Query 035300
Match_columns 68
No_of_seqs 49 out of 51
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 10:46:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035300.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035300hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13005 zf-IS66: zinc-finger 94.9 0.053 1.1E-06 29.7 3.5 41 20-60 2-47 (47)
2 PF10601 zf-LITAF-like: LITAF- 94.5 0.024 5.2E-07 33.9 1.6 51 15-66 2-71 (73)
3 PRK00464 nrdR transcriptional 94.4 0.033 7.1E-07 38.8 2.4 40 22-67 2-42 (154)
4 PF14690 zf-ISL3: zinc-finger 93.9 0.094 2E-06 28.4 3.1 38 20-59 2-47 (47)
5 COG1998 RPS31 Ribosomal protei 93.7 0.054 1.2E-06 32.6 1.9 36 9-62 11-46 (51)
6 PF04216 FdhE: Protein involve 93.3 0.039 8.4E-07 40.2 1.1 43 19-61 171-219 (290)
7 PF06906 DUF1272: Protein of u 91.4 0.092 2E-06 32.1 0.9 13 20-32 41-53 (57)
8 PF12760 Zn_Tnp_IS1595: Transp 90.9 0.4 8.7E-06 26.6 3.1 28 21-62 19-46 (46)
9 COG3813 Uncharacterized protei 90.8 0.096 2.1E-06 34.1 0.6 18 19-36 40-57 (84)
10 PF11672 DUF3268: Protein of u 90.0 0.18 4E-06 33.3 1.4 39 20-63 2-41 (102)
11 PF13248 zf-ribbon_3: zinc-rib 89.8 0.1 2.3E-06 26.3 0.1 9 22-30 4-12 (26)
12 PRK10445 endonuclease VIII; Pr 89.7 0.43 9.4E-06 34.8 3.3 34 12-60 229-262 (263)
13 PF13240 zinc_ribbon_2: zinc-r 89.7 0.098 2.1E-06 26.2 -0.0 9 23-31 2-10 (23)
14 PRK14810 formamidopyrimidine-D 89.6 0.39 8.6E-06 35.2 3.1 26 22-60 246-271 (272)
15 PRK13945 formamidopyrimidine-D 89.1 0.49 1.1E-05 34.8 3.3 34 12-60 248-281 (282)
16 TIGR03831 YgiT_finger YgiT-typ 89.1 0.87 1.9E-05 24.0 3.5 43 23-65 1-44 (46)
17 PRK12775 putative trifunctiona 88.9 0.13 2.9E-06 43.7 0.2 29 6-34 823-852 (1006)
18 TIGR03830 CxxCG_CxxCG_HTH puta 88.8 0.99 2.2E-05 28.2 4.1 41 23-64 1-42 (127)
19 PF01599 Ribosomal_S27: Riboso 88.6 0.7 1.5E-05 27.0 3.0 38 5-60 6-45 (47)
20 PRK00432 30S ribosomal protein 88.5 0.65 1.4E-05 26.9 2.9 36 7-62 11-46 (50)
21 smart00714 LITAF Possible memb 88.4 0.26 5.7E-06 29.0 1.2 49 18-67 1-66 (67)
22 PF07282 OrfB_Zn_ribbon: Putat 88.1 0.39 8.4E-06 27.9 1.8 30 19-63 27-56 (69)
23 PRK00398 rpoP DNA-directed RNA 87.7 0.92 2E-05 25.0 3.1 13 20-32 21-33 (46)
24 TIGR00577 fpg formamidopyrimid 87.5 0.73 1.6E-05 33.7 3.3 26 21-59 246-271 (272)
25 smart00661 RPOL9 RNA polymeras 87.4 0.38 8.2E-06 26.4 1.4 29 22-63 2-30 (52)
26 PF01927 Mut7-C: Mut7-C RNAse 87.3 0.6 1.3E-05 31.2 2.5 45 19-63 90-134 (147)
27 TIGR03655 anti_R_Lar restricti 86.9 0.52 1.1E-05 26.9 1.8 35 22-64 3-37 (53)
28 PRK09678 DNA-binding transcrip 86.8 0.57 1.2E-05 29.2 2.1 40 22-68 3-44 (72)
29 PRK01103 formamidopyrimidine/5 86.6 0.88 1.9E-05 33.1 3.3 28 21-61 246-273 (274)
30 cd00729 rubredoxin_SM Rubredox 85.8 1.1 2.3E-05 24.0 2.6 20 11-30 9-28 (34)
31 COG0675 Transposase and inacti 85.5 0.48 1E-05 32.5 1.4 24 19-62 308-331 (364)
32 PRK14811 formamidopyrimidine-D 85.3 1 2.2E-05 33.0 3.0 28 21-61 236-263 (269)
33 PF14369 zf-RING_3: zinc-finge 85.0 0.86 1.9E-05 24.7 2.0 15 16-30 17-31 (35)
34 smart00531 TFIIE Transcription 84.7 0.34 7.3E-06 32.5 0.3 41 18-67 97-137 (147)
35 TIGR01562 FdhE formate dehydro 84.7 0.38 8.3E-06 36.7 0.6 45 18-62 182-233 (305)
36 PRK00420 hypothetical protein; 84.3 0.81 1.7E-05 30.7 2.0 30 19-64 22-51 (112)
37 PF14803 Nudix_N_2: Nudix N-te 82.9 0.93 2E-05 24.6 1.6 29 22-61 2-30 (34)
38 PF12773 DZR: Double zinc ribb 82.1 0.36 7.9E-06 26.5 -0.3 14 50-63 26-39 (50)
39 PRK03564 formate dehydrogenase 81.9 0.86 1.9E-05 34.9 1.6 43 19-61 186-234 (309)
40 PF08271 TF_Zn_Ribbon: TFIIB z 81.7 1.6 3.5E-05 23.8 2.3 30 22-65 2-31 (43)
41 PF09297 zf-NADH-PPase: NADH p 81.5 0.98 2.1E-05 23.4 1.3 17 21-37 4-20 (32)
42 PF14354 Lar_restr_allev: Rest 81.2 1.7 3.7E-05 24.6 2.3 33 22-61 5-37 (61)
43 TIGR00373 conserved hypothetic 81.0 0.44 9.5E-06 32.6 -0.3 35 19-67 108-142 (158)
44 TIGR01206 lysW lysine biosynth 80.1 1.8 4E-05 25.6 2.3 33 21-66 3-35 (54)
45 COG1645 Uncharacterized Zn-fin 78.6 1.9 4.1E-05 29.9 2.3 27 21-64 29-55 (131)
46 COG3464 Transposase and inacti 78.2 3.3 7.1E-05 32.2 3.7 46 18-63 36-87 (402)
47 TIGR00622 ssl1 transcription f 76.9 1.2 2.7E-05 30.0 0.9 26 22-66 3-28 (112)
48 PRK06266 transcription initiat 76.6 0.62 1.3E-05 32.6 -0.6 35 19-67 116-150 (178)
49 PF05129 Elf1: Transcription e 76.4 3.5 7.6E-05 25.8 2.8 37 18-64 20-57 (81)
50 PF06827 zf-FPG_IleRS: Zinc fi 74.5 4.3 9.3E-05 20.5 2.4 14 22-35 3-16 (30)
51 COG1592 Rubrerythrin [Energy p 74.5 2.6 5.7E-05 29.9 2.1 23 6-29 136-158 (166)
52 TIGR00310 ZPR1_znf ZPR1 zinc f 74.1 3.4 7.3E-05 29.6 2.6 38 22-63 2-40 (192)
53 cd00350 rubredoxin_like Rubred 73.6 4 8.6E-05 21.3 2.2 14 17-30 14-27 (33)
54 PF03119 DNA_ligase_ZBD: NAD-d 72.6 2.8 6E-05 21.7 1.4 18 22-39 1-18 (28)
55 PF09723 Zn-ribbon_8: Zinc rib 72.3 5.8 0.00012 21.7 2.8 12 17-28 23-34 (42)
56 smart00834 CxxC_CXXC_SSSS Puta 71.3 5.9 0.00013 20.5 2.6 12 18-29 24-35 (41)
57 PF08792 A2L_zn_ribbon: A2L zi 70.3 5.9 0.00013 21.2 2.4 26 22-62 5-30 (33)
58 PF14255 Cys_rich_CPXG: Cystei 70.2 3.4 7.3E-05 24.3 1.6 11 22-32 2-12 (52)
59 smart00659 RPOLCX RNA polymera 70.0 5.8 0.00013 22.4 2.5 27 5-31 3-30 (44)
60 COG1656 Uncharacterized conser 69.4 1.5 3.3E-05 31.4 -0.0 45 17-63 94-140 (165)
61 TIGR00340 zpr1_rel ZPR1-relate 68.3 5.1 0.00011 28.0 2.4 35 23-62 1-37 (163)
62 PF04606 Ogr_Delta: Ogr/Delta- 67.2 3.6 7.8E-05 23.0 1.3 38 22-66 1-40 (47)
63 TIGR00244 transcriptional regu 66.0 4.7 0.0001 28.4 1.9 39 22-66 2-41 (147)
64 PRK09401 reverse gyrase; Revie 65.8 2.4 5.2E-05 37.3 0.5 14 20-33 7-20 (1176)
65 PF09862 DUF2089: Protein of u 65.2 5.2 0.00011 26.9 1.9 14 23-36 1-14 (113)
66 PF13894 zf-C2H2_4: C2H2-type 64.0 2.9 6.4E-05 18.6 0.4 13 54-66 1-13 (24)
