Query 033949
Match_columns 107
No_of_seqs 145 out of 412
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 08:06:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033949.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033949hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12773 DZR: Double zinc ribb 99.2 7.3E-12 1.6E-16 71.4 3.0 42 53-104 9-50 (50)
2 PF13248 zf-ribbon_3: zinc-rib 99.1 2.5E-11 5.3E-16 60.8 1.3 24 84-107 3-26 (26)
3 PF13240 zinc_ribbon_2: zinc-r 99.1 3.9E-11 8.4E-16 58.5 1.2 23 85-107 1-23 (23)
4 PRK14559 putative protein seri 99.0 4.6E-10 1E-14 92.6 3.5 50 22-107 2-51 (645)
5 PRK14714 DNA polymerase II lar 98.6 3.7E-08 8E-13 85.4 4.3 51 20-107 666-719 (1337)
6 PF10571 UPF0547: Uncharacteri 98.5 7.4E-08 1.6E-12 48.2 1.5 23 84-106 1-23 (26)
7 PF12773 DZR: Double zinc ribb 98.3 7.5E-07 1.6E-11 50.5 2.7 36 59-107 1-39 (50)
8 PF13248 zf-ribbon_3: zinc-rib 97.9 7.2E-06 1.6E-10 40.8 1.2 25 56-93 2-26 (26)
9 PF13240 zinc_ribbon_2: zinc-r 97.8 8.7E-06 1.9E-10 39.5 1.2 23 58-93 1-23 (23)
10 PRK00398 rpoP DNA-directed RNA 97.8 9.9E-06 2.1E-10 45.3 1.0 23 84-106 4-30 (46)
11 PRK04023 DNA polymerase II lar 97.6 7.4E-05 1.6E-09 64.4 3.9 50 19-107 624-673 (1121)
12 PF03833 PolC_DP2: DNA polymer 97.5 2.2E-05 4.9E-10 66.4 0.0 49 19-106 653-701 (900)
13 PRK14559 putative protein seri 97.4 0.00012 2.6E-09 60.9 3.0 36 57-107 2-37 (645)
14 COG1198 PriA Primosomal protei 97.4 0.00024 5.1E-09 59.9 4.4 50 56-106 435-484 (730)
15 COG2888 Predicted Zn-ribbon RN 97.3 0.00015 3.4E-09 42.7 2.1 10 56-65 27-36 (61)
16 PRK14890 putative Zn-ribbon RN 97.3 0.00025 5.5E-09 41.8 2.8 10 56-65 25-34 (59)
17 PRK14873 primosome assembly pr 97.1 0.00043 9.3E-09 57.9 3.6 23 82-106 409-431 (665)
18 TIGR00595 priA primosomal prot 97.1 0.00058 1.3E-08 55.3 4.2 50 56-106 213-262 (505)
19 smart00659 RPOLCX RNA polymera 97.1 0.00027 5.9E-09 39.4 1.2 26 58-93 4-29 (44)
20 PF03604 DNA_RNApol_7kD: DNA d 96.9 0.00058 1.3E-08 35.6 1.4 10 59-68 3-12 (32)
21 TIGR02098 MJ0042_CXXC MJ0042 f 96.8 0.00048 1E-08 36.7 0.6 34 57-94 3-36 (38)
22 PF10571 UPF0547: Uncharacteri 96.7 0.00088 1.9E-08 33.3 1.4 10 58-67 2-11 (26)
23 PRK05580 primosome assembly pr 96.7 0.002 4.4E-08 53.9 4.1 50 56-106 381-430 (679)
24 PRK14714 DNA polymerase II lar 96.6 0.0017 3.6E-08 57.4 2.8 36 56-107 667-702 (1337)
25 PRK00398 rpoP DNA-directed RNA 96.6 0.0016 3.5E-08 36.2 1.8 13 56-68 21-33 (46)
26 PRK04023 DNA polymerase II lar 96.5 0.0018 3.9E-08 56.2 2.7 36 55-106 625-660 (1121)
27 PF09889 DUF2116: Uncharacteri 96.5 0.00035 7.6E-09 41.3 -1.1 23 83-105 3-26 (59)
28 PF07191 zinc-ribbons_6: zinc- 96.4 0.0005 1.1E-08 41.9 -0.9 27 55-95 16-42 (70)
29 TIGR02098 MJ0042_CXXC MJ0042 f 96.4 0.0027 5.8E-08 33.7 2.0 35 21-67 2-36 (38)
30 PF13717 zinc_ribbon_4: zinc-r 96.4 0.0018 4E-08 34.4 1.3 32 57-92 3-34 (36)
31 COG1996 RPC10 DNA-directed RNA 96.3 0.0013 2.9E-08 37.4 0.6 10 58-67 8-17 (49)
32 TIGR00595 priA primosomal prot 96.3 0.004 8.7E-08 50.5 3.6 29 50-92 234-262 (505)
33 PRK14890 putative Zn-ribbon RN 96.3 0.004 8.6E-08 36.7 2.6 41 56-105 7-56 (59)
34 PF13719 zinc_ribbon_5: zinc-r 96.2 0.0026 5.7E-08 33.9 1.2 33 57-93 3-35 (37)
35 COG1198 PriA Primosomal protei 96.1 0.0064 1.4E-07 51.5 3.9 29 50-92 456-484 (730)
36 PRK00420 hypothetical protein; 96.0 0.0037 7.9E-08 41.4 1.5 24 83-106 23-49 (112)
37 COG2093 DNA-directed RNA polym 96.0 0.0036 7.7E-08 37.3 1.2 23 84-106 5-27 (64)
38 PF07191 zinc-ribbons_6: zinc- 96.0 0.0011 2.5E-08 40.3 -1.0 39 57-107 2-40 (70)
39 PRK12496 hypothetical protein; 96.0 0.0039 8.5E-08 43.7 1.6 24 84-107 128-153 (164)
40 COG2888 Predicted Zn-ribbon RN 95.9 0.008 1.7E-07 35.5 2.6 42 55-105 8-58 (61)
41 smart00834 CxxC_CXXC_SSSS Puta 95.9 0.0033 7.2E-08 33.6 0.9 33 55-93 4-36 (41)
42 PF08271 TF_Zn_Ribbon: TFIIB z 95.9 0.0034 7.5E-08 34.4 0.9 16 53-68 16-31 (43)
43 PF15616 TerY-C: TerY-C metal 95.8 0.0068 1.5E-07 41.2 2.3 31 55-96 88-118 (131)
44 smart00834 CxxC_CXXC_SSSS Puta 95.8 0.0069 1.5E-07 32.4 1.9 25 83-107 5-36 (41)
45 PF07282 OrfB_Zn_ribbon: Putat 95.8 0.0091 2E-07 35.5 2.5 42 46-96 18-59 (69)
46 TIGR01384 TFS_arch transcripti 95.7 0.019 4.2E-07 36.9 4.1 15 54-68 14-28 (104)
47 PRK13130 H/ACA RNA-protein com 95.7 0.0087 1.9E-07 35.0 2.2 12 84-95 18-29 (56)
48 PF13719 zinc_ribbon_5: zinc-r 95.7 0.0081 1.8E-07 32.0 1.9 35 21-67 2-36 (37)
49 PF09538 FYDLN_acid: Protein o 95.7 0.0075 1.6E-07 39.7 2.1 31 21-69 9-39 (108)
50 PF11023 DUF2614: Protein of u 95.7 0.0042 9E-08 41.1 0.8 12 55-66 68-79 (114)
51 smart00659 RPOLCX RNA polymera 95.5 0.01 2.3E-07 32.9 1.9 12 55-66 18-29 (44)
52 PRK14892 putative transcriptio 95.5 0.027 5.8E-07 36.5 3.9 36 18-68 18-54 (99)
53 COG1439 Predicted nucleic acid 95.4 0.0077 1.7E-07 42.8 1.5 25 83-107 139-163 (177)
54 PF09862 DUF2089: Protein of u 95.4 0.0049 1.1E-07 40.9 0.4 31 59-102 1-31 (113)
55 PF07754 DUF1610: Domain of un 95.4 0.0099 2.1E-07 29.0 1.3 24 59-91 1-24 (24)
56 PF13717 zinc_ribbon_4: zinc-r 95.3 0.012 2.7E-07 31.2 1.7 34 21-66 2-35 (36)
57 PRK03681 hypA hydrogenase nick 95.3 0.01 2.3E-07 39.2 1.7 24 83-106 70-96 (114)
58 PRK05580 primosome assembly pr 95.2 0.02 4.3E-07 48.0 3.5 28 52-93 404-431 (679)
59 cd00350 rubredoxin_like Rubred 95.2 0.016 3.5E-07 30.0 2.0 25 57-92 2-26 (33)
60 PRK12380 hydrogenase nickel in 95.2 0.012 2.6E-07 38.8 1.8 23 83-105 70-94 (113)
61 PRK14873 primosome assembly pr 95.2 0.028 6E-07 47.2 4.3 40 21-92 392-431 (665)
62 cd00729 rubredoxin_SM Rubredox 95.1 0.019 4E-07 30.1 2.0 12 57-68 3-14 (34)
63 PRK02935 hypothetical protein; 95.0 0.011 2.4E-07 38.7 1.1 24 84-107 71-96 (110)
64 PF03604 DNA_RNApol_7kD: DNA d 95.0 0.014 2.9E-07 30.4 1.2 22 85-106 2-26 (32)
65 PF10601 zf-LITAF-like: LITAF- 95.0 0.013 2.9E-07 35.4 1.4 49 19-67 5-69 (73)
66 TIGR01206 lysW lysine biosynth 95.0 0.016 3.5E-07 33.6 1.7 14 55-68 21-34 (54)
67 TIGR00100 hypA hydrogenase nic 95.0 0.016 3.5E-07 38.3 1.8 24 83-106 70-95 (115)
68 PF10083 DUF2321: Uncharacteri 94.9 0.0032 6.9E-08 43.9 -1.8 10 97-106 68-77 (158)
69 PF09297 zf-NADH-PPase: NADH p 94.8 0.012 2.6E-07 30.3 0.7 11 58-68 5-15 (32)
70 COG4260 Membrane protease subu 94.7 0.015 3.3E-07 44.4 1.3 24 84-107 316-344 (345)
71 smart00661 RPOL9 RNA polymeras 94.7 0.038 8.2E-07 30.9 2.6 15 56-70 20-34 (52)
72 PF14353 CpXC: CpXC protein 94.6 0.0098 2.1E-07 39.6 0.1 13 83-95 38-50 (128)
73 PF09723 Zn-ribbon_8: Zinc rib 94.6 0.022 4.8E-07 31.1 1.5 31 55-91 4-34 (42)
74 TIGR01206 lysW lysine biosynth 94.6 0.02 4.3E-07 33.2 1.3 32 57-95 3-34 (54)
75 PRK03564 formate dehydrogenase 94.6 0.049 1.1E-06 41.9 3.8 48 20-92 186-235 (309)
76 cd00350 rubredoxin_like Rubred 94.5 0.036 7.9E-07 28.7 2.2 23 84-106 2-26 (33)
77 PF14446 Prok-RING_1: Prokaryo 94.4 0.02 4.4E-07 33.2 1.1 28 56-94 5-32 (54)
78 cd00729 rubredoxin_SM Rubredox 94.4 0.032 7E-07 29.2 1.8 23 84-106 3-27 (34)
79 PF09538 FYDLN_acid: Protein o 94.4 0.027 5.9E-07 37.0 1.8 30 56-96 9-39 (108)
80 PRK03824 hypA hydrogenase nick 94.4 0.026 5.6E-07 38.4 1.7 15 55-69 69-83 (135)
81 COG1645 Uncharacterized Zn-fin 94.4 0.03 6.6E-07 38.0 2.0 28 21-67 28-55 (131)
82 PF09723 Zn-ribbon_8: Zinc rib 94.3 0.018 3.8E-07 31.5 0.6 30 21-64 5-34 (42)
83 PF04216 FdhE: Protein involve 94.2 0.01 2.3E-07 44.7 -0.6 14 55-68 196-209 (290)
84 TIGR02300 FYDLN_acid conserved 94.2 0.037 8.1E-07 37.4 2.1 31 21-69 9-39 (129)
85 smart00714 LITAF Possible memb 94.1 0.013 2.8E-07 35.0 -0.2 48 20-67 2-63 (67)
86 PF12172 DUF35_N: Rubredoxin-l 94.1 0.024 5.3E-07 29.9 0.9 23 83-105 11-33 (37)
87 PF14803 Nudix_N_2: Nudix N-te 94.0 0.015 3.3E-07 30.6 0.0 30 57-91 1-30 (34)
88 COG2051 RPS27A Ribosomal prote 94.0 0.035 7.5E-07 33.5 1.6 33 20-68 18-50 (67)
89 COG1594 RPB9 DNA-directed RNA 93.9 0.13 2.7E-06 34.0 4.3 32 23-70 4-36 (113)
90 PRK00415 rps27e 30S ribosomal 93.7 0.065 1.4E-06 31.6 2.3 34 19-68 9-42 (59)
91 PF08274 PhnA_Zn_Ribbon: PhnA 93.6 0.025 5.4E-07 29.0 0.4 11 83-93 19-29 (30)
92 smart00661 RPOL9 RNA polymeras 93.6 0.04 8.6E-07 30.8 1.2 33 58-97 2-34 (52)
93 PRK00564 hypA hydrogenase nick 93.5 0.041 8.9E-07 36.5 1.4 23 83-105 71-96 (117)
94 COG1645 Uncharacterized Zn-fin 93.5 0.032 6.8E-07 37.9 0.8 24 82-105 27-52 (131)
95 COG1996 RPC10 DNA-directed RNA 93.4 0.048 1E-06 31.0 1.3 23 84-106 7-33 (49)
96 COG1545 Predicted nucleic-acid 93.4 0.053 1.1E-06 37.1 1.8 24 83-106 29-52 (140)
97 PRK00420 hypothetical protein; 93.3 0.07 1.5E-06 35.4 2.2 32 21-70 23-54 (112)
98 PF09855 DUF2082: Nucleic-acid 93.3 0.14 2.9E-06 30.7 3.3 39 23-65 2-45 (64)
99 PF01155 HypA: Hydrogenase exp 93.1 0.036 7.7E-07 36.5 0.6 24 83-106 70-95 (113)
100 PF02150 RNA_POL_M_15KD: RNA p 93.0 0.032 7E-07 29.4 0.2 9 58-66 3-11 (35)
101 PF11781 RRN7: RNA polymerase 92.9 0.059 1.3E-06 28.6 1.2 14 53-66 22-35 (36)
102 TIGR02605 CxxC_CxxC_SSSS putat 92.9 0.068 1.5E-06 30.0 1.5 31 55-91 4-34 (52)
103 PRK00415 rps27e 30S ribosomal 92.9 0.062 1.3E-06 31.7 1.3 30 56-94 11-41 (59)
104 PF05191 ADK_lid: Adenylate ki 92.8 0.047 1E-06 29.0 0.7 31 57-94 2-32 (36)
105 PF11023 DUF2614: Protein of u 92.7 0.088 1.9E-06 34.9 2.0 31 20-71 68-100 (114)
106 TIGR00100 hypA hydrogenase nic 92.7 0.077 1.7E-06 35.0 1.7 9 21-29 70-78 (115)
107 PRK04136 rpl40e 50S ribosomal 92.6 0.079 1.7E-06 29.9 1.5 25 82-106 13-37 (48)
108 PHA00626 hypothetical protein 92.5 0.11 2.4E-06 30.4 2.1 14 55-68 22-35 (59)
109 PRK12380 hydrogenase nickel in 92.5 0.083 1.8E-06 34.8 1.8 13 56-68 70-82 (113)
110 PF06677 Auto_anti-p27: Sjogre 92.5 0.07 1.5E-06 29.2 1.2 22 83-104 17-41 (41)
111 PF08792 A2L_zn_ribbon: A2L zi 92.3 0.13 2.8E-06 26.8 2.0 13 54-66 19-31 (33)
112 PF04216 FdhE: Protein involve 92.3 0.028 6.2E-07 42.4 -0.8 40 55-94 210-249 (290)
113 PF06906 DUF1272: Protein of u 92.2 0.071 1.5E-06 31.1 1.0 13 58-70 7-19 (57)
114 PF15616 TerY-C: TerY-C metal 92.1 0.11 2.4E-06 35.3 2.0 12 95-106 103-114 (131)
115 smart00531 TFIIE Transcription 92.0 0.06 1.3E-06 36.9 0.7 40 53-95 96-135 (147)
116 PF14319 Zn_Tnp_IS91: Transpos 92.0 0.15 3.2E-06 33.5 2.5 7 99-105 62-68 (111)
117 smart00531 TFIIE Transcription 91.9 0.058 1.3E-06 36.9 0.5 12 57-68 124-135 (147)
118 PRK00432 30S ribosomal protein 91.8 0.12 2.5E-06 29.4 1.6 7 58-64 22-28 (50)
119 PF14446 Prok-RING_1: Prokaryo 91.7 0.11 2.4E-06 30.1 1.4 30 20-68 4-33 (54)
120 PRK08351 DNA-directed RNA poly 91.5 0.11 2.5E-06 30.8 1.4 9 58-66 5-13 (61)
121 PF05876 Terminase_GpA: Phage 91.5 0.11 2.4E-06 42.8 1.7 13 83-95 229-241 (557)
122 PLN03086 PRLI-interacting fact 91.4 0.13 2.8E-06 42.6 2.0 11 19-29 405-415 (567)
123 PRK14892 putative transcriptio 91.3 0.11 2.4E-06 33.6 1.3 10 55-64 20-29 (99)
124 PRK03824 hypA hydrogenase nick 91.3 0.13 2.8E-06 34.9 1.7 12 20-31 69-80 (135)
125 TIGR01384 TFS_arch transcripti 91.2 0.16 3.4E-06 32.5 1.9 11 58-68 2-12 (104)
126 PRK06393 rpoE DNA-directed RNA 91.2 0.12 2.6E-06 30.9 1.3 23 55-92 4-26 (64)
127 PHA02942 putative transposase; 91.2 0.23 5.1E-06 39.1 3.2 42 45-96 314-355 (383)
128 PF13453 zf-TFIIB: Transcripti 91.1 0.086 1.9E-06 28.4 0.6 28 58-92 1-28 (41)
129 PRK12286 rpmF 50S ribosomal pr 91.1 0.13 2.8E-06 30.1 1.3 21 84-105 28-48 (57)
130 PF12760 Zn_Tnp_IS1595: Transp 91.1 0.28 6E-06 27.1 2.6 10 20-29 17-26 (46)
131 TIGR01562 FdhE formate dehydro 90.8 0.24 5.2E-06 38.1 2.9 24 56-92 210-233 (305)
132 PF08772 NOB1_Zn_bind: Nin one 90.8 0.13 2.9E-06 31.5 1.2 12 55-66 8-19 (73)
133 PF01155 HypA: Hydrogenase exp 90.5 0.05 1.1E-06 35.8 -0.9 27 55-92 69-95 (113)
134 PRK02935 hypothetical protein; 90.4 0.31 6.8E-06 32.0 2.7 31 20-71 69-101 (110)
135 TIGR02300 FYDLN_acid conserved 90.3 0.23 5E-06 33.6 2.2 29 56-95 9-38 (129)
136 TIGR00515 accD acetyl-CoA carb 90.3 0.13 2.9E-06 39.1 1.1 24 83-106 26-54 (285)
137 PF10058 DUF2296: Predicted in 90.3 0.21 4.6E-06 28.8 1.7 33 55-92 21-53 (54)
138 CHL00174 accD acetyl-CoA carbo 90.3 0.13 2.9E-06 39.3 1.1 24 83-106 38-66 (296)
139 COG2093 DNA-directed RNA polym 90.3 0.12 2.5E-06 30.9 0.6 24 56-92 4-27 (64)
140 PF01485 IBR: IBR domain; Int 90.3 0.23 4.9E-06 28.4 1.9 16 84-105 41-56 (64)
141 PRK00564 hypA hydrogenase nick 90.2 0.23 5E-06 32.9 2.1 13 56-68 71-83 (117)
142 PRK06266 transcription initiat 90.1 0.18 3.9E-06 35.8 1.6 11 56-66 117-127 (178)
143 PRK03681 hypA hydrogenase nick 90.1 0.2 4.4E-06 33.0 1.7 12 56-67 70-81 (114)
144 PRK12495 hypothetical protein; 90.1 0.16 3.6E-06 37.3 1.4 25 82-106 41-67 (226)
145 TIGR03831 YgiT_finger YgiT-typ 89.9 0.69 1.5E-05 24.8 3.5 6 24-29 1-6 (46)
146 PF14354 Lar_restr_allev: Rest 89.7 0.29 6.4E-06 28.2 2.0 10 55-64 28-37 (61)
147 PF01667 Ribosomal_S27e: Ribos 89.6 0.24 5.2E-06 28.8 1.6 30 21-67 7-37 (55)
148 PF01783 Ribosomal_L32p: Ribos 89.5 0.23 5E-06 28.7 1.5 20 84-104 27-46 (56)
149 PRK05978 hypothetical protein; 89.5 0.27 6E-06 34.0 2.1 33 21-70 33-66 (148)
150 PF03833 PolC_DP2: DNA polymer 89.4 0.11 2.3E-06 44.8 0.0 39 20-95 666-704 (900)
151 TIGR00373 conserved hypothetic 89.3 0.18 3.9E-06 35.0 1.1 33 55-95 108-140 (158)
152 KOG2906 RNA polymerase III sub 89.1 0.42 9.1E-06 31.0 2.6 34 23-71 3-36 (105)
153 PF14369 zf-RING_3: zinc-finge 88.9 0.36 7.8E-06 25.4 1.8 22 84-105 3-29 (35)
154 PRK12496 hypothetical protein; 88.9 0.36 7.7E-06 33.8 2.3 12 57-68 128-139 (164)
155 COG0375 HybF Zn finger protein 88.6 0.25 5.5E-06 32.8 1.4 23 83-105 70-94 (115)
156 TIGR01031 rpmF_bact ribosomal 88.5 0.23 5.1E-06 28.7 1.0 19 85-104 28-46 (55)
157 COG4306 Uncharacterized protei 88.5 0.12 2.7E-06 35.1 -0.2 10 84-93 69-78 (160)
158 PRK00762 hypA hydrogenase nick 88.5 0.24 5.3E-06 33.1 1.3 11 56-67 70-80 (124)
159 PRK05654 acetyl-CoA carboxylas 88.5 0.21 4.5E-06 38.1 1.0 24 83-106 27-55 (292)
160 COG1096 Predicted RNA-binding 88.5 0.27 5.8E-06 35.4 1.5 13 56-68 149-161 (188)
161 PRK12775 putative trifunctiona 88.4 0.38 8.3E-06 42.2 2.7 51 55-107 795-848 (1006)
162 COG4888 Uncharacterized Zn rib 88.3 0.4 8.7E-06 31.2 2.1 40 19-70 20-60 (104)
163 PF14205 Cys_rich_KTR: Cystein 88.2 0.71 1.5E-05 26.8 2.8 14 55-68 27-40 (55)
164 COG1594 RPB9 DNA-directed RNA 88.1 0.25 5.3E-06 32.7 1.0 33 56-95 2-34 (113)
165 PF05129 Elf1: Transcription e 88.0 0.24 5.2E-06 30.9 0.9 35 19-68 20-58 (81)
166 smart00647 IBR In Between Ring 87.8 0.56 1.2E-05 26.7 2.4 11 55-65 39-49 (64)
167 TIGR03826 YvyF flagellar opero 87.8 0.17 3.8E-06 34.6 0.2 23 82-105 80-102 (137)
168 PRK14973 DNA topoisomerase I; 87.7 0.93 2E-05 39.7 4.6 66 21-105 588-665 (936)
169 PRK00464 nrdR transcriptional 87.7 0.46 1E-05 33.1 2.2 12 57-68 29-40 (154)
170 smart00547 ZnF_RBZ Zinc finger 87.6 0.36 7.9E-06 23.1 1.2 22 85-106 4-25 (26)
171 PRK08579 anaerobic ribonucleos 87.3 0.36 7.7E-06 40.5 1.8 24 83-106 568-591 (625)
172 COG2260 Predicted Zn-ribbon RN 87.3 0.42 9.1E-06 28.1 1.6 9 85-93 19-27 (59)
173 PLN00209 ribosomal protein S27 87.3 0.48 1E-05 30.0 1.9 33 20-68 35-67 (86)
174 PF04981 NMD3: NMD3 family ; 87.3 0.43 9.4E-06 35.0 2.0 13 83-95 35-47 (236)
175 COG1592 Rubrerythrin [Energy p 87.1 0.52 1.1E-05 33.2 2.3 25 56-92 134-158 (166)
176 PRK15103 paraquat-inducible me 87.1 0.43 9.3E-06 38.1 2.0 21 86-106 224-244 (419)
177 TIGR00373 conserved hypothetic 87.1 0.19 4E-06 35.0 -0.0 25 83-107 109-138 (158)
178 COG1096 Predicted RNA-binding 87.0 0.27 5.8E-06 35.4 0.8 23 83-105 149-173 (188)
179 PF00641 zf-RanBP: Zn-finger i 87.0 0.4 8.6E-06 24.0 1.2 22 85-106 6-27 (30)
180 COG0675 Transposase and inacti 86.8 0.63 1.4E-05 34.4 2.7 13 84-96 323-335 (364)
181 TIGR01562 FdhE formate dehydro 86.5 0.67 1.4E-05 35.7 2.7 41 55-95 223-264 (305)
182 COG1552 RPL40A Ribosomal prote 86.5 0.14 3E-06 29.1 -0.7 25 82-106 13-37 (50)
183 PRK03564 formate dehydrogenase 86.3 0.8 1.7E-05 35.3 3.1 53 20-95 211-264 (309)
184 PF07295 DUF1451: Protein of u 86.3 0.64 1.4E-05 32.1 2.3 13 17-29 108-120 (146)
185 PF02591 DUF164: Putative zinc 86.3 0.38 8.2E-06 27.5 1.0 22 84-105 23-54 (56)
186 PF13901 DUF4206: Domain of un 86.2 0.64 1.4E-05 33.5 2.4 34 20-68 151-184 (202)
187 PRK00464 nrdR transcriptional 86.2 0.43 9.3E-06 33.2 1.4 10 84-93 29-38 (154)
188 PTZ00083 40S ribosomal protein 86.2 0.59 1.3E-05 29.5 1.9 33 20-68 34-66 (85)
189 PF06827 zf-FPG_IleRS: Zinc fi 86.0 0.23 4.9E-06 24.9 -0.0 19 85-103 3-27 (30)
190 PRK05978 hypothetical protein; 86.0 0.49 1.1E-05 32.8 1.6 11 84-94 53-63 (148)
191 PRK06266 transcription initiat 85.9 0.24 5.3E-06 35.1 0.1 12 20-31 116-127 (178)
192 PRK07418 acetolactate synthase 85.9 0.41 8.9E-06 39.5 1.4 26 82-107 591-616 (616)
193 PF09567 RE_MamI: MamI restric 85.8 0.37 8.1E-06 36.4 1.0 24 83-106 82-105 (314)
194 PF01396 zf-C4_Topoisom: Topoi 85.7 1 2.2E-05 24.1 2.5 32 22-68 2-36 (39)
195 smart00440 ZnF_C2C2 C2C2 Zinc 85.7 1.5 3.2E-05 23.6 3.1 7 23-29 2-8 (40)
196 PF09986 DUF2225: Uncharacteri 85.7 0.78 1.7E-05 33.3 2.6 10 20-29 4-13 (214)
197 PRK08270 anaerobic ribonucleos 85.6 0.52 1.1E-05 39.7 1.9 23 83-106 626-648 (656)
198 PRK08271 anaerobic ribonucleos 85.3 0.53 1.2E-05 39.5 1.8 23 83-105 566-588 (623)
199 PRK07219 DNA topoisomerase I; 85.3 1.3 2.7E-05 38.3 4.1 21 86-106 672-697 (822)
200 KOG0320 Predicted E3 ubiquitin 85.2 0.2 4.4E-06 35.8 -0.6 21 86-106 156-176 (187)
201 PF06044 DRP: Dam-replacing fa 85.2 0.31 6.8E-06 36.4 0.4 37 20-70 30-67 (254)
202 PRK06260 threonine synthase; V 85.1 0.69 1.5E-05 36.3 2.3 11 57-67 4-14 (397)
203 PRK11595 DNA utilization prote 85.1 0.58 1.3E-05 34.0 1.7 21 84-104 35-55 (227)
204 PF13597 NRDD: Anaerobic ribon 85.0 0.3 6.5E-06 40.2 0.2 10 56-65 491-500 (546)
205 COG0068 HypF Hydrogenase matur 84.9 0.52 1.1E-05 40.1 1.6 73 18-106 98-182 (750)
206 COG4640 Predicted membrane pro 84.8 0.52 1.1E-05 37.6 1.4 8 59-66 18-25 (465)
207 COG0777 AccD Acetyl-CoA carbox 84.3 0.48 1E-05 36.1 1.1 10 96-105 46-55 (294)
208 PRK11032 hypothetical protein; 84.3 0.86 1.9E-05 32.0 2.3 14 16-29 119-132 (160)
209 PRK10445 endonuclease VIII; Pr 84.3 0.49 1.1E-05 35.4 1.1 21 84-104 236-262 (263)
210 PRK14810 formamidopyrimidine-D 84.1 0.5 1.1E-05 35.5 1.0 22 83-104 244-271 (272)
211 PRK03922 hypothetical protein; 84.1 0.63 1.4E-05 30.7 1.4 13 83-95 49-61 (113)
212 PRK01103 formamidopyrimidine/5 83.8 0.51 1.1E-05 35.4 1.0 22 84-105 246-273 (274)
213 PF14353 CpXC: CpXC protein 83.7 1.6 3.5E-05 28.8 3.3 29 19-47 36-70 (128)
214 PF06221 zf-C2HC5: Putative zi 83.7 0.69 1.5E-05 27.0 1.3 11 56-66 18-28 (57)
215 COG1592 Rubrerythrin [Energy p 83.7 0.75 1.6E-05 32.5 1.7 24 83-106 134-158 (166)
216 TIGR00577 fpg formamidopyrimid 83.5 0.56 1.2E-05 35.2 1.1 20 84-103 246-271 (272)
217 cd01675 RNR_III Class III ribo 83.2 0.74 1.6E-05 38.0 1.8 23 84-106 519-541 (555)
218 COG1545 Predicted nucleic-acid 83.2 0.7 1.5E-05 31.5 1.4 12 55-66 42-53 (140)
219 PRK03988 translation initiatio 83.1 1.9 4.1E-05 29.5 3.5 33 21-68 102-135 (138)
220 PF03119 DNA_ligase_ZBD: NAD-d 83.0 0.4 8.7E-06 23.9 0.1 8 59-66 2-9 (28)
221 COG1998 RPS31 Ribosomal protei 83.0 0.93 2E-05 25.8 1.6 11 55-65 36-46 (51)
222 TIGR00311 aIF-2beta translatio 82.9 2 4.3E-05 29.2 3.5 33 21-68 97-130 (133)
223 PF04475 DUF555: Protein of un 82.8 0.75 1.6E-05 29.9 1.3 13 83-95 47-59 (102)
224 COG1997 RPL43A Ribosomal prote 82.7 0.97 2.1E-05 28.7 1.8 31 20-68 34-65 (89)
225 COG4391 Uncharacterized protei 82.6 1 2.2E-05 26.7 1.8 14 17-30 44-57 (62)
226 smart00653 eIF2B_5 domain pres 82.4 1.7 3.7E-05 28.5 3.0 29 21-64 80-109 (110)
227 COG1885 Uncharacterized protei 82.4 0.84 1.8E-05 30.0 1.4 13 83-95 49-61 (115)
228 TIGR00155 pqiA_fam integral me 82.3 0.95 2E-05 36.0 2.0 15 54-68 31-45 (403)
229 TIGR03655 anti_R_Lar restricti 82.2 2.4 5.2E-05 23.9 3.2 13 56-68 26-38 (53)
230 PRK14811 formamidopyrimidine-D 82.0 0.66 1.4E-05 34.8 1.0 21 84-104 236-262 (269)
231 TIGR00354 polC DNA polymerase, 82.0 0.77 1.7E-05 40.4 1.5 22 83-106 625-646 (1095)
232 COG2816 NPY1 NTP pyrophosphohy 82.0 0.76 1.7E-05 35.0 1.3 25 82-106 110-138 (279)
233 PF09986 DUF2225: Uncharacteri 81.9 0.91 2E-05 33.0 1.7 16 55-70 4-19 (214)
234 TIGR00155 pqiA_fam integral me 81.9 1.6 3.6E-05 34.6 3.2 34 55-95 12-45 (403)
235 PF14569 zf-UDP: Zinc-binding 81.7 0.9 1.9E-05 28.3 1.3 14 56-69 9-22 (80)
236 PF01363 FYVE: FYVE zinc finge 81.6 0.71 1.5E-05 27.1 0.9 16 53-68 6-21 (69)
237 PRK09678 DNA-binding transcrip 81.6 0.92 2E-05 27.7 1.3 38 22-68 2-41 (72)
238 PRK00481 NAD-dependent deacety 81.6 1.8 3.9E-05 31.7 3.2 13 55-67 121-133 (242)
239 PRK07591 threonine synthase; V 81.5 1 2.2E-05 35.8 1.9 12 57-68 34-45 (421)
240 TIGR02487 NrdD anaerobic ribon 81.3 0.97 2.1E-05 37.5 1.8 24 83-106 524-547 (579)
241 COG1579 Zn-ribbon protein, pos 81.1 0.78 1.7E-05 34.2 1.1 22 84-105 198-229 (239)
242 PF07295 DUF1451: Protein of u 81.1 1 2.2E-05 31.1 1.5 29 55-92 111-139 (146)
243 PRK09710 lar restriction allev 81.1 2.5 5.3E-05 25.3 3.0 34 23-70 8-41 (64)
244 TIGR00310 ZPR1_znf ZPR1 zinc f 80.8 1.1 2.4E-05 32.2 1.7 39 23-67 2-41 (192)
245 COG2995 PqiA Uncharacterized p 80.7 1.1 2.3E-05 35.8 1.8 35 54-95 16-50 (418)
246 COG0333 RpmF Ribosomal protein 80.6 1.1 2.4E-05 26.2 1.4 21 84-105 28-48 (57)
247 PF09334 tRNA-synt_1g: tRNA sy 80.6 0.42 9.2E-06 37.6 -0.5 36 57-106 137-175 (391)
248 PF04502 DUF572: Family of unk 80.5 0.95 2.1E-05 34.9 1.4 42 19-68 38-89 (324)
249 PF13005 zf-IS66: zinc-finger 80.3 2.3 5E-05 23.1 2.6 7 23-29 4-10 (47)
250 PF04606 Ogr_Delta: Ogr/Delta- 80.2 0.45 9.7E-06 26.4 -0.4 7 24-30 2-8 (47)
251 PRK11827 hypothetical protein; 80.1 2.7 5.9E-05 24.8 3.0 33 21-70 8-40 (60)
252 PRK13945 formamidopyrimidine-D 80.0 0.85 1.9E-05 34.4 1.0 21 84-104 255-281 (282)
253 cd01411 SIR2H SIR2H: Uncharact 79.9 2.7 5.8E-05 30.6 3.6 13 84-96 137-149 (225)
254 TIGR03844 cysteate_syn cysteat 79.8 1.4 3.1E-05 34.8 2.2 9 22-30 3-11 (398)
255 PF01020 Ribosomal_L40e: Ribos 79.5 1.6 3.4E-05 25.1 1.7 24 82-105 16-41 (52)
256 TIGR00570 cdk7 CDK-activating 79.4 1.1 2.4E-05 34.5 1.5 8 22-29 4-11 (309)
257 PRK00423 tfb transcription ini 79.2 1.7 3.6E-05 33.2 2.4 33 20-68 10-42 (310)
258 PF06397 Desulfoferrod_N: Desu 79.1 1.3 2.7E-05 23.6 1.2 16 20-35 5-20 (36)
259 PRK04179 rpl37e 50S ribosomal 79.1 1.2 2.7E-05 26.4 1.3 24 20-64 16-40 (62)
260 COG2816 NPY1 NTP pyrophosphohy 79.1 1.3 2.9E-05 33.7 1.8 11 55-65 128-138 (279)
261 COG3357 Predicted transcriptio 79.1 1.6 3.4E-05 28.0 1.8 30 58-96 60-89 (97)
262 PF01927 Mut7-C: Mut7-C RNAse 78.5 1.4 3E-05 30.1 1.6 9 83-91 124-132 (147)
263 COG0777 AccD Acetyl-CoA carbox 78.5 0.61 1.3E-05 35.5 -0.2 14 56-69 47-60 (294)
264 PRK07591 threonine synthase; V 78.3 1.2 2.5E-05 35.4 1.4 30 55-96 17-46 (421)
265 PRK08270 anaerobic ribonucleos 78.3 1.8 4E-05 36.5 2.5 33 46-94 618-650 (656)
266 COG1326 Uncharacterized archae 78.2 0.79 1.7E-05 33.2 0.3 33 20-66 5-40 (201)
267 PF00301 Rubredoxin: Rubredoxi 78.1 1.5 3.3E-05 24.5 1.4 36 57-92 2-43 (47)
268 cd01412 SIRT5_Af1_CobB SIRT5_A 77.9 3.2 6.9E-05 29.9 3.4 13 84-96 131-143 (224)
269 TIGR02827 RNR_anaer_Bdell anae 77.7 1.5 3.1E-05 36.7 1.8 22 84-105 533-554 (586)
270 TIGR00143 hypF [NiFe] hydrogen 77.7 1.1 2.4E-05 38.1 1.1 75 16-107 63-150 (711)
271 PF11672 DUF3268: Protein of u 77.7 2.1 4.5E-05 27.9 2.1 43 21-69 2-44 (102)
272 PRK00241 nudC NADH pyrophospha 77.6 1.1 2.5E-05 33.3 1.0 24 82-105 98-125 (256)
273 smart00064 FYVE Protein presen 77.5 2.3 5E-05 24.8 2.2 10 57-66 27-36 (68)
274 PRK09263 anaerobic ribonucleos 77.5 1.5 3.3E-05 37.3 1.9 9 56-64 641-649 (711)
275 PF13597 NRDD: Anaerobic ribon 77.2 0.93 2E-05 37.3 0.5 20 85-105 493-512 (546)
276 PHA02998 RNA polymerase subuni 77.0 6.2 0.00013 28.4 4.5 15 56-70 171-185 (195)
277 COG1656 Uncharacterized conser 76.8 1.4 2.9E-05 31.2 1.2 12 56-67 97-108 (165)
278 TIGR00686 phnA alkylphosphonat 76.8 2.5 5.5E-05 27.8 2.4 29 23-69 4-32 (109)
279 COG0143 MetG Methionyl-tRNA sy 76.7 2.1 4.6E-05 35.5 2.5 36 56-105 142-180 (558)
280 PRK06319 DNA topoisomerase I/S 76.7 5 0.00011 34.9 4.8 35 20-68 591-628 (860)
281 PRK11032 hypothetical protein; 76.6 1.6 3.4E-05 30.7 1.4 29 55-92 123-151 (160)
282 COG0068 HypF Hydrogenase matur 76.5 1.7 3.8E-05 37.1 1.9 56 22-93 124-183 (750)
283 PF05876 Terminase_GpA: Phage 76.5 2.3 4.9E-05 35.2 2.6 37 22-69 201-242 (557)
284 cd01413 SIR2_Af2 SIR2_Af2: Arc 76.4 3.6 7.8E-05 29.8 3.3 13 84-96 137-149 (222)
285 PF05502 Dynactin_p62: Dynacti 76.3 2.6 5.6E-05 34.4 2.8 40 55-95 25-64 (483)
286 KOG3507 DNA-directed RNA polym 76.3 0.76 1.6E-05 27.1 -0.2 23 83-105 20-45 (62)
287 PF12660 zf-TFIIIC: Putative z 76.2 2.1 4.5E-05 27.5 1.8 44 22-66 15-65 (99)
288 PF05605 zf-Di19: Drought indu 76.2 1.5 3.3E-05 24.8 1.1 36 56-93 2-41 (54)
289 PF01873 eIF-5_eIF-2B: Domain 76.1 2.6 5.7E-05 28.3 2.4 30 22-65 94-123 (125)
290 PRK00241 nudC NADH pyrophospha 75.9 1.9 4.1E-05 32.2 1.8 29 56-93 99-127 (256)
291 PLN03086 PRLI-interacting fact 75.9 3.4 7.4E-05 34.4 3.4 49 55-106 406-462 (567)
292 KOG2612 Predicted integral mem 75.6 1.2 2.5E-05 28.5 0.5 21 6-29 62-82 (103)
293 PRK14704 anaerobic ribonucleos 75.3 1.8 4E-05 36.3 1.8 22 83-105 559-580 (618)
294 PF09845 DUF2072: Zn-ribbon co 75.2 1.4 3E-05 30.0 0.8 9 59-67 4-12 (131)
295 TIGR00340 zpr1_rel ZPR1-relate 75.2 2 4.3E-05 30.2 1.7 38 24-67 1-39 (163)
296 COG0266 Nei Formamidopyrimidin 75.0 1.4 3.1E-05 33.4 0.9 22 83-104 245-272 (273)
297 COG4068 Uncharacterized protei 75.0 1.2 2.6E-05 26.3 0.4 19 83-101 8-26 (64)
298 PRK10220 hypothetical protein; 74.7 3.4 7.4E-05 27.3 2.6 30 23-70 5-34 (111)
299 COG1040 ComFC Predicted amidop 74.6 0.62 1.3E-05 34.1 -1.0 36 57-105 25-60 (225)
300 PF06044 DRP: Dam-replacing fa 74.5 1.1 2.4E-05 33.6 0.2 32 57-94 32-64 (254)
301 PRK07111 anaerobic ribonucleos 74.3 1.9 4E-05 37.0 1.6 22 83-105 680-701 (735)
302 COG0675 Transposase and inacti 73.7 1.6 3.4E-05 32.3 0.9 23 83-106 309-331 (364)
303 PLN02638 cellulose synthase A 73.5 2.1 4.4E-05 38.2 1.7 37 14-66 10-46 (1079)
304 PRK12336 translation initiatio 73.5 4.6 0.0001 29.1 3.3 36 21-71 98-134 (201)
305 PF06750 DiS_P_DiS: Bacterial 73.3 2.6 5.6E-05 26.7 1.7 38 56-95 33-70 (92)
306 cd00730 rubredoxin Rubredoxin; 73.3 3.6 7.9E-05 23.3 2.2 36 57-92 2-43 (50)
307 COG1779 C4-type Zn-finger prot 73.2 1.2 2.6E-05 32.3 0.2 44 18-67 11-54 (201)
308 PRK01110 rpmF 50S ribosomal pr 73.2 2.2 4.7E-05 25.1 1.2 20 84-105 28-47 (60)
309 cd01407 SIR2-fam SIR2 family o 73.2 2.9 6.2E-05 30.1 2.2 45 49-96 102-146 (218)
310 PRK15103 paraquat-inducible me 73.1 2.9 6.3E-05 33.4 2.3 12 55-66 29-40 (419)
311 PF10122 Mu-like_Com: Mu-like 73.0 0.98 2.1E-05 25.8 -0.3 15 56-70 24-38 (51)
312 COG3058 FdhE Uncharacterized p 72.9 0.4 8.8E-06 36.6 -2.4 10 20-29 184-193 (308)
313 COG2331 Uncharacterized protei 72.9 0.53 1.1E-05 29.2 -1.5 14 55-68 11-24 (82)
314 PF05495 zf-CHY: CHY zinc fing 72.8 1.3 2.8E-05 26.7 0.2 23 83-105 41-69 (71)
315 COG1439 Predicted nucleic acid 72.7 2.2 4.7E-05 30.5 1.4 12 56-67 139-150 (177)
316 PRK11788 tetratricopeptide rep 72.6 2 4.3E-05 32.4 1.3 21 84-104 355-375 (389)
317 PRK08271 anaerobic ribonucleos 72.5 3.4 7.3E-05 34.8 2.7 33 45-92 557-589 (623)
318 PRK01343 zinc-binding protein; 72.5 2.2 4.8E-05 24.9 1.2 13 83-95 9-21 (57)
319 PF10263 SprT-like: SprT-like 72.2 1.7 3.7E-05 29.3 0.8 33 55-94 122-154 (157)
320 cd04476 RPA1_DBD_C RPA1_DBD_C: 72.0 3.2 6.9E-05 28.5 2.1 35 48-93 27-61 (166)
321 COG1328 NrdD Oxygen-sensitive 71.9 2.3 4.9E-05 36.3 1.6 24 83-106 641-664 (700)
322 PF03367 zf-ZPR1: ZPR1 zinc-fi 71.8 3 6.5E-05 29.1 1.9 39 22-66 2-40 (161)
323 PF08646 Rep_fac-A_C: Replicat 71.7 5.8 0.00013 26.6 3.3 31 53-93 15-47 (146)
324 COG1110 Reverse gyrase [DNA re 71.6 1.9 4.2E-05 38.3 1.1 25 82-106 693-717 (1187)
325 PF09526 DUF2387: Probable met 71.3 5 0.00011 24.4 2.6 37 22-71 9-45 (71)
326 PRK06450 threonine synthase; V 71.3 3 6.6E-05 32.2 2.0 12 57-68 19-30 (338)
327 PRK08665 ribonucleotide-diphos 71.2 2.6 5.7E-05 36.1 1.8 23 84-106 725-749 (752)
328 COG3877 Uncharacterized protei 71.1 1.9 4.1E-05 28.5 0.7 26 57-95 7-32 (122)
329 PRK07220 DNA topoisomerase I; 70.8 6.9 0.00015 33.5 4.2 9 22-30 590-598 (740)
330 TIGR02443 conserved hypothetic 70.5 6 0.00013 23.3 2.7 38 21-71 9-46 (59)
331 smart00778 Prim_Zn_Ribbon Zinc 70.5 5 0.00011 21.3 2.2 8 22-29 4-11 (37)
332 COG1773 Rubredoxin [Energy pro 70.4 5.5 0.00012 23.1 2.5 15 56-70 3-17 (55)
333 PF01907 Ribosomal_L37e: Ribos 70.0 2.2 4.9E-05 24.7 0.8 26 20-66 14-40 (55)
334 cd01410 SIRT7 SIRT7: Eukaryoti 69.9 3.2 7E-05 29.8 1.8 13 55-67 94-106 (206)
335 PRK08579 anaerobic ribonucleos 69.8 4.1 9E-05 34.3 2.6 25 55-92 567-591 (625)
336 COG1571 Predicted DNA-binding 69.8 2.7 5.8E-05 33.8 1.4 11 58-68 352-362 (421)
337 PRK11595 DNA utilization prote 69.7 2.2 4.7E-05 31.0 0.9 8 58-65 36-43 (227)
338 COG0846 SIR2 NAD-dependent pro 69.6 5 0.00011 30.0 2.8 18 50-67 116-133 (250)
339 KOG2879 Predicted E3 ubiquitin 69.6 2.5 5.4E-05 32.3 1.2 12 84-95 277-288 (298)
340 TIGR03847 conserved hypothetic 69.3 2.8 6.1E-05 29.8 1.3 20 83-102 156-175 (177)
341 PRK00133 metG methionyl-tRNA s 69.1 3.4 7.3E-05 34.8 2.0 35 58-106 141-178 (673)
342 PRK07111 anaerobic ribonucleos 69.1 4.6 9.9E-05 34.6 2.8 23 55-91 679-701 (735)
343 smart00709 Zpr1 Duplicated dom 68.9 4.3 9.3E-05 28.3 2.2 39 23-67 2-40 (160)
344 COG3364 Zn-ribbon containing p 68.9 1.6 3.4E-05 28.6 0.0 11 58-68 4-14 (112)
345 PRK00423 tfb transcription ini 68.8 2.9 6.2E-05 31.9 1.4 32 55-95 10-42 (310)
346 PF03884 DUF329: Domain of unk 68.8 3 6.5E-05 24.4 1.2 21 84-104 3-25 (57)
347 PRK11788 tetratricopeptide rep 68.3 3.6 7.9E-05 31.0 1.9 13 54-66 366-378 (389)
348 PF03854 zf-P11: P-11 zinc fin 68.1 0.67 1.5E-05 26.2 -1.6 25 83-107 21-45 (50)
349 PF09334 tRNA-synt_1g: tRNA sy 67.9 3.1 6.7E-05 32.8 1.5 29 55-93 148-176 (391)
350 PF07503 zf-HYPF: HypF finger; 67.4 1.2 2.6E-05 23.4 -0.7 8 85-92 23-30 (35)
351 PTZ00410 NAD-dependent SIR2; P 67.3 4.6 9.9E-05 31.7 2.2 46 48-96 139-184 (349)
352 PRK14704 anaerobic ribonucleos 67.2 2.7 5.8E-05 35.3 1.0 24 55-92 558-581 (618)
353 COG3809 Uncharacterized protei 66.9 2.3 5.1E-05 26.6 0.5 11 56-66 21-31 (88)
354 PF04135 Nop10p: Nucleolar RNA 66.8 4.4 9.6E-05 23.3 1.6 12 84-95 18-29 (53)
355 PF14690 zf-ISL3: zinc-finger 66.7 8.6 0.00019 20.6 2.7 8 22-29 3-10 (47)
356 CHL00174 accD acetyl-CoA carbo 66.7 1.6 3.5E-05 33.5 -0.4 12 57-68 58-69 (296)
357 TIGR00375 conserved hypothetic 66.7 3 6.5E-05 33.0 1.2 13 56-68 240-252 (374)
358 PTZ00255 60S ribosomal protein 66.6 1.9 4.2E-05 27.5 0.1 31 20-68 35-66 (90)
359 PRK14289 chaperone protein Dna 66.5 8.6 0.00019 30.2 3.7 23 83-105 197-219 (386)
360 TIGR02827 RNR_anaer_Bdell anae 66.5 5 0.00011 33.6 2.4 32 46-92 524-555 (586)
361 PF04810 zf-Sec23_Sec24: Sec23 66.3 1.5 3.3E-05 23.4 -0.4 20 48-67 16-35 (40)
362 PRK14715 DNA polymerase II lar 65.9 3.4 7.4E-05 37.8 1.4 22 83-106 674-695 (1627)
363 COG3791 Uncharacterized conser 65.8 2.7 5.9E-05 28.2 0.7 9 99-107 71-79 (133)
364 PF15135 UPF0515: Uncharacteri 65.7 9.2 0.0002 28.9 3.5 66 20-107 111-184 (278)
365 COG5525 Bacteriophage tail ass 65.6 2.1 4.6E-05 35.8 0.1 39 23-66 229-269 (611)
366 PRK07219 DNA topoisomerase I; 65.5 11 0.00024 32.6 4.4 11 84-94 734-744 (822)
367 TIGR00515 accD acetyl-CoA carb 65.1 1.8 4E-05 32.9 -0.3 15 55-69 44-58 (285)
368 COG4530 Uncharacterized protei 65.0 3.3 7.1E-05 27.6 0.9 31 21-69 9-39 (129)
369 COG1040 ComFC Predicted amidop 64.9 1.2 2.5E-05 32.6 -1.3 22 85-106 26-47 (225)
370 PRK04011 peptide chain release 64.9 3.7 8.1E-05 32.7 1.4 10 56-65 328-337 (411)
371 PF14634 zf-RING_5: zinc-RING 64.9 1.9 4E-05 23.3 -0.2 21 85-105 24-44 (44)
372 PF03811 Zn_Tnp_IS1: InsA N-te 64.9 4.6 9.9E-05 21.3 1.3 10 21-30 5-14 (36)
373 COG2126 RPL37A Ribosomal prote 64.7 4.3 9.2E-05 23.9 1.2 26 19-65 14-40 (61)
374 TIGR02420 dksA RNA polymerase- 64.6 1.9 4E-05 28.0 -0.3 23 83-105 80-109 (110)
375 PF10276 zf-CHCC: Zinc-finger 64.5 3.1 6.6E-05 22.5 0.6 11 55-65 28-38 (40)
376 COG1571 Predicted DNA-binding 64.5 4.6 0.0001 32.5 1.8 15 56-70 367-381 (421)
377 COG4640 Predicted membrane pro 64.3 4.1 9E-05 32.7 1.5 27 56-95 1-27 (465)
378 PRK08197 threonine synthase; V 64.2 5 0.00011 31.4 2.0 9 22-30 8-16 (394)
379 PRK14138 NAD-dependent deacety 64.2 3.5 7.7E-05 30.4 1.1 44 49-95 112-155 (244)
380 PLN02189 cellulose synthase 63.8 4.5 9.8E-05 36.0 1.8 12 55-66 52-63 (1040)
381 TIGR00280 L37a ribosomal prote 63.8 3.3 7.1E-05 26.5 0.7 31 20-68 34-65 (91)
382 TIGR01405 polC_Gram_pos DNA po 63.7 4.2 9.1E-05 36.8 1.6 10 97-106 708-717 (1213)
383 TIGR00398 metG methionyl-tRNA 63.6 4.8 0.0001 32.6 1.8 24 84-107 150-176 (530)
384 PF01780 Ribosomal_L37ae: Ribo 63.6 2.2 4.8E-05 27.2 -0.1 32 20-68 34-65 (90)
385 PF06957 COPI_C: Coatomer (COP 63.6 2.1 4.6E-05 34.4 -0.2 31 40-70 364-394 (422)
386 PF14311 DUF4379: Domain of un 63.3 5.6 0.00012 22.4 1.6 13 56-68 28-40 (55)
387 COG3478 Predicted nucleic-acid 62.9 6.1 0.00013 23.8 1.7 11 55-65 39-49 (68)
388 COG1107 Archaea-specific RecJ- 62.9 3.7 7.9E-05 34.6 1.0 24 83-106 80-104 (715)
389 PRK06386 replication factor A; 62.8 4.6 0.0001 31.8 1.5 22 82-105 235-256 (358)
390 PTZ00408 NAD-dependent deacety 62.8 7.4 0.00016 28.8 2.6 13 55-67 116-128 (242)
391 TIGR00622 ssl1 transcription f 62.7 4.7 0.0001 26.7 1.3 85 22-106 16-112 (112)
392 COG0551 TopA Zn-finger domain 62.1 16 0.00036 24.3 4.0 12 19-30 58-69 (140)
393 PF13824 zf-Mss51: Zinc-finger 62.1 6.6 0.00014 22.8 1.7 8 85-92 16-23 (55)
394 PF04828 GFA: Glutathione-depe 61.7 1.9 4.1E-05 26.0 -0.6 11 83-93 48-58 (92)
395 KOG2041 WD40 repeat protein [G 61.4 7.8 0.00017 33.8 2.7 63 20-106 1116-1183(1189)
396 PF01258 zf-dskA_traR: Prokary 61.3 1.7 3.7E-05 22.6 -0.8 11 85-95 5-15 (36)
397 PTZ00409 Sir2 (Silent Informat 61.2 7 0.00015 29.4 2.2 19 50-68 131-149 (271)
398 PF14255 Cys_rich_CPXG: Cystei 61.1 4.2 9.1E-05 23.2 0.8 11 85-95 2-12 (52)
399 COG5349 Uncharacterized protei 61.1 3.6 7.7E-05 27.7 0.5 15 55-69 39-53 (126)
400 COG5525 Bacteriophage tail ass 61.1 8 0.00017 32.5 2.7 42 54-95 225-271 (611)
401 KOG2907 RNA polymerase I trans 61.0 2.8 6E-05 27.9 0.0 17 55-71 24-40 (116)
402 TIGR03830 CxxCG_CxxCG_HTH puta 60.6 4.6 0.0001 26.1 1.0 6 24-29 1-6 (127)
403 PLN02436 cellulose synthase A 60.4 5.7 0.00012 35.5 1.8 12 55-66 54-65 (1094)
404 PF04438 zf-HIT: HIT zinc fing 60.4 4.6 9.9E-05 20.4 0.8 10 83-92 13-22 (30)
405 PRK09521 exosome complex RNA-b 60.4 4.4 9.5E-05 28.6 0.9 23 83-105 149-174 (189)
406 PRK11823 DNA repair protein Ra 60.2 9.7 0.00021 30.6 3.0 26 20-66 6-31 (446)
407 PLN02569 threonine synthase 60.2 6.3 0.00014 32.1 1.9 28 56-95 49-76 (484)
408 PF03966 Trm112p: Trm112p-like 60.1 1.1 2.3E-05 26.6 -1.9 19 51-69 48-66 (68)
409 cd00296 SIR2 SIR2 superfamily 60.0 10 0.00023 26.8 2.9 21 47-67 104-124 (222)
410 PRK03976 rpl37ae 50S ribosomal 59.8 4.2 9.1E-05 25.9 0.7 31 20-68 35-66 (90)
411 PRK12775 putative trifunctiona 59.6 9.9 0.00021 33.7 3.1 56 20-95 795-850 (1006)
