss_pred eeccccccceeEeec-CeeecCCCCCCCc
Q 032810 103 RRCEVCGGSGLVLRE-KDYFKCPECGMSY 130 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~-~~~~kC~~CGGFl 130 (133)
-+|..|+--=.|.-. ....+|..||--|
T Consensus 20 VkCpdC~N~q~vFshast~V~C~~CG~~l 48 (67)
T COG2051 20 VKCPDCGNEQVVFSHASTVVTCLICGTTL 48 (67)
T ss_pred EECCCCCCEEEEeccCceEEEecccccEE
Confidence 478888888777754 4688888888544
No 259
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=22.78 E-value=66 Score=23.59 Aligned_cols=26 Identities=23% Similarity=0.659 Sum_probs=17.0
Q ss_pred eeccccccceeEe----ecCeeecCCCCCCC
Q 032810 103 RRCEVCGGSGLVL----REKDYFKCPECGMS 129 (133)
Q Consensus 103 ~rCe~C~GsGLV~----r~~~~~kC~~CGGF 129 (133)
-.|+.|+ +-.|. +++....|+.||=.
T Consensus 22 f~CP~Cg-e~~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 22 FECPRCG-KVSISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred eECCCCC-CeEeeeecCCCcceEECCCCCCc
Confidence 4688888 33442 34567888888843
No 260
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=22.75 E-value=40 Score=20.92 Aligned_cols=9 Identities=44% Similarity=0.984 Sum_probs=6.8
Q ss_pred eecCCCCCC
Q 032810 120 YFKCPECGM 128 (133)
Q Consensus 120 ~~kC~~CGG 128 (133)
..-||.|||
T Consensus 3 ~~pCP~CGG 11 (37)
T smart00778 3 HGPCPNCGG 11 (37)
T ss_pred ccCCCCCCC
Confidence 356899987
No 261
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=22.72 E-value=33 Score=24.23 Aligned_cols=12 Identities=42% Similarity=1.622 Sum_probs=9.6
Q ss_pred eeecCCCCCCCc
Q 032810 119 DYFKCPECGMSY 130 (133)
Q Consensus 119 ~~~kC~~CGGFl 130 (133)
..+|||.||..+
T Consensus 16 ~~lrCPRC~~~F 27 (65)
T COG4049 16 EFLRCPRCGMVF 27 (65)
T ss_pred eeeeCCchhHHH
Confidence 588999999654
No 262
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=22.54 E-value=22 Score=31.19 Aligned_cols=23 Identities=30% Similarity=0.832 Sum_probs=18.4
Q ss_pred EEEeee-eccceeEEeeeeeceee
Q 032810 77 IIVGAI-AGVTPFVVAGIEFSKRI 99 (133)
Q Consensus 77 i~vG~i-AGv~PFvvAg~EF~KRI 99 (133)
.+||.. .|=||||++|.|+.+.+
T Consensus 132 vvvgIaASGrTPYvigal~yAr~~ 155 (298)
T COG2103 132 VVVGIAASGRTPYVIGALEYARQR 155 (298)
T ss_pred EEEEEecCCCCchhhHHHHHHHhc
Confidence 566644 48899999999998875
No 263
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=22.40 E-value=46 Score=29.23 Aligned_cols=25 Identities=32% Similarity=0.848 Sum_probs=13.3
Q ss_pred eccccccceeEeecC---------eeecCCCCCC
Q 032810 104 RCEVCGGSGLVLREK---------DYFKCPECGM 128 (133)
Q Consensus 104 rCe~C~GsGLV~r~~---------~~~kC~~CGG 128 (133)
.|..|.|+|.-.+-. .-..|..|+|
T Consensus 145 ~C~~C~GsGv~~~~~~~gPg~~qs~q~~C~~C~G 178 (337)
T KOG0712|consen 145 KCTTCRGSGVQTRTRQMGPGMVQSPQLVCDSCNG 178 (337)
T ss_pred CCCCCCCCCceeEEEeccccccccceeEeccCCC
Confidence 566666666544221 2355666665
No 264
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=22.39 E-value=58 Score=21.35 Aligned_cols=18 Identities=28% Similarity=0.554 Sum_probs=11.3
Q ss_pred eeeeccccccceeEeecC
Q 032810 101 AQRRCEVCGGSGLVLREK 118 (133)
Q Consensus 101 ~Q~rCe~C~GsGLV~r~~ 118 (133)
+-..|+.|+|.=|+..+.