67 COG1110 Reverse gyrase [DNA re 63.5 3.2 7E-05 37.3 0.8 20 20-39 8-27 (1187)
68 PF06221 zf-C2HC5: Putative zi 63.5 3.8 8.2E-05 24.7 0.9 24 11-34 25-49 (57)
69 TIGR02098 MJ0042_CXXC MJ0042 f 63.4 5.2 0.00011 20.8 1.4 13 52-64 24-36 (38)
70 PRK11827 hypothetical protein; 63.2 6.3 0.00014 23.9 1.8 27 22-63 10-36 (60)
71 PF14353 CpXC: CpXC protein 63.2 6.7 0.00015 25.1 2.1 36 11-46 29-70 (128)
72 PF05191 ADK_lid: Adenylate ki 63.0 4.8 0.0001 21.9 1.2 15 17-31 18-32 (36)
73 PF07038 DUF1324: Protein of u 62.8 6.1 0.00013 24.1 1.7 15 37-51 7-21 (59)
74 COG4391 Uncharacterized protei 62.1 6.8 0.00015 24.3 1.9 47 11-66 15-61 (62)
75 COG1996 RPC10 DNA-directed RNA 61.9 5.2 0.00011 23.6 1.3 15 19-33 23-37 (49)
76 COG1933 Archaeal DNA polymeras 61.9 1.4 3.1E-05 33.6 -1.4 23 7-29 141-163 (253)
77 PF14787 zf-CCHC_5: GAG-polypr 61.5 3.7 8E-05 23.1 0.6 10 20-29 2-11 (36)
78 smart00778 Prim_Zn_Ribbon Zinc 61.4 4.6 9.9E-05 22.3 0.9 10 20-29 3-12 (37)
79 TIGR01384 TFS_arch transcripti 60.4 4.9 0.00011 25.0 1.1 9 22-30 2-10 (104)
80 PRK09710 lar restriction allev 60.4 14 0.00029 23.0 3.0 30 21-62 7-36 (64)
81 TIGR01054 rgy reverse gyrase. 60.4 3.7 8.1E-05 36.1 0.7 13 20-32 7-19 (1171)
82 PRK04023 DNA polymerase II lar 60.1 4.7 0.0001 36.2 1.2 39 21-67 639-677 (1121)
83 PRK12380 hydrogenase nickel in 59.8 6.5 0.00014 25.6 1.6 18 11-28 61-78 (113)
84 PF01396 zf-C4_Topoisom: Topoi 59.5 6.7 0.00015 21.3 1.4 13 21-33 2-14 (39)
85 TIGR02605 CxxC_CxxC_SSSS putat 58.9 25 0.00054 19.2 3.7 11 18-28 24-34 (52)
86 PF06677 Auto_anti-p27: Sjogre 58.5 5.4 0.00012 22.4 0.9 17 44-60 25-41 (41)
87 PF09947 DUF2180: Uncharacteri 57.9 1.8 4E-05 27.0 -1.2 57 4-63 3-66 (68)
88 PF08273 Prim_Zn_Ribbon: Zinc- 57.7 4 8.7E-05 22.9 0.3 31 20-60 3-33 (40)
89 PF10263 SprT-like: SprT-like 56.7 10 0.00022 24.5 2.1 14 52-65 142-155 (157)
90 PF13453 zf-TFIIB: Transcripti 56.4 12 0.00027 20.0 2.1 13 23-35 2-14 (41)
91 PRK00241 nudC NADH pyrophospha 56.1 8 0.00017 28.2 1.7 13 20-32 99-111 (256)
92 PF09538 FYDLN_acid: Protein o 55.9 6.4 0.00014 26.0 1.1 16 18-33 24-39 (108)
93 PRK05580 primosome assembly pr 55.7 9.2 0.0002 31.4 2.2 27 21-62 391-417 (679)
94 PF13465 zf-H2C2_2: Zinc-finge 55.6 6.9 0.00015 19.3 0.9 14 50-63 11-24 (26)
95 PF07754 DUF1610: Domain of un 54.8 6 0.00013 20.3 0.6 10 18-27 14-23 (24)
96 PF04438 zf-HIT: HIT zinc fing 53.6 5.2 0.00011 21.0 0.3 23 40-65 3-25 (30)
97 PF12171 zf-C2H2_jaz: Zinc-fin 53.4 4.1 8.8E-05 19.9 -0.1 13 53-65 1-13 (27)
98 smart00709 Zpr1 Duplicated dom 53.3 16 0.00034 25.4 2.7 34 22-62 2-38 (160)
99 PRK14873 primosome assembly pr 53.0 11 0.00024 31.4 2.2 12 21-32 393-404 (665)
100 PRK14892 putative transcriptio 52.0 15 0.00034 24.0 2.4 33 18-62 19-51 (99)
101 PF03604 DNA_RNApol_7kD: DNA d 51.6 15 0.00033 19.6 1.9 14 17-30 14-27 (32)
102 PRK14701 reverse gyrase; Provi 51.5 6.9 0.00015 35.9 0.9 17 20-36 6-22 (1638)
103 smart00132 LIM Zinc-binding do 51.3 7 0.00015 19.1 0.6 35 23-64 2-38 (39)
104 PF03966 Trm112p: Trm112p-like 51.1 21 0.00046 20.9 2.7 16 49-64 49-64 (68)
105 PF04828 GFA: Glutathione-depe 50.8 9.3 0.0002 22.0 1.1 19 47-65 42-60 (92)
106 TIGR00100 hypA hydrogenase nic 50.6 12 0.00027 24.3 1.8 18 11-28 61-78 (115)
107 PF09855 DUF2082: Nucleic-acid 50.3 22 0.00047 21.6 2.7 12 51-62 34-45 (64)
108 COG2093 DNA-directed RNA polym 50.3 11 0.00023 23.6 1.3 16 22-37 20-44 (64)
109 COG1439 Predicted nucleic acid 49.5 18 0.0004 26.1 2.7 25 6-32 141-165 (177)
110 TIGR00595 priA primosomal prot 49.2 14 0.0003 29.4 2.2 26 22-62 224-249 (505)
111 PF10571 UPF0547: Uncharacteri 48.8 9.1 0.0002 19.5 0.8 13 18-30 12-24 (26)
112 PF02701 zf-Dof: Dof domain, z 48.6 7.7 0.00017 24.1 0.5 36 18-61 3-38 (63)
113 PRK09521 exosome complex RNA-b 48.5 16 0.00035 25.1 2.2 25 22-62 151-175 (189)
114 PHA00626 hypothetical protein 48.3 21 0.00046 22.0 2.4 32 22-63 2-33 (59)
115 PF06750 DiS_P_DiS: Bacterial 47.5 3.3 7.2E-05 26.2 -1.2 38 19-64 32-69 (92)
116 PRK03824 hypA hydrogenase nick 47.1 16 0.00035 24.4 1.9 50 11-62 61-116 (135)
117 COG1571 Predicted DNA-binding 47.0 12 0.00026 30.2 1.6 34 16-65 346-379 (421)
118 PRK05320 rhodanese superfamily 47.0 13 0.00029 27.1 1.7 28 4-31 226-255 (257)
119 PF05605 zf-Di19: Drought indu 47.0 9.2 0.0002 21.5 0.7 37 22-63 4-41 (54)
120 PF12172 DUF35_N: Rubredoxin-l 46.5 22 0.00049 18.5 2.1 23 5-29 12-34 (37)
121 COG1675 TFA1 Transcription ini 45.9 7.9 0.00017 27.7 0.3 14 21-34 133-146 (176)
122 PRK00762 hypA hydrogenase nick 45.7 9.7 0.00021 25.1 0.7 10 21-30 93-102 (124)
123 PRK04351 hypothetical protein; 45.5 23 0.00049 24.3 2.5 17 50-66 129-145 (149)
124 TIGR00155 pqiA_fam integral me 45.1 13 0.00029 29.0 1.5 31 22-65 15-45 (403)
125 PF06689 zf-C4_ClpX: ClpX C4-t 45.1 7.1 0.00015 21.5 -0.0 10 54-63 2-11 (41)
126 PF02150 RNA_POL_M_15KD: RNA p 44.9 22 0.00048 18.9 1.9 15 22-36 3-17 (35)
127 COG1867 TRM1 N2,N2-dimethylgua 44.8 20 0.00043 28.8 2.4 30 3-32 239-269 (380)
128 PF00096 zf-C2H2: Zinc finger, 44.3 13 0.00028 17.0 0.8 12 54-65 1-12 (23)
129 PF01485 IBR: IBR domain; Int 43.0 4.4 9.6E-05 22.2 -1.1 26 14-39 12-39 (64)
130 PF04423 Rad50_zn_hook: Rad50 42.7 11 0.00023 21.2 0.5 13 18-30 18-30 (54)
131 PF07503 zf-HYPF: HypF finger; 42.7 7.8 0.00017 21.1 -0.1 18 17-34 18-35 (35)
132 PRK03681 hypA hydrogenase nick 42.3 23 0.00051 23.0 2.1 19 10-28 60-78 (114)
133 PRK00423 tfb transcription ini 42.2 23 0.0005 26.3 2.3 31 20-64 11-41 (310)
134 PRK00564 hypA hydrogenase nick 42.2 16 0.00034 23.9 1.3 18 10-27 61-78 (117)
135 PF06054 CoiA: Competence prot 42.1 20 0.00043 27.6 2.0 16 18-33 28-43 (375)
136 cd04476 RPA1_DBD_C RPA1_DBD_C: 41.5 15 0.00033 24.3 1.2 11 52-62 50-60 (166)