412 PRK08329 threonine synthase; V 59.6 6.2 0.00013 30.4 1.7 9 22-30 2-10 (347)
413 PLN02610 probable methionyl-tR 59.3 6.7 0.00014 34.0 2.0 23 84-106 171-196 (801)
414 PF09567 RE_MamI: MamI restric 59.2 4.1 9E-05 30.9 0.7 24 22-66 83-106 (314)
415 PLN02400 cellulose synthase 59.1 7 0.00015 35.0 2.1 12 55-66 54-65 (1085)
416 PRK05333 NAD-dependent deacety 58.6 11 0.00024 28.3 3.0 13 84-96 180-192 (285)
417 PF08209 Sgf11: Sgf11 (transcr 58.5 4.5 9.7E-05 21.0 0.5 13 83-95 4-16 (33)
418 PF12647 RNHCP: RNHCP domain; 58.1 9.1 0.0002 24.5 2.0 35 20-70 3-38 (92)
419 PHA02942 putative transposase; 57.7 5.2 0.00011 31.6 1.0 24 83-106 325-351 (383)
420 COG1327 Predicted transcriptio 57.3 6.9 0.00015 27.3 1.5 9 84-92 29-37 (156)
421 KOG3362 Predicted BBOX Zn-fing 57.2 4.9 0.00011 27.9 0.7 23 55-93 117-139 (156)
422 PRK00133 metG methionyl-tRNA s 57.1 16 0.00035 30.8 3.9 11 58-68 154-164 (673)
423 PRK14894 glycyl-tRNA synthetas 56.7 9.8 0.00021 31.6 2.5 16 55-70 87-102 (539)
424 PF08882 Acetone_carb_G: Aceto 56.6 5 0.00011 26.5 0.7 16 82-97 73-88 (112)
425 TIGR00244 transcriptional regu 56.5 7.6 0.00017 26.9 1.6 7 23-29 2-8 (147)
426 TIGR00416 sms DNA repair prote 56.2 10 0.00023 30.5 2.5 26 21-67 7-32 (454)
427 PRK07218 replication factor A; 56.1 6.6 0.00014 31.6 1.4 22 82-105 296-317 (423)
428 PRK09263 anaerobic ribonucleos 56.1 13 0.00028 31.9 3.1 23 83-105 641-667 (711)
429 COG2835 Uncharacterized conser 56.0 17 0.00036 21.5 2.7 34 21-71 8-41 (60)
430 COG0143 MetG Methionyl-tRNA sy 55.8 13 0.00027 31.1 3.0 13 56-68 155-167 (558)
431 KOG1247 Methionyl-tRNA synthet 55.7 4.7 0.0001 32.9 0.5 26 56-95 152-177 (567)
432 PLN02915 cellulose synthase A 55.6 9.8 0.00021 34.0 2.4 12 55-66 33-44 (1044)
433 PLN03208 E3 ubiquitin-protein 55.5 9.1 0.0002 27.7 1.9 13 83-95 68-80 (193)
434 PF10146 zf-C4H2: Zinc finger- 55.4 2.9 6.3E-05 30.9 -0.7 25 82-106 193-217 (230)
435 COG2995 PqiA Uncharacterized p 55.3 13 0.00028 29.8 2.9 36 18-68 15-50 (418)
436 PLN02610 probable methionyl-tR 55.2 13 0.00027 32.3 3.0 11 84-94 188-198 (801)
437 PRK05638 threonine synthase; V 55.1 8.9 0.00019 30.6 2.0 12 56-68 16-27 (442)
438 PF13913 zf-C2HC_2: zinc-finge 55.0 3.8 8.3E-05 19.6 -0.1 10 57-66 3-12 (25)
439 TIGR02487 NrdD anaerobic ribon 55.0 12 0.00025 31.3 2.7 25 55-92 523-547 (579)
440 PF14952 zf-tcix: Putative tre 55.0 7.2 0.00016 21.6 1.0 12 84-95 12-23 (44)
441 PRK08665 ribonucleotide-diphos 54.9 7.2 0.00016 33.5 1.5 24 57-91 725-748 (752)
442 COG5257 GCD11 Translation init 54.8 8.6 0.00019 30.5 1.8 9 85-93 74-82 (415)
443 PRK04338 N(2),N(2)-dimethylgua 54.8 8.5 0.00019 30.3 1.8 24 83-106 244-270 (382)
444 KOG1598 Transcription initiati 54.7 6.7 0.00015 32.4 1.2 34 23-72 2-35 (521)
445 COG1933 Archaeal DNA polymeras 54.5 5.2 0.00011 30.0 0.5 28 55-93 166-193 (253)
446 COG3024 Uncharacterized protei 54.5 6.6 0.00014 23.5 0.9 13 83-95 7-19 (65)
447 PLN02195 cellulose synthase A 54.5 11 0.00023 33.5 2.5 11 56-66 25-35 (977)
448 TIGR00398 metG methionyl-tRNA 54.4 11 0.00023 30.7 2.3 13 83-95 166-178 (530)
449 PRK00448 polC DNA polymerase I 54.4 7.4 0.00016 35.9 1.5 9 98-106 934-942 (1437)
450 KOG2462 C2H2-type Zn-finger pr 54.2 20 0.00044 27.4 3.6 50 55-106 160-224 (279)
451 cd01408 SIRT1 SIRT1: Eukaryoti 54.1 5.1 0.00011 29.3 0.5 11 56-66 116-126 (235)
452 PF01096 TFIIS_C: Transcriptio 54.1 6.8 0.00015 20.8 0.8 7 23-29 2-8 (39)
453 COG1379 PHP family phosphoeste 54.1 3 6.6E-05 32.8 -0.8 42 6-66 234-275 (403)
454 cd01409 SIRT4 SIRT4: Eukaryoti 54.0 18 0.00039 26.9 3.4 20 48-67 110-129 (260)
455 PF03117 Herpes_UL49_1: UL49 f 53.9 13 0.00028 27.9 2.5 33 39-71 78-120 (245)
456 PRK11823 DNA repair protein Ra 53.7 13 0.00029 29.8 2.8 8 58-65 9-16 (446)
457 smart00401 ZnF_GATA zinc finge 53.6 10 0.00022 21.4 1.6 35 21-68 3-37 (52)
458 PTZ00073 60S ribosomal protein 53.5 6.7 0.00015 25.0 0.8 25 20-65 15-40 (91)
459 PF08996 zf-DNA_Pol: DNA Polym 53.4 3.5 7.6E-05 29.2 -0.5 73 20-103 17-107 (188)
460 cd01675 RNR_III Class III ribo 53.3 14 0.0003 30.6 2.8 22 58-92 520-541 (555)
461 KOG2923 Uncharacterized conser 52.9 5.8 0.00013 23.8 0.5 41 49-94 13-55 (67)
462 TIGR00354 polC DNA polymerase, 52.6 12 0.00025 33.4 2.4 30 55-95 1011-1040(1095)
463 TIGR01385 TFSII transcription 52.5 21 0.00045 27.4 3.5 11 19-29 256-266 (299)
464 PF02146 SIR2: Sir2 family; I 52.4 7.7 0.00017 26.8 1.1 43 50-95 99-141 (178)
465 PRK00418 DNA gyrase inhibitor; 52.1 8.9 0.00019 22.8 1.2 11 84-94 7-17 (62)
466 TIGR03829 YokU_near_AblA uncha 52.1 41 0.00089 21.3 4.3 15 54-68 33-47 (89)
467 TIGR00375 conserved hypothetic 51.9 7.8 0.00017 30.7 1.2 22 85-107 242-268 (374)
468 PF04161 Arv1: Arv1-like famil 51.8 6.9 0.00015 28.2 0.8 7 23-29 2-8 (208)
469 PF14206 Cys_rich_CPCC: Cystei 51.6 15 0.00033 22.7 2.2 29 22-69 2-33 (78)
470 COG2176 PolC DNA polymerase II 51.5 9.6 0.00021 34.8 1.7 10 84-93 940-949 (1444)
471 KOG1842 FYVE finger-containing 51.4 4.9 0.00011 32.7 0.0 24 47-70 171-194 (505)
472 COG4357 Zinc finger domain con 51.1 3.3 7.1E-05 26.9 -0.9 11 85-95 82-92 (105)
473 cd01121 Sms Sms (bacterial rad 50.9 11 0.00023 29.7 1.8 10 55-64 13-22 (372)
474 KOG2846 Predicted membrane pro 50.9 8.2 0.00018 30.1 1.1 16 56-71 242-257 (328)
475 PF01529 zf-DHHC: DHHC palmito 50.4 9.1 0.0002 25.9 1.2 24 82-105 47-70 (174)
476 COG1328 NrdD Oxygen-sensitive 50.0 16 0.00035 31.3 2.8 35 55-102 640-675 (700)
477 TIGR00416 sms DNA repair prote 49.9 16 0.00035 29.5 2.7 11 56-66 7-17 (454)
478 TIGR02419 C4_traR_proteo phage 49.8 5.2 0.00011 23.6 -0.1 20 84-103 32-58 (63)
479 TIGR02820 formald_GSH S-(hydro 49.8 7.8 0.00017 27.7 0.8 11 97-107 89-99 (182)
480 PRK13715 conjugal transfer pro 49.7 4.1 8.8E-05 24.8 -0.6 19 85-103 36-61 (73)
481 KOG2807 RNA polymerase II tran 49.6 9.3 0.0002 30.0 1.2 24 83-106 276-299 (378)
482 PF06107 DUF951: Bacterial pro 49.6 10 0.00022 22.2 1.1 29 26-69 15-44 (57)
483 PRK13264 3-hydroxyanthranilate 49.6 4.1 8.9E-05 29.1 -0.6 41 56-96 120-170 (177)
484 TIGR00143 hypF [NiFe] hydrogen 49.5 11 0.00025 32.2 1.8 57 22-94 91-151 (711)
485 COG5082 AIR1 Arginine methyltr 49.5 14 0.00029 26.7 2.0 13 18-30 57-69 (190)
486 PF11648 RIG-I_C-RD: C-termina 49.0 15 0.00033 24.3 2.1 29 20-51 59-87 (123)
487 PHA00080 DksA-like zinc finger 48.9 5.3 0.00011 24.2 -0.2 10 85-94 33-42 (72)
488 cd07973 Spt4 Transcription elo 48.8 12 0.00025 24.2 1.4 11 57-67 4-14 (98)
489 PF14447 Prok-RING_4: Prokaryo 48.7 17 0.00038 21.0 2.0 12 85-96 41-52 (55)
490 PF14149 YhfH: YhfH-like prote 48.5 3 6.5E-05 22.3 -1.1 12 84-95 14-25 (37)
491 PF01599 Ribosomal_S27: Riboso 48.3 11 0.00024 21.1 1.1 24 82-105 17-46 (47)
492 PF11331 DUF3133: Protein of u 48.3 12 0.00027 20.8 1.3 39 54-94 4-42 (46)
493 COG1503 eRF1 Peptide chain rel 48.2 8.9 0.00019 30.8 1.0 11 56-66 327-337 (411)
494 COG1110 Reverse gyrase [DNA re 47.8 5.8 0.00012 35.5 -0.1 28 56-96 694-721 (1187)
495 cd00065 FYVE FYVE domain; Zinc 47.5 15 0.00033 20.3 1.7 11 56-66 18-28 (57)
496 PRK10996 thioredoxin 2; Provis 47.5 27 0.00059 23.1 3.2 14 54-67 20-33 (139)
497 PF09332 Mcm10: Mcm10 replicat 47.5 12 0.00027 29.3 1.7 10 56-65 285-294 (344)
498 TIGR03676 aRF1/eRF1 peptide ch 47.4 11 0.00025 29.9 1.5 9 98-106 343-351 (403)
499 PF11290 DUF3090: Protein of u 47.4 11 0.00024 26.7 1.3 18 83-100 154-171 (171)
500 KOG3084 NADH pyrophosphatase I 47.4 8.9 0.00019 30.0 0.8 11 97-107 150-160 (345)
No 1
>PF12773 DZR: Double zinc ribbon
Probab=99.23 E-value=7.3e-12 Score=71.41 Aligned_cols=42 Identities=31% Similarity=0.755 Sum_probs=34.8
Q ss_pred CCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCC
Q 033949 53 KEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCG 104 (107)
Q Consensus 53 ~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG 104 (107)
.....+|++||..+..... ....|++||++++.+++||++||
T Consensus 9 ~~~~~fC~~CG~~l~~~~~----------~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLPPPDQ----------SKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CccccCChhhcCChhhccC----------CCCCCcCCcCCCcCCcCccCccc
Confidence 3579999999999872111 25789999999999999999998
No 2
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=99.11 E-value=2.5e-11 Score=60.84 Aligned_cols=24 Identities=42% Similarity=1.032 Sum_probs=22.8
Q ss_pred cccccCCceecCCCccCcCCCCCC
Q 033949 84 SKCRFCDRLVEPDFSFCPYCGSAL 107 (107)
Q Consensus 84 ~~C~~CG~~i~~~~~fCP~CG~~l 107 (107)
+.||+||++++++++|||+||++|
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred CCCcccCCcCCcccccChhhCCCC
Confidence 579999999999999999999987
No 3
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=99.08 E-value=3.9e-11 Score=58.50 Aligned_cols=23 Identities=43% Similarity=1.024 Sum_probs=21.8
Q ss_pred ccccCCceecCCCccCcCCCCCC
Q 033949 85 KCRFCDRLVEPDFSFCPYCGSAL 107 (107)
Q Consensus 85 ~C~~CG~~i~~~~~fCP~CG~~l 107 (107)
+||+||++|+.+++|||+||++|
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCcC
Confidence 49999999999999999999986
No 4
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=98.95 E-value=4.6e-10 Score=92.56 Aligned_cols=50 Identities=26% Similarity=0.602 Sum_probs=42.9
Q ss_pred EECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCc
Q 033949 22 GRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCP 101 (107)
Q Consensus 22 ~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP 101 (107)
.+||+||... .....+|+.||..+. ...||+||++++.+++|||
T Consensus 2 ~~Cp~Cg~~n---------------------~~~akFC~~CG~~l~---------------~~~Cp~CG~~~~~~~~fC~ 45 (645)
T PRK14559 2 LICPQCQFEN---------------------PNNNRFCQKCGTSLT---------------HKPCPQCGTEVPVDEAHCP 45 (645)
T ss_pred CcCCCCCCcC---------------------CCCCccccccCCCCC---------------CCcCCCCCCCCCccccccc
Confidence 4799999943 347999999999973 2479999999999999999
Q ss_pred CCCCCC
Q 033949 102 YCGSAL 107 (107)
Q Consensus 102 ~CG~~l 107 (107)
+||+++
T Consensus 46 ~CG~~~ 51 (645)
T PRK14559 46 NCGAET 51 (645)
T ss_pred ccCCcc
Confidence 999875
No 5
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=98.61 E-value=3.7e-08 Score=85.44 Aligned_cols=51 Identities=33% Similarity=0.671 Sum_probs=41.2
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCC---
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPD--- 96 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~--- 96 (107)
...+||+||... +..+||.||+..+. .+.||+||++++++
T Consensus 666 ~~rkCPkCG~~t-----------------------~~~fCP~CGs~te~--------------vy~CPsCGaev~~des~ 708 (1337)
T PRK14714 666 GRRRCPSCGTET-----------------------YENRCPDCGTHTEP--------------VYVCPDCGAEVPPDESG 708 (1337)
T ss_pred EEEECCCCCCcc-----------------------ccccCcccCCcCCC--------------ceeCccCCCccCCCccc
Confidence 357899999942 33499999999743 35899999999876
Q ss_pred CccCcCCCCCC
Q 033949 97 FSFCPYCGSAL 107 (107)
Q Consensus 97 ~~fCP~CG~~l 107 (107)
+.+||+||+++
T Consensus 709 a~~CP~CGtpl 719 (1337)
T PRK14714 709 RVECPRCDVEL 719 (1337)
T ss_pred cccCCCCCCcc
Confidence 88999999875
No 6
>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=98.47 E-value=7.4e-08 Score=48.15 Aligned_cols=23 Identities=35% Similarity=0.805 Sum_probs=21.1
Q ss_pred cccccCCceecCCCccCcCCCCC
Q 033949 84 SKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 84 ~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
+.||+|+++|+.++++||.||..
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGYD 23 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCCC
Confidence 46999999999999999999975
No 7
>PF12773 DZR: Double zinc ribbon
Probab=98.26 E-value=7.5e-07 Score=50.46 Aligned_cols=36 Identities=25% Similarity=0.698 Sum_probs=29.3
Q ss_pred CCCCCCCCCCCCCCCCCCCCCccCccccccCCceec---CCCccCcCCCCCC
Q 033949 59 CNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE---PDFSFCPYCGSAL 107 (107)
Q Consensus 59 C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~---~~~~fCP~CG~~l 107 (107)
||+||+.++.+ ...|++||+.+. ....+||.||+.+
T Consensus 1 Cp~Cg~~~~~~-------------~~fC~~CG~~l~~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 1 CPHCGTPNPDD-------------AKFCPHCGTPLPPPDQSKKICPNCGAEN 39 (50)
T ss_pred CCCcCCcCCcc-------------ccCChhhcCChhhccCCCCCCcCCcCCC
Confidence 78999997653 368999999998 3578999999864
No 8
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=97.85 E-value=7.2e-06 Score=40.77 Aligned_cols=25 Identities=24% Similarity=0.646 Sum_probs=16.4
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV 93 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i 93 (107)
.+.||+||+.++.+ .+.|++||+.+
T Consensus 2 ~~~Cp~Cg~~~~~~-------------~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPD-------------AKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcc-------------cccChhhCCCC
Confidence 35688888865432 35788888764
No 9
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=97.82 E-value=8.7e-06 Score=39.45 Aligned_cols=23 Identities=22% Similarity=0.641 Sum_probs=15.6
Q ss_pred eCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949 58 FCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV 93 (107)
Q Consensus 58 ~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i 93 (107)
+||+||+.++.+ .+.|++||++|
T Consensus 1 ~Cp~CG~~~~~~-------------~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIEDD-------------AKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCCCCc-------------CcchhhhCCcC
Confidence 477888877542 35688888764
No 10
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=97.77 E-value=9.9e-06 Score=45.32 Aligned_cols=23 Identities=48% Similarity=0.873 Sum_probs=11.2
Q ss_pred cccccCCceecC----CCccCcCCCCC
Q 033949 84 SKCRFCDRLVEP----DFSFCPYCGSA 106 (107)
Q Consensus 84 ~~C~~CG~~i~~----~~~fCP~CG~~ 106 (107)
++|++||++++. ....||+||++
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCe
Confidence 445555555422 23455555554
No 11
>PRK04023 DNA polymerase II large subunit; Validated
Probab=97.57 E-value=7.4e-05 Score=64.36 Aligned_cols=50 Identities=28% Similarity=0.539 Sum_probs=37.6
Q ss_pred CCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCc
Q 033949 19 SGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFS 98 (107)
Q Consensus 19 ~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~ 98 (107)
.....||.||.. .....||+||+.-+ ..+.||.||..... .
T Consensus 624 Vg~RfCpsCG~~-----------------------t~~frCP~CG~~Te--------------~i~fCP~CG~~~~~--y 664 (1121)
T PRK04023 624 IGRRKCPSCGKE-----------------------TFYRRCPFCGTHTE--------------PVYRCPRCGIEVEE--D 664 (1121)
T ss_pred ccCccCCCCCCc-----------------------CCcccCCCCCCCCC--------------cceeCccccCcCCC--C
Confidence 345679999994 15578999999832 24689999998654 5
Q ss_pred cCcCCCCCC
Q 033949 99 FCPYCGSAL 107 (107)
Q Consensus 99 fCP~CG~~l 107 (107)
.||+||.++
T Consensus 665 ~CPKCG~El 673 (1121)
T PRK04023 665 ECEKCGREP 673 (1121)
T ss_pred cCCCCCCCC
Confidence 599999864
No 12
>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=97.50 E-value=2.2e-05 Score=66.42 Aligned_cols=49 Identities=35% Similarity=0.647 Sum_probs=0.0
Q ss_pred CCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCc
Q 033949 19 SGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFS 98 (107)
Q Consensus 19 ~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~ 98 (107)
.....||.||.. ++...||.||+.-+. .+.||.||.++..+
T Consensus 653 i~~r~Cp~Cg~~-----------------------t~~~~Cp~CG~~T~~--------------~~~Cp~C~~~~~~~-- 693 (900)
T PF03833_consen 653 IGRRRCPKCGKE-----------------------TFYNRCPECGSHTEP--------------VYVCPDCGIEVEED-- 693 (900)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred eecccCcccCCc-----------------------chhhcCcccCCcccc--------------ceeccccccccCcc--
Confidence 345679999993 367889999998643 57899999998877
Q ss_pred cCcCCCCC
Q 033949 99 FCPYCGSA 106 (107)
Q Consensus 99 fCP~CG~~ 106 (107)
.||.||.+
T Consensus 694 ~C~~C~~~ 701 (900)
T PF03833_consen 694 ECPKCGRE 701 (900)
T ss_dssp --------
T ss_pred cccccccc
Confidence 99999975
No 13
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=97.40 E-value=0.00012 Score=60.95 Aligned_cols=36 Identities=28% Similarity=0.768 Sum_probs=28.1
Q ss_pred eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCCC
Q 033949 57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL 107 (107)
Q Consensus 57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~l 107 (107)
+.||.||+....+ .+.|++||+.+.. +.||.||+.+
T Consensus 2 ~~Cp~Cg~~n~~~-------------akFC~~CG~~l~~--~~Cp~CG~~~ 37 (645)
T PRK14559 2 LICPQCQFENPNN-------------NRFCQKCGTSLTH--KPCPQCGTEV 37 (645)
T ss_pred CcCCCCCCcCCCC-------------CccccccCCCCCC--CcCCCCCCCC
Confidence 5799999987543 3689999998753 6899999864
No 14
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=97.37 E-value=0.00024 Score=59.92 Aligned_cols=50 Identities=26% Similarity=0.591 Sum_probs=30.8
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCC
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
.+.|..||+..+-.+-...+..+.......|+.||.. ..-...||.||+.
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~-~~~p~~Cp~Cgs~ 484 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQ-EPIPQSCPECGSE 484 (730)
T ss_pred eeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCC-CCCCCCCCCCCCC
Confidence 3445555544433322222222222346789999999 8889999999986
No 15
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=97.33 E-value=0.00015 Score=42.72 Aligned_cols=10 Identities=30% Similarity=0.770 Sum_probs=5.0
Q ss_pred ceeCCCCCCC
Q 033949 56 ALFCNNCNLL 65 (107)
Q Consensus 56 ~~~C~~CG~~ 65 (107)
.-.||+||+.
T Consensus 27 ~F~CPnCGe~ 36 (61)
T COG2888 27 KFPCPNCGEV 36 (61)
T ss_pred EeeCCCCCce
Confidence 3345555543
No 16
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=97.30 E-value=0.00025 Score=41.79 Aligned_cols=10 Identities=30% Similarity=0.962 Sum_probs=5.8
Q ss_pred ceeCCCCCCC
Q 033949 56 ALFCNNCNLL 65 (107)
Q Consensus 56 ~~~C~~CG~~ 65 (107)
.-.||+||+.
T Consensus 25 ~F~CPnCG~~ 34 (59)
T PRK14890 25 KFLCPNCGEV 34 (59)
T ss_pred EeeCCCCCCe
Confidence 4456666654
No 17
>PRK14873 primosome assembly protein PriA; Provisional
Probab=97.14 E-value=0.00043 Score=57.86 Aligned_cols=23 Identities=39% Similarity=0.924 Sum_probs=19.0
Q ss_pred CccccccCCceecCCCccCcCCCCC
Q 033949 82 DVSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 82 ~~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
....|+.||... ....||+||+.
T Consensus 409 ~~l~Ch~CG~~~--~p~~Cp~Cgs~ 431 (665)
T PRK14873 409 GTPRCRWCGRAA--PDWRCPRCGSD 431 (665)
T ss_pred CeeECCCCcCCC--cCccCCCCcCC
Confidence 357899999974 37899999985
No 18
>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=97.13 E-value=0.00058 Score=55.31 Aligned_cols=50 Identities=24% Similarity=0.520 Sum_probs=32.0
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCC
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
.+.|..||+...-.+-..++..+.......|+.||.. .+-...||.||+.
T Consensus 213 ~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~-~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 213 NLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQ-EPIPKTCPQCGSE 262 (505)
T ss_pred eeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCc-CCCCCCCCCCCCC
Confidence 5667777776644333333333333346789999988 4445799999985
No 19
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=97.06 E-value=0.00027 Score=39.38 Aligned_cols=26 Identities=27% Similarity=0.584 Sum_probs=13.6
Q ss_pred eCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949 58 FCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV 93 (107)
Q Consensus 58 ~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i 93 (107)
.|..||..++++.. ....||+||..|
T Consensus 4 ~C~~Cg~~~~~~~~----------~~irC~~CG~rI 29 (44)
T smart00659 4 ICGECGRENEIKSK----------DVVRCRECGYRI 29 (44)
T ss_pred ECCCCCCEeecCCC----------CceECCCCCceE
Confidence 46666666555321 134566666555
No 20
>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=96.88 E-value=0.00058 Score=35.57 Aligned_cols=10 Identities=20% Similarity=0.607 Sum_probs=4.6
Q ss_pred CCCCCCCCCC
Q 033949 59 CNNCNLLFPS 68 (107)
Q Consensus 59 C~~CG~~~~~ 68 (107)
|..||+..++
T Consensus 3 C~~Cg~~~~~ 12 (32)
T PF03604_consen 3 CGECGAEVEL 12 (32)
T ss_dssp ESSSSSSE-B
T ss_pred CCcCCCeeEc
Confidence 4555555543
No 21
>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=96.76 E-value=0.00048 Score=36.70 Aligned_cols=34 Identities=18% Similarity=0.351 Sum_probs=17.5
Q ss_pred eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949 57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE 94 (107)
Q Consensus 57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~ 94 (107)
+.||+||+.+.++.+..... .....|++||+.+.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~----~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGAN----GGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCC----CCEEECCCCCCEEE
Confidence 46777777666544321000 01356777776654
No 22
>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=96.75 E-value=0.00088 Score=33.28 Aligned_cols=10 Identities=30% Similarity=0.830 Sum_probs=5.0
Q ss_pred eCCCCCCCCC
Q 033949 58 FCNNCNLLFP 67 (107)
Q Consensus 58 ~C~~CG~~~~ 67 (107)
.||.|++.+.
T Consensus 2 ~CP~C~~~V~ 11 (26)
T PF10571_consen 2 TCPECGAEVP 11 (26)
T ss_pred cCCCCcCCch
Confidence 3555555543
No 23
>PRK05580 primosome assembly protein PriA; Validated
Probab=96.70 E-value=0.002 Score=53.89 Aligned_cols=50 Identities=20% Similarity=0.398 Sum_probs=29.3
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCC
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
++.|..||+...-.+-..++..+.......|+.||.... -...||.||+.
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~-~~~~Cp~Cg~~ 430 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEP-IPKACPECGST 430 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCC-CCCCCCCCcCC
Confidence 555666666553322222222222224678999998844 44679999975
No 24
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=96.57 E-value=0.0017 Score=57.42 Aligned_cols=36 Identities=28% Similarity=0.705 Sum_probs=28.1
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCCC
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL 107 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~l 107 (107)
...||.||+... ...||+||+.+.+.+ .||.||.++
T Consensus 667 ~rkCPkCG~~t~---------------~~fCP~CGs~te~vy-~CPsCGaev 702 (1337)
T PRK14714 667 RRRCPSCGTETY---------------ENRCPDCGTHTEPVY-VCPDCGAEV 702 (1337)
T ss_pred EEECCCCCCccc---------------cccCcccCCcCCCce-eCccCCCcc
Confidence 368999999642 247999999987655 899999853
No 25
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=96.56 E-value=0.0016 Score=36.22 Aligned_cols=13 Identities=15% Similarity=0.358 Sum_probs=8.3
Q ss_pred ceeCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPS 68 (107)
Q Consensus 56 ~~~C~~CG~~~~~ 68 (107)
.+.||.||+.+..
T Consensus 21 ~~~Cp~CG~~~~~ 33 (46)
T PRK00398 21 GVRCPYCGYRILF 33 (46)
T ss_pred ceECCCCCCeEEE
Confidence 5677777766544
No 26
>PRK04023 DNA polymerase II large subunit; Validated
Probab=96.52 E-value=0.0018 Score=56.16 Aligned_cols=36 Identities=25% Similarity=0.562 Sum_probs=29.2
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCC
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
...+|+.||.... ...||+||+. .....+||.||..
T Consensus 625 g~RfCpsCG~~t~---------------~frCP~CG~~-Te~i~fCP~CG~~ 660 (1121)
T PRK04023 625 GRRKCPSCGKETF---------------YRRCPFCGTH-TEPVYRCPRCGIE 660 (1121)
T ss_pred cCccCCCCCCcCC---------------cccCCCCCCC-CCcceeCccccCc
Confidence 4568999999851 3689999999 5677899999975
No 27
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=96.51 E-value=0.00035 Score=41.30 Aligned_cols=23 Identities=39% Similarity=1.003 Sum_probs=19.7
Q ss_pred ccccccCCceecCCCccC-cCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFC-PYCGS 105 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fC-P~CG~ 105 (107)
.++|++||++|+++-.|| +.|++
T Consensus 3 HkHC~~CG~~Ip~~~~fCS~~C~~ 26 (59)
T PF09889_consen 3 HKHCPVCGKPIPPDESFCSPKCRE 26 (59)
T ss_pred CCcCCcCCCcCCcchhhhCHHHHH
Confidence 368999999999999999 57764
No 28
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=96.41 E-value=0.0005 Score=41.93 Aligned_cols=27 Identities=19% Similarity=0.454 Sum_probs=13.9
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
....|..|+..+.. ...||.||.+++.
T Consensus 16 ~~~~C~~C~~~~~~--------------~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 16 GHYHCEACQKDYKK--------------EAFCPDCGQPLEV 42 (70)
T ss_dssp TEEEETTT--EEEE--------------EEE-TTT-SB-EE
T ss_pred CEEECcccccccee--------------cccCCCcccHHHH
Confidence 56777777776643 3467777776654
No 29
>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=96.40 E-value=0.0027 Score=33.73 Aligned_cols=35 Identities=20% Similarity=0.368 Sum_probs=22.7
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP 67 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~ 67 (107)
.+.||+|+..+. ||-=+....+..+.|++||+.+.
T Consensus 2 ~~~CP~C~~~~~------------v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPNCKTSFR------------VVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEE------------eCHHHcCCCCCEEECCCCCCEEE
Confidence 368999999542 22222223345799999998763
No 30
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=96.39 E-value=0.0018 Score=34.41 Aligned_cols=32 Identities=22% Similarity=0.586 Sum_probs=20.6
Q ss_pred eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
+.||+|++.|+++++..+-. ....+|++||..
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~----g~~v~C~~C~~~ 34 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPK----GRKVRCSKCGHV 34 (36)
T ss_pred EECCCCCCEEeCCHHHCCCC----CcEEECCCCCCE
Confidence 57888888887766533211 125678888865
No 31
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=96.34 E-value=0.0013 Score=37.39 Aligned_cols=10 Identities=20% Similarity=0.491 Sum_probs=4.9
Q ss_pred eCCCCCCCCC
Q 033949 58 FCNNCNLLFP 67 (107)
Q Consensus 58 ~C~~CG~~~~ 67 (107)
.|..||..++
T Consensus 8 ~C~~Cg~~~~ 17 (49)
T COG1996 8 KCARCGREVE 17 (49)
T ss_pred EhhhcCCeee
Confidence 3555555543
No 32
>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=96.32 E-value=0.004 Score=50.46 Aligned_cols=29 Identities=28% Similarity=0.563 Sum_probs=22.7
Q ss_pred cCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 50 WPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 50 ~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
++++...+.|.+||...++. ..||+||..
T Consensus 234 ~h~~~~~l~Ch~Cg~~~~~~--------------~~Cp~C~s~ 262 (505)
T TIGR00595 234 YHKKEGKLRCHYCGYQEPIP--------------KTCPQCGSE 262 (505)
T ss_pred EecCCCeEEcCCCcCcCCCC--------------CCCCCCCCC
Confidence 34456799999999998653 379999985
No 33
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=96.32 E-value=0.004 Score=36.72 Aligned_cols=41 Identities=20% Similarity=0.455 Sum_probs=28.0
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce-ecC--------CCccCcCCCC
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL-VEP--------DFSFCPYCGS 105 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~-i~~--------~~~fCP~CG~ 105 (107)
...|++||..+...+.. ....|||||++ |.. +.-.||+||-
T Consensus 7 ~~~CtSCg~~i~~~~~~---------~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 7 PPKCTSCGIEIAPREKA---------VKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred CccccCCCCcccCCCcc---------CEeeCCCCCCeeEeechhHHhcCCceECCCCCC
Confidence 45799999988543311 24679999998 432 5667999984
No 34
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=96.18 E-value=0.0026 Score=33.95 Aligned_cols=33 Identities=21% Similarity=0.500 Sum_probs=17.1
Q ss_pred eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949 57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV 93 (107)
Q Consensus 57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i 93 (107)
+.||+|++.+.++.+..+.. ....+|++||...
T Consensus 3 i~CP~C~~~f~v~~~~l~~~----~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAG----GRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccC----CcEEECCCCCcEe
Confidence 45777777766655421100 0245677776543
No 35
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=96.13 E-value=0.0064 Score=51.48 Aligned_cols=29 Identities=21% Similarity=0.387 Sum_probs=23.0
Q ss_pred cCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 50 WPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 50 ~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
+++....+.|.+||+...+ ...||+||.+
T Consensus 456 ~H~~~~~L~CH~Cg~~~~~--------------p~~Cp~Cgs~ 484 (730)
T COG1198 456 LHKATGQLRCHYCGYQEPI--------------PQSCPECGSE 484 (730)
T ss_pred EecCCCeeEeCCCCCCCCC--------------CCCCCCCCCC
Confidence 4445689999999999654 2479999998
No 36
>PRK00420 hypothetical protein; Validated
Probab=95.99 E-value=0.0037 Score=41.44 Aligned_cols=24 Identities=21% Similarity=0.466 Sum_probs=14.9
Q ss_pred ccccccCCceec---CCCccCcCCCCC
Q 033949 83 VSKCRFCDRLVE---PDFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~---~~~~fCP~CG~~ 106 (107)
..+||.||+++- .+..+||.||+.
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCCe
Confidence 356777776654 366677777654
No 37
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=95.98 E-value=0.0036 Score=37.32 Aligned_cols=23 Identities=43% Similarity=1.058 Sum_probs=16.7
Q ss_pred cccccCCceecCCCccCcCCCCC
Q 033949 84 SKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 84 ~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
+-|.+|+..++.+.+.||.||+.
T Consensus 5 kAC~~Ck~l~~~d~e~CP~Cgs~ 27 (64)
T COG2093 5 KACKNCKRLTPEDTEICPVCGST 27 (64)
T ss_pred HHHhhccccCCCCCccCCCCCCc
Confidence 45777777777777777777764
No 38
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=95.96 E-value=0.0011 Score=40.35 Aligned_cols=39 Identities=26% Similarity=0.582 Sum_probs=21.7
Q ss_pred eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCCC
Q 033949 57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL 107 (107)
Q Consensus 57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~l 107 (107)
+.||.|+..++... ..++|..|+..... -.+||.||++|
T Consensus 2 ~~CP~C~~~L~~~~-----------~~~~C~~C~~~~~~-~a~CPdC~~~L 40 (70)
T PF07191_consen 2 NTCPKCQQELEWQG-----------GHYHCEACQKDYKK-EAFCPDCGQPL 40 (70)
T ss_dssp -B-SSS-SBEEEET-----------TEEEETTT--EEEE-EEE-TTT-SB-
T ss_pred CcCCCCCCccEEeC-----------CEEECcccccccee-cccCCCcccHH
Confidence 46888888865533 25789999887554 34799998876
No 39
>PRK12496 hypothetical protein; Provisional
Probab=95.96 E-value=0.0039 Score=43.70 Aligned_cols=24 Identities=25% Similarity=0.639 Sum_probs=17.7
Q ss_pred cccccCCceecC--CCccCcCCCCCC
Q 033949 84 SKCRFCDRLVEP--DFSFCPYCGSAL 107 (107)
Q Consensus 84 ~~C~~CG~~i~~--~~~fCP~CG~~l 107 (107)
+.|+.||...+. ...+||-||++|
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~~~ 153 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGSPV 153 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCChh
Confidence 568888888764 446788888875
No 40
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=95.95 E-value=0.008 Score=35.50 Aligned_cols=42 Identities=19% Similarity=0.383 Sum_probs=29.2
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC---------CCccCcCCCC
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP---------DFSFCPYCGS 105 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~---------~~~fCP~CG~ 105 (107)
+...|++||..+.+.+.- ....|||||+++.. +--.||+||-
T Consensus 8 ~~~~CtSCg~~i~p~e~~---------v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 8 DPPVCTSCGREIAPGETA---------VKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred CCceeccCCCEeccCCce---------eEeeCCCCCceeeehhhhHHHcCCceECCCcCc
Confidence 356899999998664421 24679999954433 5667999984
No 41
>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=95.92 E-value=0.0033 Score=33.62 Aligned_cols=33 Identities=18% Similarity=0.353 Sum_probs=16.0
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV 93 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i 93 (107)
|...|+.||+.++......+ .....||+||+++
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~~------~~~~~CP~Cg~~~ 36 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKISD------DPLATCPECGGDV 36 (41)
T ss_pred EEEEcCCCCCEEEEEEecCC------CCCCCCCCCCCcc
Confidence 34466666666654221110 0134577777654
No 42
>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=95.90 E-value=0.0034 Score=34.39 Aligned_cols=16 Identities=31% Similarity=0.789 Sum_probs=9.8
Q ss_pred CCCceeCCCCCCCCCC
Q 033949 53 KEPALFCNNCNLLFPS 68 (107)
Q Consensus 53 ~~~~~~C~~CG~~~~~ 68 (107)
....+.|+.||..++.
T Consensus 16 ~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 16 ERGELVCPNCGLVLEE 31 (43)
T ss_dssp TTTEEEETTT-BBEE-
T ss_pred CCCeEECCCCCCEeec
Confidence 3467788888877654
No 43
>PF15616 TerY-C: TerY-C metal binding domain
Probab=95.84 E-value=0.0068 Score=41.20 Aligned_cols=31 Identities=19% Similarity=0.368 Sum_probs=23.0
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCC
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPD 96 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~ 96 (107)
.++.| .||..+-++.+ ....||.||.....+
T Consensus 88 ~fa~C-~CGkl~Ci~g~----------~~~~CPwCg~~g~~~ 118 (131)
T PF15616_consen 88 AFAVC-GCGKLFCIDGE----------GEVTCPWCGNEGSFG 118 (131)
T ss_pred cEEEe-cCCCEEEeCCC----------CCEECCCCCCeeeec
Confidence 56777 79999876553 257899999987654
No 44
>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=95.82 E-value=0.0069 Score=32.36 Aligned_cols=25 Identities=28% Similarity=0.743 Sum_probs=19.2
Q ss_pred ccccccCCceecC-------CCccCcCCCCCC
Q 033949 83 VSKCRFCDRLVEP-------DFSFCPYCGSAL 107 (107)
Q Consensus 83 ~~~C~~CG~~i~~-------~~~fCP~CG~~l 107 (107)
.+.|++||...+. ....||.||.++
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 4789999996643 456899999853
No 45
>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=95.79 E-value=0.0091 Score=35.55 Aligned_cols=42 Identities=17% Similarity=0.223 Sum_probs=25.5
Q ss_pred eeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCC
Q 033949 46 PVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPD 96 (107)
Q Consensus 46 P~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~ 96 (107)
+++..+.......||.||...+.... .....|++||...+.|
T Consensus 18 ~v~~v~~~~TSq~C~~CG~~~~~~~~---------~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 18 QVVEVDEAYTSQTCPRCGHRNKKRRS---------GRVFTCPNCGFEMDRD 59 (69)
T ss_pred EEEEECCCCCccCccCcccccccccc---------cceEEcCCCCCEECcH
Confidence 34444554446678888887755111 1256788888887664
No 46
>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=95.74 E-value=0.019 Score=36.87 Aligned_cols=15 Identities=13% Similarity=0.366 Sum_probs=11.2
Q ss_pred CCceeCCCCCCCCCC
Q 033949 54 EPALFCNNCNLLFPS 68 (107)
Q Consensus 54 ~~~~~C~~CG~~~~~ 68 (107)
+..+.|+.||...+.