T Consensus 13 al~~Cp~C~~~~l~~~~~ 30 (55)
T PF08063_consen 13 ALEPCPKCKGGQLYFDGS 30 (55)
T ss_dssp EE---SSSSE-EEEEETT
T ss_pred CCCCCCCCCCCeEEecCC
Confidence 356899999988888777
No 265
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=22.39 E-value=41 Score=26.51 Aligned_cols=27 Identities=30% Similarity=0.744 Sum_probs=16.1
Q ss_pred eeeccccccceeEeec----CeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVLRE----KDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~----~~~~kC~~CGGFl 130 (133)
.-+|..|+-. ...+ ....+||.|||.|
T Consensus 122 ~~~C~~C~~~--~~~~~~~~~~~p~C~~Cgg~l 152 (242)
T PRK00481 122 RARCTKCGQT--YDLDEYLKPEPPRCPKCGGIL 152 (242)
T ss_pred ceeeCCCCCC--cChhhhccCCCCCCCCCCCcc
Confidence 4579999431 1111 1245699999965
No 266
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=22.06 E-value=54 Score=22.85 Aligned_cols=25 Identities=28% Similarity=0.533 Sum_probs=14.0
Q ss_pred eccccccc---eeEeecCeeecCCCCCC
Q 032810 104 RCEVCGGS---GLVLREKDYFKCPECGM 128 (133)
Q Consensus 104 rCe~C~Gs---GLV~r~~~~~kC~~CGG 128 (133)
+|+-|+.. =-|..++..++|.+||.
T Consensus 35 ~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~ 62 (97)
T PF01807_consen 35 LCPFHDDKTPSFSINPDKNRFKCFGCGK 62 (97)
T ss_dssp --SSS--SS--EEEETTTTEEEETTT--
T ss_pred ECcCCCCCCCceEEECCCCeEEECCCCC
Confidence 48888753 34555678999999984
No 267
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=21.83 E-value=44 Score=30.08 Aligned_cols=17 Identities=18% Similarity=0.122 Sum_probs=11.6
Q ss_pred ccccccccccccccccc
Q 032810 50 RRWAAPSAASNDVSSVA 66 (133)
Q Consensus 50 rr~~~~~~~~~~v~~~a 66 (133)
|...++....+|++.-.
T Consensus 131 ~s~~~r~~~~DEvD~~p 147 (557)
T PF05876_consen 131 RSRPARYLLLDEVDRYP 147 (557)
T ss_pred ccCCcCEEEEechhhcc
Confidence 45566777788887654
No 268
>COG4734 ArdA Antirestriction protein [General function prediction only]
Probab=21.75 E-value=32 Score=28.53 Aligned_cols=12 Identities=42% Similarity=0.899 Sum_probs=10.1
Q ss_pred eeecCCCCCCCc
Q 032810 119 DYFKCPECGMSY 130 (133)
Q Consensus 119 ~~~kC~~CGGFl 130 (133)
-++|||.|-||+
T Consensus 46 vmVkCpnceg~~ 57 (193)
T COG4734 46 VMVKCPNCEGFY 57 (193)
T ss_pred ceeeccchhhHH
Confidence 478999999986
No 269
>PRK07218 replication factor A; Provisional
Probab=21.72 E-value=44 Score=29.75 Aligned_cols=20 Identities=30% Similarity=0.689 Sum_probs=13.1
Q ss_pred eeccccccceeEeecCeeecCCCCCC
Q 032810 103 RRCEVCGGSGLVLREKDYFKCPECGM 128 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~~~~~kC~~CGG 128 (133)
+||+.|+= -| ++..|+.||-
T Consensus 298 ~rCP~C~r-~v-----~~~~C~~hG~ 317 (423)
T PRK07218 298 ERCPECGR-VI-----QKGQCRSHGA 317 (423)
T ss_pred ecCcCccc-cc-----cCCcCCCCCC
Confidence 58888862 11 3367888884
No 270
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=21.66 E-value=66 Score=20.28 Aligned_cols=23 Identities=22% Similarity=0.553 Sum_probs=15.0
Q ss_pred eccccccceeEeecCeeecCCCCCCC
Q 032810 104 RCEVCGGSGLVLREKDYFKCPECGMS 129 (133)
Q Consensus 104 rCe~C~GsGLV~r~~~~~kC~~CGGF 129 (133)
.|..|.-..++ + ..++|..|..|
T Consensus 2 ~C~~C~~~~i~--g-~R~~C~~C~dy 24 (49)
T cd02345 2 SCSACRKQDIS--G-IRFPCQVCRDY 24 (49)
T ss_pred cCCCCCCCCce--E-eeEECCCCCCc
Confidence 37777766666 3 34488888765
No 271
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=21.22 E-value=52 Score=30.04 Aligned_cols=26 Identities=27% Similarity=0.511 Sum_probs=17.7
Q ss_pred eeeccccccceeEeecCeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVLREKDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~~~~~kC~~CGGFl 130 (133)
-.+|+.|..+ +.--..-+|+.||.-.