137 COG2260 Predicted Zn-ribbon RN 41.3 11 0.00025 23.1 0.5 12 21-32 18-29 (59)
138 COG1779 C4-type Zn-finger prot 40.9 28 0.0006 25.8 2.5 41 18-63 12-53 (201)
139 PF05280 FlhC: Flagellar trans 40.6 14 0.0003 26.1 0.9 26 22-60 136-161 (175)
140 cd00730 rubredoxin Rubredoxin; 40.0 29 0.00063 20.0 2.1 13 18-30 32-44 (50)
141 TIGR00354 polC DNA polymerase, 39.8 21 0.00045 32.2 2.0 20 14-33 1022-1041(1095)
142 PF01155 HypA: Hydrogenase exp 39.8 5.6 0.00012 25.7 -1.1 21 11-31 61-81 (113)
143 PF13395 HNH_4: HNH endonuclea 39.7 10 0.00022 21.5 0.1 13 23-35 1-13 (54)
144 PLN03086 PRLI-interacting fact 39.5 5.4 0.00012 33.1 -1.5 45 19-63 452-514 (567)
145 PF03367 zf-ZPR1: ZPR1 zinc-fi 39.4 33 0.00072 23.7 2.6 37 22-63 3-40 (161)
146 PF09889 DUF2116: Uncharacteri 39.4 14 0.0003 22.3 0.7 11 21-31 4-14 (59)
147 PF03884 DUF329: Domain of unk 39.3 8.4 0.00018 23.1 -0.3 14 22-35 4-17 (57)
148 PRK04023 DNA polymerase II lar 38.9 22 0.00047 32.2 2.0 20 14-33 1047-1066(1121)
149 PF01096 TFIIS_C: Transcriptio 38.0 22 0.00048 19.2 1.3 11 22-32 2-12 (39)
150 COG1096 Predicted RNA-binding 37.4 28 0.00061 25.5 2.1 25 21-62 150-174 (188)
151 PRK05978 hypothetical protein; 37.4 17 0.00037 25.3 1.0 35 18-66 31-65 (148)
152 COG5349 Uncharacterized protei 37.3 14 0.00031 25.6 0.5 12 18-29 19-30 (126)
153 PRK14714 DNA polymerase II lar 37.1 24 0.00051 32.5 1.9 20 14-33 1263-1282(1337)
154 KOG3799 Rab3 effector RIM1 and 36.6 9.3 0.0002 27.6 -0.5 30 22-66 91-120 (169)
155 KOG3456 NADH:ubiquinone oxidor 36.4 16 0.00034 25.2 0.6 12 17-28 101-112 (120)
156 PRK08173 DNA topoisomerase III 36.4 34 0.00073 29.4 2.7 14 17-30 723-736 (862)
157 PF08394 Arc_trans_TRASH: Arch 36.3 17 0.00037 20.2 0.7 30 23-63 1-33 (37)
158 PF11793 FANCL_C: FANCL C-term 36.1 14 0.0003 22.1 0.3 16 17-32 52-67 (70)
159 PF06957 COPI_C: Coatomer (COP 35.9 26 0.00056 28.2 1.8 30 35-65 360-392 (422)
160 TIGR00375 conserved hypothetic 35.7 17 0.00036 28.6 0.8 11 20-31 259-269 (374)
161 PF12874 zf-met: Zinc-finger o 35.7 21 0.00045 16.5 0.8 12 54-65 1-12 (25)
162 PRK14715 DNA polymerase II lar 35.7 26 0.00056 32.8 2.0 20 14-33 1551-1570(1627)
163 PF12660 zf-TFIIIC: Putative z 35.3 20 0.00044 22.8 1.0 14 17-30 85-98 (99)
164 PF08209 Sgf11: Sgf11 (transcr 35.2 15 0.00033 19.9 0.3 15 22-36 6-20 (33)
165 smart00019 SF_P Pulmonary surf 35.0 15 0.00032 26.9 0.3 21 5-25 102-122 (191)
166 PRK06393 rpoE DNA-directed RNA 35.0 22 0.00049 21.9 1.1 9 21-29 18-26 (64)
167 PRK15103 paraquat-inducible me 34.7 27 0.00059 27.5 1.7 31 21-64 11-41 (419)
168 PF14375 Cys_rich_CWC: Cystein 34.6 20 0.00043 20.2 0.8 11 23-33 1-11 (50)
169 PF07213 DAP10: DAP10 membrane 34.5 18 0.00038 23.3 0.6 15 14-28 16-30 (79)
170 COG1405 SUA7 Transcription ini 34.4 35 0.00075 25.8 2.2 30 21-64 2-31 (285)
171 KOG1598 Transcription initiati 34.0 24 0.00051 29.4 1.4 29 22-64 2-30 (521)
172 PHA02942 putative transposase; 34.0 24 0.00052 27.3 1.3 28 20-63 325-352 (383)
173 PRK06260 threonine synthase; V 33.4 43 0.00093 25.4 2.6 28 6-33 5-32 (397)
174 PRK14714 DNA polymerase II lar 32.9 18 0.00038 33.3 0.5 13 55-67 711-723 (1337)
175 PF02176 zf-TRAF: TRAF-type zi 32.5 9.1 0.0002 21.1 -0.9 39 19-64 8-53 (60)
176 TIGR00308 TRM1 tRNA(guanine-26 32.5 33 0.00071 26.5 1.9 16 15-30 247-262 (374)
177 smart00507 HNHc HNH nucleases. 32.4 25 0.00053 17.7 0.9 11 21-31 11-21 (52)
178 PRK14559 putative protein seri 32.3 18 0.0004 30.2 0.5 10 55-64 43-52 (645)
179 PRK08351 DNA-directed RNA poly 32.3 20 0.00044 21.8 0.6 8 22-29 17-24 (61)
180 PF02591 DUF164: Putative zinc 32.0 21 0.00046 20.2 0.6 35 20-63 22-56 (56)
181 PF04879 Molybdop_Fe4S4: Molyb 32.0 11 0.00024 20.8 -0.5 13 17-29 2-14 (55)
182 COG1594 RPB9 DNA-directed RNA 32.0 48 0.001 21.8 2.3 11 22-32 4-14 (113)
183 TIGR02300 FYDLN_acid conserved 31.7 26 0.00056 24.4 1.1 15 17-31 23-37 (129)
184 KOG4317 Predicted Zn-finger pr 31.4 21 0.00045 28.7 0.6 22 43-64 9-30 (383)
185 cd04467 S1_aIF5A S1_aIF5A: Arc 30.9 29 0.00062 20.7 1.1 15 27-41 13-27 (57)
186 PF05741 zf-nanos: Nanos RNA b 30.9 16 0.00034 21.9 -0.1 11 52-62 32-42 (55)
187 PRK01343 zinc-binding protein; 30.6 18 0.0004 21.8 0.2 13 19-31 8-20 (57)
188 COG3809 Uncharacterized protei 30.4 26 0.00057 23.0 0.9 8 21-28 22-29 (88)
189 COG1885 Uncharacterized protei 30.4 87 0.0019 21.5 3.5 32 19-50 48-79 (115)
190 smart00440 ZnF_C2C2 C2C2 Zinc 30.4 41 0.00089 18.2 1.6 11 22-32 2-12 (40)
191 smart00064 FYVE Protein presen 30.0 34 0.00074 19.4 1.3 27 20-63 10-36 (68)
192 PF09334 tRNA-synt_1g: tRNA sy 29.9 30 0.00064 26.6 1.3 22 6-27 122-143 (391)
193 PF13966 zf-RVT: zinc-binding 29.9 29 0.00063 20.7 1.0 15 17-31 56-70 (86)
194 COG2888 Predicted Zn-ribbon RN 29.5 22 0.00048 22.0 0.4 12 16-27 46-57 (61)
195 TIGR03031 cas_csx12 CRISPR-ass 29.5 25 0.00054 30.6 0.9 13 18-30 758-770 (802)
196 PRK12722 transcriptional activ 29.5 27 0.00058 25.3 0.9 14 21-34 135-148 (187)
197 PF13912 zf-C2H2_6: C2H2-type 29.3 17 0.00036 17.2 -0.1 13 54-66 2-14 (27)
198 smart00647 IBR In Between Ring 29.2 49 0.0011 17.9 1.8 17 18-34 16-34 (64)
199 COG4888 Uncharacterized Zn rib 28.7 30 0.00064 23.4 0.9 15 51-65 20-34 (104)
200 KOG2807 RNA polymerase II tran 28.6 30 0.00065 27.8 1.1 30 19-67 275-304 (378)
201 PF09845 DUF2072: Zn-ribbon co 28.5 25 0.00053 24.4 0.5 8 22-29 21-28 (131)
202 PRK06450 threonine synthase; V 28.5 56 0.0012 24.6 2.5 16 18-33 16-31 (338)
203 COG3024 Uncharacterized protei 28.5 23 0.0005 22.2 0.4 17 20-36 7-23 (65)
204 COG4311 SoxD Sarcosine oxidase 28.3 26 0.00056 23.4 0.6 7 22-28 5-11 (97)
205 cd01407 SIR2-fam SIR2 family o 28.1 28 0.00061 24.2 0.8 11 20-30 133-143 (218)
206 TIGR02443 conserved hypothetic 27.9 32 0.0007 21.0 0.9 18 14-31 3-20 (59)