T Consensus 14 ~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 14 NGVYVCPSCGYEKEK 28 (104)
T ss_pred CCeEECcCCCCcccc
Confidence 367888888877665
No 47
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=95.74 E-value=0.0087 Score=34.97 Aligned_cols=12 Identities=17% Similarity=0.490 Sum_probs=6.2
Q ss_pred cccccCCceecC
Q 033949 84 SKCRFCDRLVEP 95 (107)
Q Consensus 84 ~~C~~CG~~i~~ 95 (107)
..||.||+.+..
T Consensus 18 ~~CP~CG~~t~~ 29 (56)
T PRK13130 18 EICPVCGGKTKN 29 (56)
T ss_pred ccCcCCCCCCCC
Confidence 346666655433
No 48
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=95.73 E-value=0.0081 Score=32.01 Aligned_cols=35 Identities=31% Similarity=0.539 Sum_probs=23.4
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP 67 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~ 67 (107)
.++||+|+..+. ||-=++..++..+.|+.|++.+.
T Consensus 2 ~i~CP~C~~~f~------------v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 2 IITCPNCQTRFR------------VPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EEECCCCCceEE------------cCHHHcccCCcEEECCCCCcEee
Confidence 468999999543 22122334456999999998763
No 49
>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=95.71 E-value=0.0075 Score=39.70 Aligned_cols=31 Identities=26% Similarity=0.787 Sum_probs=23.9
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCC
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSS 69 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~ 69 (107)
..+||+||.++ +-+++. + +.||+||+.+.+.
T Consensus 9 KR~Cp~CG~kF----------------YDLnk~-P-ivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKF----------------YDLNKD-P-IVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchh----------------ccCCCC-C-ccCCCCCCccCcc
Confidence 45799999965 345653 4 6799999999887
No 50
>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=95.69 E-value=0.0042 Score=41.11 Aligned_cols=12 Identities=25% Similarity=0.454 Sum_probs=6.5
Q ss_pred CceeCCCCCCCC
Q 033949 55 PALFCNNCNLLF 66 (107)
Q Consensus 55 ~~~~C~~CG~~~ 66 (107)
..+.||+||+..
T Consensus 68 v~V~CP~C~K~T 79 (114)
T PF11023_consen 68 VQVECPNCGKQT 79 (114)
T ss_pred eeeECCCCCChH
Confidence 455555555554
No 51
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=95.53 E-value=0.01 Score=32.92 Aligned_cols=12 Identities=17% Similarity=0.595 Sum_probs=8.2
Q ss_pred CceeCCCCCCCC
Q 033949 55 PALFCNNCNLLF 66 (107)
Q Consensus 55 ~~~~C~~CG~~~ 66 (107)
+.+.||+||+.+
T Consensus 18 ~~irC~~CG~rI 29 (44)
T smart00659 18 DVVRCRECGYRI 29 (44)
T ss_pred CceECCCCCceE
Confidence 567777777665
No 52
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=95.45 E-value=0.027 Score=36.55 Aligned_cols=36 Identities=22% Similarity=0.393 Sum_probs=26.0
Q ss_pred CCCcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 18 KSGAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 18 ~~~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
....+.||+||+ ++. +++++....+.|++||..+..
T Consensus 18 lpt~f~CP~Cge~~v~---------------v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 18 LPKIFECPRCGKVSIS---------------VKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred CCcEeECCCCCCeEee---------------eecCCCcceEECCCCCCccCE
Confidence 356778999997 332 334444579999999998865
No 53
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=95.44 E-value=0.0077 Score=42.83 Aligned_cols=25 Identities=40% Similarity=0.940 Sum_probs=21.4
Q ss_pred ccccccCCceecCCCccCcCCCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGSAL 107 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~~l 107 (107)
.+.|..|+...+....+||.||+++
T Consensus 139 ~~rC~GC~~~f~~~~~~Cp~CG~~~ 163 (177)
T COG1439 139 RLRCHGCKRIFPEPKDFCPICGSPL 163 (177)
T ss_pred eEEEecCceecCCCCCcCCCCCCce
Confidence 5679999999888999999999874
No 54
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=95.40 E-value=0.0049 Score=40.88 Aligned_cols=31 Identities=23% Similarity=0.464 Sum_probs=22.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcC
Q 033949 59 CNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPY 102 (107)
Q Consensus 59 C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~ 102 (107)
||.||..+.++. ..|++||+.|...+..+..
T Consensus 1 CPvCg~~l~vt~-------------l~C~~C~t~i~G~F~l~~~ 31 (113)
T PF09862_consen 1 CPVCGGELVVTR-------------LKCPSCGTEIEGEFELPWF 31 (113)
T ss_pred CCCCCCceEEEE-------------EEcCCCCCEEEeeeccchh
Confidence 788888876543 6788888888877766654
No 55
>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=95.37 E-value=0.0099 Score=28.97 Aligned_cols=24 Identities=17% Similarity=0.375 Sum_probs=13.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCccCccccccCCc
Q 033949 59 CNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDR 91 (107)
Q Consensus 59 C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~ 91 (107)
|.+||..+...+.. ..+.|||||.
T Consensus 1 C~sC~~~i~~r~~~---------v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQA---------VPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccC---------ceEeCCCCCC
Confidence 56677766543211 2467888874
No 56
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=95.32 E-value=0.012 Score=31.16 Aligned_cols=34 Identities=26% Similarity=0.576 Sum_probs=22.6
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCC
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLF 66 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~ 66 (107)
.+.||+|+..+++-. =++..++..+.|+.||+.+
T Consensus 2 ~i~Cp~C~~~y~i~d------------~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCPNCQAKYEIDD------------EKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEEeCCH------------HHCCCCCcEEECCCCCCEe
Confidence 468999999543221 1233445689999999875
No 57
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=95.30 E-value=0.01 Score=39.18 Aligned_cols=24 Identities=25% Similarity=0.519 Sum_probs=14.6
Q ss_pred ccccccCCceecCCC---ccCcCCCCC
Q 033949 83 VSKCRFCDRLVEPDF---SFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~---~fCP~CG~~ 106 (107)
..+|++||...+... ..||.||+.
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 70 ECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred EEEcccCCCeeecCCccCCcCcCcCCC
Confidence 456777777665532 337777753
No 58
>PRK05580 primosome assembly protein PriA; Validated
Probab=95.24 E-value=0.02 Score=48.04 Aligned_cols=28 Identities=21% Similarity=0.444 Sum_probs=21.7
Q ss_pred CCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949 52 AKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV 93 (107)
Q Consensus 52 ~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i 93 (107)
+....+.|..||...... ..||+||...
T Consensus 404 ~~~~~l~Ch~Cg~~~~~~--------------~~Cp~Cg~~~ 431 (679)
T PRK05580 404 RFQRRLRCHHCGYQEPIP--------------KACPECGSTD 431 (679)
T ss_pred CCCCeEECCCCcCCCCCC--------------CCCCCCcCCe
Confidence 445789999999987653 3799998863
No 59
>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=95.23 E-value=0.016 Score=30.01 Aligned_cols=25 Identities=16% Similarity=0.511 Sum_probs=15.4
Q ss_pred eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
..|+.||..++.... ...||.||+.
T Consensus 2 ~~C~~CGy~y~~~~~-----------~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEEA-----------PWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCcC-----------CCcCcCCCCc
Confidence 357777777655331 2467777764
No 60
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=95.22 E-value=0.012 Score=38.84 Aligned_cols=23 Identities=30% Similarity=0.632 Sum_probs=12.8
Q ss_pred ccccccCCceecCCCc--cCcCCCC
Q 033949 83 VSKCRFCDRLVEPDFS--FCPYCGS 105 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~--fCP~CG~ 105 (107)
..+|++||.+.+.... .||.||+
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQVVEIHQHDAQCPHCHG 94 (113)
T ss_pred EEEcccCCCEEecCCcCccCcCCCC
Confidence 4556666665554322 2777765
No 61
>PRK14873 primosome assembly protein PriA; Provisional
Probab=95.22 E-value=0.028 Score=47.25 Aligned_cols=40 Identities=20% Similarity=0.434 Sum_probs=28.0
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
...||+|+.... ++++...+.|.+||... . ...||+||..
T Consensus 392 ~~~C~~C~~~L~-----------------~h~~~~~l~Ch~CG~~~-~--------------p~~Cp~Cgs~ 431 (665)
T PRK14873 392 PARCRHCTGPLG-----------------LPSAGGTPRCRWCGRAA-P--------------DWRCPRCGSD 431 (665)
T ss_pred eeECCCCCCcee-----------------EecCCCeeECCCCcCCC-c--------------CccCCCCcCC
Confidence 456777777433 33445789999999864 2 2479999986
No 62
>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=95.11 E-value=0.019 Score=30.11 Aligned_cols=12 Identities=17% Similarity=0.620 Sum_probs=7.3
Q ss_pred eeCCCCCCCCCC
Q 033949 57 LFCNNCNLLFPS 68 (107)
Q Consensus 57 ~~C~~CG~~~~~ 68 (107)
..|+.||..++.
T Consensus 3 ~~C~~CG~i~~g 14 (34)
T cd00729 3 WVCPVCGYIHEG 14 (34)
T ss_pred EECCCCCCEeEC
Confidence 456777766543
No 63
>PRK02935 hypothetical protein; Provisional
Probab=95.02 E-value=0.011 Score=38.71 Aligned_cols=24 Identities=21% Similarity=0.548 Sum_probs=11.5
Q ss_pred cccccCCceecC--CCccCcCCCCCC
Q 033949 84 SKCRFCDRLVEP--DFSFCPYCGSAL 107 (107)
Q Consensus 84 ~~C~~CG~~i~~--~~~fCP~CG~~l 107 (107)
..||+|++++.- ....|.+|+++|
T Consensus 71 V~CP~C~K~TKmLGrvD~CM~C~~PL 96 (110)
T PRK02935 71 VICPSCEKPTKMLGRVDACMHCNQPL 96 (110)
T ss_pred eECCCCCchhhhccceeecCcCCCcC
Confidence 345555554433 344555555543
No 64
>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=95.01 E-value=0.014 Score=30.37 Aligned_cols=22 Identities=41% Similarity=0.712 Sum_probs=12.7
Q ss_pred ccccCCceecC---CCccCcCCCCC
Q 033949 85 KCRFCDRLVEP---DFSFCPYCGSA 106 (107)
Q Consensus 85 ~C~~CG~~i~~---~~~fCP~CG~~ 106 (107)
.|..||++++. +...||+||.+
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-S
T ss_pred CCCcCCCeeEcCCCCcEECCcCCCe
Confidence 46667766654 45567777654
No 65
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=95.01 E-value=0.013 Score=35.44 Aligned_cols=49 Identities=20% Similarity=0.399 Sum_probs=29.4
Q ss_pred CCcEECCCCCC-CcEEEEEee-EE--------------EEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949 19 SGAGRCINCGS-TADLVEYEK-VL--------------KAFFVPVWKWPAKEPALFCNNCNLLFP 67 (107)
Q Consensus 19 ~~~~~C~~Cg~-~~~~~~~~~-~f--------------~lFFIP~~~~~~~~~~~~C~~CG~~~~ 67 (107)
+..+.||+|++ ....+++.. +. -++|||++==.-++-...||+|+..+.
T Consensus 5 p~~~~CP~C~~~~~T~v~~~~g~~t~~~~~~l~~~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg 69 (73)
T PF10601_consen 5 PVRIYCPYCQQQVQTRVEYKSGTMTYICAALLCLFGCWPCCCIPFCCDSCKDVYHYCPNCGAFLG 69 (73)
T ss_pred ceeeECCCCCCEEEEEEEEEeChHHHHHHHHHHHHHHHHHhhHhhccccccCceEECCCCCCEeE
Confidence 45688999999 555555433 21 135666433333435777777777654
No 66
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=95.00 E-value=0.016 Score=33.58 Aligned_cols=14 Identities=14% Similarity=0.574 Sum_probs=6.7
Q ss_pred CceeCCCCCCCCCC
Q 033949 55 PALFCNNCNLLFPS 68 (107)
Q Consensus 55 ~~~~C~~CG~~~~~ 68 (107)
..+.|+.||+.+++
T Consensus 21 eiV~Cp~CGaeleV 34 (54)
T TIGR01206 21 ELVICDECGAELEV 34 (54)
T ss_pred CEEeCCCCCCEEEE
Confidence 34455555554443
No 67
>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=94.95 E-value=0.016 Score=38.30 Aligned_cols=24 Identities=29% Similarity=0.748 Sum_probs=12.8
Q ss_pred ccccccCCceecCC--CccCcCCCCC
Q 033949 83 VSKCRFCDRLVEPD--FSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~~--~~fCP~CG~~ 106 (107)
..+|++||...+.. ..-||.||+.
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 70 ECECEDCSEEVSPEIDLYRCPKCHGI 95 (115)
T ss_pred EEEcccCCCEEecCCcCccCcCCcCC
Confidence 34566666655553 2236666653
No 68
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=94.89 E-value=0.0032 Score=43.89 Aligned_cols=10 Identities=40% Similarity=1.032 Sum_probs=5.6
Q ss_pred CccCcCCCCC
Q 033949 97 FSFCPYCGSA 106 (107)
Q Consensus 97 ~~fCP~CG~~ 106 (107)
.+||-+||++
T Consensus 68 PsYC~~CGkp 77 (158)
T PF10083_consen 68 PSYCHNCGKP 77 (158)
T ss_pred ChhHHhCCCC
Confidence 3556666654
No 69
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=94.83 E-value=0.012 Score=30.25 Aligned_cols=11 Identities=27% Similarity=0.763 Sum_probs=4.0
Q ss_pred eCCCCCCCCCC
Q 033949 58 FCNNCNLLFPS 68 (107)
Q Consensus 58 ~C~~CG~~~~~ 68 (107)
+|+.||.....
T Consensus 5 fC~~CG~~t~~ 15 (32)
T PF09297_consen 5 FCGRCGAPTKP 15 (32)
T ss_dssp B-TTT--BEEE
T ss_pred ccCcCCccccC
Confidence 45555555433
No 70
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=94.69 E-value=0.015 Score=44.44 Aligned_cols=24 Identities=29% Similarity=0.715 Sum_probs=17.2
Q ss_pred cccccCCceecC-----CCccCcCCCCCC
Q 033949 84 SKCRFCDRLVEP-----DFSFCPYCGSAL 107 (107)
Q Consensus 84 ~~C~~CG~~i~~-----~~~fCP~CG~~l 107 (107)
+.|++||--..+ .++|||.||.++
T Consensus 316 nfc~ncG~~~t~~~~ng~a~fcp~cgq~~ 344 (345)
T COG4260 316 NFCLNCGCGTTADFDNGKAKFCPECGQGF 344 (345)
T ss_pred ccccccCcccccCCccchhhhChhhcCCC
Confidence 478888822222 789999999874
No 71
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=94.65 E-value=0.038 Score=30.92 Aligned_cols=15 Identities=20% Similarity=0.527 Sum_probs=9.6
Q ss_pred ceeCCCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPSSL 70 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~ 70 (107)
...|+.||....++.
T Consensus 20 ~~vC~~Cg~~~~~~~ 34 (52)
T smart00661 20 RFVCRKCGYEEPIEQ 34 (52)
T ss_pred EEECCcCCCeEECCC
Confidence 566777777665543
No 72
>PF14353 CpXC: CpXC protein
Probab=94.62 E-value=0.0098 Score=39.57 Aligned_cols=13 Identities=15% Similarity=0.319 Sum_probs=8.3
Q ss_pred ccccccCCceecC
Q 033949 83 VSKCRFCDRLVEP 95 (107)
Q Consensus 83 ~~~C~~CG~~i~~ 95 (107)
...||+||+....
T Consensus 38 ~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 38 SFTCPSCGHKFRL 50 (128)
T ss_pred EEECCCCCCceec
Confidence 5667777776544
No 73
>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=94.62 E-value=0.022 Score=31.10 Aligned_cols=31 Identities=19% Similarity=0.350 Sum_probs=19.3
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCc
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDR 91 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~ 91 (107)
|.-.|+.||+.++.-....+ . ....||.||.
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~-~-----~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSISE-D-----DPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEEcCC-C-----CCCcCCCCCC
Confidence 55678888888765332211 0 2457888887
No 74
>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=94.57 E-value=0.02 Score=33.19 Aligned_cols=32 Identities=19% Similarity=0.419 Sum_probs=22.6
Q ss_pred eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
..||.||+.+++..... .....|+.||++++.
T Consensus 3 ~~CP~CG~~iev~~~~~-------GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 3 FECPDCGAEIELENPEL-------GELVICDECGAELEV 34 (54)
T ss_pred cCCCCCCCEEecCCCcc-------CCEEeCCCCCCEEEE
Confidence 37999999887754311 124689999999864
No 75
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=94.56 E-value=0.049 Score=41.89 Aligned_cols=48 Identities=25% Similarity=0.441 Sum_probs=27.4
Q ss_pred CcEECCCCCC-C-cEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 20 GAGRCINCGS-T-ADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 20 ~~~~C~~Cg~-~-~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
....||-||+ . ..+++. .=....-++.|+-|++...... ..|++||..
T Consensus 186 ~~~~CPvCGs~P~~s~v~~------------~~~~G~RyL~CslC~teW~~~R-------------~~C~~Cg~~ 235 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQI------------GTTQGLRYLHCNLCESEWHVVR-------------VKCSNCEQS 235 (309)
T ss_pred CCCCCCCCCCcchhheeec------------cCCCCceEEEcCCCCCcccccC-------------ccCCCCCCC
Confidence 4568999999 3 222210 0011113788888888775432 467777753
No 76
>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=94.53 E-value=0.036 Score=28.67 Aligned_cols=23 Identities=26% Similarity=0.723 Sum_probs=19.2
Q ss_pred cccccCCceecC--CCccCcCCCCC
Q 033949 84 SKCRFCDRLVEP--DFSFCPYCGSA 106 (107)
Q Consensus 84 ~~C~~CG~~i~~--~~~fCP~CG~~ 106 (107)
..|..||...+. ....||.||.+
T Consensus 2 ~~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCcCCCcCcCCCCc
Confidence 579999999776 47799999974
No 77
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=94.43 E-value=0.02 Score=33.18 Aligned_cols=28 Identities=21% Similarity=0.416 Sum_probs=15.6
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE 94 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~ 94 (107)
...|+.||..+.... +...||.||++--
T Consensus 5 ~~~C~~Cg~~~~~~d-----------DiVvCp~CgapyH 32 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGD-----------DIVVCPECGAPYH 32 (54)
T ss_pred CccChhhCCcccCCC-----------CEEECCCCCCccc
Confidence 345666666664322 2456666666543
No 78
>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=94.42 E-value=0.032 Score=29.19 Aligned_cols=23 Identities=30% Similarity=0.753 Sum_probs=15.5
Q ss_pred cccccCCceecCC--CccCcCCCCC
Q 033949 84 SKCRFCDRLVEPD--FSFCPYCGSA 106 (107)
Q Consensus 84 ~~C~~CG~~i~~~--~~fCP~CG~~ 106 (107)
..|..||...+.+ ...||.||.+
T Consensus 3 ~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 3 WVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred EECCCCCCEeECCcCCCcCcCCCCc
Confidence 5677788775543 4678888764
No 79
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=94.40 E-value=0.027 Score=37.03 Aligned_cols=30 Identities=23% Similarity=0.484 Sum_probs=17.7
Q ss_pred ceeCCCCCCCC-CCCCCCCCCCCCCccCccccccCCceecCC
Q 033949 56 ALFCNNCNLLF-PSSLPPPPPPPPLVSDVSKCRFCDRLVEPD 96 (107)
Q Consensus 56 ~~~C~~CG~~~-~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~ 96 (107)
.-.||+||+.| .+++ .-.+||+||+.....
T Consensus 9 KR~Cp~CG~kFYDLnk-----------~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLNK-----------DPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchhccCCC-----------CCccCCCCCCccCcc
Confidence 34678888766 2222 124578887776554
No 80
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=94.36 E-value=0.026 Score=38.37 Aligned_cols=15 Identities=27% Similarity=0.552 Sum_probs=11.1
Q ss_pred CceeCCCCCCCCCCC
Q 033949 55 PALFCNNCNLLFPSS 69 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~ 69 (107)
....|+.||..+..+
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 567788888777664
No 81
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=94.36 E-value=0.03 Score=38.03 Aligned_cols=28 Identities=29% Similarity=0.772 Sum_probs=21.6
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP 67 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~ 67 (107)
..+||.||.. ||+ +++.++||.||....
T Consensus 28 ~~hCp~Cg~P----------------LF~---KdG~v~CPvC~~~~~ 55 (131)
T COG1645 28 AKHCPKCGTP----------------LFR---KDGEVFCPVCGYREV 55 (131)
T ss_pred HhhCcccCCc----------------cee---eCCeEECCCCCceEE
Confidence 4579999994 466 458999999996543
No 82
>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=94.26 E-value=0.018 Score=31.48 Aligned_cols=30 Identities=20% Similarity=0.554 Sum_probs=17.4
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCC
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNL 64 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~ 64 (107)
...|+.||+..++. .+.+. ...+.||.||.
T Consensus 5 ey~C~~Cg~~fe~~-------------~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVL-------------QSISE-DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEE-------------EEcCC-CCCCcCCCCCC
Confidence 45677777733322 22333 36777777777
No 83
>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=94.16 E-value=0.01 Score=44.71 Aligned_cols=14 Identities=21% Similarity=0.427 Sum_probs=7.8
Q ss_pred CceeCCCCCCCCCC
Q 033949 55 PALFCNNCNLLFPS 68 (107)
Q Consensus 55 ~~~~C~~CG~~~~~ 68 (107)
-++.|+.||+....
T Consensus 196 R~L~Cs~C~t~W~~ 209 (290)
T PF04216_consen 196 RYLHCSLCGTEWRF 209 (290)
T ss_dssp EEEEETTT--EEE-
T ss_pred EEEEcCCCCCeeee
Confidence 37778888877654
No 84
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=94.16 E-value=0.037 Score=37.41 Aligned_cols=31 Identities=19% Similarity=0.262 Sum_probs=23.5
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCC
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSS 69 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~ 69 (107)
..+||+||.++ +-+++ .-+.||+||+.+.+.
T Consensus 9 Kr~Cp~cg~kF----------------YDLnk--~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 9 KRICPNTGSKF----------------YDLNR--RPAVSPYTGEQFPPE 39 (129)
T ss_pred cccCCCcCccc----------------cccCC--CCccCCCcCCccCcc
Confidence 45799999965 23443 578899999999775
No 85
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=94.09 E-value=0.013 Score=34.96 Aligned_cols=48 Identities=23% Similarity=0.346 Sum_probs=26.1
Q ss_pred CcEECCCCCC-CcEEEEEee-EEE---------EEEEeeeec---CCCCCceeCCCCCCCCC
Q 033949 20 GAGRCINCGS-TADLVEYEK-VLK---------AFFVPVWKW---PAKEPALFCNNCNLLFP 67 (107)
Q Consensus 20 ~~~~C~~Cg~-~~~~~~~~~-~f~---------lFFIP~~~~---~~~~~~~~C~~CG~~~~ 67 (107)
..+.||+|++ ..+.+++.. ..+ +++..++|| +-++-...||+||..+.
T Consensus 2 ~~i~Cp~C~~~~~T~v~~~~g~~t~~~~~ll~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg 63 (67)
T smart00714 2 YQLFCPRCQNNVTTRVETETGVCAWLICCLLFLLCFCCCLPCCLDSFKDVNHYCPNCGAFLG 63 (67)
T ss_pred cceECCCCCCEEEEEEEEEeChHHHHHHHHHHHHHHHHHHHHhcccccCccEECCCCCCEeE
Confidence 4578999999 555555443 111 112233443 33334666777776553
No 86
>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=94.07 E-value=0.024 Score=29.89 Aligned_cols=23 Identities=43% Similarity=0.947 Sum_probs=13.3
Q ss_pred ccccccCCceecCCCccCcCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~ 105 (107)
..+|.+||...-+-...||.||+
T Consensus 11 ~~rC~~Cg~~~~pPr~~Cp~C~s 33 (37)
T PF12172_consen 11 GQRCRDCGRVQFPPRPVCPHCGS 33 (37)
T ss_dssp EEE-TTT--EEES--SEETTTT-
T ss_pred EEEcCCCCCEecCCCcCCCCcCc
Confidence 45788888887777788888875
No 87
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=94.04 E-value=0.015 Score=30.60 Aligned_cols=30 Identities=20% Similarity=0.452 Sum_probs=13.1
Q ss_pred eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCc
Q 033949 57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDR 91 (107)
Q Consensus 57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~ 91 (107)
.+||.||..++..-...+ ......|++||.
T Consensus 1 kfC~~CG~~l~~~ip~gd-----~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGD-----DRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT------SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCC-----CccceECCCCCC
Confidence 378999998754221100 013567999886
No 88
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=94.02 E-value=0.035 Score=33.48 Aligned_cols=33 Identities=15% Similarity=0.407 Sum_probs=23.6
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
-.++||.|||.. +=|+.....+.|..||..+..
T Consensus 18 l~VkCpdC~N~q----------------~vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 18 LRVKCPDCGNEQ----------------VVFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred EEEECCCCCCEE----------------EEeccCceEEEecccccEEEe
Confidence 356899999932 225556578999999998743
No 89
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=93.92 E-value=0.13 Score=34.04 Aligned_cols=32 Identities=25% Similarity=0.454 Sum_probs=23.0
Q ss_pred ECCCCCCCcEEEEEeeEEEEEEEeeeecCC-CCCceeCCCCCCCCCCCC
Q 033949 23 RCINCGSTADLVEYEKVLKAFFVPVWKWPA-KEPALFCNNCNLLFPSSL 70 (107)
Q Consensus 23 ~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~-~~~~~~C~~CG~~~~~~~ 70 (107)
-||.||+.+ +|-.. .+..+.|+.||..++++.
T Consensus 4 FCp~Cgsll----------------~p~~~~~~~~l~C~kCgye~~~~~ 36 (113)
T COG1594 4 FCPKCGSLL----------------YPKKDDEGGKLVCRKCGYEEEASN 36 (113)
T ss_pred ccCCccCee----------------EEeEcCCCcEEECCCCCcchhccc
Confidence 599999943 22111 235999999999998875
No 90
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=93.70 E-value=0.065 Score=31.63 Aligned_cols=34 Identities=15% Similarity=0.358 Sum_probs=24.5
Q ss_pred CCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 19 SGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 19 ~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
...++||.|++.. +=|+.....+.|..||..+..
T Consensus 9 F~~VkCp~C~n~q----------------~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 9 FLKVKCPDCGNEQ----------------VVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EEEEECCCCCCeE----------------EEEecCCcEEECcccCCCccc
Confidence 3467899999922 125556579999999998844
No 91
>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=93.58 E-value=0.025 Score=28.96 Aligned_cols=11 Identities=18% Similarity=0.350 Sum_probs=7.1
Q ss_pred ccccccCCcee
Q 033949 83 VSKCRFCDRLV 93 (107)
Q Consensus 83 ~~~C~~CG~~i 93 (107)
...||.||.++
T Consensus 19 ~~vCp~C~~ew 29 (30)
T PF08274_consen 19 LLVCPECGHEW 29 (30)
T ss_dssp SEEETTTTEEE
T ss_pred EEeCCcccccC
Confidence 45677777664
No 92
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=93.58 E-value=0.04 Score=30.84 Aligned_cols=33 Identities=18% Similarity=0.333 Sum_probs=21.9
Q ss_pred eCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCC
Q 033949 58 FCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDF 97 (107)
Q Consensus 58 ~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~ 97 (107)
+||.||..+....... .....|+.||.....++
T Consensus 2 FCp~Cg~~l~~~~~~~-------~~~~vC~~Cg~~~~~~~ 34 (52)
T smart00661 2 FCPKCGNMLIPKEGKE-------KRRFVCRKCGYEEPIEQ 34 (52)
T ss_pred CCCCCCCccccccCCC-------CCEEECCcCCCeEECCC
Confidence 7999999876543211 02567999998765543
No 93
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=93.52 E-value=0.041 Score=36.48 Aligned_cols=23 Identities=26% Similarity=0.779 Sum_probs=11.4
Q ss_pred ccccccCCceecCC-C-c-cCcCCCC
Q 033949 83 VSKCRFCDRLVEPD-F-S-FCPYCGS 105 (107)
Q Consensus 83 ~~~C~~CG~~i~~~-~-~-fCP~CG~ 105 (107)
..+|.+||...+.+ . . .||.||+
T Consensus 71 ~~~C~~Cg~~~~~~~~~~~~CP~Cgs 96 (117)
T PRK00564 71 ELECKDCSHVFKPNALDYGVCEKCHS 96 (117)
T ss_pred EEEhhhCCCccccCCccCCcCcCCCC
Confidence 34566666554442 1 1 2666665
No 94
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=93.46 E-value=0.032 Score=37.94 Aligned_cols=24 Identities=29% Similarity=0.647 Sum_probs=18.6
Q ss_pred CccccccCCceecC--CCccCcCCCC
Q 033949 82 DVSKCRFCDRLVEP--DFSFCPYCGS 105 (107)
Q Consensus 82 ~~~~C~~CG~~i~~--~~~fCP~CG~ 105 (107)
+..+||.||.++-. +-.|||.||.
T Consensus 27 L~~hCp~Cg~PLF~KdG~v~CPvC~~ 52 (131)
T COG1645 27 LAKHCPKCGTPLFRKDGEVFCPVCGY 52 (131)
T ss_pred HHhhCcccCCcceeeCCeEECCCCCc
Confidence 46788888888755 7788888884
No 95
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=93.39 E-value=0.048 Score=31.03 Aligned_cols=23 Identities=52% Similarity=0.917 Sum_probs=10.8
Q ss_pred cccccCCceecC----CCccCcCCCCC
Q 033949 84 SKCRFCDRLVEP----DFSFCPYCGSA 106 (107)
Q Consensus 84 ~~C~~CG~~i~~----~~~fCP~CG~~ 106 (107)
+.|-.||++++. ...-||+||++
T Consensus 7 Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 7 YKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEhhhcCCeeehhhccCceeCCCCCcE
Confidence 445555555442 34445555543
No 96
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=93.37 E-value=0.053 Score=37.05 Aligned_cols=24 Identities=42% Similarity=1.007 Sum_probs=15.5
Q ss_pred ccccccCCceecCCCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
..+|++||+.--+--.+||+||++
T Consensus 29 g~kC~~CG~v~~PPr~~Cp~C~~~ 52 (140)
T COG1545 29 GTKCKKCGRVYFPPRAYCPKCGSE 52 (140)
T ss_pred EEEcCCCCeEEcCCcccCCCCCCC
Confidence 345666666666666666666654
No 97
>PRK00420 hypothetical protein; Validated
Probab=93.29 E-value=0.07 Score=35.36 Aligned_cols=32 Identities=16% Similarity=0.409 Sum_probs=23.4
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL 70 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~ 70 (107)
+.+||.||... |.+ +....+||.||..+....
T Consensus 23 ~~~CP~Cg~pL----------------f~l--k~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 23 SKHCPVCGLPL----------------FEL--KDGEVVCPVHGKVYIVKS 54 (112)
T ss_pred cCCCCCCCCcc----------------eec--CCCceECCCCCCeeeecc
Confidence 35799999843 444 347999999999876643
No 98
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=93.29 E-value=0.14 Score=30.71 Aligned_cols=39 Identities=23% Similarity=0.497 Sum_probs=24.0
Q ss_pred ECCCCCC-CcEEEEEe---eEEEEEEEeeeecCCC-CCceeCCCCCCC
Q 033949 23 RCINCGS-TADLVEYE---KVLKAFFVPVWKWPAK-EPALFCNNCNLL 65 (107)
Q Consensus 23 ~C~~Cg~-~~~~~~~~---~~f~lFFIP~~~~~~~-~~~~~C~~CG~~ 65 (107)
.||.||+ .++.-+.+ .-++- +|.+..+ -..+.|++||..
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~sk----iFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSK----IFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEE----EEEecCcEEEEEECCCCCCE
Confidence 5999999 44433322 23442 4666433 337889999986
No 99
>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=93.12 E-value=0.036 Score=36.48 Aligned_cols=24 Identities=42% Similarity=0.798 Sum_probs=11.3
Q ss_pred ccccccCCceecC--CCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEP--DFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~--~~~fCP~CG~~ 106 (107)
..+|.+||.+.+. ....||.||+.
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEFDFSCPRCGSP 95 (113)
T ss_dssp EEEETTTS-EEECHHCCHH-SSSSSS
T ss_pred cEECCCCCCEEecCCCCCCCcCCcCC
Confidence 3456666666544 22336666653
No 100
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=92.99 E-value=0.032 Score=29.40 Aligned_cols=9 Identities=44% Similarity=1.235 Sum_probs=4.5
Q ss_pred eCCCCCCCC
Q 033949 58 FCNNCNLLF 66 (107)
Q Consensus 58 ~C~~CG~~~ 66 (107)
+||.||..+
T Consensus 3 FCp~C~nlL 11 (35)
T PF02150_consen 3 FCPECGNLL 11 (35)
T ss_dssp BETTTTSBE
T ss_pred eCCCCCccc
Confidence 455555544
No 101
>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=92.93 E-value=0.059 Score=28.62 Aligned_cols=14 Identities=14% Similarity=0.572 Sum_probs=9.6
Q ss_pred CCCceeCCCCCCCC
Q 033949 53 KEPALFCNNCNLLF 66 (107)
Q Consensus 53 ~~~~~~C~~CG~~~ 66 (107)
.++..+|..||+..
T Consensus 22 ~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 22 DDGFYYCDRCGHQS 35 (36)
T ss_pred cCCEEEhhhCceEc
Confidence 45677777777754
No 102
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=92.88 E-value=0.068 Score=30.02 Aligned_cols=31 Identities=16% Similarity=0.343 Sum_probs=20.0
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCc
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDR 91 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~ 91 (107)
|...|+.||..+++.....+ .....||.||+
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~------~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKMSD------DPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEEEecCC------CCCCCCCCCCC
Confidence 56689999998876432111 02346999997
No 103
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=92.88 E-value=0.062 Score=31.72 Aligned_cols=30 Identities=20% Similarity=0.466 Sum_probs=17.3
Q ss_pred ceeCCCCCCCCCC-CCCCCCCCCCCccCccccccCCceec
Q 033949 56 ALFCNNCNLLFPS-SLPPPPPPPPLVSDVSKCRFCDRLVE 94 (107)
Q Consensus 56 ~~~C~~CG~~~~~-~~~~~~~~~~~~~~~~~C~~CG~~i~ 94 (107)
.++||.|+...-+ ++.. ....|..||+.+.
T Consensus 11 ~VkCp~C~n~q~vFsha~---------t~V~C~~Cg~~L~ 41 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHAS---------TVVRCLVCGKTLA 41 (59)
T ss_pred EEECCCCCCeEEEEecCC---------cEEECcccCCCcc
Confidence 5667777776533 1111 2456777777763
No 104
>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=92.78 E-value=0.047 Score=29.00 Aligned_cols=31 Identities=19% Similarity=0.544 Sum_probs=18.5
Q ss_pred eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949 57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE 94 (107)
Q Consensus 57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~ 94 (107)
..|+.||+.|.+...... ....|.+||.++.
T Consensus 2 r~C~~Cg~~Yh~~~~pP~-------~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPK-------VEGVCDNCGGELV 32 (36)
T ss_dssp EEETTTTEEEETTTB--S-------STTBCTTTTEBEB
T ss_pred cCcCCCCCccccccCCCC-------CCCccCCCCCeeE
Confidence 357888888765332111 1357888887764
No 105
>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=92.71 E-value=0.088 Score=34.89 Aligned_cols=31 Identities=23% Similarity=0.367 Sum_probs=23.3
Q ss_pred CcEECCCCCC-C-cEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCC
Q 033949 20 GAGRCINCGS-T-ADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLP 71 (107)
Q Consensus 20 ~~~~C~~Cg~-~-~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~ 71 (107)
.+++||+||. + . . +..-.|.+|++++.++++
T Consensus 68 v~V~CP~C~K~TKm------------------L---Gr~D~CM~C~~pLTLd~~ 100 (114)
T PF11023_consen 68 VQVECPNCGKQTKM------------------L---GRVDACMHCKEPLTLDPS 100 (114)
T ss_pred eeeECCCCCChHhh------------------h---chhhccCcCCCcCccCch
Confidence 5678999999 2 2 1 234589999999988765
No 106
>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=92.65 E-value=0.077 Score=35.04 Aligned_cols=9 Identities=22% Similarity=0.796 Sum_probs=4.8
Q ss_pred cEECCCCCC
Q 033949 21 AGRCINCGS 29 (107)
Q Consensus 21 ~~~C~~Cg~ 29 (107)
...|++||.
T Consensus 70 ~~~C~~Cg~ 78 (115)
T TIGR00100 70 ECECEDCSE 78 (115)
T ss_pred EEEcccCCC
Confidence 445555555
No 107
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=92.61 E-value=0.079 Score=29.94 Aligned_cols=25 Identities=20% Similarity=0.377 Sum_probs=22.3
Q ss_pred CccccccCCceecCCCccCcCCCCC
Q 033949 82 DVSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 82 ~~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
+.++|-.|+|.+++.|+.|-.||++
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~~ 37 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGYK 37 (48)
T ss_pred cccchhcccCCCCccccccccCCCC
Confidence 4678999999999999999999974
No 108
>PHA00626 hypothetical protein
Probab=92.55 E-value=0.11 Score=30.38 Aligned_cols=14 Identities=14% Similarity=0.380 Sum_probs=9.0
Q ss_pred CceeCCCCCCCCCC
Q 033949 55 PALFCNNCNLLFPS 68 (107)
Q Consensus 55 ~~~~C~~CG~~~~~ 68 (107)
+.-.|+.||..+..
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 55667777776644
No 109
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=92.52 E-value=0.083 Score=34.81 Aligned_cols=13 Identities=15% Similarity=0.583 Sum_probs=6.0
Q ss_pred ceeCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPS 68 (107)
Q Consensus 56 ~~~C~~CG~~~~~ 68 (107)
...|+.||..+++
T Consensus 70 ~~~C~~Cg~~~~~ 82 (113)
T PRK12380 70 QAWCWDCSQVVEI 82 (113)
T ss_pred EEEcccCCCEEec
Confidence 4445555544433
No 110
>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=92.49 E-value=0.07 Score=29.19 Aligned_cols=22 Identities=23% Similarity=0.576 Sum_probs=16.3
Q ss_pred ccccccCCceecC---CCccCcCCC
Q 033949 83 VSKCRFCDRLVEP---DFSFCPYCG 104 (107)
Q Consensus 83 ~~~C~~CG~~i~~---~~~fCP~CG 104 (107)
...||.||.++-. +-.+||.|+
T Consensus 17 ~~~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred cCccCCCCCeeEEecCCCEECCCCC
Confidence 4578888887754 667888885
No 111
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=92.32 E-value=0.13 Score=26.82 Aligned_cols=13 Identities=23% Similarity=0.447 Sum_probs=9.1
Q ss_pred CCceeCCCCCCCC
Q 033949 54 EPALFCNNCNLLF 66 (107)
Q Consensus 54 ~~~~~C~~CG~~~ 66 (107)
..+..|+.||..+
T Consensus 19 ~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 19 DDYEVCIFCGSSF 31 (33)
T ss_pred CCeEEcccCCcEe
Confidence 3677777777765
No 112
>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=92.31 E-value=0.028 Score=42.35 Aligned_cols=40 Identities=15% Similarity=0.184 Sum_probs=17.5
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE 94 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~ 94 (107)
..+.||+||..-..+.......++-......|.+||.-+.
T Consensus 210 ~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 210 VRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp -TTS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred cCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 4668999999865433211111111124578999998764
No 113
>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=92.24 E-value=0.071 Score=31.13 Aligned_cols=13 Identities=23% Similarity=0.603 Sum_probs=7.9
Q ss_pred eCCCCCCCCCCCC
Q 033949 58 FCNNCNLLFPSSL 70 (107)
Q Consensus 58 ~C~~CG~~~~~~~ 70 (107)
-|..|+..++.+.
T Consensus 7 nCE~C~~dLp~~s 19 (57)
T PF06906_consen 7 NCECCDKDLPPDS 19 (57)
T ss_pred CccccCCCCCCCC
Confidence 3666777666544
No 114
>PF15616 TerY-C: TerY-C metal binding domain
Probab=92.13 E-value=0.11 Score=35.33 Aligned_cols=12 Identities=33% Similarity=0.963 Sum_probs=9.4
Q ss_pred CCCccCcCCCCC
Q 033949 95 PDFSFCPYCGSA 106 (107)
Q Consensus 95 ~~~~fCP~CG~~ 106 (107)
++-..||-||+.
T Consensus 103 ~~~~~CPwCg~~ 114 (131)
T PF15616_consen 103 EGEVTCPWCGNE 114 (131)
T ss_pred CCCEECCCCCCe
Confidence 366889999975
No 115
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=92.05 E-value=0.06 Score=36.87 Aligned_cols=40 Identities=15% Similarity=0.262 Sum_probs=23.9
Q ss_pred CCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 53 KEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 53 ~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
......||+||..+...... .+.+ ......||+||+++..
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~-~~~d--~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEAN-QLLD--MDGTFTCPRCGEELEE 135 (147)
T ss_pred CCcEEECcCCCCEeeHHHHH-HhcC--CCCcEECCCCCCEEEE
Confidence 33577899999888642211 0000 0123789999999865
No 116
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=91.96 E-value=0.15 Score=33.50 Aligned_cols=7 Identities=43% Similarity=1.364 Sum_probs=3.1
Q ss_pred cCcCCCC
Q 033949 99 FCPYCGS 105 (107)
Q Consensus 99 fCP~CG~ 105 (107)
+||.||.
T Consensus 62 ~CP~C~~ 68 (111)
T PF14319_consen 62 HCPSCQA 68 (111)
T ss_pred CCCCCCC
Confidence 4444443
No 117
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=91.92 E-value=0.058 Score=36.92 Aligned_cols=12 Identities=17% Similarity=0.520 Sum_probs=7.2
Q ss_pred eeCCCCCCCCCC
Q 033949 57 LFCNNCNLLFPS 68 (107)
Q Consensus 57 ~~C~~CG~~~~~ 68 (107)
..||.||..+..
T Consensus 124 f~Cp~Cg~~l~~ 135 (147)
T smart00531 124 FTCPRCGEELEE 135 (147)
T ss_pred EECCCCCCEEEE
Confidence 566666666544
No 118
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=91.81 E-value=0.12 Score=29.43 Aligned_cols=7 Identities=43% Similarity=1.317 Sum_probs=3.4
Q ss_pred eCCCCCC
Q 033949 58 FCNNCNL 64 (107)
Q Consensus 58 ~C~~CG~ 64 (107)
+||.||+
T Consensus 22 fCP~Cg~ 28 (50)
T PRK00432 22 FCPRCGS 28 (50)
T ss_pred cCcCCCc
Confidence 4444444
No 119
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=91.70 E-value=0.11 Score=30.10 Aligned_cols=30 Identities=17% Similarity=0.533 Sum_probs=21.3
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
....|+-||..+ ..+++.+.||.||+++..
T Consensus 4 ~~~~C~~Cg~~~-------------------~~~dDiVvCp~CgapyHR 33 (54)
T PF14446_consen 4 EGCKCPVCGKKF-------------------KDGDDIVVCPECGAPYHR 33 (54)
T ss_pred cCccChhhCCcc-------------------cCCCCEEECCCCCCcccH
Confidence 345788888853 224578889999988854
No 120
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=91.52 E-value=0.11 Score=30.77 Aligned_cols=9 Identities=22% Similarity=0.888 Sum_probs=5.5
Q ss_pred eCCCCCCCC
Q 033949 58 FCNNCNLLF 66 (107)
Q Consensus 58 ~C~~CG~~~ 66 (107)
.|.+|+...
T Consensus 5 AC~~C~~i~ 13 (61)
T PRK08351 5 ACRHCHYIT 13 (61)
T ss_pred hhhhCCccc
Confidence 566666665
No 121
>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=91.51 E-value=0.11 Score=42.79 Aligned_cols=13 Identities=23% Similarity=0.455 Sum_probs=7.6
Q ss_pred ccccccCCceecC
Q 033949 83 VSKCRFCDRLVEP 95 (107)
Q Consensus 83 ~~~C~~CG~~i~~ 95 (107)
.+.||.||..|+.
T Consensus 229 ~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 229 RYVCPHCGCEIEE 241 (557)
T ss_pred EEECCCCcCCCCH
Confidence 4556666666553
No 122
>PLN03086 PRLI-interacting factor K; Provisional
Probab=91.39 E-value=0.13 Score=42.59 Aligned_cols=11 Identities=27% Similarity=0.604 Sum_probs=8.4
Q ss_pred CCcEECCCCCC
Q 033949 19 SGAGRCINCGS 29 (107)
Q Consensus 19 ~~~~~C~~Cg~ 29 (107)
...+.|+||+.
T Consensus 405 ~~~V~C~NC~~ 415 (567)
T PLN03086 405 VDTVECRNCKH 415 (567)
T ss_pred CCeEECCCCCC
Confidence 35667999988
No 123
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=91.32 E-value=0.11 Score=33.64 Aligned_cols=10 Identities=20% Similarity=0.580 Sum_probs=6.5
Q ss_pred CceeCCCCCC
Q 033949 55 PALFCNNCNL 64 (107)
Q Consensus 55 ~~~~C~~CG~ 64 (107)
....||+||+
T Consensus 20 t~f~CP~Cge 29 (99)
T PRK14892 20 KIFECPRCGK 29 (99)
T ss_pred cEeECCCCCC
Confidence 3566777774
No 124
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=91.28 E-value=0.13 Score=34.88 Aligned_cols=12 Identities=33% Similarity=0.753 Sum_probs=9.0
Q ss_pred CcEECCCCCCCc
Q 033949 20 GAGRCINCGSTA 31 (107)
Q Consensus 20 ~~~~C~~Cg~~~ 31 (107)
....|++||..+
T Consensus 69 ~~~~C~~CG~~~ 80 (135)
T PRK03824 69 AVLKCRNCGNEW 80 (135)
T ss_pred eEEECCCCCCEE
Confidence 566799999844
No 125
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=91.19 E-value=0.16 Score=32.54 Aligned_cols=11 Identities=36% Similarity=1.038 Sum_probs=8.5
Q ss_pred eCCCCCCCCCC
Q 033949 58 FCNNCNLLFPS 68 (107)
Q Consensus 58 ~C~~CG~~~~~ 68 (107)
+||.||..+..
T Consensus 2 fC~~Cg~~l~~ 12 (104)
T TIGR01384 2 FCPKCGSLMTP 12 (104)
T ss_pred CCcccCccccc
Confidence 68888888755
No 126
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=91.17 E-value=0.12 Score=30.95 Aligned_cols=23 Identities=22% Similarity=0.472 Sum_probs=15.0
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
..+.|..|+...+. ..||+||..
T Consensus 4 ~~~AC~~C~~i~~~---------------~~Cp~Cgs~ 26 (64)
T PRK06393 4 QYRACKKCKRLTPE---------------KTCPVHGDE 26 (64)
T ss_pred hhhhHhhCCcccCC---------------CcCCCCCCC
Confidence 56677777777531 357777776
No 127
>PHA02942 putative transposase; Provisional
Probab=91.15 E-value=0.23 Score=39.09 Aligned_cols=42 Identities=14% Similarity=0.169 Sum_probs=27.7
Q ss_pred EeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCC
Q 033949 45 VPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPD 96 (107)
Q Consensus 45 IP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~ 96 (107)
|+++..++......||.||+...... .....|++||...+.|
T Consensus 314 ~~Vv~V~p~yTSq~Cs~CG~~~~~l~----------~r~f~C~~CG~~~drD 355 (383)
T PHA02942 314 MIVEFVNPSYSSVSCPKCGHKMVEIA----------HRYFHCPSCGYENDRD 355 (383)
T ss_pred CEEEEECCCCCCccCCCCCCccCcCC----------CCEEECCCCCCEeCcH
Confidence 55666666644678999998653110 0246899999988764
No 128
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=91.15 E-value=0.086 Score=28.44 Aligned_cols=28 Identities=14% Similarity=0.400 Sum_probs=16.1
Q ss_pred eCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 58 FCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 58 ~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
.||.|+..+...... ++ ....|++||-.