T Consensus 57 i~kC~~c~~~---~~y~~~~~C~~cg~~~ 82 (415)
T COG5257 57 IYKCPECYRP---ECYTTEPKCPNCGAET 82 (415)
T ss_pred eEeCCCCCCC---cccccCCCCCCCCCCc
Confidence 3689999987 2222356899998643
No 272
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=20.87 E-value=62 Score=19.06 Aligned_cols=15 Identities=27% Similarity=0.656 Sum_probs=10.7
Q ss_pred eeccccccceeEeec
Q 032810 103 RRCEVCGGSGLVLRE 117 (133)
Q Consensus 103 ~rCe~C~GsGLV~r~ 117 (133)
.+|+.||..+++..+
T Consensus 3 ~~Cp~Cg~~~~~~~g 17 (47)
T PF14690_consen 3 PRCPHCGSPSVHRHG 17 (47)
T ss_pred ccCCCcCCCceECCc
Confidence 479999988855433
No 273
>KOG2824 consensus Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=20.62 E-value=71 Score=27.78 Aligned_cols=13 Identities=38% Similarity=0.958 Sum_probs=9.3
Q ss_pred eeccccccceeEe
Q 032810 103 RRCEVCGGSGLVL 115 (133)
Q Consensus 103 ~rCe~C~GsGLV~ 115 (133)
-.|+.|||-+.|+
T Consensus 230 ~~C~~CGg~rFlp 242 (281)
T KOG2824|consen 230 GVCESCGGARFLP 242 (281)
T ss_pred CcCCCcCCcceEe
Confidence 5677887777665
No 274
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=20.56 E-value=70 Score=21.93 Aligned_cols=24 Identities=33% Similarity=0.819 Sum_probs=18.0
Q ss_pred eccccccceeEe-ec-----CeeecCCCCC
Q 032810 104 RCEVCGGSGLVL-RE-----KDYFKCPECG 127 (133)
Q Consensus 104 rCe~C~GsGLV~-r~-----~~~~kC~~CG 127 (133)
.|++|++.-.+. |+ .++..||.|-
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPlyCpKCK 35 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLYCPKCK 35 (55)
T ss_pred ECCCCCCccceeeecCceeccccccCCCCC
Confidence 699999887655 22 4688899985
No 275
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=20.48 E-value=78 Score=17.66 Aligned_cols=25 Identities=20% Similarity=0.663 Sum_probs=12.2
Q ss_pred eeccccccce--eEeecCeeecCCCCC
Q 032810 103 RRCEVCGGSG--LVLREKDYFKCPECG 127 (133)
Q Consensus 103 ~rCe~C~GsG--LV~r~~~~~kC~~CG 127 (133)
+.|+.|+..= ...-++..+-|+.|-
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCc
Confidence 4688888762 122235677788773
No 276
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=20.41 E-value=51 Score=28.25 Aligned_cols=45 Identities=24% Similarity=0.590 Sum_probs=26.9
Q ss_pred eccceeEEee----eee-----c-ee-e---eeeeeccccccce---eEee-----cCeeecCCCCC
Q 032810 83 AGVTPFVVAG----IEF-----S-KR-I---IAQRRCEVCGGSG---LVLR-----EKDYFKCPECG 127 (133)
Q Consensus 83 AGv~PFvvAg----~EF-----~-KR-I---i~Q~rCe~C~GsG---LV~r-----~~~~~kC~~CG 127 (133)
+..+||++|+ +.- . ++ . -....|++||+.= +|.. +.+|-.|.-|+
T Consensus 151 ~a~apfi~AALq~~~~~~a~~l~~~~~~~~~~~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~ 217 (305)
T TIGR01562 151 AALVPFLGAALQVAWAHWALGLEGGAVVETRESRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCA 217 (305)
T ss_pred hhhhHHHHHHHHHHHHHHHHhCCccccCcccCCCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCC
Confidence 7889999998 432 1 22 1 1233899999974 4432 23565555554
No 277
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=20.39 E-value=45 Score=20.05 Aligned_cols=27 Identities=26% Similarity=0.463 Sum_probs=14.3
Q ss_pred eeccc--cccceeEeecCee--ecCCCCCCC
Q 032810 103 RRCEV--CGGSGLVLREKDY--FKCPECGMS 129 (133)
Q Consensus 103 ~rCe~--C~GsGLV~r~~~~--~kC~~CGGF 129 (133)
+.|.. |++--.+..+... +.|+.||-.