207 COG3582 Predicted nucleic acid 27.8 31 0.00067 24.6 1.0 20 14-33 104-123 (162)
208 KOG0402 60S ribosomal protein 27.8 16 0.00034 24.3 -0.5 11 52-62 35-45 (92)
209 TIGR02159 PA_CoA_Oxy4 phenylac 27.7 27 0.00059 23.9 0.7 10 20-29 105-114 (146)
210 PRK00481 NAD-dependent deacety 27.6 28 0.00061 24.6 0.7 9 22-30 144-152 (242)
211 KOG2906 RNA polymerase III sub 27.5 35 0.00076 23.1 1.1 22 8-29 53-74 (105)
212 PF13913 zf-C2HC_2: zinc-finge 27.5 6.1 0.00013 19.7 -2.0 10 22-31 4-13 (25)
213 PF11023 DUF2614: Protein of u 27.2 21 0.00046 24.4 0.1 21 7-30 75-95 (114)
214 cd01412 SIRT5_Af1_CobB SIRT5_A 26.7 31 0.00068 23.9 0.8 11 20-30 130-140 (224)
215 PRK13130 H/ACA RNA-protein com 26.6 24 0.00051 21.1 0.2 12 20-31 17-28 (56)
216 COG1933 Archaeal DNA polymeras 26.6 46 0.001 25.5 1.7 23 11-33 174-196 (253)
217 PF09856 DUF2083: Predicted tr 26.4 72 0.0016 22.3 2.6 25 2-26 12-44 (156)
218 COG2835 Uncharacterized conser 26.4 80 0.0017 19.3 2.5 28 22-64 10-37 (60)
219 cd01230 PH_EFA6 EFA6 Pleckstri 26.3 44 0.00094 22.0 1.4 23 45-67 20-42 (117)
220 PRK12860 transcriptional activ 26.3 33 0.00071 24.9 0.9 13 21-33 135-147 (189)
221 COG1198 PriA Primosomal protei 26.2 53 0.0011 28.1 2.2 13 17-29 472-484 (730)
222 PRK14724 DNA topoisomerase III 26.1 42 0.00091 29.3 1.6 14 17-30 752-765 (987)
223 PF15616 TerY-C: TerY-C metal 26.0 49 0.0011 22.7 1.7 38 21-64 78-116 (131)
224 PRK14138 NAD-dependent deacety 25.7 34 0.00073 24.6 0.9 11 20-30 143-153 (244)
225 PF05015 Plasmid_killer: Plasm 25.5 70 0.0015 19.8 2.2 19 28-46 62-80 (93)
226 PF14447 Prok-RING_4: Prokaryo 25.2 28 0.00061 21.0 0.3 16 20-35 39-54 (55)
227 cd04482 RPA2_OBF_like RPA2_OBF 24.8 40 0.00086 20.9 1.0 9 19-27 83-91 (91)
228 PF08063 PADR1: PADR1 (NUC008) 24.7 39 0.00084 19.7 0.8 17 18-34 12-28 (55)
229 PF08772 NOB1_Zn_bind: Nin one 24.4 30 0.00065 21.5 0.4 11 19-29 23-33 (73)
230 PF06044 DRP: Dam-replacing fa 24.3 67 0.0014 24.6 2.2 34 20-65 31-65 (254)
231 PF07295 DUF1451: Protein of u 24.1 92 0.002 21.4 2.7 8 21-28 131-138 (146)
232 PF04135 Nop10p: Nucleolar RNA 24.1 40 0.00086 20.0 0.8 12 21-32 18-29 (53)
233 TIGR01374 soxD sarcosine oxida 24.1 35 0.00075 22.0 0.6 6 22-27 3-8 (84)
234 PRK05333 NAD-dependent deacety 23.7 38 0.00082 24.8 0.8 10 21-30 180-189 (285)
235 PF09526 DUF2387: Probable met 23.5 46 0.001 20.5 1.1 14 17-30 5-18 (71)
236 PF13408 Zn_ribbon_recom: Reco 23.5 56 0.0012 17.5 1.3 9 22-30 7-15 (58)
237 cd01411 SIR2H SIR2H: Uncharact 23.5 39 0.00085 23.9 0.8 11 20-30 136-146 (225)
238 PRK04338 N(2),N(2)-dimethylgua 23.4 64 0.0014 24.9 2.0 13 18-30 259-271 (382)
239 PF04194 PDCD2_C: Programmed c 23.3 39 0.00084 23.0 0.8 11 20-30 97-107 (164)
240 PF01780 Ribosomal_L37ae: Ribo 22.9 33 0.00071 22.4 0.3 13 51-63 33-45 (90)
241 PF05876 Terminase_GpA: Phage 22.7 64 0.0014 26.1 2.0 37 22-63 202-239 (557)
242 KOG3362 Predicted BBOX Zn-fing 22.7 22 0.00048 25.5 -0.5 16 50-65 126-141 (156)
243 smart00451 ZnF_U1 U1-like zinc 22.6 39 0.00085 16.6 0.5 12 53-64 3-14 (35)
244 PRK07956 ligA NAD-dependent DN 22.3 70 0.0015 26.8 2.2 15 19-33 403-417 (665)
245 PF09151 DUF1936: Domain of un 22.3 64 0.0014 18.0 1.4 10 22-31 3-12 (36)
246 smart00532 LIGANc Ligase N fam 22.1 75 0.0016 25.3 2.2 16 19-34 398-413 (441)
247 cd01413 SIR2_Af2 SIR2_Af2: Arc 22.0 42 0.00092 23.6 0.8 10 21-30 137-146 (222)
248 TIGR00575 dnlj DNA ligase, NAD 22.0 74 0.0016 26.5 2.2 15 19-33 391-405 (652)
249 PF01258 zf-dskA_traR: Prokary 21.9 67 0.0015 16.6 1.4 15 20-34 3-17 (36)
250 cd07973 Spt4 Transcription elo 21.9 43 0.00093 21.9 0.7 9 19-27 19-27 (98)
251 PF13719 zinc_ribbon_5: zinc-r 21.8 40 0.00086 17.9 0.5 31 22-62 4-34 (37)
252 TIGR02646 conserved hypothetic 21.8 26 0.00056 23.2 -0.3 16 18-33 22-37 (144)
253 COG4049 Uncharacterized protei 21.8 35 0.00077 21.3 0.3 8 21-28 18-25 (65)
254 PF02146 SIR2: Sir2 family; I 21.7 69 0.0015 21.4 1.7 14 18-31 127-140 (178)
255 PF10825 DUF2752: Protein of u 21.5 38 0.00083 19.3 0.4 8 22-29 11-18 (52)
256 PF14206 Cys_rich_CPCC: Cystei 21.2 46 0.00099 21.0 0.7 11 22-32 3-13 (78)
257 KOG0373 Serine/threonine speci 21.1 86 0.0019 24.5 2.3 26 13-38 253-278 (306)
258 COG0266 Nei Formamidopyrimidin 20.9 78 0.0017 24.1 2.0 17 20-36 245-261 (273)
259 PRK14890 putative Zn-ribbon RN 20.8 43 0.00094 20.5 0.5 12 16-27 44-55 (59)
260 PF00130 C1_1: Phorbol esters/ 20.7 1.6E+02 0.0034 15.8 2.9 31 16-62 7-37 (53)
261 PF09012 FeoC: FeoC like trans 20.5 1E+02 0.0022 17.7 2.1 14 18-31 52-65 (69)
262 PF01363 FYVE: FYVE zinc finge 20.5 48 0.001 18.8 0.7 14 50-63 22-35 (69)
263 PF01844 HNH: HNH endonuclease 20.5 43 0.00092 17.3 0.4 9 23-31 1-9 (47)
264 PF04400 DUF539: Protein of un 20.4 30 0.00064 20.1 -0.2 22 13-38 2-23 (45)
265 PRK00415 rps27e 30S ribosomal 20.4 70 0.0015 19.5 1.4 21 45-65 22-42 (59)
266 cd00296 SIR2 SIR2 superfamily 20.3 45 0.00098 22.6 0.6 14 18-31 132-145 (222)
267 PF03117 Herpes_UL49_1: UL49 f 20.2 1.1E+02 0.0024 23.3 2.6 26 4-29 134-161 (245)
268 TIGR01057 topA_arch DNA topois 20.1 60 0.0013 26.5 1.4 12 19-30 588-599 (618)
269 PRK14351 ligA NAD-dependent DN 20.0 82 0.0018 26.6 2.1 15 18-32 421-435 (689)
No 1
>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=94.88 E-value=0.053 Score=29.66 Aligned_cols=41 Identities=29% Similarity=0.646 Sum_probs=29.1
Q ss_pred CCcCCCCCCceEEEEec-ceeeeEEeeeeeeec----ceEEeeccc
Q 035300 20 DAACPYCGGPVLAIDFD-AHLRFCFLPISHKVK----KKFYCTICS 60 (68)
Q Consensus 20 ~G~Cp~CGG~v~a~Dve-s~~rfCflP~~~k~k----rk~~Ct~C~ 60 (68)
+.+||.||+.+.-+-.+ .+-.|=++|.-++.. -+|.|+-|+
T Consensus 2 ~~~C~~Cg~~l~~ig~~~~~q~l~~~p~~~~V~e~~~~~y~C~~C~ 47 (47)
T PF13005_consen 2 PRACPDCGGELKEIGEEKVRQVLDLPPAKPEVTEHVRHKYACPCCG 47 (47)