T Consensus 1 ~CP~C~~~l~~~~~~-~~------~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVRLG-DV------EIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEEEC-CE------EEEECCCCCeE
Confidence 488888876542211 11 24568888753
No 129
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=91.12 E-value=0.13 Score=30.08 Aligned_cols=21 Identities=29% Similarity=0.774 Sum_probs=10.8
Q ss_pred cccccCCceecCCCccCcCCCC
Q 033949 84 SKCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 84 ~~C~~CG~~i~~~~~fCP~CG~ 105 (107)
..|++||+. ...-..||+||.
T Consensus 28 ~~C~~CG~~-~~~H~vC~~CG~ 48 (57)
T PRK12286 28 VECPNCGEP-KLPHRVCPSCGY 48 (57)
T ss_pred eECCCCCCc-cCCeEECCCCCc
Confidence 345556555 233455555554
No 130
>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=91.11 E-value=0.28 Score=27.06 Aligned_cols=10 Identities=40% Similarity=0.793 Sum_probs=6.1
Q ss_pred CcEECCCCCC
Q 033949 20 GAGRCINCGS 29 (107)
Q Consensus 20 ~~~~C~~Cg~ 29 (107)
+.+.||+||+
T Consensus 17 ~g~~CP~Cg~ 26 (46)
T PF12760_consen 17 DGFVCPHCGS 26 (46)
T ss_pred CCCCCCCCCC
Confidence 3355777776
No 131
>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=90.85 E-value=0.24 Score=38.08 Aligned_cols=24 Identities=25% Similarity=0.539 Sum_probs=16.6
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
++.|+-|++...... ..|++||..
T Consensus 210 yL~CslC~teW~~~R-------------~~C~~Cg~~ 233 (305)
T TIGR01562 210 YLSCSLCATEWHYVR-------------VKCSHCEES 233 (305)
T ss_pred EEEcCCCCCcccccC-------------ccCCCCCCC
Confidence 788888888775532 467777754
No 132
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=90.83 E-value=0.13 Score=31.54 Aligned_cols=12 Identities=25% Similarity=0.423 Sum_probs=4.3
Q ss_pred CceeCCCCCCCC
Q 033949 55 PALFCNNCNLLF 66 (107)
Q Consensus 55 ~~~~C~~CG~~~ 66 (107)
+.+.|..|-...
T Consensus 8 ~vlrC~aCf~~t 19 (73)
T PF08772_consen 8 WVLRCHACFKIT 19 (73)
T ss_dssp EEEE-SSS--EE
T ss_pred eeEEccccccCc
Confidence 445555554443
No 133
>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=90.54 E-value=0.05 Score=35.78 Aligned_cols=27 Identities=19% Similarity=0.349 Sum_probs=13.3
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
....|..||+.++++.. ...||+||..
T Consensus 69 ~~~~C~~Cg~~~~~~~~-----------~~~CP~Cgs~ 95 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEF-----------DFSCPRCGSP 95 (113)
T ss_dssp -EEEETTTS-EEECHHC-----------CHH-SSSSSS
T ss_pred CcEECCCCCCEEecCCC-----------CCCCcCCcCC
Confidence 45566666666655331 2456666664
No 134
>PRK02935 hypothetical protein; Provisional
Probab=90.40 E-value=0.31 Score=31.97 Aligned_cols=31 Identities=16% Similarity=0.232 Sum_probs=22.9
Q ss_pred CcEECCCCCC--CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCC
Q 033949 20 GAGRCINCGS--TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLP 71 (107)
Q Consensus 20 ~~~~C~~Cg~--~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~ 71 (107)
.++.||+|+. .. -+..-.|.+|+.++..+++
T Consensus 69 vqV~CP~C~K~TKm---------------------LGrvD~CM~C~~PLTLd~~ 101 (110)
T PRK02935 69 VQVICPSCEKPTKM---------------------LGRVDACMHCNQPLTLDRS 101 (110)
T ss_pred eeeECCCCCchhhh---------------------ccceeecCcCCCcCCcCcc
Confidence 4678999999 32 2345689999999877664
No 135
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=90.35 E-value=0.23 Score=33.62 Aligned_cols=29 Identities=14% Similarity=0.216 Sum_probs=16.9
Q ss_pred ceeCCCCCCCC-CCCCCCCCCCCCCccCccccccCCceecC
Q 033949 56 ALFCNNCNLLF-PSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 56 ~~~C~~CG~~~-~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
.-.||+||+.| .+.+ .-..||+||+....
T Consensus 9 Kr~Cp~cg~kFYDLnk-----------~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 9 KRICPNTGSKFYDLNR-----------RPAVSPYTGEQFPP 38 (129)
T ss_pred cccCCCcCccccccCC-----------CCccCCCcCCccCc
Confidence 34677777765 2222 23467777777554
No 136
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=90.35 E-value=0.13 Score=39.09 Aligned_cols=24 Identities=25% Similarity=0.772 Sum_probs=15.0
Q ss_pred ccccccCCceecC-----CCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEP-----DFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~-----~~~fCP~CG~~ 106 (107)
..+||+||+.+-. +...||+||..
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h 54 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHH 54 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCc
Confidence 4567777765533 56677777754
No 137
>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=90.32 E-value=0.21 Score=28.83 Aligned_cols=33 Identities=21% Similarity=0.393 Sum_probs=19.9
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
+.+.|++|......... .+....+++|++||+.
T Consensus 21 ~aLIC~~C~~hNGla~~-----~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 21 YALICSKCFSHNGLAPK-----EEFEEIQYRCPYCGAL 53 (54)
T ss_pred eeEECcccchhhccccc-----ccCCceEEEcCCCCCc
Confidence 67778888776655321 0111236788888874
No 138
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=90.30 E-value=0.13 Score=39.33 Aligned_cols=24 Identities=25% Similarity=0.578 Sum_probs=16.8
Q ss_pred ccccccCCceecC-----CCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEP-----DFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~-----~~~fCP~CG~~ 106 (107)
..+||+|++.+.. +...||+||..
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h 66 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYH 66 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCC
Confidence 5677777776643 67778888764
No 139
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=90.30 E-value=0.12 Score=30.90 Aligned_cols=24 Identities=29% Similarity=0.688 Sum_probs=14.5
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
++.|.+|+...+.+. ..||.||.+
T Consensus 4 ~kAC~~Ck~l~~~d~-------------e~CP~Cgs~ 27 (64)
T COG2093 4 EKACKNCKRLTPEDT-------------EICPVCGST 27 (64)
T ss_pred hHHHhhccccCCCCC-------------ccCCCCCCc
Confidence 456667766664422 457777766
No 140
>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=90.30 E-value=0.23 Score=28.39 Aligned_cols=16 Identities=38% Similarity=0.966 Sum_probs=9.2
Q ss_pred cccccCCceecCCCccCcCCCC
Q 033949 84 SKCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 84 ~~C~~CG~~i~~~~~fCP~CG~ 105 (107)
..|+.||.+ ||-.|+.
T Consensus 41 ~~C~~C~~~------fC~~C~~ 56 (64)
T PF01485_consen 41 VTCPSCGTE------FCFKCGE 56 (64)
T ss_dssp CCTTSCCSE------ECSSSTS
T ss_pred eECCCCCCc------CccccCc
Confidence 456666655 5655554
No 141
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=90.17 E-value=0.23 Score=32.86 Aligned_cols=13 Identities=31% Similarity=0.864 Sum_probs=5.8
Q ss_pred ceeCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPS 68 (107)
Q Consensus 56 ~~~C~~CG~~~~~ 68 (107)
...|..||..+++
T Consensus 71 ~~~C~~Cg~~~~~ 83 (117)
T PRK00564 71 ELECKDCSHVFKP 83 (117)
T ss_pred EEEhhhCCCcccc
Confidence 4445555544433
No 142
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=90.14 E-value=0.18 Score=35.77 Aligned_cols=11 Identities=45% Similarity=1.252 Sum_probs=5.6
Q ss_pred ceeCCCCCCCC
Q 033949 56 ALFCNNCNLLF 66 (107)
Q Consensus 56 ~~~C~~CG~~~ 66 (107)
+-.||.||..+
T Consensus 117 ~Y~Cp~C~~ry 127 (178)
T PRK06266 117 FFFCPNCHIRF 127 (178)
T ss_pred EEECCCCCcEE
Confidence 44455555544
No 143
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=90.12 E-value=0.2 Score=33.00 Aligned_cols=12 Identities=17% Similarity=0.717 Sum_probs=5.4
Q ss_pred ceeCCCCCCCCC
Q 033949 56 ALFCNNCNLLFP 67 (107)
Q Consensus 56 ~~~C~~CG~~~~ 67 (107)
...|+.||..++
T Consensus 70 ~~~C~~Cg~~~~ 81 (114)
T PRK03681 70 ECWCETCQQYVT 81 (114)
T ss_pred EEEcccCCCeee
Confidence 444444444443
No 144
>PRK12495 hypothetical protein; Provisional
Probab=90.11 E-value=0.16 Score=37.32 Aligned_cols=25 Identities=24% Similarity=0.627 Sum_probs=18.9
Q ss_pred CccccccCCceecC--CCccCcCCCCC
Q 033949 82 DVSKCRFCDRLVEP--DFSFCPYCGSA 106 (107)
Q Consensus 82 ~~~~C~~CG~~i~~--~~~fCP~CG~~ 106 (107)
...+|+.||.+|.. +-.+||.|+..
T Consensus 41 sa~hC~~CG~PIpa~pG~~~Cp~CQ~~ 67 (226)
T PRK12495 41 TNAHCDECGDPIFRHDGQEFCPTCQQP 67 (226)
T ss_pred chhhcccccCcccCCCCeeECCCCCCc
Confidence 45678888888876 77788888753
No 145
>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=89.89 E-value=0.69 Score=24.77 Aligned_cols=6 Identities=50% Similarity=1.365 Sum_probs=3.3
Q ss_pred CCCCCC
Q 033949 24 CINCGS 29 (107)
Q Consensus 24 C~~Cg~ 29 (107)
||.||.
T Consensus 1 C~~C~~ 6 (46)
T TIGR03831 1 CPICGG 6 (46)
T ss_pred CCCCCC
Confidence 556654
No 146
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=89.67 E-value=0.29 Score=28.21 Aligned_cols=10 Identities=20% Similarity=0.584 Sum_probs=8.2
Q ss_pred CceeCCCCCC
Q 033949 55 PALFCNNCNL 64 (107)
Q Consensus 55 ~~~~C~~CG~ 64 (107)
+++.|..||.
T Consensus 28 ~~V~C~~Cga 37 (61)
T PF14354_consen 28 YYVECTDCGA 37 (61)
T ss_pred EEEEcCCCCC
Confidence 5688999988
No 147
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=89.58 E-value=0.24 Score=28.80 Aligned_cols=30 Identities=13% Similarity=0.453 Sum_probs=17.8
Q ss_pred cEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949 21 AGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP 67 (107)
Q Consensus 21 ~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~ 67 (107)
.++||.|++ .. =|+.....+.|..||..+.
T Consensus 7 ~VkCp~C~~~q~-----------------vFSha~t~V~C~~Cg~~L~ 37 (55)
T PF01667_consen 7 DVKCPGCYNIQT-----------------VFSHAQTVVKCVVCGTVLA 37 (55)
T ss_dssp EEE-TTT-SEEE-----------------EETT-SS-EE-SSSTSEEE
T ss_pred EEECCCCCCeeE-----------------EEecCCeEEEcccCCCEec
Confidence 567999999 32 1666656888999998763
No 148
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=89.55 E-value=0.23 Score=28.74 Aligned_cols=20 Identities=35% Similarity=0.878 Sum_probs=9.6
Q ss_pred cccccCCceecCCCccCcCCC
Q 033949 84 SKCRFCDRLVEPDFSFCPYCG 104 (107)
Q Consensus 84 ~~C~~CG~~i~~~~~fCP~CG 104 (107)
..|++||+. ...-..||.||
T Consensus 27 ~~c~~cg~~-~~~H~vc~~cG 46 (56)
T PF01783_consen 27 VKCPNCGEP-KLPHRVCPSCG 46 (56)
T ss_dssp EESSSSSSE-ESTTSBCTTTB
T ss_pred eeeccCCCE-ecccEeeCCCC
Confidence 345555533 33344555554
No 149
>PRK05978 hypothetical protein; Provisional
Probab=89.47 E-value=0.27 Score=34.04 Aligned_cols=33 Identities=27% Similarity=0.647 Sum_probs=21.2
Q ss_pred cEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949 21 AGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL 70 (107)
Q Consensus 21 ~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~ 70 (107)
..+||+||+ +. |+ +--+-.-.|++||..++...
T Consensus 33 ~grCP~CG~G~L----------------F~-g~Lkv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 33 RGRCPACGEGKL----------------FR-AFLKPVDHCAACGEDFTHHR 66 (148)
T ss_pred cCcCCCCCCCcc----------------cc-cccccCCCccccCCccccCC
Confidence 457999999 54 11 00113556999999987754
No 150
>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=89.39 E-value=0.11 Score=44.81 Aligned_cols=39 Identities=31% Similarity=0.742 Sum_probs=0.0
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
....||.||+.- .....||.||..... ..||+||.+...
T Consensus 666 ~~~~Cp~CG~~T----------------------~~~~~Cp~C~~~~~~---------------~~C~~C~~~~~~ 704 (900)
T PF03833_consen 666 FYNRCPECGSHT----------------------EPVYVCPDCGIEVEE---------------DECPKCGRETTS 704 (900)
T ss_dssp ----------------------------------------------------------------------------
T ss_pred hhhcCcccCCcc----------------------ccceeccccccccCc---------------cccccccccCcc
Confidence 345799999942 367889999998753 369999998655
No 151
>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=89.33 E-value=0.18 Score=35.04 Aligned_cols=33 Identities=15% Similarity=0.282 Sum_probs=16.2
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
.+-.||.|+..+.-... .+....||.||+++..
T Consensus 108 ~~Y~Cp~c~~r~tf~eA--------~~~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEA--------MELNFTCPRCGAMLDY 140 (158)
T ss_pred CeEECCCCCcEeeHHHH--------HHcCCcCCCCCCEeee
Confidence 45556666665532110 0123456666666544
No 152
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=89.12 E-value=0.42 Score=31.05 Aligned_cols=34 Identities=24% Similarity=0.490 Sum_probs=23.1
Q ss_pred ECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCC
Q 033949 23 RCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLP 71 (107)
Q Consensus 23 ~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~ 71 (107)
.||.|||.+.+.. +..-....|+-|+..++|+.+
T Consensus 3 FCP~Cgn~Live~---------------g~~~~rf~C~tCpY~~~I~~e 36 (105)
T KOG2906|consen 3 FCPTCGNMLIVES---------------GESCNRFSCRTCPYVFPISRE 36 (105)
T ss_pred ccCCCCCEEEEec---------------CCeEeeEEcCCCCceeeEeee
Confidence 5999999442111 112257889999999988754
No 153
>PF14369 zf-RING_3: zinc-finger
Probab=88.89 E-value=0.36 Score=25.37 Aligned_cols=22 Identities=32% Similarity=0.700 Sum_probs=14.4
Q ss_pred cccccCCceecC-----CCccCcCCCC
Q 033949 84 SKCRFCDRLVEP-----DFSFCPYCGS 105 (107)
Q Consensus 84 ~~C~~CG~~i~~-----~~~fCP~CG~ 105 (107)
+.|.+|...+.. +...||+|+.
T Consensus 3 ywCh~C~~~V~~~~~~~~~~~CP~C~~ 29 (35)
T PF14369_consen 3 YWCHQCNRFVRIAPSPDSDVACPRCHG 29 (35)
T ss_pred EeCccCCCEeEeCcCCCCCcCCcCCCC
Confidence 567888866653 3334888875
No 154
>PRK12496 hypothetical protein; Provisional
Probab=88.86 E-value=0.36 Score=33.80 Aligned_cols=12 Identities=25% Similarity=0.880 Sum_probs=6.6
Q ss_pred eeCCCCCCCCCC
Q 033949 57 LFCNNCNLLFPS 68 (107)
Q Consensus 57 ~~C~~CG~~~~~ 68 (107)
..|+-||..++.
T Consensus 128 ~~C~gC~~~~~~ 139 (164)
T PRK12496 128 KVCKGCKKKYPE 139 (164)
T ss_pred EECCCCCccccC
Confidence 346666666543
No 155
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=88.63 E-value=0.25 Score=32.85 Aligned_cols=23 Identities=39% Similarity=0.554 Sum_probs=12.6
Q ss_pred ccccccCCceecC--CCccCcCCCC
Q 033949 83 VSKCRFCDRLVEP--DFSFCPYCGS 105 (107)
Q Consensus 83 ~~~C~~CG~~i~~--~~~fCP~CG~ 105 (107)
.-.|.+|+.++.. ..-.||.||+
T Consensus 70 ~~~C~~C~~~~~~e~~~~~CP~C~s 94 (115)
T COG0375 70 ECWCLDCGQEVELEELDYRCPKCGS 94 (115)
T ss_pred EEEeccCCCeecchhheeECCCCCC
Confidence 3456666666555 2223666665
No 156
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=88.55 E-value=0.23 Score=28.72 Aligned_cols=19 Identities=32% Similarity=0.931 Sum_probs=8.1
Q ss_pred ccccCCceecCCCccCcCCC
Q 033949 85 KCRFCDRLVEPDFSFCPYCG 104 (107)
Q Consensus 85 ~C~~CG~~i~~~~~fCP~CG 104 (107)
.|++||+. ...-..||.||
T Consensus 28 ~C~~cG~~-~~~H~vc~~cG 46 (55)
T TIGR01031 28 VCPNCGEF-KLPHRVCPSCG 46 (55)
T ss_pred ECCCCCCc-ccCeeECCccC
Confidence 34444443 22334444444
No 157
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=88.54 E-value=0.12 Score=35.15 Aligned_cols=10 Identities=30% Similarity=0.574 Sum_probs=6.5
Q ss_pred cccccCCcee
Q 033949 84 SKCRFCDRLV 93 (107)
Q Consensus 84 ~~C~~CG~~i 93 (107)
..|+|||+..
T Consensus 69 sfchncgs~f 78 (160)
T COG4306 69 SFCHNCGSRF 78 (160)
T ss_pred chhhcCCCCC
Confidence 4577777654
No 158
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=88.54 E-value=0.24 Score=33.08 Aligned_cols=11 Identities=18% Similarity=0.407 Sum_probs=5.2
Q ss_pred ceeCCCCCCCCC
Q 033949 56 ALFCNNCNLLFP 67 (107)
Q Consensus 56 ~~~C~~CG~~~~ 67 (107)
...| .||..++
T Consensus 70 ~~~C-~Cg~~~~ 80 (124)
T PRK00762 70 EIEC-ECGYEGV 80 (124)
T ss_pred eEEe-eCcCccc
Confidence 4445 5554443
No 159
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=88.51 E-value=0.21 Score=38.13 Aligned_cols=24 Identities=29% Similarity=0.865 Sum_probs=15.1
Q ss_pred ccccccCCceecC-----CCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEP-----DFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~-----~~~fCP~CG~~ 106 (107)
..+||+|+..+-. +...||+||..
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h 55 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHH 55 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCC
Confidence 4567777766533 56677777764
No 160
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=88.48 E-value=0.27 Score=35.36 Aligned_cols=13 Identities=15% Similarity=0.378 Sum_probs=7.2
Q ss_pred ceeCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPS 68 (107)
Q Consensus 56 ~~~C~~CG~~~~~ 68 (107)
+..|+.|++.+..
T Consensus 149 ~A~CsrC~~~L~~ 161 (188)
T COG1096 149 YARCSRCRAPLVK 161 (188)
T ss_pred EEEccCCCcceEE
Confidence 3446666666544
No 161
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=88.43 E-value=0.38 Score=42.24 Aligned_cols=51 Identities=20% Similarity=0.419 Sum_probs=32.0
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC---CCccCcCCCCCC
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP---DFSFCPYCGSAL 107 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~---~~~fCP~CG~~l 107 (107)
+...||.|+..++-+++-. .-.-.+++.+|..||+.-+- ...-||+||.+|
T Consensus 795 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 848 (1006)
T PRK12775 795 GVATCPKCHRPLEGDEEYV--CCATSELQWRCDDCGKVSEGFAFPYGMCPACGGKL 848 (1006)
T ss_pred CCccCcccCCCCCCCceeE--EecCcceeeehhhhccccccccCCcCcCcccccch
Confidence 4667888877776554310 00011246889999987655 346799999764
No 162
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=88.33 E-value=0.4 Score=31.20 Aligned_cols=40 Identities=23% Similarity=0.431 Sum_probs=25.5
Q ss_pred CCcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949 19 SGAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL 70 (107)
Q Consensus 19 ~~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~ 70 (107)
...++||+||. .+..- ..+-....+.+.|.+||..++-..
T Consensus 20 ~k~FtCp~Cghe~vs~c------------tvkk~~~~g~~~Cg~CGls~e~ev 60 (104)
T COG4888 20 PKTFTCPRCGHEKVSSC------------TVKKTVNIGTAVCGNCGLSFECEV 60 (104)
T ss_pred CceEecCccCCeeeeEE------------EEEecCceeEEEcccCcceEEEec
Confidence 35788999999 43200 012222346899999999886543
No 163
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=88.17 E-value=0.71 Score=26.78 Aligned_cols=14 Identities=21% Similarity=0.444 Sum_probs=7.8
Q ss_pred CceeCCCCCCCCCC
Q 033949 55 PALFCNNCNLLFPS 68 (107)
Q Consensus 55 ~~~~C~~CG~~~~~ 68 (107)
.-++||.|....-+
T Consensus 27 fPlyCpKCK~EtlI 40 (55)
T PF14205_consen 27 FPLYCPKCKQETLI 40 (55)
T ss_pred ccccCCCCCceEEE
Confidence 45566666655433
No 164
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=88.11 E-value=0.25 Score=32.66 Aligned_cols=33 Identities=24% Similarity=0.401 Sum_probs=21.5
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
..+||.||+.+...+.... ....|++||.+.+.
T Consensus 2 m~FCp~Cgsll~p~~~~~~-------~~l~C~kCgye~~~ 34 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEG-------GKLVCRKCGYEEEA 34 (113)
T ss_pred ccccCCccCeeEEeEcCCC-------cEEECCCCCcchhc
Confidence 4689999999866432110 24678888876544
No 165
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=87.99 E-value=0.24 Score=30.87 Aligned_cols=35 Identities=23% Similarity=0.380 Sum_probs=16.7
Q ss_pred CCcEECCCCCC--CcEEEEEeeEEEEEEEeeeecCCC--CCceeCCCCCCCCCC
Q 033949 19 SGAGRCINCGS--TADLVEYEKVLKAFFVPVWKWPAK--EPALFCNNCNLLFPS 68 (107)
Q Consensus 19 ~~~~~C~~Cg~--~~~~~~~~~~f~lFFIP~~~~~~~--~~~~~C~~CG~~~~~ 68 (107)
...+.||.||+ ++.+ .++++ ...+.|..||..++.
T Consensus 20 ~~~F~CPfC~~~~sV~v---------------~idkk~~~~~~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSV---------------KIDKKEGIGILSCRVCGESFQT 58 (81)
T ss_dssp SS----TTT--SS-EEE---------------EEETTTTEEEEEESSS--EEEE
T ss_pred CceEcCCcCCCCCeEEE---------------EEEccCCEEEEEecCCCCeEEE
Confidence 46788999996 4432 23333 348999999998754
No 166
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=87.78 E-value=0.56 Score=26.74 Aligned_cols=11 Identities=18% Similarity=0.646 Sum_probs=5.0
Q ss_pred CceeCCCCCCC
Q 033949 55 PALFCNNCNLL 65 (107)
Q Consensus 55 ~~~~C~~CG~~ 65 (107)
..+.|+.||..
T Consensus 39 ~~v~C~~C~~~ 49 (64)
T smart00647 39 NRVTCPKCGFS 49 (64)
T ss_pred CeeECCCCCCe
Confidence 34445444433
No 167
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=87.78 E-value=0.17 Score=34.57 Aligned_cols=23 Identities=17% Similarity=0.499 Sum_probs=19.8
Q ss_pred CccccccCCceecCCCccCcCCCC
Q 033949 82 DVSKCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 82 ~~~~C~~CG~~i~~~~~fCP~CG~ 105 (107)
..+.|..||+.|..+ +||+.|-.
T Consensus 80 l~~~CE~CG~~I~~G-r~C~~C~~ 102 (137)
T TIGR03826 80 LGYPCERCGTSIREG-RLCDSCAG 102 (137)
T ss_pred CcCcccccCCcCCCC-CccHHHHH
Confidence 468899999998887 99999854
No 168
>PRK14973 DNA topoisomerase I; Provisional
Probab=87.74 E-value=0.93 Score=39.75 Aligned_cols=66 Identities=17% Similarity=0.307 Sum_probs=35.9
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCC---CCCCCCCCCCC-CCCCCCCccCccccccCCcee--c
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNN---CNLLFPSSLPP-PPPPPPLVSDVSKCRFCDRLV--E 94 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~---CG~~~~~~~~~-~~~~~~~~~~~~~C~~CG~~i--~ 94 (107)
...||.||.... +++.+.+.++.|+. |+..+.+..+. .++ ......||.||..+ .
T Consensus 588 ~~~CP~CG~~l~---------------ik~~k~gkFigCS~Yp~Ck~t~~L~~~~~g~~----~~~~~~Cp~CG~p~~~~ 648 (936)
T PRK14973 588 IGPCPVCGKDLR---------------IKHIGSSQFIGCSGYPDCTFNIGLPGTTWGWA----IRTDEVCPIHHLNHVRL 648 (936)
T ss_pred cccCCcccccce---------------eecccCceeEECCCCCCCCccccCCccccccC----CCCCCCCCCCCCCceEE
Confidence 357999998431 23333334677765 88766553221 010 00124799999732 1
Q ss_pred -C----CCc-cCcCCCC
Q 033949 95 -P----DFS-FCPYCGS 105 (107)
Q Consensus 95 -~----~~~-fCP~CG~ 105 (107)
. ++- =||.|..
T Consensus 649 ~r~Gr~g~fl~CP~C~~ 665 (936)
T PRK14973 649 IRKGARPWDIGCPLCSH 665 (936)
T ss_pred eecCCCcccccCccccc
Confidence 1 222 3999864
No 169
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=87.67 E-value=0.46 Score=33.07 Aligned_cols=12 Identities=25% Similarity=0.509 Sum_probs=8.7
Q ss_pred eeCCCCCCCCCC
Q 033949 57 LFCNNCNLLFPS 68 (107)
Q Consensus 57 ~~C~~CG~~~~~ 68 (107)
..|++||..+..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 568888887743
No 170
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=87.60 E-value=0.36 Score=23.14 Aligned_cols=22 Identities=32% Similarity=0.564 Sum_probs=17.3
Q ss_pred ccccCCceecCCCccCcCCCCC
Q 033949 85 KCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 85 ~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
.|+.|+....+....|-.||++
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred cCCCCCCcChhhhccccccCCc
Confidence 5788888877888888888875
No 171
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=87.34 E-value=0.36 Score=40.48 Aligned_cols=24 Identities=33% Similarity=0.845 Sum_probs=18.2
Q ss_pred ccccccCCceecCCCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
..+|+.||..+......||.||+.
T Consensus 568 ~~~C~~CG~~~~g~~~~CP~CGs~ 591 (625)
T PRK08579 568 ITVCNKCGRSTTGLYTRCPRCGSE 591 (625)
T ss_pred CccCCCCCCccCCCCCcCcCCCCc
Confidence 567888888666667788888853
No 172
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=87.34 E-value=0.42 Score=28.11 Aligned_cols=9 Identities=33% Similarity=0.759 Sum_probs=4.5
Q ss_pred ccccCCcee
Q 033949 85 KCRFCDRLV 93 (107)
Q Consensus 85 ~C~~CG~~i 93 (107)
+||.||..+
T Consensus 19 ~Cp~CG~~t 27 (59)
T COG2260 19 KCPVCGGDT 27 (59)
T ss_pred cCCCCCCcc
Confidence 455555443
No 173
>PLN00209 ribosomal protein S27; Provisional
Probab=87.32 E-value=0.48 Score=29.96 Aligned_cols=33 Identities=12% Similarity=0.398 Sum_probs=23.3
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
..++||.|++.. +=|+.....+.|..||..+..
T Consensus 35 m~VkCp~C~n~q----------------~VFShA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 35 MDVKCQGCFNIT----------------TVFSHSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred EEEECCCCCCee----------------EEEecCceEEEccccCCEeec
Confidence 367899999921 115555568999999998743
No 174
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=87.27 E-value=0.43 Score=35.00 Aligned_cols=13 Identities=31% Similarity=0.516 Sum_probs=9.3
Q ss_pred ccccccCCceecC
Q 033949 83 VSKCRFCDRLVEP 95 (107)
Q Consensus 83 ~~~C~~CG~~i~~ 95 (107)
...|+.||+-...
T Consensus 35 v~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 35 VTICPKCGRYRIG 47 (236)
T ss_pred ceECCCCCCEECC
Confidence 4678888877655
No 175
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=87.13 E-value=0.52 Score=33.25 Aligned_cols=25 Identities=16% Similarity=0.458 Sum_probs=16.1
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
...|+.||....-.. -..||.||++
T Consensus 134 ~~vC~vCGy~~~ge~------------P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEGEA------------PEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccCCC------------CCcCCCCCCh
Confidence 677888877765422 2367777765
No 176
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=87.09 E-value=0.43 Score=38.12 Aligned_cols=21 Identities=29% Similarity=0.903 Sum_probs=9.8
Q ss_pred cccCCceecCCCccCcCCCCC
Q 033949 86 CRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 86 C~~CG~~i~~~~~fCP~CG~~ 106 (107)
|+.||...+.+...||.||+.
T Consensus 224 C~~Cd~l~~~~~a~CpRC~~~ 244 (419)
T PRK15103 224 CSCCTAILPADQPVCPRCHTK 244 (419)
T ss_pred CCCCCCCCCCCCCCCCCCCCc
Confidence 555554443333345555543
No 177
>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=87.05 E-value=0.19 Score=34.97 Aligned_cols=25 Identities=24% Similarity=0.246 Sum_probs=12.9
Q ss_pred ccccccCCceecC-----CCccCcCCCCCC
Q 033949 83 VSKCRFCDRLVEP-----DFSFCPYCGSAL 107 (107)
Q Consensus 83 ~~~C~~CG~~i~~-----~~~fCP~CG~~l 107 (107)
.+.||+||..... .-=-||.||..|
T Consensus 109 ~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L 138 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAMELNFTCPRCGAML 138 (158)
T ss_pred eEECCCCCcEeeHHHHHHcCCcCCCCCCEe
Confidence 4556666655433 123366666543
No 178
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=87.03 E-value=0.27 Score=35.36 Aligned_cols=23 Identities=26% Similarity=0.775 Sum_probs=20.2
Q ss_pred ccccccCCceecC--CCccCcCCCC
Q 033949 83 VSKCRFCDRLVEP--DFSFCPYCGS 105 (107)
Q Consensus 83 ~~~C~~CG~~i~~--~~~fCP~CG~ 105 (107)
...|.+||+++.. ....||.||+
T Consensus 149 ~A~CsrC~~~L~~~~~~l~Cp~Cg~ 173 (188)
T COG1096 149 YARCSRCRAPLVKKGNMLKCPNCGN 173 (188)
T ss_pred EEEccCCCcceEEcCcEEECCCCCC
Confidence 5679999999987 6789999996
No 179
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=86.98 E-value=0.4 Score=23.97 Aligned_cols=22 Identities=32% Similarity=0.650 Sum_probs=13.5
Q ss_pred ccccCCceecCCCccCcCCCCC
Q 033949 85 KCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 85 ~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
.|+.|+....+....|-.||++
T Consensus 6 ~C~~C~~~N~~~~~~C~~C~~~ 27 (30)
T PF00641_consen 6 KCPSCTFMNPASRSKCVACGAP 27 (30)
T ss_dssp EETTTTEEEESSSSB-TTT--B
T ss_pred cCCCCcCCchHHhhhhhCcCCC
Confidence 5777777777777777777753
No 180
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=86.79 E-value=0.63 Score=34.41 Aligned_cols=13 Identities=31% Similarity=0.577 Sum_probs=8.3
Q ss_pred cccccCCceecCC
Q 033949 84 SKCRFCDRLVEPD 96 (107)
Q Consensus 84 ~~C~~CG~~i~~~ 96 (107)
..||+||...+.|
T Consensus 323 ~~C~~cg~~~~rD 335 (364)
T COG0675 323 FKCPRCGFVHDRD 335 (364)
T ss_pred EECCCCCCeehhh
Confidence 4677777766553
No 181
>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=86.55 E-value=0.67 Score=35.67 Aligned_cols=41 Identities=12% Similarity=0.208 Sum_probs=22.3
Q ss_pred CceeCCCCCCCCCCCCCCCCCC-CCCccCccccccCCceecC
Q 033949 55 PALFCNNCNLLFPSSLPPPPPP-PPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~-~~~~~~~~~C~~CG~~i~~ 95 (107)
..+.|++||..-.+.....+-. ++.......|..|+.-+..
T Consensus 223 ~R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~ 264 (305)
T TIGR01562 223 VRVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYLKI 264 (305)
T ss_pred cCccCCCCCCCCceeeEeecCCCCCcceEEeeccccccchhh
Confidence 4789999998633221111110 0111235679999886644
No 182
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=86.51 E-value=0.14 Score=29.10 Aligned_cols=25 Identities=28% Similarity=0.563 Sum_probs=22.4
Q ss_pred CccccccCCceecCCCccCcCCCCC
Q 033949 82 DVSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 82 ~~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
+.++|-.|+|..+.+|+-|-.||++
T Consensus 13 ~kkIC~rC~Arnp~~A~kCRkC~~k 37 (50)
T COG1552 13 NKKICRRCYARNPPRATKCRKCGYK 37 (50)
T ss_pred hHHHHHHhcCCCCcchhHHhhccCC
Confidence 3678999999999999999999975
No 183
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=86.34 E-value=0.8 Score=35.32 Aligned_cols=53 Identities=15% Similarity=0.180 Sum_probs=32.3
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCC-CccCccccccCCceecC
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPP-LVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~-~~~~~~~C~~CG~~i~~ 95 (107)
.-..|+-|+..| ....+.|++||..-.+.-. .+.++ .......|..|+.-+..
T Consensus 211 RyL~CslC~teW---------------------~~~R~~C~~Cg~~~~l~y~--~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 211 RYLHCNLCESEW---------------------HVVRVKCSNCEQSGKLHYW--SLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred eEEEcCCCCCcc---------------------cccCccCCCCCCCCceeee--eecCCCcceEeeeccccccccee
Confidence 455799999987 3357899999974322111 11111 11235679999876644
No 184
>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=86.29 E-value=0.64 Score=32.07 Aligned_cols=13 Identities=38% Similarity=0.831 Sum_probs=7.6
Q ss_pred cCCCcEECCCCCC
Q 033949 17 LKSGAGRCINCGS 29 (107)
Q Consensus 17 ~~~~~~~C~~Cg~ 29 (107)
.+.+...|.+||.
T Consensus 108 ~g~G~l~C~~Cg~ 120 (146)
T PF07295_consen 108 VGPGTLVCENCGH 120 (146)
T ss_pred ecCceEecccCCC
Confidence 3445566666666
No 185
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=86.26 E-value=0.38 Score=27.55 Aligned_cols=22 Identities=36% Similarity=1.032 Sum_probs=12.5
Q ss_pred cccccCCceecC----------CCccCcCCCC
Q 033949 84 SKCRFCDRLVEP----------DFSFCPYCGS 105 (107)
Q Consensus 84 ~~C~~CG~~i~~----------~~~fCP~CG~ 105 (107)
..|..|+-.|++ .-.+||+||.
T Consensus 23 ~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 23 GTCSGCHMELPPQELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred CccCCCCEEcCHHHHHHHHcCCCeEECcCCCc
Confidence 356666665544 3456666664
No 186
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=86.21 E-value=0.64 Score=33.47 Aligned_cols=34 Identities=18% Similarity=0.461 Sum_probs=26.6
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
...+|..|++.- +||||... ....|+.|++.+..
T Consensus 151 kGfiCe~C~~~~--------------~IfPF~~~-~~~~C~~C~~v~H~ 184 (202)
T PF13901_consen 151 KGFICEICNSDD--------------IIFPFQID-TTVRCPKCKSVFHK 184 (202)
T ss_pred CCCCCccCCCCC--------------CCCCCCCC-CeeeCCcCccccch
Confidence 346788998832 57999985 89999999999843
No 187
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=86.17 E-value=0.43 Score=33.23 Aligned_cols=10 Identities=20% Similarity=0.673 Sum_probs=8.2
Q ss_pred cccccCCcee
Q 033949 84 SKCRFCDRLV 93 (107)
Q Consensus 84 ~~C~~CG~~i 93 (107)
+.|++||...
T Consensus 29 ~~c~~c~~~f 38 (154)
T PRK00464 29 RECLACGKRF 38 (154)
T ss_pred eeccccCCcc
Confidence 7899999764
No 188
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=86.15 E-value=0.59 Score=29.48 Aligned_cols=33 Identities=12% Similarity=0.409 Sum_probs=23.3
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
..++||.|++.. +=|+.....+.|..||..+..
T Consensus 34 m~VkCp~C~n~q----------------~VFShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 34 MDVKCPGCSQIT----------------TVFSHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred EEEECCCCCCee----------------EEEecCceEEEccccCCEeec
Confidence 367899999921 115555568999999998743
No 189
>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=86.03 E-value=0.23 Score=24.89 Aligned_cols=19 Identities=37% Similarity=0.884 Sum_probs=8.1
Q ss_pred ccccCCceecC------CCccCcCC
Q 033949 85 KCRFCDRLVEP------DFSFCPYC 103 (107)
Q Consensus 85 ~C~~CG~~i~~------~~~fCP~C 103 (107)
.|+.|+..++. +..+||.|
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rC 27 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRC 27 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTT
T ss_pred cCccCCCcceEeEecCCCCeECcCC
Confidence 45666655543 35566665
No 190
>PRK05978 hypothetical protein; Provisional
Probab=86.00 E-value=0.49 Score=32.79 Aligned_cols=11 Identities=18% Similarity=0.537 Sum_probs=5.7
Q ss_pred cccccCCceec
Q 033949 84 SKCRFCDRLVE 94 (107)
Q Consensus 84 ~~C~~CG~~i~ 94 (107)
..|+.||.+..
T Consensus 53 ~~C~~CG~~~~ 63 (148)
T PRK05978 53 DHCAACGEDFT 63 (148)
T ss_pred CCccccCCccc
Confidence 34555555543
No 191
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=85.95 E-value=0.24 Score=35.10 Aligned_cols=12 Identities=25% Similarity=0.121 Sum_probs=6.6
Q ss_pred CcEECCCCCCCc
Q 033949 20 GAGRCINCGSTA 31 (107)
Q Consensus 20 ~~~~C~~Cg~~~ 31 (107)
.-..||+||.++
T Consensus 116 ~~Y~Cp~C~~ry 127 (178)
T PRK06266 116 MFFFCPNCHIRF 127 (178)
T ss_pred CEEECCCCCcEE
Confidence 344566666643
No 192
>PRK07418 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=85.90 E-value=0.41 Score=39.54 Aligned_cols=26 Identities=31% Similarity=0.791 Sum_probs=23.7
Q ss_pred CccccccCCceecCCCccCcCCCCCC
Q 033949 82 DVSKCRFCDRLVEPDFSFCPYCGSAL 107 (107)
Q Consensus 82 ~~~~C~~CG~~i~~~~~fCP~CG~~l 107 (107)
....|++||+.+.+..+||+.||.+|
T Consensus 591 ~~~~~~~~~~~~~~~~~f~~~~g~~~ 616 (616)
T PRK07418 591 ELIYCSNCGAKNPSTHRFCPECGTKL 616 (616)
T ss_pred CcccCCCCCCcCccccccchhhCCCC
Confidence 45789999999999999999999986
No 193
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=85.79 E-value=0.37 Score=36.38 Aligned_cols=24 Identities=38% Similarity=0.735 Sum_probs=18.6
Q ss_pred ccccccCCceecCCCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
...|.+||+.+..=-+-||+||+.
T Consensus 82 l~~C~~CGa~V~~~e~~Cp~C~St 105 (314)
T PF09567_consen 82 LGKCNNCGANVSRLEESCPNCGST 105 (314)
T ss_pred hhhhccccceeeehhhcCCCCCcc
Confidence 356888888888777888888863
No 194
>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=85.73 E-value=1 Score=24.08 Aligned_cols=32 Identities=28% Similarity=0.538 Sum_probs=20.4
Q ss_pred EECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCC---CCCCCCC
Q 033949 22 GRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNN---CNLLFPS 68 (107)
Q Consensus 22 ~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~---CG~~~~~ 68 (107)
..||.||+.+. .+.++.+.++.|+. |.....+
T Consensus 2 ~~CP~Cg~~lv---------------~r~~k~g~F~~Cs~yP~C~~~~~~ 36 (39)
T PF01396_consen 2 EKCPKCGGPLV---------------LRRGKKGKFLGCSNYPECKYTEPL 36 (39)
T ss_pred cCCCCCCceeE---------------EEECCCCCEEECCCCCCcCCeEeC
Confidence 46999997331 33455557788865 7776544
No 195
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=85.69 E-value=1.5 Score=23.57 Aligned_cols=7 Identities=43% Similarity=1.322 Sum_probs=5.6
Q ss_pred ECCCCCC
Q 033949 23 RCINCGS 29 (107)
Q Consensus 23 ~C~~Cg~ 29 (107)
.||+||+
T Consensus 2 ~Cp~C~~ 8 (40)
T smart00440 2 PCPKCGN 8 (40)
T ss_pred cCCCCCC
Confidence 5888887
No 196
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=85.66 E-value=0.78 Score=33.32 Aligned_cols=10 Identities=30% Similarity=0.624 Sum_probs=7.8
Q ss_pred CcEECCCCCC
Q 033949 20 GAGRCINCGS 29 (107)
Q Consensus 20 ~~~~C~~Cg~ 29 (107)
++++||.|++
T Consensus 4 k~~~CPvC~~ 13 (214)
T PF09986_consen 4 KKITCPVCGK 13 (214)
T ss_pred CceECCCCCC
Confidence 5677888888
No 197
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=85.58 E-value=0.52 Score=39.71 Aligned_cols=23 Identities=35% Similarity=0.756 Sum_probs=16.9
Q ss_pred ccccccCCceecCCCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
..+|+.||.. ......||.||+.
T Consensus 626 ~~~C~~CG~~-~g~~~~CP~CG~~ 648 (656)
T PRK08270 626 FSICPKHGYL-SGEHEFCPKCGEE 648 (656)
T ss_pred CcccCCCCCc-CCCCCCCcCCcCc
Confidence 4568888873 4556789998875
No 198
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=85.35 E-value=0.53 Score=39.48 Aligned_cols=23 Identities=30% Similarity=0.766 Sum_probs=16.4
Q ss_pred ccccccCCceecCCCccCcCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~ 105 (107)
..+|++||......-..||.||+
T Consensus 566 ~~iC~~CG~~~~g~~~~CP~CGs 588 (623)
T PRK08271 566 ITICNDCHHIDKRTGKRCPICGS 588 (623)
T ss_pred CccCCCCCCcCCCCCcCCcCCCC
Confidence 45688888764555678888885
No 199
>PRK07219 DNA topoisomerase I; Validated
Probab=85.28 E-value=1.3 Score=38.29 Aligned_cols=21 Identities=33% Similarity=0.770 Sum_probs=13.0
Q ss_pred cccCCceecC-----CCccCcCCCCC
Q 033949 86 CRFCDRLVEP-----DFSFCPYCGSA 106 (107)
Q Consensus 86 C~~CG~~i~~-----~~~fCP~CG~~ 106 (107)
||.|...... .-.-||.||..
T Consensus 672 CP~C~~~~~~~~~~~~~~~CP~Cg~~ 697 (822)
T PRK07219 672 CPDCEAEKEEEDPDEVIGPCPKCGGE 697 (822)
T ss_pred CCCCCCCccccccccccccCCCCCCe
Confidence 7777765432 23568888754
No 200
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.16 E-value=0.2 Score=35.78 Aligned_cols=21 Identities=24% Similarity=0.585 Sum_probs=12.8
Q ss_pred cccCCceecCCCccCcCCCCC
Q 033949 86 CRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 86 C~~CG~~i~~~~~fCP~CG~~ 106 (107)
|..|-++......-||-|+.+
T Consensus 156 C~~Cik~alk~~~~CP~C~kk 176 (187)
T KOG0320|consen 156 CSQCIKDALKNTNKCPTCRKK 176 (187)
T ss_pred HHHHHHHHHHhCCCCCCcccc
Confidence 666666656666666666654
No 201
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=85.15 E-value=0.31 Score=36.41 Aligned_cols=37 Identities=27% Similarity=0.486 Sum_probs=15.0
Q ss_pred CcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949 20 GAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL 70 (107)
Q Consensus 20 ~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~ 70 (107)
.+..||+||+ ....++. ++..-...|++|++.|++..
T Consensus 30 ~n~yCP~Cg~~~L~~f~N--------------N~PVaDF~C~~C~eeyELKS 67 (254)
T PF06044_consen 30 ENMYCPNCGSKPLSKFEN--------------NRPVADFYCPNCNEEYELKS 67 (254)
T ss_dssp HH---TTT--SS-EE----------------------EEE-TTT--EEEEEE
T ss_pred HCCcCCCCCChhHhhccC--------------CCccceeECCCCchHHhhhh
Confidence 5778999999 4543332 33334778999999998743
No 202
>PRK06260 threonine synthase; Validated
Probab=85.13 E-value=0.69 Score=36.31 Aligned_cols=11 Identities=27% Similarity=0.658 Sum_probs=5.1
Q ss_pred eeCCCCCCCCC
Q 033949 57 LFCNNCNLLFP 67 (107)
Q Consensus 57 ~~C~~CG~~~~ 67 (107)
+.|..||..++
T Consensus 4 ~~C~~cg~~~~ 14 (397)
T PRK06260 4 LKCIECGKEYD 14 (397)
T ss_pred EEECCCCCCCC
Confidence 44444444443
No 203
>PRK11595 DNA utilization protein GntX; Provisional
Probab=85.06 E-value=0.58 Score=34.04 Aligned_cols=21 Identities=19% Similarity=0.338 Sum_probs=14.5
Q ss_pred cccccCCceecCCCccCcCCC
Q 033949 84 SKCRFCDRLVEPDFSFCPYCG 104 (107)
Q Consensus 84 ~~C~~CG~~i~~~~~fCP~CG 104 (107)
..|+.||.++......|+.|-
T Consensus 35 ~~C~~Cg~~~~~~~~~C~~C~ 55 (227)
T PRK11595 35 TCCPQCGLPATHPHLPCGRCL 55 (227)
T ss_pred CcCccCCCcCCCCCCCcHHHH
Confidence 469999987654334688874
No 204
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=85.04 E-value=0.3 Score=40.20 Aligned_cols=10 Identities=20% Similarity=0.790 Sum_probs=3.6
Q ss_pred ceeCCCCCCC
Q 033949 56 ALFCNNCNLL 65 (107)
Q Consensus 56 ~~~C~~CG~~ 65 (107)
.-.|+.||..