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 49 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTE 49 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSE
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCc
Confidence 47866 8776666666555 888888754
No 278
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=20.37 E-value=68 Score=22.75 Aligned_cols=15 Identities=40% Similarity=1.070 Sum_probs=8.2
Q ss_pred ecCeeecCCCCCCCc
Q 032810 116 REKDYFKCPECGMSY 130 (133)
Q Consensus 116 r~~~~~kC~~CGGFl 130 (133)
.+-.++.||.||...
T Consensus 61 ENMs~~~Cp~Cg~~~ 75 (81)
T PF10609_consen 61 ENMSYFVCPHCGERI 75 (81)
T ss_dssp ECT-EEE-TTT--EE
T ss_pred ECCCccCCCCCCCee
Confidence 456799999999753
No 279
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.22 E-value=71 Score=28.31 Aligned_cols=19 Identities=37% Similarity=0.996 Sum_probs=14.3
Q ss_pred eccccccceeEeecCeeecCCCCCCCcc
Q 032810 104 RCEVCGGSGLVLREKDYFKCPECGMSYG 131 (133)
Q Consensus 104 rCe~C~GsGLV~r~~~~~kC~~CGGFl~ 131 (133)
.|..|| ...+||.|++.|-
T Consensus 215 ~C~~Cg---------~~~~C~~C~~~l~ 233 (505)
T TIGR00595 215 LCRSCG---------YILCCPNCDVSLT 233 (505)
T ss_pred EhhhCc---------CccCCCCCCCceE
Confidence 577775 4578999998774
No 280
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=20.11 E-value=88 Score=23.91 Aligned_cols=29 Identities=24% Similarity=0.572 Sum_probs=20.7
Q ss_pred eecccccccee--EeecC-eeecCCCCCCCcc
Q 032810 103 RRCEVCGGSGL--VLREK-DYFKCPECGMSYG 131 (133)
Q Consensus 103 ~rCe~C~GsGL--V~r~~-~~~kC~~CGGFl~ 131 (133)
-.|..|+..-- +..++ +..+|-+||..-|
T Consensus 103 VlC~~C~spdT~l~k~~r~~~l~C~ACGa~~~ 134 (138)
T PRK03988 103 VICPECGSPDTKLIKEGRIWVLKCEACGAETP 134 (138)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCCCCc
Confidence 46999998764 43334 5889999997543
No 281
>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=20.03 E-value=48 Score=24.93 Aligned_cols=27 Identities=33% Similarity=0.816 Sum_probs=17.4
Q ss_pred eeeccccccceeEeec-----CeeecCCCCCCCc
Q 032810 102 QRRCEVCGGSGLVLRE-----KDYFKCPECGMSY 130 (133)
Q Consensus 102 Q~rCe~C~GsGLV~r~-----~~~~kC~~CGGFl 130 (133)
+-+|..|+.. ...+ ....+|+.|||.|
T Consensus 113 ~~~C~~C~~~--~~~~~~~~~~~~p~C~~C~~~l 144 (222)
T cd00296 113 RVRCTSCGKE--YPRDEVLEREKPPRCPKCGGLL 144 (222)
T ss_pred ccEECCCCCC--cchhhhhhccCCCCCCCCCCcc
Confidence 4578888743 2211 2357899999965
Done!