T ss_pred CCcCCCCCceeeECCceeeEEEEeecccceEEEEEEeceEECCCCC
Confidence 56899999998866555 556666788766544 366777774
No 2
>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=94.48 E-value=0.024 Score=33.92 Aligned_cols=51 Identities=22% Similarity=0.461 Sum_probs=37.9
Q ss_pred eecCCCCcCCCCCCceEEEEecce-----------------eeeEEeeeeeee--cceEEeecccceeeec
Q 035300 15 RRNGADAACPYCGGPVLAIDFDAH-----------------LRFCFLPISHKV--KKKFYCTICSRRLVPA 66 (68)
Q Consensus 15 ~~~~A~G~Cp~CGG~v~a~Dves~-----------------~rfCflP~~~k~--krk~~Ct~C~r~L~~~ 66 (68)
+++|..-.||+||-.+. +.++.+ |-+|+||++.+. ...++|+.|++.|-.|
T Consensus 2 ~~~p~~~~CP~C~~~~~-T~v~~~~g~~t~~~~~~l~~~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~~ 71 (73)
T PF10601_consen 2 GPEPVRIYCPYCQQQVQ-TRVEYKSGTMTYICAALLCLFGCWPCCCIPFCCDSCKDVYHYCPNCGAFLGTY 71 (73)
T ss_pred CCCceeeECCCCCCEEE-EEEEEEeChHHHHHHHHHHHHHHHHHhhHhhccccccCceEECCCCCCEeEEE
Confidence 46788889999998764 334422 345789999854 4579999999998776
No 3
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=94.44 E-value=0.033 Score=38.75 Aligned_cols=40 Identities=25% Similarity=0.652 Sum_probs=27.4
Q ss_pred cCCCCCCce-EEEEecceeeeEEeeeeeeecceEEeecccceeeecc
Q 035300 22 ACPYCGGPV-LAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPAT 67 (68)
Q Consensus 22 ~Cp~CGG~v-~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~~ 67 (68)
.|||||++. .|.|=+. ++==.-.+|++.|..||++...|-
T Consensus 2 ~cp~c~~~~~~~~~s~~------~~~~~~~~~~~~c~~c~~~f~~~e 42 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRP------AEDGNAIRRRRECLACGKRFTTFE 42 (154)
T ss_pred cCCCCCCCCCEeEeccc------cCCCCceeeeeeccccCCcceEeE
Confidence 499999976 6655431 111123677799999999987764
No 4
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=93.92 E-value=0.094 Score=28.41 Aligned_cols=38 Identities=32% Similarity=0.751 Sum_probs=23.2
Q ss_pred CCcCCCCCCceEEE--EecceeeeEEeee-----eee-ecceEEeecc
Q 035300 20 DAACPYCGGPVLAI--DFDAHLRFCFLPI-----SHK-VKKKFYCTIC 59 (68)
Q Consensus 20 ~G~Cp~CGG~v~a~--Dves~~rfCflP~-----~~k-~krk~~Ct~C 59 (68)
|-.||+||..-..- -.+..|+ .+|+ +.+ .+++|.|..|
T Consensus 2 ~~~Cp~Cg~~~~~~~g~~~r~i~--~l~~~~~~~~L~i~~~R~~C~~C 47 (47)
T PF14690_consen 2 PPRCPHCGSPSVHRHGYKTRRIR--HLPIGGRPVYLRIRKRRYRCKNC 47 (47)
T ss_pred CccCCCcCCCceECCceEEEEEe--ecccCCEEEEEEEEeEEEECcCC
Confidence 56899999776332 2333444 4444 433 3678888876
No 5
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=93.65 E-value=0.054 Score=32.57 Aligned_cols=36 Identities=39% Similarity=0.708 Sum_probs=25.7
Q ss_pred CceeeeeecCCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300 9 LREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR 62 (68)
Q Consensus 9 e~~kv~~~~~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (68)
+.+||++.++ -||+||-++-.+| ++.++.|-.||-.
T Consensus 11 ~~~kv~rk~~---~CPrCG~gvfmA~---------------H~dR~~CGkCgyT 46 (51)
T COG1998 11 DDEKVKRKNR---FCPRCGPGVFMAD---------------HKDRWACGKCGYT 46 (51)
T ss_pred cCCcEEEccc---cCCCCCCcchhhh---------------cCceeEeccccce
Confidence 4456776655 6999998877666 4457888888743
No 6
>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=93.29 E-value=0.039 Score=40.24 Aligned_cols=43 Identities=19% Similarity=0.508 Sum_probs=24.5
Q ss_pred CCCcCCCCCCceEEEEecce----eeeEEeeeeeeecc--eEEeecccc
Q 035300 19 ADAACPYCGGPVLAIDFDAH----LRFCFLPISHKVKK--KFYCTICSR 61 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~Dves~----~rfCflP~~~k~kr--k~~Ct~C~r 61 (68)
..|.||-||+.-++.-++.. .|+.+=.+|.-.|+ +..|+.||.
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~ 219 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGN 219 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT--
T ss_pred cCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCC
Confidence 35999999999888877764 58888788866653 568999985
No 7
>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=91.43 E-value=0.092 Score=32.14 Aligned_cols=13 Identities=38% Similarity=1.221 Sum_probs=11.1
Q ss_pred CCcCCCCCCceEE
Q 035300 20 DAACPYCGGPVLA 32 (68)
Q Consensus 20 ~G~Cp~CGG~v~a 32 (68)
.|.||+|||.++.
T Consensus 41 ~~~CPNCgGelv~ 53 (57)
T PF06906_consen 41 NGVCPNCGGELVR 53 (57)
T ss_pred cCcCcCCCCcccc
Confidence 6899999998753
No 8
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=90.86 E-value=0.4 Score=26.63 Aligned_cols=28 Identities=21% Similarity=0.790 Sum_probs=20.6
Q ss_pred CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300 21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR 62 (68)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (68)
-.||+||.. .+.-+.+ ...|.|..|+++
T Consensus 19 ~~CP~Cg~~-~~~~~~~-------------~~~~~C~~C~~q 46 (46)
T PF12760_consen 19 FVCPHCGST-KHYRLKT-------------RGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCe-eeEEeCC-------------CCeEECCCCCCc
Confidence 459999997 5555555 677888888764
No 9
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.83 E-value=0.096 Score=34.11 Aligned_cols=18 Identities=33% Similarity=0.815 Sum_probs=14.5
Q ss_pred CCCcCCCCCCceEEEEec
Q 035300 19 ADAACPYCGGPVLAIDFD 36 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~Dve 36 (68)
-.|.||+|||.+++--++
T Consensus 40 l~g~CPnCGGelv~RP~R 57 (84)
T COG3813 40 LHGLCPNCGGELVARPIR 57 (84)
T ss_pred hcCcCCCCCchhhcCcCC
Confidence 469999999999876554
No 10
>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=89.96 E-value=0.18 Score=33.29 Aligned_cols=39 Identities=28% Similarity=0.635 Sum_probs=24.3
Q ss_pred CCcCCCCCCceEEEEecceeeeEEeeeeeeecc-eEEeeccccee
Q 035300 20 DAACPYCGGPVLAIDFDAHLRFCFLPISHKVKK-KFYCTICSRRL 63 (68)
Q Consensus 20 ~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr-k~~Ct~C~r~L 63 (68)
|-.||||||++.-+|= +.. -|=-...+. -|.|+.|++-.