T Consensus 491 ~~~C~~CG~~ 500 (546)
T PF13597_consen 491 IDICPDCGYI 500 (546)
T ss_dssp EEEETTT---
T ss_pred cccccCCCcC
Confidence 4455555554
No 205
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=84.95 E-value=0.52 Score=40.07 Aligned_cols=73 Identities=25% Similarity=0.430 Sum_probs=42.7
Q ss_pred CCCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCC--CCCceeCCCCCCCCCCCCCCCCCCCCC--ccCccccccCCcee
Q 033949 18 KSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPA--KEPALFCNNCNLLFPSSLPPPPPPPPL--VSDVSKCRFCDRLV 93 (107)
Q Consensus 18 ~~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~--~~~~~~C~~CG~~~~~~~~~~~~~~~~--~~~~~~C~~CG~~i 93 (107)
.++..+|+.|-.... =|-++ ..++..|++||-.+.+-+. .|++.+- ...-.-|+.|..+-
T Consensus 98 ~pD~a~C~~Cl~Ei~---------------dp~~rrY~YPF~~CT~CGPRfTIi~a-lPYDR~nTsM~~F~lC~~C~~EY 161 (750)
T COG0068 98 PPDAATCEDCLEEIF---------------DPNSRRYLYPFINCTNCGPRFTIIEA-LPYDRENTSMADFPLCPFCDKEY 161 (750)
T ss_pred CCchhhhHHHHHHhc---------------CCCCcceeccccccCCCCcceeeecc-CCCCcccCccccCcCCHHHHHHh
Confidence 356678999987210 01111 2247789999999877442 2333221 11345688887776
Q ss_pred cC--------CCccCcCCCCC
Q 033949 94 EP--------DFSFCPYCGSA 106 (107)
Q Consensus 94 ~~--------~~~fCP~CG~~ 106 (107)
.. ...-||.||=+
T Consensus 162 ~dP~nRRfHAQp~aCp~CGP~ 182 (750)
T COG0068 162 KDPLNRRFHAQPIACPKCGPH 182 (750)
T ss_pred cCccccccccccccCcccCCC
Confidence 44 56778888854
No 206
>COG4640 Predicted membrane protein [Function unknown]
Probab=84.80 E-value=0.52 Score=37.65 Aligned_cols=8 Identities=38% Similarity=1.148 Sum_probs=3.6
Q ss_pred CCCCCCCC
Q 033949 59 CNNCNLLF 66 (107)
Q Consensus 59 C~~CG~~~ 66 (107)
|+-||+.+
T Consensus 18 C~qCG~~~ 25 (465)
T COG4640 18 CTQCGHKF 25 (465)
T ss_pred ccccCCcC
Confidence 44444444
No 207
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=84.35 E-value=0.48 Score=36.10 Aligned_cols=10 Identities=40% Similarity=1.308 Sum_probs=5.0
Q ss_pred CCccCcCCCC
Q 033949 96 DFSFCPYCGS 105 (107)
Q Consensus 96 ~~~fCP~CG~ 105 (107)
+...||+||.
T Consensus 46 n~~vcp~c~~ 55 (294)
T COG0777 46 NLKVCPKCGH 55 (294)
T ss_pred hhhcccccCc
Confidence 4555555544
No 208
>PRK11032 hypothetical protein; Provisional
Probab=84.34 E-value=0.86 Score=31.97 Aligned_cols=14 Identities=29% Similarity=0.510 Sum_probs=9.2
Q ss_pred ecCCCcEECCCCCC
Q 033949 16 VLKSGAGRCINCGS 29 (107)
Q Consensus 16 ~~~~~~~~C~~Cg~ 29 (107)
+.+.++..|.+||.
T Consensus 119 vvg~G~LvC~~Cg~ 132 (160)
T PRK11032 119 VVGLGNLVCEKCHH 132 (160)
T ss_pred eeecceEEecCCCC
Confidence 44456667777777
No 209
>PRK10445 endonuclease VIII; Provisional
Probab=84.28 E-value=0.49 Score=35.36 Aligned_cols=21 Identities=33% Similarity=0.977 Sum_probs=14.1
Q ss_pred cccccCCceecC------CCccCcCCC
Q 033949 84 SKCRFCDRLVEP------DFSFCPYCG 104 (107)
Q Consensus 84 ~~C~~CG~~i~~------~~~fCP~CG 104 (107)
..||.||..|.. +.-|||.|-
T Consensus 236 ~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 236 EACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 457777777754 667777773
No 210
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=84.08 E-value=0.5 Score=35.51 Aligned_cols=22 Identities=23% Similarity=0.676 Sum_probs=17.2
Q ss_pred ccccccCCceecC------CCccCcCCC
Q 033949 83 VSKCRFCDRLVEP------DFSFCPYCG 104 (107)
Q Consensus 83 ~~~C~~CG~~i~~------~~~fCP~CG 104 (107)
...||.||++|.. +.-|||.|-
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 3569999988865 788899884
No 211
>PRK03922 hypothetical protein; Provisional
Probab=84.06 E-value=0.63 Score=30.73 Aligned_cols=13 Identities=15% Similarity=0.549 Sum_probs=8.4
Q ss_pred ccccccCCceecC
Q 033949 83 VSKCRFCDRLVEP 95 (107)
Q Consensus 83 ~~~C~~CG~~i~~ 95 (107)
...||.||+++++
T Consensus 49 ~~~cP~cge~~~~ 61 (113)
T PRK03922 49 LTICPKCGEPFDS 61 (113)
T ss_pred cccCCCCCCcCCc
Confidence 4567777777655
No 212
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=83.77 E-value=0.51 Score=35.36 Aligned_cols=22 Identities=36% Similarity=0.881 Sum_probs=17.3
Q ss_pred cccccCCceecC------CCccCcCCCC
Q 033949 84 SKCRFCDRLVEP------DFSFCPYCGS 105 (107)
Q Consensus 84 ~~C~~CG~~i~~------~~~fCP~CG~ 105 (107)
..|+.||+.|.. +.-|||.|-.
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 246 EPCRRCGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCeeEEEEECCCCcEECcCCCC
Confidence 459999988864 7889999854
No 213
>PF14353 CpXC: CpXC protein
Probab=83.75 E-value=1.6 Score=28.77 Aligned_cols=29 Identities=24% Similarity=0.380 Sum_probs=17.0
Q ss_pred CCcEECCCCCC----CcEEEE--EeeEEEEEEEee
Q 033949 19 SGAGRCINCGS----TADLVE--YEKVLKAFFVPV 47 (107)
Q Consensus 19 ~~~~~C~~Cg~----~~~~~~--~~~~f~lFFIP~ 47 (107)
...++||+||. .+.+.. ..+.|.+++.|=
T Consensus 36 l~~~~CP~Cg~~~~~~~p~lY~D~~~~~~i~~~P~ 70 (128)
T PF14353_consen 36 LFSFTCPSCGHKFRLEYPLLYHDPEKKFMIYYFPD 70 (128)
T ss_pred cCEEECCCCCCceecCCCEEEEcCCCCEEEEEcCC
Confidence 35678888888 222222 233677777664
No 214
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=83.70 E-value=0.69 Score=27.05 Aligned_cols=11 Identities=36% Similarity=0.694 Sum_probs=6.2
Q ss_pred ceeCCCCCCCC
Q 033949 56 ALFCNNCNLLF 66 (107)
Q Consensus 56 ~~~C~~CG~~~ 66 (107)
+--|.+||..+
T Consensus 18 ~~NCl~CGkIi 28 (57)
T PF06221_consen 18 APNCLNCGKII 28 (57)
T ss_pred cccccccChhh
Confidence 33466666655
No 215
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=83.66 E-value=0.75 Score=32.45 Aligned_cols=24 Identities=33% Similarity=0.718 Sum_probs=20.6
Q ss_pred ccccccCCceecC-CCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEP-DFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~-~~~fCP~CG~~ 106 (107)
...|+-||..... ....||-||.+
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCCh
Confidence 5889999998866 68899999964
No 216
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.46 E-value=0.56 Score=35.21 Aligned_cols=20 Identities=40% Similarity=1.022 Sum_probs=16.2
Q ss_pred cccccCCceecC------CCccCcCC
Q 033949 84 SKCRFCDRLVEP------DFSFCPYC 103 (107)
Q Consensus 84 ~~C~~CG~~i~~------~~~fCP~C 103 (107)
..|+.||++|.. +.-|||.|
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCeeEEEEECCCCCEECCCC
Confidence 468999988865 78889988
No 217
>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=83.20 E-value=0.74 Score=37.96 Aligned_cols=23 Identities=35% Similarity=0.662 Sum_probs=17.5
Q ss_pred cccccCCceecCCCccCcCCCCC
Q 033949 84 SKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 84 ~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
.+|++||......-..||.||++
T Consensus 519 ~~C~~CG~~~~~~~~~CP~CGs~ 541 (555)
T cd01675 519 DICNDCGYIGEGEGFKCPKCGSE 541 (555)
T ss_pred ccCCCCCCCCcCCCCCCcCCCCc
Confidence 37999998655667889999864
No 218
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=83.18 E-value=0.7 Score=31.48 Aligned_cols=12 Identities=25% Similarity=0.753 Sum_probs=8.8
Q ss_pred CceeCCCCCCCC
Q 033949 55 PALFCNNCNLLF 66 (107)
Q Consensus 55 ~~~~C~~CG~~~ 66 (107)
+...|+.||+.-
T Consensus 42 Pr~~Cp~C~~~~ 53 (140)
T COG1545 42 PRAYCPKCGSET 53 (140)
T ss_pred CcccCCCCCCCC
Confidence 567788888774
No 219
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=83.06 E-value=1.9 Score=29.49 Aligned_cols=33 Identities=27% Similarity=0.516 Sum_probs=20.9
Q ss_pred cEECCCCCCCc-EEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 21 AGRCINCGSTA-DLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 21 ~~~C~~Cg~~~-~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
-+.|+.||+.- .+++ ..+...+.|..||+.-.+
T Consensus 102 yVlC~~C~spdT~l~k---------------~~r~~~l~C~ACGa~~~V 135 (138)
T PRK03988 102 YVICPECGSPDTKLIK---------------EGRIWVLKCEACGAETPV 135 (138)
T ss_pred cEECCCCCCCCcEEEE---------------cCCeEEEEcccCCCCCcC
Confidence 46799999932 2222 123367889889887544
No 220
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=83.04 E-value=0.4 Score=23.93 Aligned_cols=8 Identities=25% Similarity=0.754 Sum_probs=2.4
Q ss_pred CCCCCCCC
Q 033949 59 CNNCNLLF 66 (107)
Q Consensus 59 C~~CG~~~ 66 (107)
||.||+.+
T Consensus 2 CP~C~s~l 9 (28)
T PF03119_consen 2 CPVCGSKL 9 (28)
T ss_dssp -TTT--BE
T ss_pred cCCCCCEe
Confidence 45555544
No 221
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=83.00 E-value=0.93 Score=25.82 Aligned_cols=11 Identities=18% Similarity=0.576 Sum_probs=8.2
Q ss_pred CceeCCCCCCC
Q 033949 55 PALFCNNCNLL 65 (107)
Q Consensus 55 ~~~~C~~CG~~ 65 (107)
+.+.|..||..
T Consensus 36 dR~~CGkCgyT 46 (51)
T COG1998 36 DRWACGKCGYT 46 (51)
T ss_pred ceeEeccccce
Confidence 57778888765
No 222
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=82.86 E-value=2 Score=29.21 Aligned_cols=33 Identities=18% Similarity=0.441 Sum_probs=21.0
Q ss_pred cEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 21 AGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 21 ~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
-+.|+.|++ .-.+++. .+.+.+.|..||+.-.+
T Consensus 97 yVlC~~C~sPdT~l~k~---------------~r~~~l~C~ACGa~~~v 130 (133)
T TIGR00311 97 YVICRECNRPDTRIIKE---------------GRVSLLKCEACGAKAPL 130 (133)
T ss_pred eEECCCCCCCCcEEEEe---------------CCeEEEecccCCCCCcc
Confidence 467999999 3222221 23357789999987654
No 223
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=82.84 E-value=0.75 Score=29.86 Aligned_cols=13 Identities=15% Similarity=0.460 Sum_probs=9.0
Q ss_pred ccccccCCceecC
Q 033949 83 VSKCRFCDRLVEP 95 (107)
Q Consensus 83 ~~~C~~CG~~i~~ 95 (107)
...||.||.++++
T Consensus 47 ~~~cP~Cge~~~~ 59 (102)
T PF04475_consen 47 DTICPKCGEELDS 59 (102)
T ss_pred cccCCCCCCccCc
Confidence 4567777777765
No 224
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=82.66 E-value=0.97 Score=28.69 Aligned_cols=31 Identities=23% Similarity=0.486 Sum_probs=22.3
Q ss_pred CcEECCCCCCC-cEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 20 GAGRCINCGST-ADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 20 ~~~~C~~Cg~~-~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
+...||.||.. +. + .......|.+||+.+.-
T Consensus 34 ~~~~Cp~C~~~~Vk--R----------------~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRTTVK--R----------------IATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCccee--e----------------eccCeEEcCCCCCeecc
Confidence 34579999993 31 1 13479999999999854
No 225
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.60 E-value=1 Score=26.73 Aligned_cols=14 Identities=21% Similarity=0.437 Sum_probs=7.2
Q ss_pred cCCCcEECCCCCCC
Q 033949 17 LKSGAGRCINCGST 30 (107)
Q Consensus 17 ~~~~~~~C~~Cg~~ 30 (107)
++.+.+.||+|+..
T Consensus 44 g~~gev~CPYC~t~ 57 (62)
T COG4391 44 GDEGEVVCPYCSTR 57 (62)
T ss_pred CCCCcEecCccccE
Confidence 33445555555553
No 226
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=82.44 E-value=1.7 Score=28.54 Aligned_cols=29 Identities=28% Similarity=0.557 Sum_probs=17.6
Q ss_pred cEECCCCCCC-cEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCC
Q 033949 21 AGRCINCGST-ADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNL 64 (107)
Q Consensus 21 ~~~C~~Cg~~-~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~ 64 (107)
-+.|+.|+++ -++++. .+...+.|..||+
T Consensus 80 yVlC~~C~spdT~l~k~---------------~r~~~l~C~aCGa 109 (110)
T smart00653 80 YVLCPECGSPDTELIKE---------------NRLFFLKCEACGA 109 (110)
T ss_pred cEECCCCCCCCcEEEEe---------------CCeEEEEccccCC
Confidence 3679999982 222221 1335777888886
No 227
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=82.36 E-value=0.84 Score=29.98 Aligned_cols=13 Identities=23% Similarity=0.557 Sum_probs=8.3
Q ss_pred ccccccCCceecC
Q 033949 83 VSKCRFCDRLVEP 95 (107)
Q Consensus 83 ~~~C~~CG~~i~~ 95 (107)
...||.||+.+++
T Consensus 49 ~t~CP~Cg~~~e~ 61 (115)
T COG1885 49 STSCPKCGEPFES 61 (115)
T ss_pred cccCCCCCCccce
Confidence 3457777776655
No 228
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=82.31 E-value=0.95 Score=35.98 Aligned_cols=15 Identities=13% Similarity=0.366 Sum_probs=11.3
Q ss_pred CCceeCCCCCCCCCC
Q 033949 54 EPALFCNNCNLLFPS 68 (107)
Q Consensus 54 ~~~~~C~~CG~~~~~ 68 (107)
++...||.||+....
T Consensus 31 g~~a~CpRCg~~L~~ 45 (403)
T TIGR00155 31 GQKAACPRCGTTLTV 45 (403)
T ss_pred CCeeECCCCCCCCcC
Confidence 367888888888744
No 229
>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=82.21 E-value=2.4 Score=23.92 Aligned_cols=13 Identities=23% Similarity=0.483 Sum_probs=8.8
Q ss_pred ceeCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPS 68 (107)
Q Consensus 56 ~~~C~~CG~~~~~ 68 (107)
+..|+.||+..+.
T Consensus 26 ~~~C~~Cga~~~~ 38 (53)
T TIGR03655 26 YFECSTCGASGPV 38 (53)
T ss_pred EEECCCCCCCccc
Confidence 3468888877654
No 230
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=82.02 E-value=0.66 Score=34.80 Aligned_cols=21 Identities=33% Similarity=0.869 Sum_probs=13.3
Q ss_pred cccccCCceecC------CCccCcCCC
Q 033949 84 SKCRFCDRLVEP------DFSFCPYCG 104 (107)
Q Consensus 84 ~~C~~CG~~i~~------~~~fCP~CG 104 (107)
..|+.||+.|.. +.-|||.|-
T Consensus 236 ~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 236 QPCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred CCCCcCCCeeEEEEECCCCcEECCCCc
Confidence 357777766654 566777764
No 231
>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=81.97 E-value=0.77 Score=40.38 Aligned_cols=22 Identities=32% Similarity=0.830 Sum_probs=17.7
Q ss_pred ccccccCCceecCCCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
.++||+||.. .-...||.||++
T Consensus 625 ~RKCPkCG~y--Tlk~rCP~CG~~ 646 (1095)
T TIGR00354 625 IRKCPQCGKE--SFWLKCPVCGEL 646 (1095)
T ss_pred EEECCCCCcc--cccccCCCCCCc
Confidence 5779999987 556789999975
No 232
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=81.97 E-value=0.76 Score=34.97 Aligned_cols=25 Identities=28% Similarity=0.585 Sum_probs=19.0
Q ss_pred CccccccCCceecC----CCccCcCCCCC
Q 033949 82 DVSKCRFCDRLVEP----DFSFCPYCGSA 106 (107)
Q Consensus 82 ~~~~C~~CG~~i~~----~~~fCP~CG~~ 106 (107)
..+.|+.||+++.+ -+..||.||..
T Consensus 110 ~~RFCg~CG~~~~~~~~g~~~~C~~cg~~ 138 (279)
T COG2816 110 SHRFCGRCGTKTYPREGGWARVCPKCGHE 138 (279)
T ss_pred hCcCCCCCCCcCccccCceeeeCCCCCCc
Confidence 35778888888876 57788888864
No 233
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=81.95 E-value=0.91 Score=32.97 Aligned_cols=16 Identities=19% Similarity=0.436 Sum_probs=12.8
Q ss_pred CceeCCCCCCCCCCCC
Q 033949 55 PALFCNNCNLLFPSSL 70 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~ 70 (107)
..+.||.|++.+....
T Consensus 4 k~~~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKK 19 (214)
T ss_pred CceECCCCCCeeeeeE
Confidence 4689999999997643
No 234
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=81.89 E-value=1.6 Score=34.64 Aligned_cols=34 Identities=15% Similarity=0.476 Sum_probs=22.3
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
+...|+.||..++...-.. .....||.||+++..
T Consensus 12 ~~~~C~~Cd~l~~~~~l~~-------g~~a~CpRCg~~L~~ 45 (403)
T TIGR00155 12 KHILCSQCDMLVALPRIES-------GQKAACPRCGTTLTV 45 (403)
T ss_pred CeeeCCCCCCcccccCCCC-------CCeeECCCCCCCCcC
Confidence 4667999998876533111 024579999998854
No 235
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=81.73 E-value=0.9 Score=28.27 Aligned_cols=14 Identities=14% Similarity=0.266 Sum_probs=3.7
Q ss_pred ceeCCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPSS 69 (107)
Q Consensus 56 ~~~C~~CG~~~~~~ 69 (107)
...|..||..+.++
T Consensus 9 ~qiCqiCGD~VGl~ 22 (80)
T PF14569_consen 9 GQICQICGDDVGLT 22 (80)
T ss_dssp S-B-SSS--B--B-
T ss_pred CcccccccCccccC
Confidence 34555566555443
No 236
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=81.61 E-value=0.71 Score=27.13 Aligned_cols=16 Identities=25% Similarity=0.353 Sum_probs=5.8
Q ss_pred CCCceeCCCCCCCCCC
Q 033949 53 KEPALFCNNCNLLFPS 68 (107)
Q Consensus 53 ~~~~~~C~~CG~~~~~ 68 (107)
+.....|..|+..+..
T Consensus 6 d~~~~~C~~C~~~F~~ 21 (69)
T PF01363_consen 6 DSEASNCMICGKKFSL 21 (69)
T ss_dssp GGG-SB-TTT--B-BS
T ss_pred CCCCCcCcCcCCcCCC
Confidence 3345566666666643
No 237
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=81.60 E-value=0.92 Score=27.74 Aligned_cols=38 Identities=24% Similarity=0.417 Sum_probs=25.5
Q ss_pred EECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCC--CCCCCCCC
Q 033949 22 GRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCN--NCNLLFPS 68 (107)
Q Consensus 22 ~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~--~CG~~~~~ 68 (107)
..||.||+.+ .++.+++.+- ..+.-+-.|. .||..+..
T Consensus 2 m~CP~Cg~~a-~irtSr~~s~--------~~~~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 2 FHCPLCQHAA-HARTSRYITD--------TTKERYHQCQNVNCSATFIT 41 (72)
T ss_pred ccCCCCCCcc-EEEEChhcCh--------hhheeeeecCCCCCCCEEEE
Confidence 4699999965 5666666551 1123577788 89998854
No 238
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=81.59 E-value=1.8 Score=31.71 Aligned_cols=13 Identities=15% Similarity=0.485 Sum_probs=7.1
Q ss_pred CceeCCCCCCCCC
Q 033949 55 PALFCNNCNLLFP 67 (107)
Q Consensus 55 ~~~~C~~CG~~~~ 67 (107)
..+.|..|+..++
T Consensus 121 ~~~~C~~C~~~~~ 133 (242)
T PRK00481 121 LRARCTKCGQTYD 133 (242)
T ss_pred CceeeCCCCCCcC
Confidence 4555666655543
No 239
>PRK07591 threonine synthase; Validated
Probab=81.52 E-value=1 Score=35.80 Aligned_cols=12 Identities=17% Similarity=0.382 Sum_probs=6.2
Q ss_pred eeCCCCCCCCCC
Q 033949 57 LFCNNCNLLFPS 68 (107)
Q Consensus 57 ~~C~~CG~~~~~ 68 (107)
..||.||..++.
T Consensus 34 ~~C~~cg~~l~~ 45 (421)
T PRK07591 34 HVCEECFGPLEV 45 (421)
T ss_pred ccCCCCCCeEEE
Confidence 455555554443
No 240
>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=81.32 E-value=0.97 Score=37.50 Aligned_cols=24 Identities=38% Similarity=0.603 Sum_probs=15.3
Q ss_pred ccccccCCceecCCCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
..+|++||..-+.....||.||++
T Consensus 524 ~~~C~~CG~~g~~~~~~CP~Cgs~ 547 (579)
T TIGR02487 524 VDVCEDCGYTGEGLNDKCPKCGSH 547 (579)
T ss_pred CccCCCCCCCCCCCCCcCcCCCCc
Confidence 456888887322233578888864
No 241
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=81.09 E-value=0.78 Score=34.16 Aligned_cols=22 Identities=36% Similarity=1.025 Sum_probs=12.7
Q ss_pred cccccCCceecC----------CCccCcCCCC
Q 033949 84 SKCRFCDRLVEP----------DFSFCPYCGS 105 (107)
Q Consensus 84 ~~C~~CG~~i~~----------~~~fCP~CG~ 105 (107)
..|..|+-.|++ +-.+||+||+
T Consensus 198 ~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgR 229 (239)
T COG1579 198 RVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGR 229 (239)
T ss_pred CcccCCeeeecHHHHHHHhcCCCCccCCccch
Confidence 456666555544 4566666664
No 242
>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=81.06 E-value=1 Score=31.13 Aligned_cols=29 Identities=24% Similarity=0.571 Sum_probs=18.8
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
+.+.|.+||+.+.+.... . ...||.||..
T Consensus 111 G~l~C~~Cg~~~~~~~~~-~--------l~~Cp~C~~~ 139 (146)
T PF07295_consen 111 GTLVCENCGHEVELTHPE-R--------LPPCPKCGHT 139 (146)
T ss_pred ceEecccCCCEEEecCCC-c--------CCCCCCCCCC
Confidence 577788888877665421 1 2368888764
No 243
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=81.05 E-value=2.5 Score=25.32 Aligned_cols=34 Identities=21% Similarity=0.227 Sum_probs=21.2
Q ss_pred ECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949 23 RCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL 70 (107)
Q Consensus 23 ~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~ 70 (107)
-||.||....+++.. ...+++.|..||+.-+...
T Consensus 8 PCPFCG~~~~~v~~~--------------~g~~~v~C~~CgA~~~~~~ 41 (64)
T PRK09710 8 PCPFCGCPSVTVKAI--------------SGYYRAKCNGCESRTGYGG 41 (64)
T ss_pred CCCCCCCceeEEEec--------------CceEEEEcCCCCcCccccc
Confidence 399999954444431 1223688999998765533
No 244
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=80.75 E-value=1.1 Score=32.25 Aligned_cols=39 Identities=21% Similarity=0.542 Sum_probs=21.3
Q ss_pred ECCCCCCCcEEEEEeeEEEEEE-EeeeecCCCCCceeCCCCCCCCC
Q 033949 23 RCINCGSTADLVEYEKVLKAFF-VPVWKWPAKEPALFCNNCNLLFP 67 (107)
Q Consensus 23 ~C~~Cg~~~~~~~~~~~f~lFF-IP~~~~~~~~~~~~C~~CG~~~~ 67 (107)
.||+||...... ..+.= ||-|+==.- -...|++||....
T Consensus 2 ~Cp~C~~~~~~~-----~~~~~~IP~F~evii-~sf~C~~CGyr~~ 41 (192)
T TIGR00310 2 DCPSCGGECETV-----MKTVNDIPYFGEVLE-TSTICEHCGYRSN 41 (192)
T ss_pred cCCCCCCCCEEE-----EEEEcCCCCcceEEE-EEEECCCCCCccc
Confidence 599999832111 11222 554441111 2567999999863
No 245
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=80.72 E-value=1.1 Score=35.82 Aligned_cols=35 Identities=14% Similarity=0.440 Sum_probs=19.6
Q ss_pred CCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 54 EPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 54 ~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
.....|+.|+.......-.. ...-.||.||+.+..
T Consensus 16 ~~~~~C~eCd~~~~~P~l~~-------~q~A~CPRC~~~l~~ 50 (418)
T COG2995 16 GHLILCPECDMLVSLPRLDS-------GQSAYCPRCGHTLTR 50 (418)
T ss_pred cceecCCCCCceeccccCCC-------CCcccCCCCCCcccc
Confidence 35667777777665432110 023567777777655
No 246
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=80.56 E-value=1.1 Score=26.23 Aligned_cols=21 Identities=29% Similarity=0.610 Sum_probs=11.6
Q ss_pred cccccCCceecCCCccCcCCCC
Q 033949 84 SKCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 84 ~~C~~CG~~i~~~~~fCP~CG~ 105 (107)
..|++||... -.-..|++||.
T Consensus 28 ~~c~~cG~~~-l~Hrvc~~cg~ 48 (57)
T COG0333 28 SVCPNCGEYK-LPHRVCLKCGY 48 (57)
T ss_pred eeccCCCCcc-cCceEcCCCCC
Confidence 4566666653 33455666664
No 247
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=80.55 E-value=0.42 Score=37.63 Aligned_cols=36 Identities=31% Similarity=0.594 Sum_probs=21.9
Q ss_pred eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC---CCccCcCCCCC
Q 033949 57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP---DFSFCPYCGSA 106 (107)
Q Consensus 57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~---~~~fCP~CG~~ 106 (107)
-.||.||..-.. ...|.+||..+++ ..-.|.-||++
T Consensus 137 g~CP~C~~~~a~--------------g~~Ce~cG~~~~~~~l~~p~~~~~g~~ 175 (391)
T PF09334_consen 137 GTCPYCGSDKAR--------------GDQCENCGRPLEPEELINPVCKICGSP 175 (391)
T ss_dssp CEETTT--SSCT--------------TTEETTTSSBEECCCSECEEETTTS-B
T ss_pred ccccCcCccccC--------------CCcccCCCCCcccccccCCcccccccc
Confidence 579999854321 3468888888875 45566666654
No 248
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=80.47 E-value=0.95 Score=34.87 Aligned_cols=42 Identities=17% Similarity=0.374 Sum_probs=30.3
Q ss_pred CCcEECCCCCC------CcEEEEE--ee--EEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 19 SGAGRCINCGS------TADLVEY--EK--VLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 19 ~~~~~C~~Cg~------~~~~~~~--~~--~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
+-++.|..||+ ++...+. .+ |++ ||||.|. +.|+.|+..+.+
T Consensus 38 Pf~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls---~~I~rF~-----~kC~~C~~~i~~ 89 (324)
T PF04502_consen 38 PFNIWCNTCGEYIYKGVRFNARKEKVGNEKYLS---TPIYRFY-----IKCPRCSNEIEF 89 (324)
T ss_pred CccCcCCCCccccccceeeeeeeEecCCCcccc---ceEEEEE-----EEcCCCCCEEee
Confidence 56788999999 2223322 34 665 9999865 569999999876
No 249
>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=80.32 E-value=2.3 Score=23.07 Aligned_cols=7 Identities=43% Similarity=1.379 Sum_probs=4.0
Q ss_pred ECCCCCC
Q 033949 23 RCINCGS 29 (107)
Q Consensus 23 ~C~~Cg~ 29 (107)
.||.||.
T Consensus 4 ~C~~Cg~ 10 (47)
T PF13005_consen 4 ACPDCGG 10 (47)
T ss_pred cCCCCCc
Confidence 4555555
No 250
>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=80.19 E-value=0.45 Score=26.43 Aligned_cols=7 Identities=57% Similarity=1.450 Sum_probs=3.8
Q ss_pred CCCCCCC
Q 033949 24 CINCGST 30 (107)
Q Consensus 24 C~~Cg~~ 30 (107)
||+||+.
T Consensus 2 CP~Cg~~ 8 (47)
T PF04606_consen 2 CPHCGSK 8 (47)
T ss_pred cCCCCCe
Confidence 5555553
No 251
>PRK11827 hypothetical protein; Provisional
Probab=80.06 E-value=2.7 Score=24.77 Aligned_cols=33 Identities=24% Similarity=0.385 Sum_probs=24.6
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL 70 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~ 70 (107)
-..||.|+.... ++.....+.|..||-.|++..
T Consensus 8 ILaCP~ckg~L~-----------------~~~~~~~Lic~~~~laYPI~d 40 (60)
T PRK11827 8 IIACPVCNGKLW-----------------YNQEKQELICKLDNLAFPLRD 40 (60)
T ss_pred heECCCCCCcCe-----------------EcCCCCeEECCccCeeccccC
Confidence 357999998542 344446899999999998854
No 252
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=79.95 E-value=0.85 Score=34.38 Aligned_cols=21 Identities=33% Similarity=0.907 Sum_probs=15.9
Q ss_pred cccccCCceecC------CCccCcCCC
Q 033949 84 SKCRFCDRLVEP------DFSFCPYCG 104 (107)
Q Consensus 84 ~~C~~CG~~i~~------~~~fCP~CG 104 (107)
..|+.||+.|.. +.-|||.|-
T Consensus 255 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 255 KPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred CCCCcCCCeeEEEEECCCccEECCCCc
Confidence 468888888865 677888884
No 253
>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=79.90 E-value=2.7 Score=30.60 Aligned_cols=13 Identities=23% Similarity=0.547 Sum_probs=7.4
Q ss_pred cccccCCceecCC
Q 033949 84 SKCRFCDRLVEPD 96 (107)
Q Consensus 84 ~~C~~CG~~i~~~ 96 (107)
..|+.||..+.++
T Consensus 137 p~C~~Cgg~lrP~ 149 (225)
T cd01411 137 PYHAKCGGVIRPD 149 (225)
T ss_pred CCCCCCCCEeCCC
Confidence 3566666665553
No 254
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=79.82 E-value=1.4 Score=34.84 Aligned_cols=9 Identities=44% Similarity=1.032 Sum_probs=5.0
Q ss_pred EECCCCCCC
Q 033949 22 GRCINCGST 30 (107)
Q Consensus 22 ~~C~~Cg~~ 30 (107)
..|++||..
T Consensus 3 l~C~~Cg~~ 11 (398)
T TIGR03844 3 LRCPGCGEV 11 (398)
T ss_pred EEeCCCCCc
Confidence 456666654
No 255
>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=79.54 E-value=1.6 Score=25.09 Aligned_cols=24 Identities=33% Similarity=0.686 Sum_probs=17.0
Q ss_pred CccccccCCceecCCCccCcC--CCC
Q 033949 82 DVSKCRFCDRLVEPDFSFCPY--CGS 105 (107)
Q Consensus 82 ~~~~C~~CG~~i~~~~~fCP~--CG~ 105 (107)
+.++|..|.+.+.+.|..|-. ||.
T Consensus 16 ~k~ICrkCyarl~~~A~nCRKkkCGh 41 (52)
T PF01020_consen 16 DKMICRKCYARLPPRATNCRKKKCGH 41 (52)
T ss_dssp S-EEETTT--EE-TTSSS-TSSSCTS
T ss_pred cceecccccCcCCCCccceecccCCC
Confidence 468899999999999999998 985
No 256
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=79.39 E-value=1.1 Score=34.54 Aligned_cols=8 Identities=25% Similarity=0.796 Sum_probs=6.0
Q ss_pred EECCCCCC
Q 033949 22 GRCINCGS 29 (107)
Q Consensus 22 ~~C~~Cg~ 29 (107)
..||.|..
T Consensus 4 ~~CP~Ck~ 11 (309)
T TIGR00570 4 QGCPRCKT 11 (309)
T ss_pred CCCCcCCC
Confidence 35888888
No 257
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=79.22 E-value=1.7 Score=33.20 Aligned_cols=33 Identities=24% Similarity=0.658 Sum_probs=23.1
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
....||.||..- ++ .+.+.+.+.|..||..++.
T Consensus 10 ~~~~Cp~Cg~~~-iv---------------~d~~~Ge~vC~~CG~Vl~e 42 (310)
T PRK00423 10 EKLVCPECGSDK-LI---------------YDYERGEIVCADCGLVIEE 42 (310)
T ss_pred cCCcCcCCCCCC-ee---------------EECCCCeEeecccCCcccc
Confidence 455799999821 11 1224589999999998855
No 258
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=79.15 E-value=1.3 Score=23.57 Aligned_cols=16 Identities=25% Similarity=0.675 Sum_probs=7.8
Q ss_pred CcEECCCCCCCcEEEE
Q 033949 20 GAGRCINCGSTADLVE 35 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~ 35 (107)
+-.+|..|||-++++.
T Consensus 5 ~~YkC~~CGniVev~~ 20 (36)
T PF06397_consen 5 EFYKCEHCGNIVEVVH 20 (36)
T ss_dssp EEEE-TTT--EEEEEE
T ss_pred cEEEccCCCCEEEEEE
Confidence 3457999999554443
No 259
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=79.13 E-value=1.2 Score=26.41 Aligned_cols=24 Identities=25% Similarity=0.718 Sum_probs=18.1
Q ss_pred CcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCC
Q 033949 20 GAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNL 64 (107)
Q Consensus 20 ~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~ 64 (107)
.-+.|.+||+ +++ .+...|..||.
T Consensus 16 tHt~CrRCG~~syh---------------------~qK~~CasCGy 40 (62)
T PRK04179 16 THIRCRRCGRHSYN---------------------VRKKYCAACGF 40 (62)
T ss_pred ccchhcccCccccc---------------------ccccchhhcCC
Confidence 4567999999 652 36778999998
No 260
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=79.11 E-value=1.3 Score=33.68 Aligned_cols=11 Identities=27% Similarity=0.422 Sum_probs=5.4
Q ss_pred CceeCCCCCCC
Q 033949 55 PALFCNNCNLL 65 (107)
Q Consensus 55 ~~~~C~~CG~~ 65 (107)
....|++||+.
T Consensus 128 ~~~~C~~cg~~ 138 (279)
T COG2816 128 WARVCPKCGHE 138 (279)
T ss_pred eeeeCCCCCCc
Confidence 34455555543
No 261
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=79.05 E-value=1.6 Score=28.04 Aligned_cols=30 Identities=20% Similarity=0.441 Sum_probs=15.4
Q ss_pred eCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCC
Q 033949 58 FCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPD 96 (107)
Q Consensus 58 ~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~ 96 (107)
.|.+||..+..+.-. .-.+||.|.++-...
T Consensus 60 ~CkkCGfef~~~~ik---------~pSRCP~CKSE~Ie~ 89 (97)
T COG3357 60 RCKKCGFEFRDDKIK---------KPSRCPKCKSEWIEE 89 (97)
T ss_pred hhcccCccccccccC---------CcccCCcchhhcccC
Confidence 466666666543211 124566666654443
No 262
>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=78.53 E-value=1.4 Score=30.06 Aligned_cols=9 Identities=22% Similarity=0.711 Sum_probs=4.5
Q ss_pred ccccccCCc
Q 033949 83 VSKCRFCDR 91 (107)
Q Consensus 83 ~~~C~~CG~ 91 (107)
-..|+.||.
T Consensus 124 f~~C~~C~k 132 (147)
T PF01927_consen 124 FWRCPGCGK 132 (147)
T ss_pred EEECCCCCC
Confidence 344555554
No 263
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=78.48 E-value=0.61 Score=35.55 Aligned_cols=14 Identities=21% Similarity=0.415 Sum_probs=7.0
Q ss_pred ceeCCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPSS 69 (107)
Q Consensus 56 ~~~C~~CG~~~~~~ 69 (107)
...||+||+.+.++
T Consensus 47 ~~vcp~c~~h~ri~ 60 (294)
T COG0777 47 LKVCPKCGHHMRIS 60 (294)
T ss_pred hhcccccCcccccC
Confidence 44455555555443
No 264
>PRK07591 threonine synthase; Validated
Probab=78.34 E-value=1.2 Score=35.42 Aligned_cols=30 Identities=27% Similarity=0.521 Sum_probs=22.4
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCC
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPD 96 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~ 96 (107)
..+.|..||..++++. .+.||.||..++..
T Consensus 17 ~~l~C~~Cg~~~~~~~------------~~~C~~cg~~l~~~ 46 (421)
T PRK07591 17 VALKCRECGAEYPLGP------------IHVCEECFGPLEVA 46 (421)
T ss_pred eEEEeCCCCCcCCCCC------------CccCCCCCCeEEEE
Confidence 4588999999987643 25799998877654
No 265
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=78.25 E-value=1.8 Score=36.52 Aligned_cols=33 Identities=18% Similarity=0.258 Sum_probs=21.8
Q ss_pred eeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949 46 PVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE 94 (107)
Q Consensus 46 P~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~ 94 (107)
|.|-++. ..-.|+.||..... ...||.||++++
T Consensus 618 ~Y~~in~--~~~~C~~CG~~~g~--------------~~~CP~CG~~~~ 650 (656)
T PRK08270 618 PYITITP--TFSICPKHGYLSGE--------------HEFCPKCGEETE 650 (656)
T ss_pred ceEEeCC--CCcccCCCCCcCCC--------------CCCCcCCcCccc
Confidence 3344443 57789999985322 357999998754
No 266
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=78.21 E-value=0.79 Score=33.20 Aligned_cols=33 Identities=24% Similarity=0.610 Sum_probs=22.7
Q ss_pred CcEECCCCCC-Cc--EEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCC
Q 033949 20 GAGRCINCGS-TA--DLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLF 66 (107)
Q Consensus 20 ~~~~C~~Cg~-~~--~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~ 66 (107)
..+.||+||. .. ++++ .....+.+.|++||...
T Consensus 5 iy~~Cp~Cg~eev~hEVik--------------~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 5 IYIECPSCGSEEVSHEVIK--------------ERGREPLVRCEECGTVH 40 (201)
T ss_pred EEEECCCCCcchhhHHHHH--------------hcCCceEEEccCCCcEe
Confidence 3568999996 32 4443 22233689999999988
No 267
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=78.10 E-value=1.5 Score=24.52 Aligned_cols=36 Identities=19% Similarity=0.383 Sum_probs=19.7
Q ss_pred eeCCCCCCCCCCCCCCC--CCC----CCCccCccccccCCce
Q 033949 57 LFCNNCNLLFPSSLPPP--PPP----PPLVSDVSKCRFCDRL 92 (107)
Q Consensus 57 ~~C~~CG~~~~~~~~~~--~~~----~~~~~~~~~C~~CG~~ 92 (107)
..|+.||..|+...-.. .|. ++.......||.||+.
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 47999999997744310 111 1111245789999986
No 268
>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=77.94 E-value=3.2 Score=29.93 Aligned_cols=13 Identities=31% Similarity=0.894 Sum_probs=7.7
Q ss_pred cccccCCceecCC
Q 033949 84 SKCRFCDRLVEPD 96 (107)
Q Consensus 84 ~~C~~CG~~i~~~ 96 (107)
..||.||..+.++
T Consensus 131 p~C~~Cgg~lrp~ 143 (224)
T cd01412 131 PRCPKCGGLLRPG 143 (224)
T ss_pred CCCCCCCCccCCc
Confidence 4566666665553
No 269
>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=77.73 E-value=1.5 Score=36.69 Aligned_cols=22 Identities=32% Similarity=0.852 Sum_probs=10.4
Q ss_pred cccccCCceecCCCccCcCCCC
Q 033949 84 SKCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 84 ~~C~~CG~~i~~~~~fCP~CG~ 105 (107)
.+|+.||......-..||.||+
T Consensus 533 siC~~CGy~~g~~~~~CP~CGs 554 (586)
T TIGR02827 533 TICNDCHHIDKRTLHRCPVCGS 554 (586)
T ss_pred eecCCCCCcCCCcCCcCcCCCC
Confidence 3466666521112255666663
No 270
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=77.72 E-value=1.1 Score=38.08 Aligned_cols=75 Identities=23% Similarity=0.460 Sum_probs=47.1
Q ss_pred ecCCCcEECCCCCCCc-EEEEEeeEEEEEEEeeeecCC--CCCceeCCCCCCCCCCCCCCCCCCCC--CccCccccccCC
Q 033949 16 VLKSGAGRCINCGSTA-DLVEYEKVLKAFFVPVWKWPA--KEPALFCNNCNLLFPSSLPPPPPPPP--LVSDVSKCRFCD 90 (107)
Q Consensus 16 ~~~~~~~~C~~Cg~~~-~~~~~~~~f~lFFIP~~~~~~--~~~~~~C~~CG~~~~~~~~~~~~~~~--~~~~~~~C~~CG 90 (107)
...++..+|+.|-+.. + |=++ ..++.-|++||=.+.+-.. .+++.+ .......|+.|-
T Consensus 63 ~ippD~a~C~~Cl~E~~d----------------p~~Rry~YpF~nCt~CGPr~~i~~~-lpydr~~t~m~~f~~C~~C~ 125 (711)
T TIGR00143 63 IIPADVATCSDCLEEMLD----------------KNDRRYLYPFISCTHCGPRFTIIEA-LPYDRENTSMADFPLCPDCA 125 (711)
T ss_pred ecCCchhhHHHHHHHhcC----------------CCcccccCCcccccCCCCCeEEeec-CCCCCCCcCCCCCcCCHHHH
Confidence 3356777899998721 1 1112 2348889999999977443 122211 112456799999
Q ss_pred ceecC--------CCccCcCCCCCC
Q 033949 91 RLVEP--------DFSFCPYCGSAL 107 (107)
Q Consensus 91 ~~i~~--------~~~fCP~CG~~l 107 (107)
+|... ...-||.||=+|
T Consensus 126 ~ey~~p~~rr~h~~~~~C~~Cgp~l 150 (711)
T TIGR00143 126 KEYKDPLDRRFHAQPIACPRCGPQL 150 (711)
T ss_pred HHhcCCccccCCCCCccCCCCCcEE
Confidence 99844 567799999543
No 271
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=77.69 E-value=2.1 Score=27.90 Aligned_cols=43 Identities=19% Similarity=0.426 Sum_probs=23.6
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCC
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSS 69 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~ 69 (107)
.+.||+||..+.++.....+ | =..+.......|+.|++-...-
T Consensus 2 p~~CpYCg~~~~l~~~~~iY-----g-~~~~~~~~~y~C~~C~AyVG~H 44 (102)
T PF11672_consen 2 PIICPYCGGPAELVDGSEIY-----G-HRYDDGPYLYVCTPCDAYVGCH 44 (102)
T ss_pred CcccCCCCCeeEEcccchhc-----C-ccCCCCceeEECCCCCceeeee
Confidence 46799999966554432211 1 1111111247788888877553
No 272
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=77.59 E-value=1.1 Score=33.34 Aligned_cols=24 Identities=25% Similarity=0.706 Sum_probs=17.8
Q ss_pred CccccccCCceecC----CCccCcCCCC
Q 033949 82 DVSKCRFCDRLVEP----DFSFCPYCGS 105 (107)
Q Consensus 82 ~~~~C~~CG~~i~~----~~~fCP~CG~ 105 (107)
..+.|+.||+.+.. ....||.||.
T Consensus 98 ~~~fC~~CG~~~~~~~~~~~~~C~~c~~ 125 (256)
T PRK00241 98 SHRFCGYCGHPMHPSKTEWAMLCPHCRE 125 (256)
T ss_pred cCccccccCCCCeecCCceeEECCCCCC
Confidence 46778888888654 4677888885
No 273
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=77.48 E-value=1.5 Score=37.31 Aligned_cols=9 Identities=22% Similarity=0.600 Sum_probs=4.4
Q ss_pred ceeCCCCCC
Q 033949 56 ALFCNNCNL 64 (107)
Q Consensus 56 ~~~C~~CG~ 64 (107)
.-.|+.||.
T Consensus 641 ~~~C~~CG~ 649 (711)
T PRK09263 641 IDECYECGF 649 (711)
T ss_pred CcccCCCCC
Confidence 344555554
No 275
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=77.16 E-value=0.93 Score=37.34 Aligned_cols=20 Identities=35% Similarity=0.688 Sum_probs=5.9
Q ss_pred ccccCCceecCCCccCcCCCC
Q 033949 85 KCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 85 ~C~~CG~~i~~~~~fCP~CG~ 105 (107)
+|++||..... ...||.||+
T Consensus 493 ~C~~CG~~~~~-~~~CP~CGs 512 (546)
T PF13597_consen 493 ICPDCGYIGGE-GDKCPKCGS 512 (546)
T ss_dssp EETTT---S---EEE-CCC--
T ss_pred cccCCCcCCCC-CCCCCCCCC
Confidence 45555554333 444555554
No 276
>PHA02998 RNA polymerase subunit; Provisional
Probab=76.96 E-value=6.2 Score=28.36 Aligned_cols=15 Identities=20% Similarity=0.503 Sum_probs=10.2
Q ss_pred ceeCCCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPSSL 70 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~ 70 (107)
+..|..||..+.+..
T Consensus 171 FYkC~~CG~~wkppk 185 (195)
T PHA02998 171 RHACRDCKKHFKPPK 185 (195)
T ss_pred EEEcCCCCCccCCcc
Confidence 456888888776543
No 277
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=76.80 E-value=1.4 Score=31.15 Aligned_cols=12 Identities=25% Similarity=0.376 Sum_probs=7.8
Q ss_pred ceeCCCCCCCCC
Q 033949 56 ALFCNNCNLLFP 67 (107)
Q Consensus 56 ~~~C~~CG~~~~ 67 (107)
...||.|+..+.
T Consensus 97 ~~RCp~CN~~L~ 108 (165)
T COG1656 97 FSRCPECNGELE 108 (165)
T ss_pred cccCcccCCEec
Confidence 556777777653
No 278
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=76.78 E-value=2.5 Score=27.81 Aligned_cols=29 Identities=21% Similarity=0.566 Sum_probs=20.6
Q ss_pred ECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCC
Q 033949 23 RCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSS 69 (107)
Q Consensus 23 ~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~ 69 (107)
.||.|++.+. |. .+..+.||.|++.....
T Consensus 4 ~CP~C~seyt-----------------Y~-dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYT-----------------YH-DGTQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcce-----------------Ee-cCCeeECcccccccccc
Confidence 4999999432 11 34689999999988554
No 279
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=76.70 E-value=2.1 Score=35.53 Aligned_cols=36 Identities=22% Similarity=0.465 Sum_probs=23.6
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC---CCccCcCCCC
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP---DFSFCPYCGS 105 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~---~~~fCP~CG~ 105 (107)
.-.||.||....- ...|.+||+.+.+ ..-.|--||+
T Consensus 142 ~g~cp~cg~~~ar--------------GD~Ce~Cg~~~~P~~l~~p~~~i~g~ 180 (558)
T COG0143 142 EGTCPKCGGEDAR--------------GDQCENCGRTLDPTELINPVCVISGA 180 (558)
T ss_pred eccCCCcCccccC--------------cchhhhccCcCCchhcCCCeeEeeCC
Confidence 5668888865422 2468888888877 3556666654
No 280
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=76.69 E-value=5 Score=34.93 Aligned_cols=35 Identities=14% Similarity=0.313 Sum_probs=20.6
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCC---CCCCCCC
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNN---CNLLFPS 68 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~---CG~~~~~ 68 (107)
....||.||....+ +++++.+.++.|++ |.....+
T Consensus 591 ~~~~CP~Cg~~~L~--------------~k~gr~G~Fl~Cs~yP~C~~t~~~ 628 (860)
T PRK06319 591 TEIDCPKCHKGKLV--------------KIWAKNRYFYGCSEYPECDYKTSE 628 (860)
T ss_pred cCcccCCCCCccee--------------EEecCCCceeeccCCccccccCCc
Confidence 34679999873222 34555556777744 6555443
No 281
>PRK11032 hypothetical protein; Provisional
Probab=76.56 E-value=1.6 Score=30.67 Aligned_cols=29 Identities=21% Similarity=0.465 Sum_probs=18.8
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
+.+.|.+||+.+.+.... ....||.||..