T Consensus 2 p~~CpYCg~~~~l~~~-~~i----Yg~~~~~~~~~y~C~~C~AyV 41 (102)
T PF11672_consen 2 PIICPYCGGPAELVDG-SEI----YGHRYDDGPYLYVCTPCDAYV 41 (102)
T ss_pred CcccCCCCCeeEEccc-chh----cCccCCCCceeEECCCCCcee
Confidence 5689999999998772 221 131111123 38999998753
No 11
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=89.77 E-value=0.1 Score=26.30 Aligned_cols=9 Identities=44% Similarity=1.353 Sum_probs=6.7
Q ss_pred cCCCCCCce
Q 035300 22 ACPYCGGPV 30 (68)
Q Consensus 22 ~Cp~CGG~v 30 (68)
.||+||-.+
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 588888743
No 12
>PRK10445 endonuclease VIII; Provisional
Probab=89.70 E-value=0.43 Score=34.78 Aligned_cols=34 Identities=29% Similarity=0.746 Sum_probs=23.4
Q ss_pred eeeeecCCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccc
Q 035300 12 KVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60 (68)
Q Consensus 12 kv~~~~~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~ 60 (68)
+|-++ +...||+||+.+.-+.+-. ...|+|+.|-
T Consensus 229 ~Vy~r--~g~~Cp~Cg~~I~~~~~~g-------------R~t~~CP~CQ 262 (263)
T PRK10445 229 KVFHR--DGEACERCGGIIEKTTLSS-------------RPFYWCPGCQ 262 (263)
T ss_pred EEeCC--CCCCCCCCCCEeEEEEECC-------------CCcEECCCCc
Confidence 44443 3456999999999887763 5566777663
No 13
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=89.69 E-value=0.098 Score=26.17 Aligned_cols=9 Identities=44% Similarity=1.335 Sum_probs=6.5
Q ss_pred CCCCCCceE
Q 035300 23 CPYCGGPVL 31 (68)
Q Consensus 23 Cp~CGG~v~ 31 (68)
||+||-.+.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 777877664
No 14
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=89.65 E-value=0.39 Score=35.15 Aligned_cols=26 Identities=23% Similarity=0.737 Sum_probs=20.1
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccc
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~ 60 (68)
.||+||+++.-..+.. ...|+|+.|-
T Consensus 246 pCprCG~~I~~~~~~g-------------R~t~~CP~CQ 271 (272)
T PRK14810 246 PCLNCKTPIRRVVVAG-------------RSSHYCPHCQ 271 (272)
T ss_pred cCCCCCCeeEEEEECC-------------CccEECcCCc
Confidence 5999999998777753 5667777774
No 15
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=89.13 E-value=0.49 Score=34.75 Aligned_cols=34 Identities=29% Similarity=0.745 Sum_probs=23.4
Q ss_pred eeeeecCCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccc
Q 035300 12 KVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60 (68)
Q Consensus 12 kv~~~~~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~ 60 (68)
+|-++. ...||+||+.+.-.-+.. ...|+|+.|-
T Consensus 248 ~Vy~R~--g~pC~~Cg~~I~~~~~~g-------------R~t~~CP~CQ 281 (282)
T PRK13945 248 WVYRRT--GKPCRKCGTPIERIKLAG-------------RSTHWCPNCQ 281 (282)
T ss_pred EEeCCC--cCCCCcCCCeeEEEEECC-------------CccEECCCCc
Confidence 354443 346999999998877754 5667777763
No 16
>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=89.07 E-value=0.87 Score=24.02 Aligned_cols=43 Identities=21% Similarity=0.336 Sum_probs=25.2
Q ss_pred CCCCCCceEEEEecceeeeEE-eeeeeeecceEEeecccceeee
Q 035300 23 CPYCGGPVLAIDFDAHLRFCF-LPISHKVKKKFYCTICSRRLVP 65 (68)
Q Consensus 23 Cp~CGG~v~a~Dves~~rfCf-lP~~~k~krk~~Ct~C~r~L~~ 65 (68)
||-|||....-++++.+.--- -=+..+.=..+.|+.||..+-+
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~~~~~~i~~vp~~~C~~CGE~~~~ 44 (46)
T TIGR03831 1 CPICGGEELEGKTTTETYEYGGELIVIENVPALVCPQCGEEYLD 44 (46)
T ss_pred CCCCCCceecceEEEEEEEeCCEEEEEeCCCccccccCCCEeeC
Confidence 888988877777654432111 1122334456678988877643
No 17
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=88.90 E-value=0.13 Score=43.74 Aligned_cols=29 Identities=34% Similarity=0.507 Sum_probs=22.1
Q ss_pred EeCCceeeeeecCCC-CcCCCCCCceEEEE
Q 035300 6 IFDLREKVIRRNGAD-AACPYCGGPVLAID 34 (68)
Q Consensus 6 vcde~~kv~~~~~A~-G~Cp~CGG~v~a~D 34 (68)
=||.-+||----.+| |.||+|||.+++.|
T Consensus 823 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 852 (1006)
T PRK12775 823 RCDDCGKVSEGFAFPYGMCPACGGKLQALD 852 (1006)
T ss_pred ehhhhccccccccCCcCcCcccccchhhhh
Confidence 456666665555666 99999999998876
No 18
>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=88.85 E-value=0.99 Score=28.17 Aligned_cols=41 Identities=27% Similarity=0.576 Sum_probs=31.1
Q ss_pred CCCCCCceEEEEecc-eeeeEEeeeeeeecceEEeecccceee
Q 035300 23 CPYCGGPVLAIDFDA-HLRFCFLPISHKVKKKFYCTICSRRLV 64 (68)
Q Consensus 23 Cp~CGG~v~a~Dves-~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (68)
||.||++....+++. .+.+.-.-+-+ .-..+.|+.||..+.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v-~~~~~~C~~CGe~~~ 42 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITI-GVPGWYCPACGEELL 42 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEE-eeeeeECCCCCCEEE
Confidence 899997666677776 44677777777 667788999998654
No 19
>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=88.58 E-value=0.7 Score=27.05 Aligned_cols=38 Identities=34% Similarity=0.697 Sum_probs=25.8
Q ss_pred EEeCCceeeeeecCCCCcCC--CCCCceEEEEecceeeeEEeeeeeeecceEEeeccc
Q 035300 5 SIFDLREKVIRRNGADAACP--YCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60 (68)
Q Consensus 5 ~vcde~~kv~~~~~A~G~Cp--~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~ 60 (68)
+=+|+++||.+.+ -.|| +||.+|-.++- +.+++|-.||
T Consensus 6 Ykvd~~Gkv~r~r---k~CP~~~CG~GvFMA~H---------------~dR~~CGKCg 45 (47)
T PF01599_consen 6 YKVDENGKVKRLR---KECPSPRCGAGVFMAEH---------------KDRHYCGKCG 45 (47)
T ss_dssp CEEETTTEEEESS---EE-TSTTTTSSSEEEE----------------SSEEEETTTS
T ss_pred EEECCCCcEEEhh---hcCCCcccCCceEeeec---------------CCCccCCCcc
Confidence 3468888887654 4699 99999865543 4577777776
No 20
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=88.47 E-value=0.65 Score=26.89 Aligned_cols=36 Identities=33% Similarity=0.623 Sum_probs=23.3
Q ss_pred eCCceeeeeecCCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300 7 FDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR 62 (68)
Q Consensus 7 cde~~kv~~~~~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (68)
+|.+ +|....+ -||+||..+.+. ++.++.|..||..
T Consensus 11 v~~~-~v~~~~~---fCP~Cg~~~m~~----------------~~~r~~C~~Cgyt 46 (50)
T PRK00432 11 VDGG-KVKRKNK---FCPRCGSGFMAE----------------HLDRWHCGKCGYT 46 (50)
T ss_pred ECCC-EEEEccC---cCcCCCcchhec----------------cCCcEECCCcCCE
Confidence 4544 6665444 899999752222 2368889999864
No 21
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=88.45 E-value=0.26 Score=28.99 Aligned_cols=49 Identities=22% Similarity=0.428 Sum_probs=32.2
Q ss_pred CCCCcCCCCCCceEEEEeccee---------------eeEEeeeeeee--cceEEeecccceeeecc
Q 035300 18 GADAACPYCGGPVLAIDFDAHL---------------RFCFLPISHKV--KKKFYCTICSRRLVPAT 67 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~a~Dves~~---------------rfCflP~~~k~--krk~~Ct~C~r~L~~~~ 67 (68)
|+.-.||+||.-++ +.+|.+. =+|+||++.+. ...++|+.|++.|-.|.
T Consensus 1 p~~i~Cp~C~~~~~-T~v~~~~g~~t~~~~~ll~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~~~ 66 (67)
T smart00714 1 PYQLFCPRCQNNVT-TRVETETGVCAWLICCLLFLLCFCCCLPCCLDSFKDVNHYCPNCGAFLGTYN 66 (67)
T ss_pred CcceECCCCCCEEE-EEEEEEeChHHHHHHHHHHHHHHHHHHHHhcccccCccEECCCCCCEeEEec
Confidence 45567999987543 4444222 24568985443 45689999999988764
No 22
>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=88.13 E-value=0.39 Score=27.86 Aligned_cols=30 Identities=23% Similarity=0.644 Sum_probs=23.0
Q ss_pred CCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccccee
Q 035300 19 ADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRL 63 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (68)
..-.||.||..... ..+.|.|.|+.||...
T Consensus 27 TSq~C~~CG~~~~~---------------~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK---------------RRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCccCccccccc---------------ccccceEEcCCCCCEE
Confidence 35579999987765 4577889999998753
No 23
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.75 E-value=0.92 Score=25.02 Aligned_cols=13 Identities=46% Similarity=1.140 Sum_probs=8.1
Q ss_pred CCcCCCCCCceEE
Q 035300 20 DAACPYCGGPVLA 32 (68)
Q Consensus 20 ~G~Cp~CGG~v~a 32 (68)
+..||+||+.+..
T Consensus 21 ~~~Cp~CG~~~~~ 33 (46)
T PRK00398 21 GVRCPYCGYRILF 33 (46)
T ss_pred ceECCCCCCeEEE
Confidence 4567777766553
No 24
>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=87.52 E-value=0.73 Score=33.69 Aligned_cols=26 Identities=27% Similarity=0.855 Sum_probs=19.8
Q ss_pred CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecc
Q 035300 21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTIC 59 (68)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C 59 (68)
-.||+||+.+.-.-+.. ...|+|+.|
T Consensus 246 ~pC~~Cg~~I~~~~~~g-------------R~t~~CP~C 271 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVGG-------------RGTHFCPQC 271 (272)
T ss_pred CCCCCCCCeeEEEEECC-------------CCCEECCCC
Confidence 36999999998877763 566777766
No 25
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=87.41 E-value=0.38 Score=26.41 Aligned_cols=29 Identities=28% Similarity=0.724 Sum_probs=18.3
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccccee
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRL 63 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (68)
-||.||..+..-+.+. ...+.|+.||...
T Consensus 2 FCp~Cg~~l~~~~~~~-------------~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCPKCGNMLIPKEGKE-------------KRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCccccccCCC-------------CCEEECCcCCCeE
Confidence 4899998665443331 2367788887543
No 26
>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=87.30 E-value=0.6 Score=31.17 Aligned_cols=45 Identities=16% Similarity=0.331 Sum_probs=31.0
Q ss_pred CCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccccee
Q 035300 19 ADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRL 63 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (68)
....||.|+|.++.++-|....----.++..+..=+.|+.||+.+
T Consensus 90 ~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 90 IFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 348999999999888766544432222333445667899999864
No 27
>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=86.85 E-value=0.52 Score=26.88 Aligned_cols=35 Identities=26% Similarity=0.663 Sum_probs=19.3
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV 64 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (68)
-||.|||....+.-. + - -...+.-|.|+-||....
T Consensus 3 PCPfCGg~~~~~~~~----~--~--~~~~~~~~~C~~Cga~~~ 37 (53)
T TIGR03655 3 PCPFCGGADVYLRRG----F--D--PLDLSHYFECSTCGASGP 37 (53)
T ss_pred CCCCCCCcceeeEec----c--C--CCCCEEEEECCCCCCCcc
Confidence 499999987743210 0 0 011122346889987654
No 28
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=86.81 E-value=0.57 Score=29.24 Aligned_cols=40 Identities=20% Similarity=0.342 Sum_probs=28.0
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEee--cccceeeeccC
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCT--ICSRRLVPATS 68 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct--~C~r~L~~~~~ 68 (68)
-||.||..+.+.|=+-.. +. -..+.+.|+ .||.+.+++.+
T Consensus 3 ~CP~Cg~~a~irtSr~~s-----~~--~~~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 3 HCPLCQHAAHARTSRYIT-----DT--TKERYHQCQNVNCSATFITYES 44 (72)
T ss_pred cCCCCCCccEEEEChhcC-----hh--hheeeeecCCCCCCCEEEEEEE
Confidence 499999999666544222 22 245677899 99999988753
No 29
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=86.55 E-value=0.88 Score=33.15 Aligned_cols=28 Identities=29% Similarity=0.889 Sum_probs=20.6
Q ss_pred CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccc
Q 035300 21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSR 61 (68)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r 61 (68)
-.||+||+.+.-..+-. ...|+|+.|-+
T Consensus 246 ~pC~~Cg~~I~~~~~~g-------------R~t~~CP~CQ~ 273 (274)
T PRK01103 246 EPCRRCGTPIEKIKQGG-------------RSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCeeEEEEECC-------------CCcEECcCCCC
Confidence 35999999998777753 55677777753
No 30
>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=85.84 E-value=1.1 Score=23.97 Aligned_cols=20 Identities=30% Similarity=0.695 Sum_probs=14.2
Q ss_pred eeeeeecCCCCcCCCCCCce
Q 035300 11 EKVIRRNGADAACPYCGGPV 30 (68)
Q Consensus 11 ~kv~~~~~A~G~Cp~CGG~v 30 (68)
+-+.....+|..||-||.+-
T Consensus 9 G~i~~g~~~p~~CP~Cg~~~ 28 (34)
T cd00729 9 GYIHEGEEAPEKCPICGAPK 28 (34)
T ss_pred CCEeECCcCCCcCcCCCCch
Confidence 33444456899999999864
No 31
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=85.53 E-value=0.48 Score=32.49 Aligned_cols=24 Identities=29% Similarity=0.747 Sum_probs=19.2
Q ss_pred CCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300 19 ADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR 62 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (68)
..-.||.||. .+.|.+.|+.||-.
T Consensus 308 tS~~C~~cg~--------------------~~~r~~~C~~cg~~ 331 (364)
T COG0675 308 TSKTCPCCGH--------------------LSGRLFKCPRCGFV 331 (364)
T ss_pred CcccccccCC--------------------ccceeEECCCCCCe
Confidence 3357999999 45788999999964
No 32
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=85.26 E-value=1 Score=33.04 Aligned_cols=28 Identities=29% Similarity=0.844 Sum_probs=21.2
Q ss_pred CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccc
Q 035300 21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSR 61 (68)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r 61 (68)
-.||+||+.+.-.-+-. ...|+|+.|-+
T Consensus 236 ~pC~~Cg~~I~~~~~~g-------------R~ty~Cp~CQ~ 263 (269)
T PRK14811 236 QPCPRCGTPIEKIVVGG-------------RGTHFCPQCQP 263 (269)
T ss_pred CCCCcCCCeeEEEEECC-------------CCcEECCCCcC
Confidence 35999999998877753 56677777754
No 33
>PF14369 zf-RING_3: zinc-finger
Probab=85.04 E-value=0.86 Score=24.66 Aligned_cols=15 Identities=40% Similarity=0.884 Sum_probs=10.6
Q ss_pred ecCCCCcCCCCCCce
Q 035300 16 RNGADAACPYCGGPV 30 (68)
Q Consensus 16 ~~~A~G~Cp~CGG~v 30 (68)
.....-+||+|+|+-
T Consensus 17 ~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 17 SPDSDVACPRCHGGF 31 (35)
T ss_pred CCCCCcCCcCCCCcE
Confidence 344455699999975
No 34
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=84.68 E-value=0.34 Score=32.46 Aligned_cols=41 Identities=22% Similarity=0.433 Sum_probs=27.9
Q ss_pred CCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeeecc
Q 035300 18 GADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPAT 67 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~~ 67 (68)
.+-=.||+||-...+.|.....- | -..|.|+.||..|+.+.
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~d----~-----~~~f~Cp~Cg~~l~~~d 137 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLLD----M-----DGTFTCPRCGEELEEDD 137 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhcC----C-----CCcEECCCCCCEEEEcC
Confidence 44557999998887655432111 1 25599999999998764
No 35
>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=84.65 E-value=0.38 Score=36.70 Aligned_cols=45 Identities=22% Similarity=0.528 Sum_probs=34.3
Q ss_pred CCCCcCCCCCCceEEEEe-----cceeeeEEeeeeeeecc--eEEeecccce
Q 035300 18 GADAACPYCGGPVLAIDF-----DAHLRFCFLPISHKVKK--KFYCTICSRR 62 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~a~Dv-----es~~rfCflP~~~k~kr--k~~Ct~C~r~ 62 (68)
...|.||-||+.-.+.-+ +...|+..=++|.--|+ |..|+.||..
T Consensus 182 ~~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 182 ESRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CCCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 457799999999766544 34578888888876664 7899999863
No 36
>PRK00420 hypothetical protein; Validated
Probab=84.28 E-value=0.81 Score=30.70 Aligned_cols=30 Identities=20% Similarity=0.569 Sum_probs=22.0
Q ss_pred CCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300 19 ADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV 64 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (68)
....||.||. |++.=...+.+|..||..+.
T Consensus 22 l~~~CP~Cg~----------------pLf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCGL----------------PLFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCCC----------------cceecCCCceECCCCCCeee
Confidence 4578999986 44443667889999998765
No 37
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=82.93 E-value=0.93 Score=24.62 Aligned_cols=29 Identities=28% Similarity=0.731 Sum_probs=13.6
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccc
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSR 61 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r 61 (68)
-||.||++++-.=.+- -...|+.|+.||.