T Consensus 123 G~LvC~~Cg~~~~~~~p~---------~i~pCp~C~~~ 151 (160)
T PRK11032 123 GNLVCEKCHHHLAFYTPE---------VLPLCPKCGHD 151 (160)
T ss_pred ceEEecCCCCEEEecCCC---------cCCCCCCCCCC
Confidence 577888888887664421 12368888764
No 282
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=76.55 E-value=1.7 Score=37.05 Aligned_cols=56 Identities=18% Similarity=0.440 Sum_probs=38.6
Q ss_pred EECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCC----ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949 22 GRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEP----ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV 93 (107)
Q Consensus 22 ~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~----~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i 93 (107)
+.|.+||-+++.++. +||++... +.-|+.|.+.|+....+ +......-||.||=.+
T Consensus 124 ~~CT~CGPRfTIi~a-----------lPYDR~nTsM~~F~lC~~C~~EY~dP~nR-----RfHAQp~aCp~CGP~~ 183 (750)
T COG0068 124 INCTNCGPRFTIIEA-----------LPYDRENTSMADFPLCPFCDKEYKDPLNR-----RFHAQPIACPKCGPHL 183 (750)
T ss_pred cccCCCCcceeeecc-----------CCCCcccCccccCcCCHHHHHHhcCcccc-----ccccccccCcccCCCe
Confidence 459999999887775 78887644 44599999988653321 1111245799999754
No 283
>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=76.48 E-value=2.3 Score=35.17 Aligned_cols=37 Identities=24% Similarity=0.557 Sum_probs=24.0
Q ss_pred EECCCCCCCcEEE-EEeeEEEEEEEeeeecCC----CCCceeCCCCCCCCCCC
Q 033949 22 GRCINCGSTADLV-EYEKVLKAFFVPVWKWPA----KEPALFCNNCNLLFPSS 69 (107)
Q Consensus 22 ~~C~~Cg~~~~~~-~~~~~f~lFFIP~~~~~~----~~~~~~C~~CG~~~~~~ 69 (107)
+.||+||....+. +. ++|+. ..-...|++||..++..
T Consensus 201 vpCPhCg~~~~l~~~~-----------l~w~~~~~~~~a~y~C~~Cg~~i~e~ 242 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWEN-----------LKWDKGEAPETARYVCPHCGCEIEEH 242 (557)
T ss_pred ccCCCCCCCccccccc-----------eeecCCCCccceEEECCCCcCCCCHH
Confidence 4699999933322 22 44442 23488899999998653
No 284
>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=76.36 E-value=3.6 Score=29.83 Aligned_cols=13 Identities=31% Similarity=1.014 Sum_probs=7.2
Q ss_pred cccccCCceecCC
Q 033949 84 SKCRFCDRLVEPD 96 (107)
Q Consensus 84 ~~C~~CG~~i~~~ 96 (107)
..||.||..+.++
T Consensus 137 p~C~~Cgg~lrP~ 149 (222)
T cd01413 137 PRCPKCGGIIRPD 149 (222)
T ss_pred CcCCCCCCccCCC
Confidence 3566666655543
No 285
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=76.31 E-value=2.6 Score=34.36 Aligned_cols=40 Identities=20% Similarity=0.395 Sum_probs=19.0
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
...+||+|-..+...+...+-. .=...-..||.|++.+..
T Consensus 25 ~~~yCp~CL~~~p~~e~~~~~n-rC~r~Cf~CP~C~~~L~~ 64 (483)
T PF05502_consen 25 DSYYCPNCLFEVPSSEARSEKN-RCSRNCFDCPICFSPLSV 64 (483)
T ss_pred ceeECccccccCChhhheeccc-eeccccccCCCCCCccee
Confidence 4667777777765543211000 000023457777766543
No 286
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=76.28 E-value=0.76 Score=27.12 Aligned_cols=23 Identities=26% Similarity=0.504 Sum_probs=13.0
Q ss_pred ccccccCCceecC---CCccCcCCCC
Q 033949 83 VSKCRFCDRLVEP---DFSFCPYCGS 105 (107)
Q Consensus 83 ~~~C~~CG~~i~~---~~~fCP~CG~ 105 (107)
.+.|-.||++..- ++--|-.||.
T Consensus 20 iYiCgdC~~en~lk~~D~irCReCG~ 45 (62)
T KOG3507|consen 20 IYICGDCGQENTLKRGDVIRCRECGY 45 (62)
T ss_pred EEEeccccccccccCCCcEehhhcch
Confidence 4556666665543 5555666654
No 287
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=76.24 E-value=2.1 Score=27.51 Aligned_cols=44 Identities=16% Similarity=0.272 Sum_probs=11.2
Q ss_pred EECCCCCC--CcEEEE-----EeeEEEEEEEeeeecCCCCCceeCCCCCCCC
Q 033949 22 GRCINCGS--TADLVE-----YEKVLKAFFVPVWKWPAKEPALFCNNCNLLF 66 (107)
Q Consensus 22 ~~C~~Cg~--~~~~~~-----~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~ 66 (107)
-.|+-|+. .++-.+ ....|.-+.+-+.++... .+..|+.||..+
T Consensus 15 E~C~~C~~~i~~~~~~~~~C~~GH~w~RC~lT~l~i~~~-~~r~C~~C~~~~ 65 (99)
T PF12660_consen 15 EKCPICGAPIPFDDLDEAQCENGHVWPRCALTFLPIQTP-GVRVCPVCGRRA 65 (99)
T ss_dssp --------------SSEEE-TTS-EEEB-SSS-SBS-SS--EEE-TTT--EE
T ss_pred ccccccccccccCCcCEeECCCCCEEeeeeeeeeeeccC-CeeEcCCCCCEE
Confidence 46888888 322211 111444445555555543 346666666554
No 288
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=76.20 E-value=1.5 Score=24.76 Aligned_cols=36 Identities=22% Similarity=0.319 Sum_probs=18.2
Q ss_pred ceeCCCCCCCCCCCCCC----CCCCCCCccCccccccCCcee
Q 033949 56 ALFCNNCNLLFPSSLPP----PPPPPPLVSDVSKCRFCDRLV 93 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~----~~~~~~~~~~~~~C~~CG~~i 93 (107)
...||.||+.+...... .... .......||=|.+.+
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~H~--~~~~~v~CPiC~~~~ 41 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDEHR--SESKNVVCPICSSRV 41 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhHCc--CCCCCccCCCchhhh
Confidence 35799999944321110 0011 111356788887654
No 289
>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=76.10 E-value=2.6 Score=28.28 Aligned_cols=30 Identities=23% Similarity=0.389 Sum_probs=18.5
Q ss_pred EECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCC
Q 033949 22 GRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLL 65 (107)
Q Consensus 22 ~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~ 65 (107)
+.|+.|++.-+.+.. +.+...+.|..||+.
T Consensus 94 VlC~~C~spdT~l~k--------------~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 94 VLCPECGSPDTELIK--------------EGRLIFLKCKACGAS 123 (125)
T ss_dssp SSCTSTSSSSEEEEE--------------ETTCCEEEETTTSCE
T ss_pred EEcCCCCCCccEEEE--------------cCCEEEEEecccCCc
Confidence 569999993322221 124478888888874
No 290
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=75.92 E-value=1.9 Score=32.15 Aligned_cols=29 Identities=21% Similarity=0.381 Sum_probs=16.1
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV 93 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i 93 (107)
..+|+.||+.+...... ....|++||...
T Consensus 99 ~~fC~~CG~~~~~~~~~---------~~~~C~~c~~~~ 127 (256)
T PRK00241 99 HRFCGYCGHPMHPSKTE---------WAMLCPHCRERY 127 (256)
T ss_pred CccccccCCCCeecCCc---------eeEECCCCCCEE
Confidence 44677777765443211 235677777654
No 291
>PLN03086 PRLI-interacting factor K; Provisional
Probab=75.86 E-value=3.4 Score=34.44 Aligned_cols=49 Identities=22% Similarity=0.467 Sum_probs=27.5
Q ss_pred CceeCCCCCCCCCCCCCCC--CCCCCCccCcccccc--CCceecC----CCccCcCCCCC
Q 033949 55 PALFCNNCNLLFPSSLPPP--PPPPPLVSDVSKCRF--CDRLVEP----DFSFCPYCGSA 106 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~--~~~~~~~~~~~~C~~--CG~~i~~----~~~fCP~CG~~ 106 (107)
..+.|++|...++...... ... ......||+ ||..+.. +...|++||..
T Consensus 406 ~~V~C~NC~~~i~l~~l~lHe~~C---~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~ 462 (567)
T PLN03086 406 DTVECRNCKHYIPSRSIALHEAYC---SRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQA 462 (567)
T ss_pred CeEECCCCCCccchhHHHHHHhhC---CCcceeCCcccccceeeccccccCccCCCCCCc
Confidence 4678999999986643210 000 002345764 7766644 34457777653
No 292
>KOG2612 consensus Predicted integral membrane protein [Function unknown]
Probab=75.59 E-value=1.2 Score=28.50 Aligned_cols=21 Identities=29% Similarity=0.512 Sum_probs=15.3
Q ss_pred EcccccceeeecCCCcEECCCCCC
Q 033949 6 VGGVNQQVSRVLKSGAGRCINCGS 29 (107)
Q Consensus 6 ifG~~~~~k~~~~~~~~~C~~Cg~ 29 (107)
|||++.. -..+...+|+||++
T Consensus 62 I~Giqkq---aek~~~~hCeNC~R 82 (103)
T KOG2612|consen 62 IFGIQKQ---AEKPMDCHCENCDR 82 (103)
T ss_pred hhhhhhh---ccCCccccCCCCcc
Confidence 6788752 34567788999998
No 293
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=75.35 E-value=1.8 Score=36.27 Aligned_cols=22 Identities=32% Similarity=0.756 Sum_probs=12.5
Q ss_pred ccccccCCceecCCCccCcCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~ 105 (107)
..+|++||.. ...-..||.||+
T Consensus 559 ~~~C~~CGy~-g~~~~~CP~CG~ 580 (618)
T PRK14704 559 VDRCKCCSYH-GVIGNECPSCGN 580 (618)
T ss_pred CeecCCCCCC-CCcCccCcCCCC
Confidence 3457777763 222256777775
No 294
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=75.20 E-value=1.4 Score=30.01 Aligned_cols=9 Identities=33% Similarity=1.139 Sum_probs=4.2
Q ss_pred CCCCCCCCC
Q 033949 59 CNNCNLLFP 67 (107)
Q Consensus 59 C~~CG~~~~ 67 (107)
|+.||..++
T Consensus 4 Ct~Cg~~f~ 12 (131)
T PF09845_consen 4 CTKCGRVFE 12 (131)
T ss_pred cCcCCCCcC
Confidence 444444443
No 295
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=75.19 E-value=2 Score=30.15 Aligned_cols=38 Identities=24% Similarity=0.479 Sum_probs=20.8
Q ss_pred CCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949 24 CINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP 67 (107)
Q Consensus 24 C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~ 67 (107)
||.||+ ...... .+-=||-|+==.- -...|++||....
T Consensus 1 CP~Cg~~~~~~~~-----~~~~IP~F~evii-~sf~C~~CGyr~~ 39 (163)
T TIGR00340 1 CPVCGSRTLKAVT-----YDYDIPYFGKIML-STYICEKCGYRST 39 (163)
T ss_pred CCCCCCcceEeee-----EeccCCCcceEEE-EEEECCCCCCchh
Confidence 899998 333321 1233444331110 2557999999863
No 296
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=74.98 E-value=1.4 Score=33.44 Aligned_cols=22 Identities=32% Similarity=0.812 Sum_probs=17.3
Q ss_pred ccccccCCceecC------CCccCcCCC
Q 033949 83 VSKCRFCDRLVEP------DFSFCPYCG 104 (107)
Q Consensus 83 ~~~C~~CG~~i~~------~~~fCP~CG 104 (107)
...|+.||..|.. +.-|||.|-
T Consensus 245 GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 245 GEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 4568888888866 788888884
No 297
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=74.96 E-value=1.2 Score=26.32 Aligned_cols=19 Identities=26% Similarity=0.777 Sum_probs=14.4
Q ss_pred ccccccCCceecCCCccCc
Q 033949 83 VSKCRFCDRLVEPDFSFCP 101 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP 101 (107)
.++|+-||+.|++|-.+|+
T Consensus 8 H~HC~VCg~aIp~de~~CS 26 (64)
T COG4068 8 HRHCVVCGKAIPPDEQVCS 26 (64)
T ss_pred CccccccCCcCCCccchHH
Confidence 3578888888888877775
No 298
>PRK10220 hypothetical protein; Provisional
Probab=74.68 E-value=3.4 Score=27.27 Aligned_cols=30 Identities=17% Similarity=0.504 Sum_probs=21.5
Q ss_pred ECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949 23 RCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL 70 (107)
Q Consensus 23 ~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~ 70 (107)
.||.|++.+. |. .+..+.||.|++......
T Consensus 5 ~CP~C~seyt-----------------Y~-d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 5 HCPKCNSEYT-----------------YE-DNGMYICPECAHEWNDAE 34 (111)
T ss_pred cCCCCCCcce-----------------Ec-CCCeEECCcccCcCCccc
Confidence 4999999432 12 346899999999886644
No 299
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=74.63 E-value=0.62 Score=34.09 Aligned_cols=36 Identities=19% Similarity=0.464 Sum_probs=25.2
Q ss_pred eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCC
Q 033949 57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~ 105 (107)
..|+.|+..++... ..|+.||.++...+-.|+.|-.
T Consensus 25 ~~C~~C~~~~~~~~-------------~~C~~C~~~l~~~~~~~~~~~~ 60 (225)
T COG1040 25 GLCSGCQADLPLIG-------------NLCPLCGLPLSSHACRCGECLA 60 (225)
T ss_pred CcChhhhhchhHHH-------------hhhHhhhChhccccccCHHHhc
Confidence 67888888775422 2688888888877777776643
No 300
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=74.52 E-value=1.1 Score=33.59 Aligned_cols=32 Identities=25% Similarity=0.385 Sum_probs=9.0
Q ss_pred eeCCCCCCCCCC-CCCCCCCCCCCccCccccccCCceec
Q 033949 57 LFCNNCNLLFPS-SLPPPPPPPPLVSDVSKCRFCDRLVE 94 (107)
Q Consensus 57 ~~C~~CG~~~~~-~~~~~~~~~~~~~~~~~C~~CG~~i~ 94 (107)
..||+||+..-. -....++ ....|++|+.+-+
T Consensus 32 ~yCP~Cg~~~L~~f~NN~PV------aDF~C~~C~eeyE 64 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFENNRPV------ADFYCPNCNEEYE 64 (254)
T ss_dssp ---TTT--SS-EE--------------EEE-TTT--EEE
T ss_pred CcCCCCCChhHhhccCCCcc------ceeECCCCchHHh
Confidence 567777776211 1111111 2456777776654
No 301
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=74.30 E-value=1.9 Score=36.95 Aligned_cols=22 Identities=41% Similarity=0.798 Sum_probs=12.9
Q ss_pred ccccccCCceecCCCccCcCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~ 105 (107)
..+|+.||..-. ....||.||+
T Consensus 680 ~~~C~~CG~~~~-~~~~CP~CG~ 701 (735)
T PRK07111 680 VDRCPVCGYLGV-IEDKCPKCGS 701 (735)
T ss_pred CeecCCCCCCCC-cCccCcCCCC
Confidence 345777775322 3467777774
No 302
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=73.69 E-value=1.6 Score=32.31 Aligned_cols=23 Identities=26% Similarity=0.723 Sum_probs=18.4
Q ss_pred ccccccCCceecCCCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
...|+.||. +....-.||.||..
T Consensus 309 S~~C~~cg~-~~~r~~~C~~cg~~ 331 (364)
T COG0675 309 SKTCPCCGH-LSGRLFKCPRCGFV 331 (364)
T ss_pred cccccccCC-ccceeEECCCCCCe
Confidence 468999999 55566789999974
No 303
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=73.54 E-value=2.1 Score=38.16 Aligned_cols=37 Identities=22% Similarity=0.496 Sum_probs=20.8
Q ss_pred eeecCCCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCC
Q 033949 14 SRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLF 66 (107)
Q Consensus 14 k~~~~~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~ 66 (107)
|.+.....-+|.-||-.+.+-. + .+.++.|..||...
T Consensus 10 k~~~~~~~qiCqICGD~vg~~~---------------~-Ge~FVAC~eC~FPV 46 (1079)
T PLN02638 10 KPMKHGGGQVCQICGDNVGKTV---------------D-GEPFVACDVCAFPV 46 (1079)
T ss_pred CCccccCCceeeecccccCcCC---------------C-CCEEEEeccCCCcc
Confidence 3444445557888887332111 1 22377788887764
No 304
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=73.49 E-value=4.6 Score=29.10 Aligned_cols=36 Identities=25% Similarity=0.426 Sum_probs=24.9
Q ss_pred cEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCC
Q 033949 21 AGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLP 71 (107)
Q Consensus 21 ~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~ 71 (107)
-+.|+.|++ .-.+++. .+...+.|..||+.-.++..
T Consensus 98 yV~C~~C~~pdT~l~k~---------------~~~~~l~C~aCGa~~~v~~~ 134 (201)
T PRK12336 98 YVICSECGLPDTRLVKE---------------DRVLMLRCDACGAHRPVKKR 134 (201)
T ss_pred eEECCCCCCCCcEEEEc---------------CCeEEEEcccCCCCcccccc
Confidence 478999999 3233221 23468899999999877544
No 305
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=73.34 E-value=2.6 Score=26.71 Aligned_cols=38 Identities=18% Similarity=0.357 Sum_probs=22.9
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
.-.|++|++.+..-+. .|+-.- -...-+|.+|++.|+.
T Consensus 33 rS~C~~C~~~L~~~~l-IPi~S~-l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDL-IPILSY-LLLRGRCRYCGAPIPP 70 (92)
T ss_pred CCcCcCCCCcCccccc-chHHHH-HHhCCCCcccCCCCCh
Confidence 4579999998855331 111000 0135689999998875
No 306
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=73.32 E-value=3.6 Score=23.26 Aligned_cols=36 Identities=19% Similarity=0.368 Sum_probs=21.0
Q ss_pred eeCCCCCCCCCCCCCCC--CCC----CCCccCccccccCCce
Q 033949 57 LFCNNCNLLFPSSLPPP--PPP----PPLVSDVSKCRFCDRL 92 (107)
Q Consensus 57 ~~C~~CG~~~~~~~~~~--~~~----~~~~~~~~~C~~CG~~ 92 (107)
..|+.||..|+...-.. .|. ++.......||.||+.
T Consensus 2 y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 2 YECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred cCCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 46999999998643210 111 0101135689999975
No 307
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=73.24 E-value=1.2 Score=32.33 Aligned_cols=44 Identities=18% Similarity=0.325 Sum_probs=24.5
Q ss_pred CCCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949 18 KSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP 67 (107)
Q Consensus 18 ~~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~ 67 (107)
....+.||.||+...++.+ +.=||-|. ..-.+...|.+||....
T Consensus 11 ~~~~~~CPvCg~~l~~~~~-----~~~IPyFG-~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 11 FETRIDCPVCGGTLKAHMY-----LYDIPYFG-EVLISTGVCERCGYRST 54 (201)
T ss_pred eeeeecCCcccceeeEEEe-----eecCCccc-eEEEEEEEccccCCccc
Confidence 3456779999994333322 12233332 11124677999998763
No 308
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=73.19 E-value=2.2 Score=25.10 Aligned_cols=20 Identities=20% Similarity=0.177 Sum_probs=10.4
Q ss_pred cccccCCceecCCCccCcCCCC
Q 033949 84 SKCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 84 ~~C~~CG~~i~~~~~fCP~CG~ 105 (107)
..|++||+...+. ..|| ||.
T Consensus 28 ~~c~~cg~~~~pH-~vc~-cG~ 47 (60)
T PRK01110 28 SVDKTTGEYHLPH-HVSP-KGY 47 (60)
T ss_pred eEcCCCCceeccc-eecC-Ccc
Confidence 4566666664442 2366 663
No 309
>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=73.18 E-value=2.9 Score=30.11 Aligned_cols=45 Identities=20% Similarity=0.438 Sum_probs=20.1
Q ss_pred ecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCC
Q 033949 49 KWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPD 96 (107)
Q Consensus 49 ~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~ 96 (107)
...-.-..+.|..|+..+..+.....+. ......||+||..+.++
T Consensus 102 elHG~~~~~~C~~C~~~~~~~~~~~~~~---~~~~p~C~~Cg~~lrP~ 146 (218)
T cd01407 102 ELHGSLFRVRCTKCGKEYPRDELQADID---REEVPRCPKCGGLLRPD 146 (218)
T ss_pred ECcCCcCcceeCCCcCCCcHHHHhHhhc---cCCCCcCCCCCCccCCC
Confidence 3333334566666666554321000000 00134577777666553
No 310
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=73.06 E-value=2.9 Score=33.44 Aligned_cols=12 Identities=17% Similarity=0.503 Sum_probs=6.2
Q ss_pred CceeCCCCCCCC
Q 033949 55 PALFCNNCNLLF 66 (107)
Q Consensus 55 ~~~~C~~CG~~~ 66 (107)
+...||.||+.+
T Consensus 29 ~~a~CpRCg~~L 40 (419)
T PRK15103 29 QKAACPRCGTTL 40 (419)
T ss_pred CeeECCCCCCCC
Confidence 345555555554
No 311
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=73.03 E-value=0.98 Score=25.84 Aligned_cols=15 Identities=13% Similarity=0.392 Sum_probs=11.5
Q ss_pred ceeCCCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPSSL 70 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~ 70 (107)
.++||.||+...+..
T Consensus 24 eIKCpRC~tiN~~~a 38 (51)
T PF10122_consen 24 EIKCPRCKTINHVRA 38 (51)
T ss_pred EEECCCCCccceEec
Confidence 678999998876644
No 312
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=72.91 E-value=0.4 Score=36.58 Aligned_cols=10 Identities=40% Similarity=0.800 Sum_probs=7.9
Q ss_pred CcEECCCCCC
Q 033949 20 GAGRCINCGS 29 (107)
Q Consensus 20 ~~~~C~~Cg~ 29 (107)
....||-||+
T Consensus 184 ~~~~CPvCGS 193 (308)
T COG3058 184 SRQYCPVCGS 193 (308)
T ss_pred ccccCCCcCC
Confidence 4446999999
No 313
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=72.87 E-value=0.53 Score=29.23 Aligned_cols=14 Identities=21% Similarity=0.453 Sum_probs=7.3
Q ss_pred CceeCCCCCCCCCC
Q 033949 55 PALFCNNCNLLFPS 68 (107)
Q Consensus 55 ~~~~C~~CG~~~~~ 68 (107)
|...|..||..++.
T Consensus 11 Y~Y~c~~cg~~~dv 24 (82)
T COG2331 11 YSYECTECGNRFDV 24 (82)
T ss_pred eEEeecccchHHHH
Confidence 44455555555543
No 314
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=72.79 E-value=1.3 Score=26.72 Aligned_cols=23 Identities=35% Similarity=0.658 Sum_probs=14.9
Q ss_pred ccccccCCceecCC------CccCcCCCC
Q 033949 83 VSKCRFCDRLVEPD------FSFCPYCGS 105 (107)
Q Consensus 83 ~~~C~~CG~~i~~~------~~fCP~CG~ 105 (107)
...|-.|+.+...+ ..+||.|+.
T Consensus 41 ~v~Cg~C~~~~~~~~~~c~~~~~C~~C~~ 69 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEYSCGADYFCPICGL 69 (71)
T ss_dssp EEEETTT--EEES-SBTT--SEEETTTTE
T ss_pred CeECCCCCCccChhhhhcCCCccCcCcCC
Confidence 56788888887774 358888874
No 315
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=72.74 E-value=2.2 Score=30.45 Aligned_cols=12 Identities=42% Similarity=1.132 Sum_probs=6.3
Q ss_pred ceeCCCCCCCCC
Q 033949 56 ALFCNNCNLLFP 67 (107)
Q Consensus 56 ~~~C~~CG~~~~ 67 (107)
.+.|.-|+..++
T Consensus 139 ~~rC~GC~~~f~ 150 (177)
T COG1439 139 RLRCHGCKRIFP 150 (177)
T ss_pred eEEEecCceecC
Confidence 444555555554
No 316
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=72.57 E-value=2 Score=32.41 Aligned_cols=21 Identities=29% Similarity=0.744 Sum_probs=9.9
Q ss_pred cccccCCceecCCCccCcCCC
Q 033949 84 SKCRFCDRLVEPDFSFCPYCG 104 (107)
Q Consensus 84 ~~C~~CG~~i~~~~~fCP~CG 104 (107)
..|.+||.....=.-.||.||
T Consensus 355 ~~c~~cg~~~~~~~~~c~~c~ 375 (389)
T PRK11788 355 YRCRNCGFTARTLYWHCPSCK 375 (389)
T ss_pred EECCCCCCCCccceeECcCCC
Confidence 334444444444444444444
No 317
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=72.54 E-value=3.4 Score=34.82 Aligned_cols=33 Identities=15% Similarity=0.484 Sum_probs=20.1
Q ss_pred EeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 45 VPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 45 IP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
||-|-++. ..-.|+.||..... ....||.||.+
T Consensus 557 i~Yf~in~--~~~iC~~CG~~~~g-------------~~~~CP~CGs~ 589 (623)
T PRK08271 557 CNYFAFNV--KITICNDCHHIDKR-------------TGKRCPICGSE 589 (623)
T ss_pred CceEEeCC--CCccCCCCCCcCCC-------------CCcCCcCCCCc
Confidence 34444453 57778899876322 13579999854
No 318
>PRK01343 zinc-binding protein; Provisional
Probab=72.51 E-value=2.2 Score=24.93 Aligned_cols=13 Identities=15% Similarity=0.409 Sum_probs=8.3
Q ss_pred ccccccCCceecC
Q 033949 83 VSKCRFCDRLVEP 95 (107)
Q Consensus 83 ~~~C~~CG~~i~~ 95 (107)
.+.||.||++...
T Consensus 9 ~~~CP~C~k~~~~ 21 (57)
T PRK01343 9 TRPCPECGKPSTR 21 (57)
T ss_pred CCcCCCCCCcCcC
Confidence 4567777776553
No 319
>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=72.22 E-value=1.7 Score=29.27 Aligned_cols=33 Identities=12% Similarity=0.269 Sum_probs=16.7
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE 94 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~ 94 (107)
+...|+.||..+...... ....+.|+.||.++.
T Consensus 122 ~~~~C~~C~~~~~r~~~~-------~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 122 YVYRCPSCGREYKRHRRS-------KRKRYRCGRCGGPLV 154 (157)
T ss_pred eEEEcCCCCCEeeeeccc-------chhhEECCCCCCEEE
Confidence 566677777665332211 012355666666543
No 320
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=72.05 E-value=3.2 Score=28.49 Aligned_cols=35 Identities=20% Similarity=0.222 Sum_probs=23.1
Q ss_pred eecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949 48 WKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV 93 (107)
Q Consensus 48 ~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i 93 (107)
|..+ +-++..||.|+..+..... ..+.|++|+..+
T Consensus 27 I~~~-~~~Y~aC~~C~kkv~~~~~----------~~~~C~~C~~~~ 61 (166)
T cd04476 27 IKPD-NWWYPACPGCNKKVVEEGN----------GTYRCEKCNKSV 61 (166)
T ss_pred EcCC-CeEEccccccCcccEeCCC----------CcEECCCCCCcC
Confidence 3344 3468889999888654321 257899998876
No 321
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=71.93 E-value=2.3 Score=36.29 Aligned_cols=24 Identities=38% Similarity=0.653 Sum_probs=18.1
Q ss_pred ccccccCCceecCCCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
...|..||+..+...+-||.||+.
T Consensus 641 i~~C~~cg~~~~~~~~~Cp~CG~~ 664 (700)
T COG1328 641 ISVCNRCGYSGEGLRTRCPKCGSE 664 (700)
T ss_pred ceeeccCCcccccccccCCCCCCc
Confidence 456888888877666668888864
No 322
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=71.80 E-value=3 Score=29.10 Aligned_cols=39 Identities=21% Similarity=0.379 Sum_probs=19.5
Q ss_pred EECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCC
Q 033949 22 GRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLF 66 (107)
Q Consensus 22 ~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~ 66 (107)
..||+||+.... ..-+-=||.|+=-.= ....|++||...
T Consensus 2 s~Cp~C~~~~~~-----~~~~~~IP~F~evii-~sf~C~~CGyk~ 40 (161)
T PF03367_consen 2 SLCPNCGENGTT-----RILLTDIPYFKEVII-MSFECEHCGYKN 40 (161)
T ss_dssp EE-TTTSSCCEE-----EEEEEEETTTEEEEE-EEEE-TTT--EE
T ss_pred CcCCCCCCCcEE-----EEEEEcCCCCceEEE-EEeECCCCCCEe
Confidence 479999993321 113445665552211 255799999976
No 323
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=71.68 E-value=5.8 Score=26.60 Aligned_cols=31 Identities=19% Similarity=0.349 Sum_probs=18.7
Q ss_pred CCCceeCC--CCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949 53 KEPALFCN--NCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV 93 (107)
Q Consensus 53 ~~~~~~C~--~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i 93 (107)
+-.+..|| .|+..+....+ ..+.|++|+..+
T Consensus 15 ~~~Y~aC~~~~C~kKv~~~~~----------~~y~C~~C~~~~ 47 (146)
T PF08646_consen 15 NWYYPACPNEKCNKKVTENGD----------GSYRCEKCNKTV 47 (146)
T ss_dssp TTEEEE-TSTTTS-B-EEETT----------TEEEETTTTEEE
T ss_pred CcEECCCCCccCCCEeecCCC----------cEEECCCCCCcC
Confidence 33588899 89887644321 247888888876
No 324
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=71.57 E-value=1.9 Score=38.34 Aligned_cols=25 Identities=32% Similarity=0.751 Sum_probs=19.3
Q ss_pred CccccccCCceecCCCccCcCCCCC
Q 033949 82 DVSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 82 ~~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
..++|..||+....+.+.||.||++
T Consensus 693 tIKrC~dcg~q~~~~~~~cP~Cgs~ 717 (1187)
T COG1110 693 TIKRCRDCGEQFVDSEDKCPRCGSR 717 (1187)
T ss_pred HHHHHhhcCceeccccccCCCCCCc
Confidence 3567888888887777788888874
No 325
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=71.34 E-value=5 Score=24.38 Aligned_cols=37 Identities=14% Similarity=0.355 Sum_probs=24.1
Q ss_pred EECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCC
Q 033949 22 GRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLP 71 (107)
Q Consensus 22 ~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~ 71 (107)
..||.|+....+.. |.=+. ..++.|-.||+.......
T Consensus 9 a~CP~C~~~D~i~~------------~~e~~-ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 9 AVCPKCQAMDTIMM------------WRENG-VEYVECVECGYTERQPDQ 45 (71)
T ss_pred ccCCCCcCccEEEE------------EEeCC-ceEEEecCCCCeeccCCc
Confidence 47999999333222 11122 369999999998866443
No 326
>PRK06450 threonine synthase; Validated
Probab=71.30 E-value=3 Score=32.19 Aligned_cols=12 Identities=25% Similarity=0.628 Sum_probs=6.7
Q ss_pred eeCCCCCCCCCC
Q 033949 57 LFCNNCNLLFPS 68 (107)
Q Consensus 57 ~~C~~CG~~~~~ 68 (107)
..||.||..++.
T Consensus 19 ~~C~~cg~~l~~ 30 (338)
T PRK06450 19 IRCKKCGGPFEI 30 (338)
T ss_pred ccCCcCCCEeEE
Confidence 456666655544
No 327
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=71.22 E-value=2.6 Score=36.13 Aligned_cols=23 Identities=26% Similarity=0.725 Sum_probs=19.1
Q ss_pred cccccCCceec--CCCccCcCCCCC
Q 033949 84 SKCRFCDRLVE--PDFSFCPYCGSA 106 (107)
Q Consensus 84 ~~C~~CG~~i~--~~~~fCP~CG~~ 106 (107)
..||.||..+. .+-..|..||.+
T Consensus 725 ~~Cp~Cg~~l~~~~GC~~C~~CG~s 749 (752)
T PRK08665 725 GACPECGSILEHEEGCVVCHSCGYS 749 (752)
T ss_pred CCCCCCCcccEECCCCCcCCCCCCC
Confidence 46999998876 489999999974
No 328
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.09 E-value=1.9 Score=28.51 Aligned_cols=26 Identities=23% Similarity=0.400 Sum_probs=14.2
Q ss_pred eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
..||.||..+-+++ .+|++|+..+..
T Consensus 7 ~~cPvcg~~~iVTe-------------L~c~~~etTVrg 32 (122)
T COG3877 7 NRCPVCGRKLIVTE-------------LKCSNCETTVRG 32 (122)
T ss_pred CCCCcccccceeEE-------------EecCCCCceEec
Confidence 45666666554322 456666665544
No 329
>PRK07220 DNA topoisomerase I; Validated
Probab=70.80 E-value=6.9 Score=33.47 Aligned_cols=9 Identities=56% Similarity=1.313 Sum_probs=7.3
Q ss_pred EECCCCCCC
Q 033949 22 GRCINCGST 30 (107)
Q Consensus 22 ~~C~~Cg~~ 30 (107)
..||.||..
T Consensus 590 ~~CP~Cg~~ 598 (740)
T PRK07220 590 GKCPLCGSD 598 (740)
T ss_pred cccccCCCe
Confidence 479999984
No 330
>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=70.50 E-value=6 Score=23.29 Aligned_cols=38 Identities=18% Similarity=0.355 Sum_probs=23.9
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCC
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLP 71 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~ 71 (107)
...||.|+....+.. |.=+. ...+.|-.||+.......
T Consensus 9 GA~CP~C~~~Dtl~~------------~~e~~-~e~vECv~Cg~~~~~~~~ 46 (59)
T TIGR02443 9 GAVCPACSAQDTLAM------------WKENN-IELVECVECGYQEQQKDQ 46 (59)
T ss_pred cccCCCCcCccEEEE------------EEeCC-ceEEEeccCCCccccCCc
Confidence 347999999333221 11122 258999999998766443
No 331
>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=70.45 E-value=5 Score=21.33 Aligned_cols=8 Identities=63% Similarity=1.535 Sum_probs=5.5
Q ss_pred EECCCCCC
Q 033949 22 GRCINCGS 29 (107)
Q Consensus 22 ~~C~~Cg~ 29 (107)
..||.||.
T Consensus 4 ~pCP~CGG 11 (37)
T smart00778 4 GPCPNCGG 11 (37)
T ss_pred cCCCCCCC
Confidence 35777777
No 332
>COG1773 Rubredoxin [Energy production and conversion]
Probab=70.36 E-value=5.5 Score=23.11 Aligned_cols=15 Identities=13% Similarity=0.496 Sum_probs=11.8
Q ss_pred ceeCCCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPSSL 70 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~ 70 (107)
...|..||..|+.++
T Consensus 3 ~~~C~~CG~vYd~e~ 17 (55)
T COG1773 3 RWRCSVCGYVYDPEK 17 (55)
T ss_pred ceEecCCceEecccc
Confidence 467999999997744
No 333
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=69.97 E-value=2.2 Score=24.74 Aligned_cols=26 Identities=19% Similarity=0.432 Sum_probs=17.4
Q ss_pred CcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCC
Q 033949 20 GAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLF 66 (107)
Q Consensus 20 ~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~ 66 (107)
.-+.|.+||+ +++ .+...|..||..-
T Consensus 14 tH~~CrRCG~~syH---------------------~qK~~CasCGyp~ 40 (55)
T PF01907_consen 14 THTLCRRCGRRSYH---------------------IQKKTCASCGYPA 40 (55)
T ss_dssp SEEE-TTTSSEEEE---------------------TTTTEETTTBTTT
T ss_pred cEeeecccCCeeee---------------------cCCCcccccCCCc
Confidence 3457999999 542 3567888888764
No 334
>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=69.92 E-value=3.2 Score=29.84 Aligned_cols=13 Identities=15% Similarity=0.411 Sum_probs=6.9
Q ss_pred CceeCCCCCCCCC
Q 033949 55 PALFCNNCNLLFP 67 (107)
Q Consensus 55 ~~~~C~~CG~~~~ 67 (107)
....|+.|+..+.
T Consensus 94 ~~~~C~~C~~~~~ 106 (206)
T cd01410 94 FIEVCKSCGPEYV 106 (206)
T ss_pred CcccCCCCCCccc
Confidence 4555666665443
No 335
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=69.82 E-value=4.1 Score=34.28 Aligned_cols=25 Identities=20% Similarity=0.473 Sum_probs=16.9
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
..-.|+.||..+.- ....||.||..
T Consensus 567 ~~~~C~~CG~~~~g-------------~~~~CP~CGs~ 591 (625)
T PRK08579 567 AITVCNKCGRSTTG-------------LYTRCPRCGSE 591 (625)
T ss_pred CCccCCCCCCccCC-------------CCCcCcCCCCc
Confidence 57789999985421 13479999854
No 336
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=69.77 E-value=2.7 Score=33.83 Aligned_cols=11 Identities=27% Similarity=0.591 Sum_probs=5.3
Q ss_pred eCCCCCCCCCC
Q 033949 58 FCNNCNLLFPS 68 (107)
Q Consensus 58 ~C~~CG~~~~~ 68 (107)
.||.||..++.
T Consensus 352 ~Cp~Cg~~m~S 362 (421)
T COG1571 352 VCPRCGGRMKS 362 (421)
T ss_pred CCCccCCchhh
Confidence 35555555443
No 337
>PRK11595 DNA utilization protein GntX; Provisional
Probab=69.71 E-value=2.2 Score=30.99 Aligned_cols=8 Identities=38% Similarity=1.003 Sum_probs=4.3
Q ss_pred eCCCCCCC
Q 033949 58 FCNNCNLL 65 (107)
Q Consensus 58 ~C~~CG~~ 65 (107)
.|+.||..
T Consensus 36 ~C~~Cg~~ 43 (227)
T PRK11595 36 CCPQCGLP 43 (227)
T ss_pred cCccCCCc
Confidence 45556544
No 338
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=69.65 E-value=5 Score=30.02 Aligned_cols=18 Identities=11% Similarity=0.296 Sum_probs=10.3
Q ss_pred cCCCCCceeCCCCCCCCC
Q 033949 50 WPAKEPALFCNNCNLLFP 67 (107)
Q Consensus 50 ~~~~~~~~~C~~CG~~~~ 67 (107)
++-+-....|..||..+.
T Consensus 116 lHGsl~~~~C~~C~~~~~ 133 (250)
T COG0846 116 LHGSLKRVRCSKCGNQYY 133 (250)
T ss_pred eccceeeeEeCCCcCccc
Confidence 333434566777776665
No 339
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.56 E-value=2.5 Score=32.27 Aligned_cols=12 Identities=42% Similarity=0.930 Sum_probs=8.8
Q ss_pred cccccCCceecC
Q 033949 84 SKCRFCDRLVEP 95 (107)
Q Consensus 84 ~~C~~CG~~i~~ 95 (107)
..||.||++.++
T Consensus 277 f~Cp~Cg~~~~~ 288 (298)
T KOG2879|consen 277 FTCPLCGENVEP 288 (298)
T ss_pred cccCccCCCCcc
Confidence 578888887763
No 340
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=69.30 E-value=2.8 Score=29.85 Aligned_cols=20 Identities=35% Similarity=0.923 Sum_probs=18.0
Q ss_pred ccccccCCceecCCCccCcC
Q 033949 83 VSKCRFCDRLVEPDFSFCPY 102 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~ 102 (107)
...||.||.+|+++-.+||.
T Consensus 156 RP~CPlCg~PldP~GH~Cpr 175 (177)
T TIGR03847 156 RPPCPLCGRPIDPDGHICPR 175 (177)
T ss_pred CCCCCCCCCCCCCCCccCCC
Confidence 56799999999999999984
No 341
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=69.14 E-value=3.4 Score=34.79 Aligned_cols=35 Identities=17% Similarity=0.328 Sum_probs=20.5
Q ss_pred eCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC---CCccCcCCCCC
Q 033949 58 FCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP---DFSFCPYCGSA 106 (107)
Q Consensus 58 ~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~---~~~fCP~CG~~ 106 (107)
.||.||+.-. ....|.+||..+++ .-..|.-||++
T Consensus 141 ~cp~C~~~d~--------------~g~~ce~cg~~~~~~~l~~~~~~~~g~~ 178 (673)
T PRK00133 141 TCPKCGAEDQ--------------YGDNCEVCGATYSPTELINPKSAISGAT 178 (673)
T ss_pred ccCCCCCccc--------------CCchhhhccccCChHhhcCCccccCCCc
Confidence 4888887611 12347777776554 23457777765
No 342
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=69.10 E-value=4.6 Score=34.63 Aligned_cols=23 Identities=30% Similarity=0.530 Sum_probs=15.7
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCc
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDR 91 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~ 91 (107)
..-.|+.||..-.+ ...||.||.
T Consensus 679 ~~~~C~~CG~~~~~--------------~~~CP~CG~ 701 (735)
T PRK07111 679 PVDRCPVCGYLGVI--------------EDKCPKCGS 701 (735)
T ss_pred CCeecCCCCCCCCc--------------CccCcCCCC
Confidence 46778888864432 246999985
No 343
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=68.92 E-value=4.3 Score=28.35 Aligned_cols=39 Identities=15% Similarity=0.377 Sum_probs=21.5
Q ss_pred ECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949 23 RCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP 67 (107)
Q Consensus 23 ~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~ 67 (107)
.||+||.... +...+-=||-|+==. --...|++||....
T Consensus 2 ~Cp~C~~~~~-----~~~~~~~IP~F~evi-i~sf~C~~CGyk~~ 40 (160)
T smart00709 2 DCPSCGGNGT-----TRMLLTSIPYFREVI-IMSFECEHCGYRNN 40 (160)
T ss_pred cCCCCCCCCE-----EEEEEecCCCcceEE-EEEEECCCCCCccc
Confidence 4999998321 122233355443111 02556999999863
No 344
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=68.91 E-value=1.6 Score=28.62 Aligned_cols=11 Identities=27% Similarity=0.830 Sum_probs=5.6
Q ss_pred eCCCCCCCCCC
Q 033949 58 FCNNCNLLFPS 68 (107)
Q Consensus 58 ~C~~CG~~~~~ 68 (107)
.|+.||+.++.
T Consensus 4 ~CtrCG~vf~~ 14 (112)
T COG3364 4 QCTRCGEVFDD 14 (112)
T ss_pred eeccccccccc
Confidence 35555555543
No 345
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=68.81 E-value=2.9 Score=31.94 Aligned_cols=32 Identities=19% Similarity=0.328 Sum_probs=20.0
Q ss_pred CceeCCCCCCCCCC-CCCCCCCCCCCccCccccccCCceecC
Q 033949 55 PALFCNNCNLLFPS-SLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 55 ~~~~C~~CG~~~~~-~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
....||.||..--+ +.. .....|.+||.-++.
T Consensus 10 ~~~~Cp~Cg~~~iv~d~~---------~Ge~vC~~CG~Vl~e 42 (310)
T PRK00423 10 EKLVCPECGSDKLIYDYE---------RGEIVCADCGLVIEE 42 (310)
T ss_pred cCCcCcCCCCCCeeEECC---------CCeEeecccCCcccc
Confidence 45689999973211 111 124689999987755
No 346
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=68.77 E-value=3 Score=24.35 Aligned_cols=21 Identities=38% Similarity=0.907 Sum_probs=9.5
Q ss_pred cccccCCceecC--CCccCcCCC
Q 033949 84 SKCRFCDRLVEP--DFSFCPYCG 104 (107)
Q Consensus 84 ~~C~~CG~~i~~--~~~fCP~CG 104 (107)
..||.||+.+.. +..|=|+|.
T Consensus 3 v~CP~C~k~~~~~~~n~~rPFCS 25 (57)
T PF03884_consen 3 VKCPICGKPVEWSPENPFRPFCS 25 (57)
T ss_dssp EE-TTT--EEE-SSSSS--SSSS
T ss_pred ccCCCCCCeecccCCCCcCCccc
Confidence 468888877765 445556664
No 347
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=68.29 E-value=3.6 Score=30.99 Aligned_cols=13 Identities=15% Similarity=0.324 Sum_probs=8.8
Q ss_pred CCceeCCCCCCCC
Q 033949 54 EPALFCNNCNLLF 66 (107)
Q Consensus 54 ~~~~~C~~CG~~~ 66 (107)
..+..||+||+--
T Consensus 366 ~~~~~c~~c~~~~ 378 (389)
T PRK11788 366 TLYWHCPSCKAWE 378 (389)
T ss_pred cceeECcCCCCcc
Confidence 3677777777753
No 348
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=68.10 E-value=0.67 Score=26.25 Aligned_cols=25 Identities=32% Similarity=0.611 Sum_probs=19.0
Q ss_pred ccccccCCceecCCCccCcCCCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGSAL 107 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~~l 107 (107)
.+-|-+|-..+-....+||-||.+|
T Consensus 21 HYLCl~CLt~ml~~s~~C~iC~~~L 45 (50)
T PF03854_consen 21 HYLCLNCLTLMLSRSDRCPICGKPL 45 (50)
T ss_dssp -EEEHHHHHHT-SSSSEETTTTEE-
T ss_pred hhHHHHHHHHHhccccCCCcccCcC
Confidence 5778888888888899999998765
No 349
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=67.92 E-value=3.1 Score=32.80 Aligned_cols=29 Identities=17% Similarity=0.332 Sum_probs=16.5
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV 93 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i 93 (107)
..-.|..||..++..+. ....|.-||+..
T Consensus 148 ~g~~Ce~cG~~~~~~~l----------~~p~~~~~g~~~ 176 (391)
T PF09334_consen 148 RGDQCENCGRPLEPEEL----------INPVCKICGSPP 176 (391)
T ss_dssp TTTEETTTSSBEECCCS----------ECEEETTTS-B-
T ss_pred CCCcccCCCCCcccccc----------cCCccccccccC
Confidence 44677888887764332 134677777654
No 350
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=67.40 E-value=1.2 Score=23.43 Aligned_cols=8 Identities=25% Similarity=0.700 Sum_probs=3.4
Q ss_pred ccccCCce
Q 033949 85 KCRFCDRL 92 (107)
Q Consensus 85 ~C~~CG~~ 92 (107)
.|++||-.
T Consensus 23 sC~~CGPr 30 (35)
T PF07503_consen 23 SCTNCGPR 30 (35)
T ss_dssp -BTTCC-S
T ss_pred cCCCCCCC
Confidence 46666543
No 351
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=67.27 E-value=4.6 Score=31.72 Aligned_cols=46 Identities=20% Similarity=0.341 Sum_probs=22.4
Q ss_pred eecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCC
Q 033949 48 WKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPD 96 (107)
Q Consensus 48 ~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~ 96 (107)
+.++-.-..+.|..|+..++.+....++. ......|+.||..+.++
T Consensus 139 iElHGsl~~~~C~~C~~~~~~~~~~~~~~---~~~vP~C~~CgG~lRPd 184 (349)
T PTZ00410 139 VEAHGSFSAASCIECHTPYDIEQAYLEAR---SGKVPHCSTCGGIVKPD 184 (349)
T ss_pred EEeccCCCeeEeCCCCCCcchhHHHHHhh---cCCCCCCCCCCCccCCc
Confidence 44444445667777776654422110000 00134577777766654
No 352
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=67.22 E-value=2.7 Score=35.33 Aligned_cols=24 Identities=21% Similarity=0.396 Sum_probs=16.3
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
..-.|+.||..-++ ...||.||..
T Consensus 558 ~~~~C~~CGy~g~~--------------~~~CP~CG~~ 581 (618)
T PRK14704 558 PVDRCKCCSYHGVI--------------GNECPSCGNE 581 (618)
T ss_pred CCeecCCCCCCCCc--------------CccCcCCCCC
Confidence 56779999874322 2469999965
No 353
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.90 E-value=2.3 Score=26.58 Aligned_cols=11 Identities=18% Similarity=0.727 Sum_probs=5.1
Q ss_pred ceeCCCCCCCC
Q 033949 56 ALFCNNCNLLF 66 (107)
Q Consensus 56 ~~~C~~CG~~~ 66 (107)
.-.||.|+...
T Consensus 21 iD~CPrCrGVW 31 (88)
T COG3809 21 IDYCPRCRGVW 31 (88)
T ss_pred eeeCCccccEe
Confidence 33455555443
No 354
>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=66.84 E-value=4.4 Score=23.30 Aligned_cols=12 Identities=33% Similarity=0.634 Sum_probs=7.9
Q ss_pred cccccCCceecC
Q 033949 84 SKCRFCDRLVEP 95 (107)
Q Consensus 84 ~~C~~CG~~i~~ 95 (107)
..||.||.++..
T Consensus 18 ~~cp~cG~~T~~ 29 (53)
T PF04135_consen 18 DKCPPCGGPTES 29 (53)
T ss_dssp SBBTTTSSBSEE
T ss_pred CccCCCCCCCcC
Confidence 367777777644
No 355
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=66.71 E-value=8.6 Score=20.58 Aligned_cols=8 Identities=63% Similarity=1.394 Sum_probs=6.4
Q ss_pred EECCCCCC
Q 033949 22 GRCINCGS 29 (107)
Q Consensus 22 ~~C~~Cg~ 29 (107)
..||+||+
T Consensus 3 ~~Cp~Cg~ 10 (47)
T PF14690_consen 3 PRCPHCGS 10 (47)
T ss_pred ccCCCcCC
Confidence 46899998
No 356
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=66.69 E-value=1.6 Score=33.50 Aligned_cols=12 Identities=17% Similarity=0.587 Sum_probs=5.6
Q ss_pred eeCCCCCCCCCC
Q 033949 57 LFCNNCNLLFPS 68 (107)
Q Consensus 57 ~~C~~CG~~~~~ 68 (107)
..||+||+.+.+
T Consensus 58 ~vcp~c~~h~rl 69 (296)
T CHL00174 58 NICEQCGYHLKM 69 (296)
T ss_pred CCCCCCCCCcCC
Confidence 345555554433
No 357
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=66.69 E-value=3 Score=32.98 Aligned_cols=13 Identities=23% Similarity=0.340 Sum_probs=6.8
Q ss_pred ceeCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPS 68 (107)
Q Consensus 56 ~~~C~~CG~~~~~ 68 (107)
.-.|..|+..++.
T Consensus 240 ~~~c~~C~~~~~~ 252 (374)
T TIGR00375 240 QTACEACGEPAVS 252 (374)
T ss_pred hhhhcccCCcCCc
Confidence 4455555555543
No 358
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=66.60 E-value=1.9 Score=27.46 Aligned_cols=31 Identities=16% Similarity=0.333 Sum_probs=21.7
Q ss_pred CcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 20 GAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 20 ~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
....||.||. .+. ......+.|..||..+.-
T Consensus 35 a~y~CpfCgk~~vk------------------R~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHAVK------------------RQAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCcee------------------eeeeEEEEcCCCCCEEeC
Confidence 4667999998 431 112368999999998754
No 359
>PRK14289 chaperone protein DnaJ; Provisional
Probab=66.51 E-value=8.6 Score=30.19 Aligned_cols=23 Identities=26% Similarity=0.456 Sum_probs=16.3
Q ss_pred ccccccCCceecCCCccCcCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~ 105 (107)
...|+.|+-.=......|+.|+.
T Consensus 197 ~~~C~~C~G~G~~~~~~C~~C~G 219 (386)
T PRK14289 197 QSTCPTCNGEGKIIKKKCKKCGG 219 (386)
T ss_pred EEecCCCCccccccCcCCCCCCC
Confidence 35688887665556677888874
No 360
>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=66.47 E-value=5 Score=33.60 Aligned_cols=32 Identities=16% Similarity=0.521 Sum_probs=18.9
Q ss_pred eeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 46 PVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 46 P~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
|.|-++. ..-.|+.||..... ....||.||.+
T Consensus 524 ~Y~tin~--~~siC~~CGy~~g~-------------~~~~CP~CGs~ 555 (586)
T TIGR02827 524 NYFCFNI--KITICNDCHHIDKR-------------TLHRCPVCGSA 555 (586)
T ss_pred ceEEeCC--CCeecCCCCCcCCC-------------cCCcCcCCCCc
Confidence 3344443 57788888874221 12468889843
No 361
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=66.29 E-value=1.5 Score=23.43 Aligned_cols=20 Identities=20% Similarity=0.446 Sum_probs=10.8
Q ss_pred eecCCCCCceeCCCCCCCCC
Q 033949 48 WKWPAKEPALFCNNCNLLFP 67 (107)
Q Consensus 48 ~~~~~~~~~~~C~~CG~~~~ 67 (107)
..++..+....|+.|+...+
T Consensus 16 ~~~~~~~~~w~C~~C~~~N~ 35 (40)
T PF04810_consen 16 CQFDDGGKTWICNFCGTKNP 35 (40)
T ss_dssp SEEETTTTEEEETTT--EEE
T ss_pred ceEcCCCCEEECcCCCCcCC
Confidence 44554555777777776543
No 362
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=65.90 E-value=3.4 Score=37.84 Aligned_cols=22 Identities=32% Similarity=1.007 Sum_probs=17.9
Q ss_pred ccccccCCceecCCCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
..+||+||.. .-...||.||++
T Consensus 674 ~~~Cp~Cg~~--~~~~~Cp~CG~~ 695 (1627)
T PRK14715 674 FFKCPKCGKV--GLYHVCPFCGTR 695 (1627)
T ss_pred eeeCCCCCCc--cccccCcccCCc
Confidence 5779999987 556789999975
No 363
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=65.82 E-value=2.7 Score=28.18 Aligned_cols=9 Identities=78% Similarity=1.804 Sum_probs=5.8
Q ss_pred cCcCCCCCC
Q 033949 99 FCPYCGSAL 107 (107)
Q Consensus 99 fCP~CG~~l 107 (107)
|||.||+.|
T Consensus 71 FC~~CGs~l 79 (133)
T COG3791 71 FCPTCGSPL 79 (133)
T ss_pred ecccCCCce
Confidence 666666654
No 364
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=65.68 E-value=9.2 Score=28.91 Aligned_cols=66 Identities=17% Similarity=0.297 Sum_probs=42.6
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCC---CCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC-
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPA---KEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP- 95 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~---~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~- 95 (107)
.++.|..|...| |.+ +...-.|..|...|+.-..... -.....+|++|+.....
T Consensus 111 rqFaC~~Cd~~W------------------wRrvp~rKeVSRCr~C~~rYDPVP~dkm----wG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 111 RQFACSSCDHMW------------------WRRVPQRKEVSRCRKCRKRYDPVPCDKM----WGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred eeeeccccchHH------------------HhccCcccccccccccccccCCCccccc----cceeeeecccccccchhh
Confidence 577899998855 322 3357779999999976332100 01124789999887654
Q ss_pred ----CCccCcCCCCCC
Q 033949 96 ----DFSFCPYCGSAL 107 (107)
Q Consensus 96 ----~~~fCP~CG~~l 107 (107)
...=|-.||..+
T Consensus 169 ~qm~v~sPCy~C~~~v 184 (278)
T PF15135_consen 169 AQMGVPSPCYGCGNPV 184 (278)
T ss_pred hhcCCCCCccCCCCcc
Confidence 556677777653
No 365
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=65.59 E-value=2.1 Score=35.78 Aligned_cols=39 Identities=18% Similarity=0.393 Sum_probs=17.1
Q ss_pred ECCCCCC--CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCC
Q 033949 23 RCINCGS--TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLF 66 (107)
Q Consensus 23 ~C~~Cg~--~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~ 66 (107)
.||+||. ....-+...++.+.+-|. ...++.|++|+..+
T Consensus 229 pCPHCGe~q~l~~~e~~~~~g~~~~~~-----~~~~~~c~h~~~~i 269 (611)
T COG5525 229 PCPHCGEEQQLKFGEKSGPRGLKDTPA-----EAAFIQCEHCGCVI 269 (611)
T ss_pred eCCCCCchhhccccccCCCcCcccchh-----hhhhhhccccCcee
Confidence 3555555 111113333444444443 12344555555554
No 366
>PRK07219 DNA topoisomerase I; Validated
Probab=65.49 E-value=11 Score=32.59 Aligned_cols=11 Identities=27% Similarity=0.492 Sum_probs=7.3
Q ss_pred cccccCCceec
Q 033949 84 SKCRFCDRLVE 94 (107)
Q Consensus 84 ~~C~~CG~~i~ 94 (107)
..||.||..+.
T Consensus 734 ~~CpkCg~~l~ 744 (822)
T PRK07219 734 EKCPECGLPLL 744 (822)
T ss_pred CCCCCCCCeEE
Confidence 56777777544
No 367
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=65.12 E-value=1.8 Score=32.92 Aligned_cols=15 Identities=13% Similarity=0.364 Sum_probs=10.1
Q ss_pred CceeCCCCCCCCCCC
Q 033949 55 PALFCNNCNLLFPSS 69 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~ 69 (107)
....||+||+.+.++
T Consensus 44 ~~~vc~~c~~h~rl~ 58 (285)
T TIGR00515 44 NLEVCPKCDHHMRMD 58 (285)
T ss_pred hCCCCCCCCCcCcCC
Confidence 356777777777653
No 368
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.00 E-value=3.3 Score=27.57 Aligned_cols=31 Identities=10% Similarity=0.093 Sum_probs=22.1
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCC
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSS 69 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~ 69 (107)
..+||+||+.+ .-+++ .-+.||+||..++.+
T Consensus 9 KridPetg~KF----------------YDLNr--dPiVsPytG~s~P~s 39 (129)
T COG4530 9 KRIDPETGKKF----------------YDLNR--DPIVSPYTGKSYPRS 39 (129)
T ss_pred cccCccccchh----------------hccCC--CccccCcccccchHH
Confidence 45799999943 22443 467899999999653
No 369
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=64.94 E-value=1.2 Score=32.63 Aligned_cols=22 Identities=27% Similarity=0.608 Sum_probs=10.6
Q ss_pred ccccCCceecCCCccCcCCCCC
Q 033949 85 KCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 85 ~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
.|+.|++.++....+||.||.+
T Consensus 26 ~C~~C~~~~~~~~~~C~~C~~~ 47 (225)
T COG1040 26 LCSGCQADLPLIGNLCPLCGLP 47 (225)
T ss_pred cChhhhhchhHHHhhhHhhhCh
Confidence 4555555554443355555543
No 370
>PRK04011 peptide chain release factor 1; Provisional
Probab=64.92 E-value=3.7 Score=32.70 Aligned_cols=10 Identities=30% Similarity=0.693 Sum_probs=5.1
Q ss_pred ceeCCCCCCC
Q 033949 56 ALFCNNCNLL 65 (107)
Q Consensus 56 ~~~C~~CG~~ 65 (107)
...|+.||..
T Consensus 328 ~~~c~~c~~~ 337 (411)
T PRK04011 328 TYKCPNCGYE 337 (411)
T ss_pred EEEcCCCCcc
Confidence 4445555544
No 371
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=64.91 E-value=1.9 Score=23.26 Aligned_cols=21 Identities=24% Similarity=0.591 Sum_probs=16.4
Q ss_pred ccccCCceecCCCccCcCCCC
Q 033949 85 KCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 85 ~C~~CG~~i~~~~~fCP~CG~ 105 (107)
.|.+|-..+......||.|++
T Consensus 24 ~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 24 FCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred HHHHHHHhhcCCCCCCcCCCC
Confidence 588887777777888988874
No 372
>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=64.87 E-value=4.6 Score=21.30 Aligned_cols=10 Identities=40% Similarity=0.713 Sum_probs=7.1
Q ss_pred cEECCCCCCC
Q 033949 21 AGRCINCGST 30 (107)
Q Consensus 21 ~~~C~~Cg~~ 30 (107)
++.||.|++.
T Consensus 5 ~v~CP~C~s~ 14 (36)
T PF03811_consen 5 DVHCPRCQST 14 (36)
T ss_pred eeeCCCCCCC
Confidence 5678888874
No 373
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=64.73 E-value=4.3 Score=23.92 Aligned_cols=26 Identities=23% Similarity=0.585 Sum_probs=18.7
Q ss_pred CCcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCC
Q 033949 19 SGAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLL 65 (107)
Q Consensus 19 ~~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~ 65 (107)
..-+.|..||. +++ .....|..||..
T Consensus 14 ~tH~~CRRCGr~syh---------------------v~k~~CaaCGfg 40 (61)
T COG2126 14 KTHIRCRRCGRRSYH---------------------VRKKYCAACGFG 40 (61)
T ss_pred cceehhhhccchhee---------------------eccceecccCCC
Confidence 34567999999 542 245689999987
No 374
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=64.64 E-value=1.9 Score=28.05 Aligned_cols=23 Identities=17% Similarity=0.488 Sum_probs=17.7
Q ss_pred ccccccCCceecC-------CCccCcCCCC
Q 033949 83 VSKCRFCDRLVEP-------DFSFCPYCGS 105 (107)
Q Consensus 83 ~~~C~~CG~~i~~-------~~~fCP~CG~ 105 (107)
.-.|..||.+|+. .+.+|..|-+
T Consensus 80 yG~C~~Cge~I~~~RL~a~P~a~~Cv~Cq~ 109 (110)
T TIGR02420 80 YGYCEECGEEIGLRRLEARPTATLCIDCKT 109 (110)
T ss_pred CCchhccCCcccHHHHhhCCCccccHHhHc
Confidence 3579999999865 7888887743
No 375
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=64.53 E-value=3.1 Score=22.55 Aligned_cols=11 Identities=18% Similarity=0.552 Sum_probs=6.1
Q ss_pred CceeCCCCCCC
Q 033949 55 PALFCNNCNLL 65 (107)
Q Consensus 55 ~~~~C~~CG~~ 65 (107)
..+.|+.||..
T Consensus 28 ~~~~CpYCg~~ 38 (40)
T PF10276_consen 28 GPVVCPYCGTR 38 (40)
T ss_dssp CEEEETTTTEE
T ss_pred CeEECCCCCCE
Confidence 34566666543
No 376
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=64.45 E-value=4.6 Score=32.48 Aligned_cols=15 Identities=20% Similarity=0.518 Sum_probs=9.7
Q ss_pred ceeCCCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPSSL 70 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~ 70 (107)
...|+.||..+....
T Consensus 367 g~rC~kCg~~~~~~~ 381 (421)
T COG1571 367 GFRCKKCGTRARETL 381 (421)
T ss_pred CcccccccccCCccc
Confidence 667777777765433
No 377
>COG4640 Predicted membrane protein [Function unknown]
Probab=64.29 E-value=4.1 Score=32.70 Aligned_cols=27 Identities=19% Similarity=0.460 Sum_probs=20.3
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
+++||.||+.-..+. +.|+.||.++..
T Consensus 1 M~fC~kcG~qk~Ed~-------------~qC~qCG~~~t~ 27 (465)
T COG4640 1 MKFCPKCGSQKAEDD-------------VQCTQCGHKFTS 27 (465)
T ss_pred CCccccccccccccc-------------ccccccCCcCCc
Confidence 368999997665533 459999998765
No 378
>PRK08197 threonine synthase; Validated
Probab=64.16 E-value=5 Score=31.44 Aligned_cols=9 Identities=44% Similarity=1.010 Sum_probs=5.4
Q ss_pred EECCCCCCC
Q 033949 22 GRCINCGST 30 (107)
Q Consensus 22 ~~C~~Cg~~ 30 (107)
.+|.+||..
T Consensus 8 ~~C~~Cg~~ 16 (394)
T PRK08197 8 LECSKCGET 16 (394)
T ss_pred EEECCCCCC
Confidence 556666663
No 379
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=64.15 E-value=3.5 Score=30.40 Aligned_cols=44 Identities=20% Similarity=0.434 Sum_probs=19.8
Q ss_pred ecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 49 KWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 49 ~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
.+.-+-..+.|..|+..++.+.....+. ......||.||..+.+
T Consensus 112 elHG~~~~~~C~~C~~~~~~~~~~~~~~---~~~~p~Cp~Cgg~lrP 155 (244)
T PRK14138 112 ELHGNVEEYYCVRCGKRYTVEDVIEKLE---KSDVPRCDDCSGLIRP 155 (244)
T ss_pred EccCCcCeeEECCCCCcccHHHHHHHHh---cCCCCCCCCCCCeECC
Confidence 3433334566777776654321100000 0012457777766655
No 380
>PLN02189 cellulose synthase
Probab=63.80 E-value=4.5 Score=35.98 Aligned_cols=12 Identities=25% Similarity=0.633 Sum_probs=7.9
Q ss_pred CceeCCCCCCCC
Q 033949 55 PALFCNNCNLLF 66 (107)
Q Consensus 55 ~~~~C~~CG~~~ 66 (107)
.++.|..||...
T Consensus 52 ~fvaC~~C~fpv 63 (1040)
T PLN02189 52 LFVACNECGFPV 63 (1040)
T ss_pred EEEeeccCCCcc
Confidence 367777777664
No 381
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=63.79 E-value=3.3 Score=26.47 Aligned_cols=31 Identities=23% Similarity=0.492 Sum_probs=21.7
Q ss_pred CcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 20 GAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 20 ~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
....||.||. .+. + .....+.|..||..+.-
T Consensus 34 a~y~CpfCgk~~vk--R----------------~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 34 AKYVCPFCGKKTVK--R----------------GSTGIWTCRKCGAKFAG 65 (91)
T ss_pred cCccCCCCCCCceE--E----------------EeeEEEEcCCCCCEEeC
Confidence 4667999998 431 1 12368999999998754
No 382
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=63.72 E-value=4.2 Score=36.79 Aligned_cols=10 Identities=40% Similarity=0.919 Sum_probs=5.2
Q ss_pred CccCcCCCCC
Q 033949 97 FSFCPYCGSA 106 (107)
Q Consensus 97 ~~fCP~CG~~ 106 (107)
.+-||.||++
T Consensus 708 ~k~cp~c~~~ 717 (1213)
T TIGR01405 708 DKDCPKCGAP 717 (1213)
T ss_pred cccCcccccc
Confidence 3455555554
No 383
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=63.62 E-value=4.8 Score=32.60 Aligned_cols=24 Identities=33% Similarity=0.798 Sum_probs=16.5
Q ss_pred cccccCCceecC---CCccCcCCCCCC
Q 033949 84 SKCRFCDRLVEP---DFSFCPYCGSAL 107 (107)
Q Consensus 84 ~~C~~CG~~i~~---~~~fCP~CG~~l 107 (107)
..|.+||...++ ...+|.-||+++
T Consensus 150 ~~ce~cg~~~~~~~l~~p~~~~~~~~~ 176 (530)
T TIGR00398 150 DHCEVCGRHLEPTELINPRCKICGAKP 176 (530)
T ss_pred chhhhccccCCHHHhcCCccccCCCcc
Confidence 468888887665 455677777753
No 384
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=63.57 E-value=2.2 Score=27.21 Aligned_cols=32 Identities=22% Similarity=0.465 Sum_probs=20.8
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
....||.||... +.+. ......|..||..+.-
T Consensus 34 ~ky~Cp~Cgk~~-vkR~----------------a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTS-VKRV----------------ATGIWKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSE-EEEE----------------ETTEEEETTTTEEEE-
T ss_pred CCCcCCCCCCce-eEEe----------------eeEEeecCCCCCEEeC
Confidence 466899999932 1111 3478999999987643
No 385
>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.
Probab=63.57 E-value=2.1 Score=34.40 Aligned_cols=31 Identities=10% Similarity=0.186 Sum_probs=14.1
Q ss_pred EEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949 40 LKAFFVPVWKWPAKEPALFCNNCNLLFPSSL 70 (107)
Q Consensus 40 f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~ 70 (107)
|.++-.-+-|+.+....+.||.||+.|..+.
T Consensus 364 F~ICa~s~tPIY~G~~~v~CP~cgA~y~~~~ 394 (422)
T PF06957_consen 364 FDICAASYTPIYRGSPSVKCPYCGAKYHPEY 394 (422)
T ss_dssp EEEBTTT--EEETTS-EEE-TTT--EEEGGG
T ss_pred ceeeecccccccCCCCCeeCCCCCCccChhh
Confidence 4444333334434446788888888886543
No 386
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=63.27 E-value=5.6 Score=22.43 Aligned_cols=13 Identities=15% Similarity=0.388 Sum_probs=9.1
Q ss_pred ceeCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPS 68 (107)
Q Consensus 56 ~~~C~~CG~~~~~ 68 (107)
...|+.||+.+..
T Consensus 28 ~W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 28 WWKCPKCGHEWKA 40 (55)
T ss_pred EEECCCCCCeeEc
Confidence 5678888777754
No 387
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=62.91 E-value=6.1 Score=23.75 Aligned_cols=11 Identities=27% Similarity=0.751 Sum_probs=7.2
Q ss_pred CceeCCCCCCC
Q 033949 55 PALFCNNCNLL 65 (107)
Q Consensus 55 ~~~~C~~CG~~ 65 (107)
..+.|.+||..
T Consensus 39 ~~itCk~CgYt 49 (68)
T COG3478 39 IVITCKNCGYT 49 (68)
T ss_pred EEEEeccCCch
Confidence 36667777765
No 388
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=62.87 E-value=3.7 Score=34.63 Aligned_cols=24 Identities=29% Similarity=0.776 Sum_probs=17.4
Q ss_pred ccccccCCceecCCCc-cCcCCCCC
Q 033949 83 VSKCRFCDRLVEPDFS-FCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~-fCP~CG~~ 106 (107)
...|..||..+.+.-. .||.|-.+
T Consensus 80 v~~c~~cG~~~~~~~~~lc~~c~~~ 104 (715)
T COG1107 80 VLTCDICGDIIVPWEEGLCPECRRK 104 (715)
T ss_pred EEeeccccceecCcccccChhHhhC
Confidence 5779999998887444 48888543
No 389
>PRK06386 replication factor A; Reviewed
Probab=62.85 E-value=4.6 Score=31.80 Aligned_cols=22 Identities=23% Similarity=0.664 Sum_probs=18.4
Q ss_pred CccccccCCceecCCCccCcCCCC
Q 033949 82 DVSKCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 82 ~~~~C~~CG~~i~~~~~fCP~CG~ 105 (107)
....||.|+..+.. ..||.||.
T Consensus 235 li~rCP~C~R~l~~--g~C~~HG~ 256 (358)
T PRK06386 235 IFTKCSVCNKIIED--GVCKDHPD 256 (358)
T ss_pred eEecCcCCCeEccC--CcCCCCCC
Confidence 35789999999885 49999996
No 390
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=62.78 E-value=7.4 Score=28.76 Aligned_cols=13 Identities=15% Similarity=0.353 Sum_probs=7.0
Q ss_pred CceeCCCCCCCCC
Q 033949 55 PALFCNNCNLLFP 67 (107)
Q Consensus 55 ~~~~C~~CG~~~~ 67 (107)
..+.|..|+..++
T Consensus 116 ~~~~C~~C~~~~~ 128 (242)
T PTZ00408 116 LKVRCTATGHVFD 128 (242)
T ss_pred ceEEECCCCcccC
Confidence 3455666655543
No 391
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=62.67 E-value=4.7 Score=26.70 Aligned_cols=85 Identities=21% Similarity=0.314 Sum_probs=41.7
Q ss_pred EECCCCCCCcE--EEEEeeEEEEEEEeee---ecCCCCCceeCCCCCCCCCCCCCC--CCCCCC-----CccCccccccC
Q 033949 22 GRCINCGSTAD--LVEYEKVLKAFFVPVW---KWPAKEPALFCNNCNLLFPSSLPP--PPPPPP-----LVSDVSKCRFC 89 (107)
Q Consensus 22 ~~C~~Cg~~~~--~~~~~~~f~lFFIP~~---~~~~~~~~~~C~~CG~~~~~~~~~--~~~~~~-----~~~~~~~C~~C 89 (107)
+.||-||-++- ..=.+.|=+||=+|.| +|+.......|-.|...+...... .++... ..=....|.+|
T Consensus 16 ~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dC 95 (112)
T TIGR00622 16 VECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDC 95 (112)
T ss_pred CcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccccccccccceeCCCCCCcccccc
Confidence 35666665111 0112225566655533 455433345699998887542110 000000 00023456666
Q ss_pred CceecCCCccCcCCCCC
Q 033949 90 DRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 90 G~~i~~~~~fCP~CG~~ 106 (107)
..-|-..-..||.|.++
T Consensus 96 D~fiHe~Lh~CPGC~~~ 112 (112)
T TIGR00622 96 DVFVHESLHCCPGCIHK 112 (112)
T ss_pred chhhhhhccCCcCCCCC
Confidence 66666677788888653
No 392
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=62.15 E-value=16 Score=24.35 Aligned_cols=12 Identities=25% Similarity=0.714 Sum_probs=8.8
Q ss_pred CCcEECCCCCCC
Q 033949 19 SGAGRCINCGST 30 (107)
Q Consensus 19 ~~~~~C~~Cg~~ 30 (107)
...+.||.||..
T Consensus 58 ~~~~~Cp~C~~~ 69 (140)
T COG0551 58 KTGVKCPKCGKG 69 (140)
T ss_pred cCceeCCCCCCC
Confidence 446789999973
No 393
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=62.15 E-value=6.6 Score=22.77 Aligned_cols=8 Identities=25% Similarity=0.592 Sum_probs=3.7
Q ss_pred ccccCCce
Q 033949 85 KCRFCDRL 92 (107)
Q Consensus 85 ~C~~CG~~ 92 (107)
.||.||-+
T Consensus 16 ~Cp~cGip 23 (55)
T PF13824_consen 16 ECPDCGIP 23 (55)
T ss_pred cCCCCCCc
Confidence 45555443
No 394
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=61.68 E-value=1.9 Score=25.99 Aligned_cols=11 Identities=18% Similarity=0.368 Sum_probs=5.4
Q ss_pred ccccccCCcee
Q 033949 83 VSKCRFCDRLV 93 (107)
Q Consensus 83 ~~~C~~CG~~i 93 (107)
...|++||..+
T Consensus 48 r~FC~~CGs~l 58 (92)
T PF04828_consen 48 RYFCPTCGSPL 58 (92)
T ss_dssp EEEETTT--EE
T ss_pred CcccCCCCCee
Confidence 45677777653
No 395
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=61.41 E-value=7.8 Score=33.75 Aligned_cols=63 Identities=24% Similarity=0.571 Sum_probs=39.6
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCC-CCCCCCCccCccccccCCceecC---
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPP-PPPPPPLVSDVSKCRFCDRLVEP--- 95 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~-~~~~~~~~~~~~~C~~CG~~i~~--- 95 (107)
..+-|..||..+ ..+.+.|+.|...++..-.. .+|++. .--.|+.|.....+
T Consensus 1116 ~~vdc~~cg~~i---------------------~~~~~~c~ec~~kfP~CiasG~pIt~~---~fWlC~~CkH~a~~~EI 1171 (1189)
T KOG2041|consen 1116 AKVDCSVCGAKI---------------------DPYDLQCSECQTKFPVCIASGRPITDN---IFWLCPRCKHRAHQHEI 1171 (1189)
T ss_pred cceeeeecCCcC---------------------CccCCCChhhcCcCceeeccCCccccc---eEEEccccccccccccc
Confidence 456799999965 45788999999998763332 233321 12235555444322
Q ss_pred -CCccCcCCCCC
Q 033949 96 -DFSFCPYCGSA 106 (107)
Q Consensus 96 -~~~fCP~CG~~ 106 (107)
..++||-|.+.
T Consensus 1172 s~y~~CPLCHs~ 1183 (1189)
T KOG2041|consen 1172 SKYNCCPLCHSM 1183 (1189)
T ss_pred cccccCccccCh
Confidence 68899999764
No 396
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=61.29 E-value=1.7 Score=22.58 Aligned_cols=11 Identities=18% Similarity=0.519 Sum_probs=5.8
Q ss_pred ccccCCceecC
Q 033949 85 KCRFCDRLVEP 95 (107)
Q Consensus 85 ~C~~CG~~i~~ 95 (107)
.|..||.+|..
T Consensus 5 ~C~~CGe~I~~ 15 (36)
T PF01258_consen 5 ICEDCGEPIPE 15 (36)
T ss_dssp B-TTTSSBEEH
T ss_pred CccccCChHHH
Confidence 36666666643
No 397
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=61.18 E-value=7 Score=29.45 Aligned_cols=19 Identities=11% Similarity=0.107 Sum_probs=9.9
Q ss_pred cCCCCCceeCCCCCCCCCC
Q 033949 50 WPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 50 ~~~~~~~~~C~~CG~~~~~ 68 (107)
++-+-..+.|..|+..+..
T Consensus 131 lHG~l~~~~C~~C~~~~~~ 149 (271)
T PTZ00409 131 LHGSVFEARCCTCRKTIQL 149 (271)
T ss_pred eccCcCcceeCCCCCCccc
Confidence 3333345566666665543
No 398
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=61.11 E-value=4.2 Score=23.24 Aligned_cols=11 Identities=27% Similarity=0.939 Sum_probs=7.6
Q ss_pred ccccCCceecC
Q 033949 85 KCRFCDRLVEP 95 (107)
Q Consensus 85 ~C~~CG~~i~~ 95 (107)
.||+||+.+..
T Consensus 2 ~CPyCge~~~~ 12 (52)
T PF14255_consen 2 QCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCeeEE
Confidence 47888877644
No 399
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.08 E-value=3.6 Score=27.73 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=11.2
Q ss_pred CceeCCCCCCCCCCC
Q 033949 55 PALFCNNCNLLFPSS 69 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~ 69 (107)
..-.|..||..|.-.
T Consensus 39 ~~p~C~aCG~dyg~~ 53 (126)
T COG5349 39 VVPACEACGLDYGFA 53 (126)
T ss_pred cCchhhhccccccCC
Confidence 356699999988653
No 400
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=61.07 E-value=8 Score=32.49 Aligned_cols=42 Identities=14% Similarity=0.322 Sum_probs=27.0
Q ss_pred CCceeCCCCCCCCCCCCC-CC-CCCC--C-CccCccccccCCceecC
Q 033949 54 EPALFCNNCNLLFPSSLP-PP-PPPP--P-LVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 54 ~~~~~C~~CG~~~~~~~~-~~-~~~~--~-~~~~~~~C~~CG~~i~~ 95 (107)
.+++.||+||+..-++-. .. +... . .+.....|++|+..|.+
T Consensus 225 r~yvpCPHCGe~q~l~~~e~~~~~g~~~~~~~~~~~~c~h~~~~i~~ 271 (611)
T COG5525 225 RFYVPCPHCGEEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVIRP 271 (611)
T ss_pred eEEeeCCCCCchhhccccccCCCcCcccchhhhhhhhccccCceeee
Confidence 379999999998866442 11 1110 0 12235689999999877
No 401
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=60.99 E-value=2.8 Score=27.86 Aligned_cols=17 Identities=24% Similarity=0.679 Sum_probs=12.1
Q ss_pred CceeCCCCCCCCCCCCC
Q 033949 55 PALFCNNCNLLFPSSLP 71 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~ 71 (107)
....|..|+..+..+..
T Consensus 24 ~~~~C~~Ck~~~~v~~~ 40 (116)
T KOG2907|consen 24 STVLCIRCKIEYPVSQF 40 (116)
T ss_pred CceEeccccccCCHHHh
Confidence 45668888888876554
No 402
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=60.57 E-value=4.6 Score=26.10 Aligned_cols=6 Identities=67% Similarity=1.464 Sum_probs=3.5
Q ss_pred CCCCCC
Q 033949 24 CINCGS 29 (107)
Q Consensus 24 C~~Cg~ 29 (107)
||.||+
T Consensus 1 C~~C~~ 6 (127)
T TIGR03830 1 CPICGS 6 (127)
T ss_pred CCCCCC
Confidence 566664
No 403
>PLN02436 cellulose synthase A
Probab=60.43 E-value=5.7 Score=35.50 Aligned_cols=12 Identities=33% Similarity=0.888 Sum_probs=8.6
Q ss_pred CceeCCCCCCCC
Q 033949 55 PALFCNNCNLLF 66 (107)
Q Consensus 55 ~~~~C~~CG~~~ 66 (107)
.++.|..||..+
T Consensus 54 ~FVACn~C~fpv 65 (1094)
T PLN02436 54 PFVACNECAFPV 65 (1094)
T ss_pred EEEeeccCCCcc
Confidence 377788787765
No 404
>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=60.41 E-value=4.6 Score=20.36 Aligned_cols=10 Identities=20% Similarity=0.511 Sum_probs=5.1
Q ss_pred ccccccCCce
Q 033949 83 VSKCRFCDRL 92 (107)
Q Consensus 83 ~~~C~~CG~~ 92 (107)
.++||.||..
T Consensus 13 kY~Cp~C~~~ 22 (30)
T PF04438_consen 13 KYRCPRCGAR 22 (30)
T ss_dssp SEE-TTT--E
T ss_pred EEECCCcCCc
Confidence 5778888776
No 405
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=60.35 E-value=4.4 Score=28.65 Aligned_cols=23 Identities=26% Similarity=0.642 Sum_probs=18.2
Q ss_pred ccccccCCceecC---CCccCcCCCC
Q 033949 83 VSKCRFCDRLVEP---DFSFCPYCGS 105 (107)
Q Consensus 83 ~~~C~~CG~~i~~---~~~fCP~CG~ 105 (107)
...|+.||..+.+ +.-.||.||+
T Consensus 149 ~a~~~~~g~~~~~~~~~~~~c~~~~~ 174 (189)
T PRK09521 149 YAMCSRCRTPLVKKGENELKCPNCGN 174 (189)
T ss_pred EEEccccCCceEECCCCEEECCCCCC
Confidence 4579999998766 4578999986
No 406
>PRK11823 DNA repair protein RadA; Provisional
Probab=60.21 E-value=9.7 Score=30.56 Aligned_cols=26 Identities=23% Similarity=0.401 Sum_probs=18.3
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCC
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLF 66 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~ 66 (107)
....|.+||... ......||.||+=-
T Consensus 6 ~~y~C~~Cg~~~---------------------~~~~g~Cp~C~~w~ 31 (446)
T PRK11823 6 TAYVCQECGAES---------------------PKWLGRCPECGAWN 31 (446)
T ss_pred CeEECCcCCCCC---------------------cccCeeCcCCCCcc
Confidence 356799999832 23678899998744
No 407
>PLN02569 threonine synthase
Probab=60.20 E-value=6.3 Score=32.09 Aligned_cols=28 Identities=14% Similarity=0.068 Sum_probs=16.2
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
.+.|+.||+.++++. ..+.| .||..++.
T Consensus 49 ~l~C~~Cg~~y~~~~-----------~~~~C-~cgg~l~~ 76 (484)
T PLN02569 49 FLECPLTGEKYSLDE-----------VVYRS-KSGGLLDV 76 (484)
T ss_pred ccEeCCCCCcCCCcc-----------ccccC-CCCCeEEE
Confidence 466777777766544 13456 46666544
No 408
>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=60.05 E-value=1.1 Score=26.63 Aligned_cols=19 Identities=26% Similarity=0.581 Sum_probs=13.7
Q ss_pred CCCCCceeCCCCCCCCCCC
Q 033949 51 PAKEPALFCNNCNLLFPSS 69 (107)
Q Consensus 51 ~~~~~~~~C~~CG~~~~~~ 69 (107)
...++.+.|+.||..|+|.
T Consensus 48 ~i~eg~L~Cp~c~r~YPI~ 66 (68)
T PF03966_consen 48 EIVEGELICPECGREYPIR 66 (68)
T ss_dssp ETTTTEEEETTTTEEEEEE
T ss_pred cccCCEEEcCCCCCEEeCC
Confidence 4455788888888887663
No 409
>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=59.97 E-value=10 Score=26.84 Aligned_cols=21 Identities=19% Similarity=0.457 Sum_probs=10.8
Q ss_pred eeecCCCCCceeCCCCCCCCC
Q 033949 47 VWKWPAKEPALFCNNCNLLFP 67 (107)
Q Consensus 47 ~~~~~~~~~~~~C~~CG~~~~ 67 (107)
|+.++-+-....|..|+..++
T Consensus 104 v~~lHG~~~~~~C~~C~~~~~ 124 (222)
T cd00296 104 VIELHGSLDRVRCTSCGKEYP 124 (222)
T ss_pred EEEecCCCCccEECCCCCCcc
Confidence 444444444555666665543
No 410
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=59.80 E-value=4.2 Score=25.93 Aligned_cols=31 Identities=19% Similarity=0.452 Sum_probs=21.6
Q ss_pred CcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 20 GAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 20 ~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
....||.||. .+. ........|..||..+.-
T Consensus 35 a~y~CpfCgk~~vk------------------R~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKVK------------------RVGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCceE------------------EEEEEEEEcCCCCCEEeC
Confidence 4668999988 431 012368899999998754
No 411
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=59.64 E-value=9.9 Score=33.68 Aligned_cols=56 Identities=18% Similarity=0.327 Sum_probs=35.1
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
...+||.|++.++--+.+- =...++-...|..||+.++-... + .-.||.||..+..
T Consensus 795 ~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~--~--------~~~~~~~~~~~~~ 850 (1006)
T PRK12775 795 GVATCPKCHRPLEGDEEYV----------CCATSELQWRCDDCGKVSEGFAF--P--------YGMCPACGGKLQA 850 (1006)
T ss_pred CCccCcccCCCCCCCceeE----------EecCcceeeehhhhccccccccC--C--------cCcCcccccchhh
Confidence 4568999999554333221 12223346789999998754331 2 2479999988654
No 412
>PRK08329 threonine synthase; Validated
Probab=59.58 E-value=6.2 Score=30.42 Aligned_cols=9 Identities=56% Similarity=1.198 Sum_probs=5.6
Q ss_pred EECCCCCCC
Q 033949 22 GRCINCGST 30 (107)
Q Consensus 22 ~~C~~Cg~~ 30 (107)
.+|..||.+
T Consensus 2 l~C~~Cg~~ 10 (347)
T PRK08329 2 LRCTKCGRT 10 (347)
T ss_pred cCcCCCCCC
Confidence 357777764
No 413
>PLN02610 probable methionyl-tRNA synthetase
Probab=59.32 E-value=6.7 Score=33.95 Aligned_cols=23 Identities=26% Similarity=0.720 Sum_probs=15.2
Q ss_pred cccccCCceecC---CCccCcCCCCC
Q 033949 84 SKCRFCDRLVEP---DFSFCPYCGSA 106 (107)
Q Consensus 84 ~~C~~CG~~i~~---~~~fCP~CG~~ 106 (107)
..|.+||..+++ ....|.-||++
T Consensus 171 d~Ce~Cg~~~~p~eLi~p~c~~~g~~ 196 (801)
T PLN02610 171 DQCEKCGKLLNPTELIDPKCKVCKNT 196 (801)
T ss_pred chhhhccccCChhhhcCCcccCCCCc
Confidence 458888876665 23457777765
No 414
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=59.24 E-value=4.1 Score=30.88 Aligned_cols=24 Identities=33% Similarity=0.750 Sum_probs=18.1
Q ss_pred EECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCC
Q 033949 22 GRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLF 66 (107)
Q Consensus 22 ~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~ 66 (107)
..|-+||+.+ +.....||+||+.-
T Consensus 83 ~~C~~CGa~V---------------------~~~e~~Cp~C~Stn 106 (314)
T PF09567_consen 83 GKCNNCGANV---------------------SRLEESCPNCGSTN 106 (314)
T ss_pred hhhcccccee---------------------eehhhcCCCCCccc
Confidence 4699999955 33677899999864
No 415
>PLN02400 cellulose synthase
Probab=59.10 E-value=7 Score=35.00 Aligned_cols=12 Identities=25% Similarity=0.628 Sum_probs=7.8
Q ss_pred CceeCCCCCCCC
Q 033949 55 PALFCNNCNLLF 66 (107)
Q Consensus 55 ~~~~C~~CG~~~ 66 (107)
.++.|..|+...
T Consensus 54 ~FVAC~eCaFPV 65 (1085)
T PLN02400 54 VFVACNECAFPV 65 (1085)
T ss_pred EEEEEccCCCcc
Confidence 367777777664
No 416
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=58.61 E-value=11 Score=28.30 Aligned_cols=13 Identities=31% Similarity=0.948 Sum_probs=9.2
Q ss_pred cccccCCceecCC
Q 033949 84 SKCRFCDRLVEPD 96 (107)
Q Consensus 84 ~~C~~CG~~i~~~ 96 (107)
..|+.||..+.++
T Consensus 180 P~C~~Cgg~lrP~ 192 (285)
T PRK05333 180 PACPACGGILKPD 192 (285)
T ss_pred CCCCCCCCcccCC
Confidence 4688888777664
No 417
>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=58.51 E-value=4.5 Score=21.00 Aligned_cols=13 Identities=31% Similarity=0.624 Sum_probs=8.1
Q ss_pred ccccccCCceecC
Q 033949 83 VSKCRFCDRLVEP 95 (107)
Q Consensus 83 ~~~C~~CG~~i~~ 95 (107)
...|+||+..|.+
T Consensus 4 ~~~C~nC~R~v~a 16 (33)
T PF08209_consen 4 YVECPNCGRPVAA 16 (33)
T ss_dssp EEE-TTTSSEEEG
T ss_pred eEECCCCcCCcch
Confidence 3568888877654
No 418
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=58.15 E-value=9.1 Score=24.50 Aligned_cols=35 Identities=20% Similarity=0.387 Sum_probs=24.1
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCC-CCceeCCCCCCCCCCCC
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAK-EPALFCNNCNLLFPSSL 70 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~-~~~~~C~~CG~~~~~~~ 70 (107)
+.++|.+||..+ -|.... .+.-.||+|=+....+.
T Consensus 3 ~~F~C~~CG~~V----------------~p~~~g~~~RNHCP~CL~S~Hvd~ 38 (92)
T PF12647_consen 3 ESFTCVHCGLTV----------------SPLAAGSAHRNHCPSCLSSLHVDI 38 (92)
T ss_pred cccCccccCCCc----------------ccCCCCCCccCcCcccccccccCC
Confidence 567899999943 222222 26888999999887764
No 419
>PHA02942 putative transposase; Provisional
Probab=57.70 E-value=5.2 Score=31.57 Aligned_cols=24 Identities=25% Similarity=0.694 Sum_probs=17.7
Q ss_pred ccccccCCceecC---CCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEP---DFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~---~~~fCP~CG~~ 106 (107)
...||.||..... ..-.||.||..
T Consensus 325 Sq~Cs~CG~~~~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 325 SVSCPKCGHKMVEIAHRYFHCPSCGYE 351 (383)
T ss_pred CccCCCCCCccCcCCCCEEECCCCCCE
Confidence 4679999987653 23479999974
No 420
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=57.27 E-value=6.9 Score=27.33 Aligned_cols=9 Identities=22% Similarity=0.600 Sum_probs=4.9
Q ss_pred cccccCCce
Q 033949 84 SKCRFCDRL 92 (107)
Q Consensus 84 ~~C~~CG~~ 92 (107)
..|++||..
T Consensus 29 ReC~~C~~R 37 (156)
T COG1327 29 RECLECGER 37 (156)
T ss_pred hcccccccc
Confidence 446666654
No 421
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=57.17 E-value=4.9 Score=27.89 Aligned_cols=23 Identities=22% Similarity=0.443 Sum_probs=17.1
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV 93 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i 93 (107)
...+|..||.. ..+.|.+||+.+
T Consensus 117 ~r~fCaVCG~~----------------S~ysC~~CG~ky 139 (156)
T KOG3362|consen 117 LRKFCAVCGYD----------------SKYSCVNCGTKY 139 (156)
T ss_pred cchhhhhcCCC----------------chhHHHhcCCce
Confidence 57789999943 257899999864
No 422
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=57.06 E-value=16 Score=30.77 Aligned_cols=11 Identities=18% Similarity=0.679 Sum_probs=6.5
Q ss_pred eCCCCCCCCCC
Q 033949 58 FCNNCNLLFPS 68 (107)
Q Consensus 58 ~C~~CG~~~~~ 68 (107)
.|..||..++.
T Consensus 154 ~ce~cg~~~~~ 164 (673)
T PRK00133 154 NCEVCGATYSP 164 (673)
T ss_pred hhhhccccCCh
Confidence 46667766543
No 423
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=56.73 E-value=9.8 Score=31.57 Aligned_cols=16 Identities=19% Similarity=0.688 Sum_probs=7.9
Q ss_pred CceeCCCCCCCCCCCC
Q 033949 55 PALFCNNCNLLFPSSL 70 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~ 70 (107)
..+.|..|+..+..++
T Consensus 87 pmV~CkkCk~ryRaD~ 102 (539)
T PRK14894 87 PLVDCRDCKMRWRADH 102 (539)
T ss_pred ceeECCCCCccccCcc
Confidence 3455555555554433
No 424
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=56.55 E-value=5 Score=26.54 Aligned_cols=16 Identities=19% Similarity=0.272 Sum_probs=12.8
Q ss_pred CccccccCCceecCCC
Q 033949 82 DVSKCRFCDRLVEPDF 97 (107)
Q Consensus 82 ~~~~C~~CG~~i~~~~ 97 (107)
..+.||+||..++..+
T Consensus 73 rEyyCP~Cgt~levE~ 88 (112)
T PF08882_consen 73 REYYCPGCGTQLEVEA 88 (112)
T ss_pred EEEECCCCcceeEEcc
Confidence 3688999999987654
No 425
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=56.52 E-value=7.6 Score=26.91 Aligned_cols=7 Identities=29% Similarity=0.795 Sum_probs=4.4
Q ss_pred ECCCCCC
Q 033949 23 RCINCGS 29 (107)
Q Consensus 23 ~C~~Cg~ 29 (107)
.||.||+
T Consensus 2 ~CP~C~~ 8 (147)
T TIGR00244 2 HCPFCQH 8 (147)
T ss_pred CCCCCCC
Confidence 4666666
No 426
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=56.18 E-value=10 Score=30.51 Aligned_cols=26 Identities=19% Similarity=0.377 Sum_probs=19.0
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP 67 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~ 67 (107)
...|.+||... ......||.|++=-.
T Consensus 7 ~y~C~~Cg~~~---------------------~~~~g~Cp~C~~w~t 32 (454)
T TIGR00416 7 KFVCQHCGADS---------------------PKWQGKCPACHAWNT 32 (454)
T ss_pred eEECCcCCCCC---------------------ccccEECcCCCCccc
Confidence 57899999932 237888999987543
No 427
>PRK07218 replication factor A; Provisional
Probab=56.13 E-value=6.6 Score=31.59 Aligned_cols=22 Identities=23% Similarity=0.665 Sum_probs=17.8
Q ss_pred CccccccCCceecCCCccCcCCCC
Q 033949 82 DVSKCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 82 ~~~~C~~CG~~i~~~~~fCP~CG~ 105 (107)
....||.|+..+.. ..||.||.
T Consensus 296 li~rCP~C~r~v~~--~~C~~hG~ 317 (423)
T PRK07218 296 LIERCPECGRVIQK--GQCRSHGA 317 (423)
T ss_pred ceecCcCccccccC--CcCCCCCC
Confidence 35789999999855 68999985
No 428
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=56.08 E-value=13 Score=31.86 Aligned_cols=23 Identities=26% Similarity=0.629 Sum_probs=14.0
Q ss_pred ccccccCCce----ecCCCccCcCCCC
Q 033949 83 VSKCRFCDRL----VEPDFSFCPYCGS 105 (107)
Q Consensus 83 ~~~C~~CG~~----i~~~~~fCP~CG~ 105 (107)
..+|+.||.. +...-..||.||+
T Consensus 641 ~~~C~~CG~~Ge~~~~~~~~~CP~CG~ 667 (711)
T PRK09263 641 IDECYECGFTGEFECTEKGFTCPKCGN 667 (711)
T ss_pred CcccCCCCCCccccCCCCCCcCcCCCC
Confidence 4578888873 1111256888885
No 429
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=55.97 E-value=17 Score=21.47 Aligned_cols=34 Identities=21% Similarity=0.445 Sum_probs=25.6
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCC
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLP 71 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~ 71 (107)
-..||-|.+...+ ....+.+.|+.|+-.|+|...
T Consensus 8 iLaCP~~kg~L~~-----------------~~~~~~L~c~~~~~aYpI~dG 41 (60)
T COG2835 8 ILACPVCKGPLVY-----------------DEEKQELICPRCKLAYPIRDG 41 (60)
T ss_pred eeeccCcCCcceE-----------------eccCCEEEecccCceeecccC
Confidence 3569999995433 334579999999999988553
No 430
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=55.80 E-value=13 Score=31.08 Aligned_cols=13 Identities=23% Similarity=0.519 Sum_probs=7.5
Q ss_pred ceeCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPS 68 (107)
Q Consensus 56 ~~~C~~CG~~~~~ 68 (107)
.-.|.+||..+..
T Consensus 155 GD~Ce~Cg~~~~P 167 (558)
T COG0143 155 GDQCENCGRTLDP 167 (558)
T ss_pred cchhhhccCcCCc
Confidence 3456666666654
No 431
>KOG1247 consensus Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=55.75 E-value=4.7 Score=32.87 Aligned_cols=26 Identities=23% Similarity=0.422 Sum_probs=17.4
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
.-.||.||..-.. ...|.+||..+.+
T Consensus 152 eg~cp~C~yd~AR--------------GDqcd~cG~l~N~ 177 (567)
T KOG1247|consen 152 EGKCPFCGYDDAR--------------GDQCDKCGKLVNA 177 (567)
T ss_pred hccCCCCCCcccc--------------chhhhhhhhhcCH
Confidence 5678888876432 2358888877766
No 432
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=55.60 E-value=9.8 Score=33.97 Aligned_cols=12 Identities=25% Similarity=0.750 Sum_probs=8.1
Q ss_pred CceeCCCCCCCC
Q 033949 55 PALFCNNCNLLF 66 (107)
Q Consensus 55 ~~~~C~~CG~~~ 66 (107)
.++.|..|+...
T Consensus 33 ~FVAC~eC~fpv 44 (1044)
T PLN02915 33 PFVACHVCGFPV 44 (1044)
T ss_pred EEEEeccCCCcc
Confidence 377777777664
No 433
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=55.51 E-value=9.1 Score=27.69 Aligned_cols=13 Identities=31% Similarity=0.600 Sum_probs=9.8
Q ss_pred ccccccCCceecC
Q 033949 83 VSKCRFCDRLVEP 95 (107)
Q Consensus 83 ~~~C~~CG~~i~~ 95 (107)
...||.|.+.+..
T Consensus 68 ~~~CPvCR~~Is~ 80 (193)
T PLN03208 68 PPKCPVCKSDVSE 80 (193)
T ss_pred CCcCCCCCCcCCh
Confidence 4579999888754
No 434
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 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 family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=55.41 E-value=2.9 Score=30.91 Aligned_cols=25 Identities=20% Similarity=0.763 Sum_probs=22.3
Q ss_pred CccccccCCceecCCCccCcCCCCC
Q 033949 82 DVSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 82 ~~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
-.+.|-+|+..|-.+|-.||-|-.+
T Consensus 193 PMK~C~sC~qqIHRNAPiCPlCK~K 217 (230)
T PF10146_consen 193 PMKTCQSCHQQIHRNAPICPLCKAK 217 (230)
T ss_pred CcchhHhHHHHHhcCCCCCcccccc
Confidence 3688999999999999999999654
No 435
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=55.25 E-value=13 Score=29.84 Aligned_cols=36 Identities=14% Similarity=0.428 Sum_probs=22.6
Q ss_pred CCCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 18 KSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 18 ~~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
..+...||.|+-..+ .| +.+ +++...||.||+.+..
T Consensus 15 ~~~~~~C~eCd~~~~------------~P--~l~-~~q~A~CPRC~~~l~~ 50 (418)
T COG2995 15 PGHLILCPECDMLVS------------LP--RLD-SGQSAYCPRCGHTLTR 50 (418)
T ss_pred ccceecCCCCCceec------------cc--cCC-CCCcccCCCCCCcccc
Confidence 345566888888321 12 233 3478888888888754
No 436
>PLN02610 probable methionyl-tRNA synthetase
Probab=55.20 E-value=13 Score=32.32 Aligned_cols=11 Identities=27% Similarity=0.833 Sum_probs=7.1
Q ss_pred cccccCCceec
Q 033949 84 SKCRFCDRLVE 94 (107)
Q Consensus 84 ~~C~~CG~~i~ 94 (107)
.+|.-||++++
T Consensus 188 p~c~~~g~~~~ 198 (801)
T PLN02610 188 PKCKVCKNTPR 198 (801)
T ss_pred CcccCCCCcce
Confidence 45777777654
No 437
>PRK05638 threonine synthase; Validated
Probab=55.15 E-value=8.9 Score=30.56 Aligned_cols=12 Identities=33% Similarity=0.736 Sum_probs=7.2
Q ss_pred ceeCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPS 68 (107)
Q Consensus 56 ~~~C~~CG~~~~~ 68 (107)
...| .||..++.
T Consensus 16 ~~~C-~c~~~l~~ 27 (442)
T PRK05638 16 PPFC-ICGELLEI 27 (442)
T ss_pred ceec-CCCCcEEE
Confidence 3567 67766544
No 438
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=55.02 E-value=3.8 Score=19.63 Aligned_cols=10 Identities=30% Similarity=0.680 Sum_probs=5.3
Q ss_pred eeCCCCCCCC
Q 033949 57 LFCNNCNLLF 66 (107)
Q Consensus 57 ~~C~~CG~~~ 66 (107)
+.|+.||..+
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 3455555555
No 439
>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=54.97 E-value=12 Score=31.25 Aligned_cols=25 Identities=24% Similarity=0.533 Sum_probs=14.9
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
..-.|..||..-+.. ...||.||..
T Consensus 523 ~~~~C~~CG~~g~~~-------------~~~CP~Cgs~ 547 (579)
T TIGR02487 523 PVDVCEDCGYTGEGL-------------NDKCPKCGSH 547 (579)
T ss_pred CCccCCCCCCCCCCC-------------CCcCcCCCCc
Confidence 466788888632221 1368888854
No 440
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=54.96 E-value=7.2 Score=21.58 Aligned_cols=12 Identities=25% Similarity=0.523 Sum_probs=6.1
Q ss_pred cccccCCceecC
Q 033949 84 SKCRFCDRLVEP 95 (107)
Q Consensus 84 ~~C~~CG~~i~~ 95 (107)
++||.||+..-.
T Consensus 12 rkCp~CGt~NG~ 23 (44)
T PF14952_consen 12 RKCPKCGTYNGT 23 (44)
T ss_pred ccCCcCcCccCc
Confidence 445555555433
No 441
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=54.88 E-value=7.2 Score=33.52 Aligned_cols=24 Identities=17% Similarity=0.454 Sum_probs=14.7
Q ss_pred eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCc
Q 033949 57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDR 91 (107)
Q Consensus 57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~ 91 (107)
..||.||..+...+ --.+|++||.
T Consensus 725 ~~Cp~Cg~~l~~~~-----------GC~~C~~CG~ 748 (752)
T PRK08665 725 GACPECGSILEHEE-----------GCVVCHSCGY 748 (752)
T ss_pred CCCCCCCcccEECC-----------CCCcCCCCCC
Confidence 35888886543222 2467888886
No 442
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=54.83 E-value=8.6 Score=30.49 Aligned_cols=9 Identities=33% Similarity=0.700 Sum_probs=4.5
Q ss_pred ccccCCcee
Q 033949 85 KCRFCDRLV 93 (107)
Q Consensus 85 ~C~~CG~~i 93 (107)
.||+||++.
T Consensus 74 ~C~~cg~~~ 82 (415)
T COG5257 74 KCPNCGAET 82 (415)
T ss_pred CCCCCCCCc
Confidence 455555543
No 443
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=54.77 E-value=8.5 Score=30.32 Aligned_cols=24 Identities=33% Similarity=0.528 Sum_probs=14.0
Q ss_pred ccccccCCceecC---CCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEP---DFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~---~~~fCP~CG~~ 106 (107)
..+|++||..... ....||+||.+
T Consensus 244 ~~~C~~c~~~~~~~~~~~~~C~~c~~~ 270 (382)
T PRK04338 244 VYYCPKCLYREEVEGLPPEECPVCGGK 270 (382)
T ss_pred EEECCCCCcEEEecCCCCCCCCCCCCc
Confidence 3457777765432 23467777765
No 444
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=54.69 E-value=6.7 Score=32.38 Aligned_cols=34 Identities=21% Similarity=0.562 Sum_probs=24.0
Q ss_pred ECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCC
Q 033949 23 RCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPP 72 (107)
Q Consensus 23 ~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~ 72 (107)
.|+|||.+. |--+...+.+.|.-||...+.+...
T Consensus 2 ~C~~C~~s~----------------fe~d~a~g~~~C~~CG~v~E~~~iv 35 (521)
T KOG1598|consen 2 VCKNCGGSN----------------FERDEATGNLYCTACGTVLEYNNIV 35 (521)
T ss_pred cCCCCCCCC----------------cccccccCCceeccccceeecccee
Confidence 599999933 2233445689999999998775543
No 445
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=54.52 E-value=5.2 Score=29.98 Aligned_cols=28 Identities=25% Similarity=0.530 Sum_probs=19.6
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV 93 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i 93 (107)
+...|..|++.+.... ....|+.||..+
T Consensus 166 q~~rc~~c~~k~rr~p-----------l~g~c~kcg~~~ 193 (253)
T COG1933 166 QEFRCVKCNTKFRRPP-----------LDGKCPICGGKI 193 (253)
T ss_pred heeehHhhhhhhcCCC-----------ccccccccCCeE
Confidence 6788888888875433 245788888744
No 446
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.50 E-value=6.6 Score=23.51 Aligned_cols=13 Identities=23% Similarity=0.393 Sum_probs=7.6
Q ss_pred ccccccCCceecC
Q 033949 83 VSKCRFCDRLVEP 95 (107)
Q Consensus 83 ~~~C~~CG~~i~~ 95 (107)
++.||.||+.++-
T Consensus 7 ~v~CP~Cgkpv~w 19 (65)
T COG3024 7 TVPCPTCGKPVVW 19 (65)
T ss_pred cccCCCCCCcccc
Confidence 3556666666544
No 447
>PLN02195 cellulose synthase A
Probab=54.48 E-value=11 Score=33.51 Aligned_cols=11 Identities=18% Similarity=0.694 Sum_probs=6.3
Q ss_pred ceeCCCCCCCC
Q 033949 56 ALFCNNCNLLF 66 (107)
Q Consensus 56 ~~~C~~CG~~~ 66 (107)
++.|..||...
T Consensus 25 fvaC~eC~~pv 35 (977)
T PLN02195 25 FVACHECSYPL 35 (977)
T ss_pred EEEeccCCCcc
Confidence 56666666553
No 448
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=54.40 E-value=11 Score=30.66 Aligned_cols=13 Identities=23% Similarity=0.629 Sum_probs=7.6
Q ss_pred ccccccCCceecC
Q 033949 83 VSKCRFCDRLVEP 95 (107)
Q Consensus 83 ~~~C~~CG~~i~~ 95 (107)
..+|.-||++++.
T Consensus 166 ~p~~~~~~~~~e~ 178 (530)
T TIGR00398 166 NPRCKICGAKPEL 178 (530)
T ss_pred CCccccCCCcceE
Confidence 3456667766543
No 449
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=54.38 E-value=7.4 Score=35.89 Aligned_cols=9 Identities=44% Similarity=1.176 Sum_probs=4.3
Q ss_pred ccCcCCCCC
Q 033949 98 SFCPYCGSA 106 (107)
Q Consensus 98 ~fCP~CG~~ 106 (107)
+.||.||++
T Consensus 934 k~Cp~Cg~~ 942 (1437)
T PRK00448 934 KDCPKCGTK 942 (1437)
T ss_pred ccCcccccc
Confidence 445555544
No 450
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=54.19 E-value=20 Score=27.35 Aligned_cols=50 Identities=22% Similarity=0.422 Sum_probs=27.0
Q ss_pred CceeCCCCCCCCCCCCC-CCCCCCCCccCccccccCCceecCC--------------CccCcCCCCC
Q 033949 55 PALFCNNCNLLFPSSLP-PPPPPPPLVSDVSKCRFCDRLVEPD--------------FSFCPYCGSA 106 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~-~~~~~~~~~~~~~~C~~CG~~i~~~--------------~~fCP~CG~~ 106 (107)
....|+.||..|-.-.. ..-|. ...+.-.|+-||+....- .=-||.||+.
T Consensus 160 ka~~C~~C~K~YvSmpALkMHir--TH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kA 224 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVSMPALKMHIR--THTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKA 224 (279)
T ss_pred ccccCCCCCceeeehHHHhhHhh--ccCCCcccccccccccchHHhhcccccccCCCCccCCcccch
Confidence 46678888888733111 00000 001245688888887642 3358888764
No 451
>cd01408 SIRT1 SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
Probab=54.13 E-value=5.1 Score=29.33 Aligned_cols=11 Identities=18% Similarity=0.673 Sum_probs=5.2
Q ss_pred ceeCCCCCCCC
Q 033949 56 ALFCNNCNLLF 66 (107)
Q Consensus 56 ~~~C~~CG~~~ 66 (107)
.+.|..|+..+
T Consensus 116 ~~~C~~C~~~~ 126 (235)
T cd01408 116 TAHCIKCKHKY 126 (235)
T ss_pred ccccccCCCcC
Confidence 44455555443
No 452
>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=54.11 E-value=6.8 Score=20.76 Aligned_cols=7 Identities=43% Similarity=1.440 Sum_probs=3.1
Q ss_pred ECCCCCC
Q 033949 23 RCINCGS 29 (107)
Q Consensus 23 ~C~~Cg~ 29 (107)
.||+||+
T Consensus 2 ~Cp~Cg~ 8 (39)
T PF01096_consen 2 KCPKCGH 8 (39)
T ss_dssp --SSS-S
T ss_pred CCcCCCC
Confidence 5777777
No 453
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=54.08 E-value=3 Score=32.78 Aligned_cols=42 Identities=24% Similarity=0.305 Sum_probs=26.4
Q ss_pred EcccccceeeecCCCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCC
Q 033949 6 VGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLF 66 (107)
Q Consensus 6 ifG~~~~~k~~~~~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~ 66 (107)
..|+.+ .++++....|..|..++.+-+. ......||.||..+
T Consensus 234 NyGLdP---~LGKY~~TAC~rC~t~y~le~A----------------~~~~wrCpkCGg~i 275 (403)
T COG1379 234 NYGLDP---RLGKYHLTACSRCYTRYSLEEA----------------KSLRWRCPKCGGKI 275 (403)
T ss_pred ecCcCc---cccchhHHHHHHhhhccCcchh----------------hhhcccCcccccch
Confidence 445555 5667777778888874432211 22567789898866
No 454
>cd01409 SIRT4 SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=54.03 E-value=18 Score=26.91 Aligned_cols=20 Identities=15% Similarity=0.356 Sum_probs=11.6
Q ss_pred eecCCCCCceeCCCCCCCCC
Q 033949 48 WKWPAKEPALFCNNCNLLFP 67 (107)
Q Consensus 48 ~~~~~~~~~~~C~~CG~~~~ 67 (107)
+.++-+-....|..|+..++
T Consensus 110 ielHG~~~~~~C~~C~~~~~ 129 (260)
T cd01409 110 VELHGSLHRVVCLSCGFRTP 129 (260)
T ss_pred EEEeeecCEEEeCCCcCccC
Confidence 33444445666777777664
No 455
>PF03117 Herpes_UL49_1: UL49 family; InterPro: IPR004339 UL49 proteins are present in the viral tegument at the surface of the nucleocapsid []. Many of the nonconserved tegument proteins of alpha-herpes viruses play important roles during different steps of the viral replication cycle, such as the shutoff of host cell functions by the vhs protein encoded by UL41 and the transcriptional activation of viral immediate-early genes by the UL48 gene product, VP16. UL49 of Human herpesvirus 1 (HHV-1) has been shown to directly interact with VP16. The UL49 gene products of HHV-1 and Bovine herpesvirus 1 exhibit virus-independent intercellular trafficking of unknown biological function but are dispensable for productive viral replication. Envelope glycoprotein M (gM) and the complex formed by glycoproteins E (gE) and I (gI) are involved in the secondary envelopment of Suid herpesvirus 1 (Pseudorabies virus, PrV) particles in the cytoplasm of infected cells. In the absence of the gE-gI complex and gM, envelopment is blocked and capsids surrounded by tegument proteins accumulate in the cytoplasm. The cytoplasmic domains of gE and gM specifically interact with the C-terminal part of the UL49 gene product of PrV suggesting a role for the protein in secondary envelopment during herpesvirus virion maturation [].; GO: 0016032 viral reproduction, 0019033 viral tegument
Probab=53.86 E-value=13 Score=27.91 Aligned_cols=33 Identities=15% Similarity=0.217 Sum_probs=20.7
Q ss_pred EEEEEEEeeeecC--------CC--CCceeCCCCCCCCCCCCC
Q 033949 39 VLKAFFVPVWKWP--------AK--EPALFCNNCNLLFPSSLP 71 (107)
Q Consensus 39 ~f~lFFIP~~~~~--------~~--~~~~~C~~CG~~~~~~~~ 71 (107)
.-++.=+|++-.. +. ..++.|.+||+=+...++
T Consensus 78 lssvi~LPv~c~~~~kc~r~~~~~~~~aVvC~~CGhCLN~GK~ 120 (245)
T PF03117_consen 78 LSSVISLPVLCFCKTKCERYKKPRSYRAVVCMECGHCLNFGKG 120 (245)
T ss_pred eEEEeecccchhhhHhhHhhcCCCCeEEEEeccCCchhhccch
Confidence 4556666765332 11 247889999998766554
No 456
>PRK11823 DNA repair protein RadA; Provisional
Probab=53.75 E-value=13 Score=29.81 Aligned_cols=8 Identities=25% Similarity=0.879 Sum_probs=3.8
Q ss_pred eCCCCCCC
Q 033949 58 FCNNCNLL 65 (107)
Q Consensus 58 ~C~~CG~~ 65 (107)
.|.+||+.
T Consensus 9 ~C~~Cg~~ 16 (446)
T PRK11823 9 VCQECGAE 16 (446)
T ss_pred ECCcCCCC
Confidence 34445444
No 457
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=53.59 E-value=10 Score=21.35 Aligned_cols=35 Identities=31% Similarity=0.881 Sum_probs=22.9
Q ss_pred cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949 21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS 68 (107)
Q Consensus 21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~ 68 (107)
...|.+|+.+.. |+++-+..+....|..||-.+..
T Consensus 3 ~~~C~~C~~~~T-------------~~WR~g~~g~~~LCnaCgl~~~k 37 (52)
T smart00401 3 GRSCSNCGTTET-------------PLWRRGPSGNKTLCNACGLYYKK 37 (52)
T ss_pred CCCcCCCCCCCC-------------CccccCCCCCCcEeecccHHHHH
Confidence 346999998321 44555555445889999987644
No 458
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=53.49 E-value=6.7 Score=25.01 Aligned_cols=25 Identities=20% Similarity=0.479 Sum_probs=18.5
Q ss_pred CcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCC
Q 033949 20 GAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLL 65 (107)
Q Consensus 20 ~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~ 65 (107)
.-+.|..||+ +++ .+...|..||..
T Consensus 15 tHtlCrRCG~~syH---------------------~qK~~CasCGyp 40 (91)
T PTZ00073 15 THTLCRRCGKRSFH---------------------VQKKRCASCGYP 40 (91)
T ss_pred CcchhcccCccccc---------------------cccccchhcCCc
Confidence 3457999999 652 356679999984
No 459
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=53.38 E-value=3.5 Score=29.25 Aligned_cols=73 Identities=18% Similarity=0.292 Sum_probs=28.8
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecC---CCCCceeCCCCCCCCCCCCCCC----CCCCC---CccCcccccc-
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWP---AKEPALFCNNCNLLFPSSLPPP----PPPPP---LVSDVSKCRF- 88 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~---~~~~~~~C~~CG~~~~~~~~~~----~~~~~---~~~~~~~C~~- 88 (107)
-.+.||+|+..... =.++.=+ .....+.|++|+..+....-.. .+... .......|..
T Consensus 17 l~~~C~~C~~~~~f-----------~g~~~~~~~~~~~~~~~C~~C~~~~~~~~l~Nql~l~iR~~i~~YY~gwl~Cdd~ 85 (188)
T PF08996_consen 17 LKLTCPSCGTEFEF-----------PGVFEEDGDDVSPSGLQCPNCSTPLSPASLVNQLELQIREHISRYYEGWLVCDDP 85 (188)
T ss_dssp EEEE-TTT--EEEE------------SSS--SSEEEETTEEEETTT--B--HHHHHHHHHHHHHHHHHHHHH--CCCCTC
T ss_pred eEeECCCCCCCccc-----------cccccCCccccccCcCcCCCCCCcCCHHHHHHHHHHHHHHHHHHHHHhCceeCcc
Confidence 46789999994321 1111100 0123678999999542211000 00000 0113567876
Q ss_pred -CCceecC---CCccCc---CC
Q 033949 89 -CDRLVEP---DFSFCP---YC 103 (107)
Q Consensus 89 -CG~~i~~---~~~fCP---~C 103 (107)
||..+.. ....|| .|
T Consensus 86 ~C~~~TR~~~~~~~rC~~~~~C 107 (188)
T PF08996_consen 86 TCGNRTRQLSLYGKRCPGAPGC 107 (188)
T ss_dssp CCHHCCCSTTSTTTCST-STT-
T ss_pred cccCcccccccCCCCCCCcccc
Confidence 8877654 444587 66
No 460
>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=53.25 E-value=14 Score=30.64 Aligned_cols=22 Identities=27% Similarity=0.661 Sum_probs=15.3
Q ss_pred eCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949 58 FCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL 92 (107)
Q Consensus 58 ~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~ 92 (107)
.|..||...+. ....||.||++
T Consensus 520 ~C~~CG~~~~~-------------~~~~CP~CGs~ 541 (555)
T cd01675 520 ICNDCGYIGEG-------------EGFKCPKCGSE 541 (555)
T ss_pred cCCCCCCCCcC-------------CCCCCcCCCCc
Confidence 89999986531 13579999965
No 461
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=52.89 E-value=5.8 Score=23.78 Aligned_cols=41 Identities=20% Similarity=0.428 Sum_probs=23.6
Q ss_pred ecCCCCC--ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949 49 KWPAKEP--ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE 94 (107)
Q Consensus 49 ~~~~~~~--~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~ 94 (107)
.|+...+ +-.|| ||..+.++.+... ..+....||+|.-.|.
T Consensus 13 e~~~e~~~y~yPCp-CGDrf~It~edL~----~ge~Va~CpsCSL~I~ 55 (67)
T KOG2923|consen 13 EFDEENQTYYYPCP-CGDRFQITLEDLE----NGEDVARCPSCSLIIR 55 (67)
T ss_pred eeccCCCeEEcCCC-CCCeeeecHHHHh----CCCeeecCCCceEEEE
Confidence 3444333 44454 8999887654211 1224678999976554
No 462
>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=52.60 E-value=12 Score=33.43 Aligned_cols=30 Identities=23% Similarity=0.449 Sum_probs=20.0
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
+...|..||+.|..-. +.-.|+.||..+..
T Consensus 1011 Q~fRC~kC~~kYRR~P-----------L~G~C~kCGg~lil 1040 (1095)
T TIGR00354 1011 QEVRCTKCNTKYRRIP-----------LVGKCLKCGNNLTL 1040 (1095)
T ss_pred cceeecccCCccccCC-----------CCCcccccCCeEEE
Confidence 6778888888874422 24568888876643
No 463
>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=52.48 E-value=21 Score=27.41 Aligned_cols=11 Identities=18% Similarity=0.407 Sum_probs=8.2
Q ss_pred CCcEECCCCCC
Q 033949 19 SGAGRCINCGS 29 (107)
Q Consensus 19 ~~~~~C~~Cg~ 29 (107)
...+.||+||+
T Consensus 256 t~~~~C~~C~~ 266 (299)
T TIGR01385 256 TDLFTCGKCKQ 266 (299)
T ss_pred cccccCCCCCC
Confidence 44677888888
No 464
>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=52.42 E-value=7.7 Score=26.85 Aligned_cols=43 Identities=16% Similarity=0.278 Sum_probs=20.9
Q ss_pred cCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949 50 WPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP 95 (107)
Q Consensus 50 ~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~ 95 (107)
++-+-....|..|+..+..+.....+ .......|+.||..+.+
T Consensus 99 lHG~l~~~~C~~C~~~~~~~~~~~~~---~~~~~~~C~~C~~~lrp 141 (178)
T PF02146_consen 99 LHGSLFRLRCSKCGKEYDREDIVDSI---DEEEPPRCPKCGGLLRP 141 (178)
T ss_dssp TTEEEEEEEETTTSBEEEGHHHHHHH---HTTSSCBCTTTSCBEEE
T ss_pred HHhhhceeeecCCCccccchhhcccc---cccccccccccCccCCC
Confidence 43333467788888766432110000 00023467777776655
No 465
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=52.14 E-value=8.9 Score=22.77 Aligned_cols=11 Identities=36% Similarity=0.824 Sum_probs=6.8
Q ss_pred cccccCCceec
Q 033949 84 SKCRFCDRLVE 94 (107)
Q Consensus 84 ~~C~~CG~~i~ 94 (107)
..||.||+.++
T Consensus 7 v~CP~C~k~~~ 17 (62)
T PRK00418 7 VNCPTCGKPVE 17 (62)
T ss_pred ccCCCCCCccc
Confidence 45666666653
No 466
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=52.05 E-value=41 Score=21.34 Aligned_cols=15 Identities=20% Similarity=0.877 Sum_probs=12.2
Q ss_pred CCceeCCCCCCCCCC
Q 033949 54 EPALFCNNCNLLFPS 68 (107)
Q Consensus 54 ~~~~~C~~CG~~~~~ 68 (107)
-+.+.|++||..+-.
T Consensus 33 VPa~~C~~CGe~y~~ 47 (89)
T TIGR03829 33 TPSISCSHCGMEYQD 47 (89)
T ss_pred CCcccccCCCcEeec
Confidence 478999999998843
No 467
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=51.93 E-value=7.8 Score=30.70 Aligned_cols=22 Identities=27% Similarity=0.810 Sum_probs=13.4
Q ss_pred ccccCCceecCCC-----ccCcCCCCCC
Q 033949 85 KCRFCDRLVEPDF-----SFCPYCGSAL 107 (107)
Q Consensus 85 ~C~~CG~~i~~~~-----~fCP~CG~~l 107 (107)
-|..|+..+++.. ..|| ||.+|
T Consensus 242 ~c~~C~~~~~~~~~~~~~~~Cp-CG~~i 268 (374)
T TIGR00375 242 ACEACGEPAVSEDAETACANCP-CGGRI 268 (374)
T ss_pred hhcccCCcCCchhhhhcCCCCC-CCCcc
Confidence 4667776666544 4477 77653
No 468
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=51.76 E-value=6.9 Score=28.19 Aligned_cols=7 Identities=57% Similarity=1.516 Sum_probs=4.8
Q ss_pred ECCCCCC
Q 033949 23 RCINCGS 29 (107)
Q Consensus 23 ~C~~Cg~ 29 (107)
.|-+||+
T Consensus 2 iCIeCg~ 8 (208)
T PF04161_consen 2 ICIECGH 8 (208)
T ss_pred EeccCCC
Confidence 5677777
No 469
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=51.59 E-value=15 Score=22.69 Aligned_cols=29 Identities=21% Similarity=0.265 Sum_probs=21.2
Q ss_pred EECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCC--ceeCCCCCCCCCCC
Q 033949 22 GRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEP--ALFCNNCNLLFPSS 69 (107)
Q Consensus 22 ~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~--~~~C~~CG~~~~~~ 69 (107)
+.||-||. +. ..+.. +-.|+.|+...+..
T Consensus 2 ~~CPCCg~~Tl-------------------~~~~~~~ydIC~VC~WEdD~~ 33 (78)
T PF14206_consen 2 YPCPCCGYYTL-------------------EERGEGTYDICPVCFWEDDGV 33 (78)
T ss_pred ccCCCCCcEEe-------------------ccCCCcCceECCCCCcccCCc
Confidence 47999999 43 23334 88999999988664
No 470
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=51.49 E-value=9.6 Score=34.75 Aligned_cols=10 Identities=20% Similarity=0.627 Sum_probs=4.8
Q ss_pred cccccCCcee
Q 033949 84 SKCRFCDRLV 93 (107)
Q Consensus 84 ~~C~~CG~~i 93 (107)
+.||.||+.+
T Consensus 940 K~CPkCg~pl 949 (1444)
T COG2176 940 KDCPKCGTPL 949 (1444)
T ss_pred CCCCcCCCcc
Confidence 3455555444
No 471
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=51.41 E-value=4.9 Score=32.68 Aligned_cols=24 Identities=25% Similarity=0.537 Sum_probs=17.0
Q ss_pred eeecCCCCCceeCCCCCCCCCCCC
Q 033949 47 VWKWPAKEPALFCNNCNLLFPSSL 70 (107)
Q Consensus 47 ~~~~~~~~~~~~C~~CG~~~~~~~ 70 (107)
+.||--...++.||.|+..+.+..
T Consensus 171 vVpW~DDs~V~~CP~Ca~~F~l~r 194 (505)
T KOG1842|consen 171 VVPWLDDSSVQFCPECANSFGLTR 194 (505)
T ss_pred cccccCCCcccccccccchhhhHH
Confidence 456755556888888888887754
No 472
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=51.06 E-value=3.3 Score=26.87 Aligned_cols=11 Identities=27% Similarity=1.038 Sum_probs=5.5
Q ss_pred ccccCCceecC
Q 033949 85 KCRFCDRLVEP 95 (107)
Q Consensus 85 ~C~~CG~~i~~ 95 (107)
.||+|.++..+
T Consensus 82 ~Cp~C~spFNp 92 (105)
T COG4357 82 SCPYCQSPFNP 92 (105)
T ss_pred CCCCcCCCCCc
Confidence 45555555443
No 473
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=50.93 E-value=11 Score=29.72 Aligned_cols=10 Identities=20% Similarity=0.225 Sum_probs=5.7
Q ss_pred CceeCCCCCC
Q 033949 55 PALFCNNCNL 64 (107)
Q Consensus 55 ~~~~C~~CG~ 64 (107)
..-.||.||+
T Consensus 13 ~~g~cp~c~~ 22 (372)
T cd01121 13 WLGKCPECGE 22 (372)
T ss_pred ccEECcCCCC
Confidence 4555666655
No 474
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=50.90 E-value=8.2 Score=30.10 Aligned_cols=16 Identities=31% Similarity=0.694 Sum_probs=10.0
Q ss_pred ceeCCCCCCCCCCCCC
Q 033949 56 ALFCNNCNLLFPSSLP 71 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~ 71 (107)
.-.|++|++..+..+.
T Consensus 242 ~F~C~~Cn~LN~~~k~ 257 (328)
T KOG2846|consen 242 TFRCPHCNALNPAKKS 257 (328)
T ss_pred EEECccccccCCCcCC
Confidence 4457777777655443
No 475
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=50.42 E-value=9.1 Score=25.93 Aligned_cols=24 Identities=21% Similarity=0.656 Sum_probs=19.4
Q ss_pred CccccccCCceecCCCccCcCCCC
Q 033949 82 DVSKCRFCDRLVEPDFSFCPYCGS 105 (107)
Q Consensus 82 ~~~~C~~CG~~i~~~~~fCP~CG~ 105 (107)
..+.|+.|...-++.+.+|+.||+
T Consensus 47 ~~~~C~~C~~~kp~Rs~HC~~C~~ 70 (174)
T PF01529_consen 47 ELKYCSTCKIIKPPRSHHCRVCNR 70 (174)
T ss_pred CCEECcccCCcCCCcceecccccc
Confidence 467788888888888888888875
No 476
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=49.98 E-value=16 Score=31.30 Aligned_cols=35 Identities=26% Similarity=0.430 Sum_probs=19.1
Q ss_pred CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce-ecCCCccCcC
Q 033949 55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL-VEPDFSFCPY 102 (107)
Q Consensus 55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~-i~~~~~fCP~ 102 (107)
..-.|..||...+-.. ..||.||.. ++.-...|+|
T Consensus 640 ~i~~C~~cg~~~~~~~-------------~~Cp~CG~~dve~~~Ri~GY 675 (700)
T COG1328 640 PISVCNRCGYSGEGLR-------------TRCPKCGSEDVEVFSRITGY 675 (700)
T ss_pred CceeeccCCccccccc-------------ccCCCCCCccceeeeeeccc
Confidence 4666777777764322 237888755 3333444443
No 477
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=49.90 E-value=16 Score=29.45 Aligned_cols=11 Identities=18% Similarity=0.576 Sum_probs=6.0
Q ss_pred ceeCCCCCCCC
Q 033949 56 ALFCNNCNLLF 66 (107)
Q Consensus 56 ~~~C~~CG~~~ 66 (107)
...|.+||...
T Consensus 7 ~y~C~~Cg~~~ 17 (454)
T TIGR00416 7 KFVCQHCGADS 17 (454)
T ss_pred eEECCcCCCCC
Confidence 34566666553
No 478
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=49.84 E-value=5.2 Score=23.57 Aligned_cols=20 Identities=20% Similarity=0.634 Sum_probs=11.2
Q ss_pred cccccCCceecC-------CCccCcCC
Q 033949 84 SKCRFCDRLVEP-------DFSFCPYC 103 (107)
Q Consensus 84 ~~C~~CG~~i~~-------~~~fCP~C 103 (107)
..|..||.+|+. .+.+|-.|
T Consensus 32 g~C~~Cg~~Ip~~Rl~a~p~~~~Cv~C 58 (63)
T TIGR02419 32 RECEDCGEPIPEARREALPGVTRCVSC 58 (63)
T ss_pred CeeccCCCcChHHHHhhcCCcCCcHHH
Confidence 356666666643 45555554
No 479
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=49.82 E-value=7.8 Score=27.71 Aligned_cols=11 Identities=27% Similarity=0.691 Sum_probs=7.5
Q ss_pred CccCcCCCCCC
Q 033949 97 FSFCPYCGSAL 107 (107)
Q Consensus 97 ~~fCP~CG~~l 107 (107)
-.||+.||++|
T Consensus 89 R~FC~~CGS~L 99 (182)
T TIGR02820 89 RHACKGCGTHM 99 (182)
T ss_pred eecCCCCCCcc
Confidence 33788888765
No 480
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=49.71 E-value=4.1 Score=24.82 Aligned_cols=19 Identities=21% Similarity=0.726 Sum_probs=11.4
Q ss_pred ccccCCceecC-------CCccCcCC
Q 033949 85 KCRFCDRLVEP-------DFSFCPYC 103 (107)
Q Consensus 85 ~C~~CG~~i~~-------~~~fCP~C 103 (107)
.|..||.+|+. ++.+|-.|
T Consensus 36 ~C~~Cg~~Ip~~Rl~a~p~~~~Cv~C 61 (73)
T PRK13715 36 LCEACGNPIPEARRKIFPGVTLCVEC 61 (73)
T ss_pred cHhhcCCcCCHHHHhcCCCcCCCHHH
Confidence 56666666653 55556555
No 481
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=49.63 E-value=9.3 Score=30.01 Aligned_cols=24 Identities=25% Similarity=0.347 Sum_probs=17.1
Q ss_pred ccccccCCceecCCCccCcCCCCC
Q 033949 83 VSKCRFCDRLVEPDFSFCPYCGSA 106 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fCP~CG~~ 106 (107)
.+.||+|++.+=.=..-||-||-.
T Consensus 276 Gy~CP~CkakvCsLP~eCpiC~lt 299 (378)
T KOG2807|consen 276 GYFCPQCKAKVCSLPIECPICSLT 299 (378)
T ss_pred ceeCCcccCeeecCCccCCcccee
Confidence 567777777777777777777653
No 482
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=49.59 E-value=10 Score=22.17 Aligned_cols=29 Identities=21% Similarity=0.411 Sum_probs=20.8
Q ss_pred CCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCC
Q 033949 26 NCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSS 69 (107)
Q Consensus 26 ~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~ 69 (107)
-||+ .|++++. +-+ ..+.|..||..+.++
T Consensus 15 PCG~~~Wei~R~--------------GaD-ikikC~gCg~~imlp 44 (57)
T PF06107_consen 15 PCGSNEWEIIRI--------------GAD-IKIKCLGCGRQIMLP 44 (57)
T ss_pred CCCCCEEEEEEc--------------cCc-EEEEECCCCCEEEEe
Confidence 5888 8876664 333 688899999887553
No 483
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=49.59 E-value=4.1 Score=29.06 Aligned_cols=41 Identities=12% Similarity=0.329 Sum_probs=22.8
Q ss_pred ceeCCCCCCCCCCCCCC-CCCCC-------C--CccCccccccCCceecCC
Q 033949 56 ALFCNNCNLLFPSSLPP-PPPPP-------P--LVSDVSKCRFCDRLVEPD 96 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~-~~~~~-------~--~~~~~~~C~~CG~~i~~~ 96 (107)
..+|++|+..+-...-. .++.. + ..+..++|++||+..+..
T Consensus 120 ~wyc~~c~~~~~e~~f~~~d~~~~~~~~~~~f~~~~e~rtC~~CG~v~~~~ 170 (177)
T PRK13264 120 QWYCDECNHKVHEVEVQLTDIETDLPPVFAAFYASEELRTCDNCGTVHPGK 170 (177)
T ss_pred EEECCCCCCeEEEEEEEecChhhhhHHHHHHHhcCHhhccCCcCCcccCcc
Confidence 66799998876321111 11111 1 112478899999887654
No 484
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=49.50 E-value=11 Score=32.16 Aligned_cols=57 Identities=16% Similarity=0.435 Sum_probs=36.1
Q ss_pred EECCCCCCCcEEEEEeeEEEEEEEeeeecCCCC----CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949 22 GRCINCGSTADLVEYEKVLKAFFVPVWKWPAKE----PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE 94 (107)
Q Consensus 22 ~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~----~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~ 94 (107)
+.|.+||=++..++. +|+++.. .+.-|+.|-..|.....+- ......-|++||=.+.
T Consensus 91 ~nCt~CGPr~~i~~~-----------lpydr~~t~m~~f~~C~~C~~ey~~p~~rr-----~h~~~~~C~~Cgp~l~ 151 (711)
T TIGR00143 91 ISCTHCGPRFTIIEA-----------LPYDRENTSMADFPLCPDCAKEYKDPLDRR-----FHAQPIACPRCGPQLN 151 (711)
T ss_pred ccccCCCCCeEEeec-----------CCCCCCCcCCCCCcCCHHHHHHhcCCcccc-----CCCCCccCCCCCcEEE
Confidence 459999998765543 5566542 3566999999885433210 1112356999998773
No 485
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=49.50 E-value=14 Score=26.75 Aligned_cols=13 Identities=31% Similarity=0.853 Sum_probs=9.5
Q ss_pred CCCcEECCCCCCC
Q 033949 18 KSGAGRCINCGST 30 (107)
Q Consensus 18 ~~~~~~C~~Cg~~ 30 (107)
...+..|.+||+.
T Consensus 57 ~~~~~~C~nCg~~ 69 (190)
T COG5082 57 REENPVCFNCGQN 69 (190)
T ss_pred cccccccchhccc
Confidence 3456779999983
No 486
>PF11648 RIG-I_C-RD: C-terminal domain of RIG-I; InterPro: IPR021673 This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2RQB_A 3GA3_A 2W4R_D 3EQT_A 2RQA_A 2RMJ_A 3NCU_A 2QFD_C 2QFB_D 3TMI_A ....
Probab=48.97 E-value=15 Score=24.33 Aligned_cols=29 Identities=28% Similarity=0.464 Sum_probs=22.3
Q ss_pred CcEECCCCCCCcEEEEEeeEEEEEEEeeeecC
Q 033949 20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWP 51 (107)
Q Consensus 20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~ 51 (107)
..+.|.+||+.|.....++-+. +|++...
T Consensus 59 ~~I~C~~C~~~wG~~m~yk~~~---LP~L~ik 87 (123)
T PF11648_consen 59 GKIHCKNCGQDWGIMMKYKGVE---LPCLKIK 87 (123)
T ss_dssp EEEEETSTSBEEEEEEEETTEE---EEEE-GG
T ss_pred CEEEcCCCChHhhhheEECCcc---ccEEEee
Confidence 4678999999998888777666 6888754
No 487
>PHA00080 DksA-like zinc finger domain containing protein
Probab=48.88 E-value=5.3 Score=24.23 Aligned_cols=10 Identities=20% Similarity=0.673 Sum_probs=5.8
Q ss_pred ccccCCceec
Q 033949 85 KCRFCDRLVE 94 (107)
Q Consensus 85 ~C~~CG~~i~ 94 (107)
.|..||.+|+
T Consensus 33 ~C~~Cg~~Ip 42 (72)
T PHA00080 33 HCEECGDPIP 42 (72)
T ss_pred EecCCCCcCc
Confidence 4666666654
No 488
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=48.79 E-value=12 Score=24.17 Aligned_cols=11 Identities=27% Similarity=0.516 Sum_probs=5.9
Q ss_pred eeCCCCCCCCC
Q 033949 57 LFCNNCNLLFP 67 (107)
Q Consensus 57 ~~C~~CG~~~~ 67 (107)
..|..|+....
T Consensus 4 rAC~~C~~I~~ 14 (98)
T cd07973 4 RACLLCSLIKT 14 (98)
T ss_pred chhccCCcccc
Confidence 35555655543
No 489
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=48.72 E-value=17 Score=21.04 Aligned_cols=12 Identities=42% Similarity=0.839 Sum_probs=6.7
Q ss_pred ccccCCceecCC
Q 033949 85 KCRFCDRLVEPD 96 (107)
Q Consensus 85 ~C~~CG~~i~~~ 96 (107)
-||-||+.++.+
T Consensus 41 gCPfC~~~~~~~ 52 (55)
T PF14447_consen 41 GCPFCGTPFEFD 52 (55)
T ss_pred CCCCCCCcccCC
Confidence 466666665543
No 490
>PF14149 YhfH: YhfH-like protein
Probab=48.52 E-value=3 Score=22.29 Aligned_cols=12 Identities=33% Similarity=0.789 Sum_probs=6.7
Q ss_pred cccccCCceecC
Q 033949 84 SKCRFCDRLVEP 95 (107)
Q Consensus 84 ~~C~~CG~~i~~ 95 (107)
+.|+.||..|+.
T Consensus 14 K~C~~CG~~i~E 25 (37)
T PF14149_consen 14 KKCTECGKEIEE 25 (37)
T ss_pred cccHHHHHHHHH
Confidence 456666655544
No 491
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=48.31 E-value=11 Score=21.11 Aligned_cols=24 Identities=29% Similarity=0.596 Sum_probs=14.4
Q ss_pred Cccccc--cCCcee----cCCCccCcCCCC
Q 033949 82 DVSKCR--FCDRLV----EPDFSFCPYCGS 105 (107)
Q Consensus 82 ~~~~C~--~CG~~i----~~~~~fCP~CG~ 105 (107)
+.+.|| .||+-+ -.+-.+|-+||.
T Consensus 17 ~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 356788 788743 226677777774
No 492
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=48.30 E-value=12 Score=20.82 Aligned_cols=39 Identities=15% Similarity=0.365 Sum_probs=23.9
Q ss_pred CCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949 54 EPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE 94 (107)
Q Consensus 54 ~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~ 94 (107)
.+++.|.+|-+.+........-. ....+..|-.|.+.|.
T Consensus 4 APFv~C~~C~~lLqlP~~~~~~~--k~~~klrCGaCs~vl~ 42 (46)
T PF11331_consen 4 APFVVCSSCFELLQLPAKFSLSK--KNQQKLRCGACSEVLS 42 (46)
T ss_pred CCEeECccHHHHHcCCCccCCCc--cceeEEeCCCCceeEE
Confidence 36888999988886654321100 0112567888888765
No 493
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=48.25 E-value=8.9 Score=30.82 Aligned_cols=11 Identities=18% Similarity=0.437 Sum_probs=5.4
Q ss_pred ceeCCCCCCCC
Q 033949 56 ALFCNNCNLLF 66 (107)
Q Consensus 56 ~~~C~~CG~~~ 66 (107)
...|+.||...
T Consensus 327 ~~~c~~~~~e~ 337 (411)
T COG1503 327 TYKCPTCGYEN 337 (411)
T ss_pred eecCCCcchhh
Confidence 44455555544
No 494
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=47.84 E-value=5.8 Score=35.53 Aligned_cols=28 Identities=29% Similarity=0.488 Sum_probs=18.7
Q ss_pred ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCC
Q 033949 56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPD 96 (107)
Q Consensus 56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~ 96 (107)
.+.|..||+.+-.+. ..||.||.+...+
T Consensus 694 IKrC~dcg~q~~~~~-------------~~cP~Cgs~~v~d 721 (1187)
T COG1110 694 IKRCRDCGEQFVDSE-------------DKCPRCGSRNVED 721 (1187)
T ss_pred HHHHhhcCceecccc-------------ccCCCCCCccccc
Confidence 456888888875432 4788888865543
No 495
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=47.53 E-value=15 Score=20.32 Aligned_cols=11 Identities=36% Similarity=0.984 Sum_probs=7.4
Q ss_pred ceeCCCCCCCC
Q 033949 56 ALFCNNCNLLF 66 (107)
Q Consensus 56 ~~~C~~CG~~~ 66 (107)
...|..||..+
T Consensus 18 k~~Cr~Cg~~~ 28 (57)
T cd00065 18 RHHCRNCGRIF 28 (57)
T ss_pred ccccCcCcCCc
Confidence 45677777765
No 496
>PRK10996 thioredoxin 2; Provisional
Probab=47.50 E-value=27 Score=23.13 Aligned_cols=14 Identities=29% Similarity=0.411 Sum_probs=9.5
Q ss_pred CCceeCCCCCCCCC
Q 033949 54 EPALFCNNCNLLFP 67 (107)
Q Consensus 54 ~~~~~C~~CG~~~~ 67 (107)
.....|+.|++..-
T Consensus 20 ~~~~~~~~~~~~~~ 33 (139)
T PRK10996 20 EDAAKCGRCGHDLF 33 (139)
T ss_pred cCCCcCCCCCCccC
Confidence 35677888887653
No 497
>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=47.49 E-value=12 Score=29.28 Aligned_cols=10 Identities=20% Similarity=0.587 Sum_probs=3.9
Q ss_pred ceeCCCCCCC
Q 033949 56 ALFCNNCNLL 65 (107)
Q Consensus 56 ~~~C~~CG~~ 65 (107)
+..|+.||..
T Consensus 285 FFkC~~C~~R 294 (344)
T PF09332_consen 285 FFKCKDCGNR 294 (344)
T ss_dssp EEE-T-TS-E
T ss_pred eEECCCCCCe
Confidence 4556666654
No 498
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=47.44 E-value=11 Score=29.94 Aligned_cols=9 Identities=56% Similarity=1.302 Sum_probs=4.4
Q ss_pred ccCcCCCCC
Q 033949 98 SFCPYCGSA 106 (107)
Q Consensus 98 ~fCP~CG~~ 106 (107)
.+||+||..
T Consensus 343 ~~~~~~~~~ 351 (403)
T TIGR03676 343 EACPKCGSE 351 (403)
T ss_pred ccCcccCcc
Confidence 345555543
No 499
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=47.43 E-value=11 Score=26.73 Aligned_cols=18 Identities=22% Similarity=0.778 Sum_probs=15.0
Q ss_pred ccccccCCceecCCCccC
Q 033949 83 VSKCRFCDRLVEPDFSFC 100 (107)
Q Consensus 83 ~~~C~~CG~~i~~~~~fC 100 (107)
...||.||.+++++-.+|
T Consensus 154 RP~CPlCg~PlDP~GH~C 171 (171)
T PF11290_consen 154 RPPCPLCGEPLDPEGHIC 171 (171)
T ss_pred CCCCCCCCCCCCCCCCcC
Confidence 567999999999887766
No 500
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=47.42 E-value=8.9 Score=29.95 Aligned_cols=11 Identities=55% Similarity=1.410 Sum_probs=0.0
Q ss_pred CccCcCCCCCC
Q 033949 97 FSFCPYCGSAL 107 (107)
Q Consensus 97 ~~fCP~CG~~l 107 (107)
.+|||.||+++
T Consensus 150 ykFCp~CG~~t 160 (345)
T KOG3084|consen 150 YKFCPGCGSPT 160 (345)
T ss_pred hccCcccCCCc
Done!