T Consensus 2 fC~~CG~~l~~~ip~g-----------d~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEG-----------DDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B-EEE--TT------------SS-EEEETTTTE
T ss_pred ccccccChhhhhcCCC-----------CCccceECCCCCC
Confidence 3999999987654411 1334567788775
No 38
>PF12773 DZR: Double zinc ribbon
Probab=82.06 E-value=0.36 Score=26.50 Aligned_cols=14 Identities=21% Similarity=0.368 Sum_probs=7.9
Q ss_pred ecceEEeeccccee
Q 035300 50 VKKKFYCTICSRRL 63 (68)
Q Consensus 50 ~krk~~Ct~C~r~L 63 (68)
.....+|+.||+.+
T Consensus 26 ~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 26 DQSKKICPNCGAEN 39 (50)
T ss_pred cCCCCCCcCCcCCC
Confidence 34455666666654
No 39
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=81.90 E-value=0.86 Score=34.95 Aligned_cols=43 Identities=19% Similarity=0.529 Sum_probs=32.3
Q ss_pred CCCcCCCCCCceEE--EEe--cceeeeEEeeeeeeecc--eEEeecccc
Q 035300 19 ADAACPYCGGPVLA--IDF--DAHLRFCFLPISHKVKK--KFYCTICSR 61 (68)
Q Consensus 19 A~G~Cp~CGG~v~a--~Dv--es~~rfCflP~~~k~kr--k~~Ct~C~r 61 (68)
..|.||-||+.-++ ++. +...|++.=++|.--|+ |..|+.||.
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 57999999998533 333 34578888888877664 789999985
No 40
>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=81.73 E-value=1.6 Score=23.75 Aligned_cols=30 Identities=27% Similarity=0.696 Sum_probs=20.3
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeee
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVP 65 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~ 65 (68)
.||+||..-...|-+ .-.++|+.||..|.-
T Consensus 2 ~Cp~Cg~~~~~~D~~--------------~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPE--------------RGELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSEEEEETT--------------TTEEEETTT-BBEE-
T ss_pred CCcCCcCCceEEcCC--------------CCeEECCCCCCEeec
Confidence 599999987655533 345678899887753
No 41
>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=81.49 E-value=0.98 Score=23.38 Aligned_cols=17 Identities=24% Similarity=0.382 Sum_probs=9.5
Q ss_pred CcCCCCCCceEEEEecc
Q 035300 21 AACPYCGGPVLAIDFDA 37 (68)
Q Consensus 21 G~Cp~CGG~v~a~Dves 37 (68)
.-||+||++...++=+.
T Consensus 4 rfC~~CG~~t~~~~~g~ 20 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGW 20 (32)
T ss_dssp SB-TTT--BEEE-SSSS
T ss_pred cccCcCCccccCCCCcC
Confidence 46999999988776543
No 42
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=81.16 E-value=1.7 Score=24.63 Aligned_cols=33 Identities=27% Similarity=0.672 Sum_probs=19.6
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccc
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSR 61 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r 61 (68)
-||-||.+....+-+..+.---. -.+.|+.||.
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~-------~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMY-------YYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCE-------EEEEcCCCCC
Confidence 39999877766665433210000 3467899987
No 43
>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=80.96 E-value=0.44 Score=32.62 Aligned_cols=35 Identities=17% Similarity=0.124 Sum_probs=23.9
Q ss_pred CCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeeecc
Q 035300 19 ADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPAT 67 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~~ 67 (68)
.-=.||+||-..+..|.-+ .-|.|+.||..|+-+.
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~--------------~~F~Cp~Cg~~L~~~d 142 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME--------------LNFTCPRCGAMLDYLD 142 (158)
T ss_pred CeEECCCCCcEeeHHHHHH--------------cCCcCCCCCCEeeecc
Confidence 3346888887666655554 1588888888887664
No 44
>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=80.13 E-value=1.8 Score=25.64 Aligned_cols=33 Identities=21% Similarity=0.470 Sum_probs=22.5
Q ss_pred CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeeec
Q 035300 21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPA 66 (68)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~ 66 (68)
..||.||..+..-|.... --+.|..||+.|...
T Consensus 3 ~~CP~CG~~iev~~~~~G-------------eiV~Cp~CGaeleVv 35 (54)
T TIGR01206 3 FECPDCGAEIELENPELG-------------ELVICDECGAELEVV 35 (54)
T ss_pred cCCCCCCCEEecCCCccC-------------CEEeCCCCCCEEEEE
Confidence 479999998766443211 135899999988764
No 45
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=78.60 E-value=1.9 Score=29.87 Aligned_cols=27 Identities=33% Similarity=0.925 Sum_probs=20.8
Q ss_pred CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300 21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV 64 (68)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (68)
-.||.|| .||+. .--.++|+.|+.+-+
T Consensus 29 ~hCp~Cg----------------~PLF~-KdG~v~CPvC~~~~~ 55 (131)
T COG1645 29 KHCPKCG----------------TPLFR-KDGEVFCPVCGYREV 55 (131)
T ss_pred hhCcccC----------------Cccee-eCCeEECCCCCceEE
Confidence 4688888 67777 667899999996544
No 46
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=78.23 E-value=3.3 Score=32.15 Aligned_cols=46 Identities=22% Similarity=0.442 Sum_probs=31.0
Q ss_pred CCCCcCCCCCCceEEEEecceeeeEEeeeeee------ecceEEeeccccee
Q 035300 18 GADAACPYCGGPVLAIDFDAHLRFCFLPISHK------VKKKFYCTICSRRL 63 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k------~krk~~Ct~C~r~L 63 (68)
+....||.||++----+----.++++||+.-+ .+|+|.|+.|+..-
T Consensus 36 ~~~~~CP~Cg~~~~~~~~~~~~~I~~L~~~~~~~~L~~r~rR~~c~~c~~~~ 87 (402)
T COG3464 36 PRKHRCPECGQRTIRRHGWRIRKIQDLPLFEVPVYLFLRKRRYKCCRCGKRF 87 (402)
T ss_pred cccCCCCCCCCcceeccccceeeeeecccCCeeEEEEeccceeecccCCCCc
Confidence 33399999999971111112456788876433 57899999999864
No 47
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.86 E-value=1.2 Score=29.99 Aligned_cols=26 Identities=42% Similarity=0.980 Sum_probs=17.7
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeeec
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPA 66 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~ 66 (68)
.||+|+.+| |-|| ..|..||-.|++-
T Consensus 3 ~CPrC~skv-----------C~LP--------~~CpiCgLtLVss 28 (112)
T TIGR00622 3 FCPQCRAKV-----------CELP--------VECPICGLTLILS 28 (112)
T ss_pred cCCCCCCCc-----------cCCC--------CcCCcCCCEEecc
Confidence 588888765 6666 3567777777654
No 48
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=76.56 E-value=0.62 Score=32.62 Aligned_cols=35 Identities=20% Similarity=0.234 Sum_probs=24.7
Q ss_pred CCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeeecc
Q 035300 19 ADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPAT 67 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~~ 67 (68)
.-=.||+||-..+..|.-+ .-|.|+.||..|+-+.
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~--------------~~F~Cp~Cg~~L~~~d 150 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME--------------YGFRCPQCGEMLEEYD 150 (178)
T ss_pred CEEECCCCCcEEeHHHHhh--------------cCCcCCCCCCCCeecc
Confidence 3446888887777766543 2688888888887654
No 49
>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=76.38 E-value=3.5 Score=25.80 Aligned_cols=37 Identities=16% Similarity=0.526 Sum_probs=20.7
Q ss_pred CCCCcCCCCC-CceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300 18 GADAACPYCG-GPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV 64 (68)
Q Consensus 18 ~A~G~Cp~CG-G~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (68)
+.-=.||.|| ...+.++|+.. ...-...|..||....
T Consensus 20 ~~~F~CPfC~~~~sV~v~idkk----------~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVKIDKK----------EGIGILSCRVCGESFQ 57 (81)
T ss_dssp SS----TTT--SS-EEEEEETT----------TTEEEEEESSS--EEE
T ss_pred CceEcCCcCCCCCeEEEEEEcc----------CCEEEEEecCCCCeEE
Confidence 3456799999 77788888765 3345678999987654
No 50
>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=74.54 E-value=4.3 Score=20.49 Aligned_cols=14 Identities=29% Similarity=0.638 Sum_probs=8.6
Q ss_pred cCCCCCCceEEEEe
Q 035300 22 ACPYCGGPVLAIDF 35 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dv 35 (68)
.||+||..+.-+.+
T Consensus 3 ~C~rC~~~~~~~~~ 16 (30)
T PF06827_consen 3 KCPRCWNYIEDIGI 16 (30)
T ss_dssp B-TTT--BBEEEEE
T ss_pred cCccCCCcceEeEe
Confidence 59999999877666
No 51
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=74.47 E-value=2.6 Score=29.92 Aligned_cols=23 Identities=26% Similarity=0.596 Sum_probs=15.7
Q ss_pred EeCCceeeeeecCCCCcCCCCCCc
Q 035300 6 IFDLREKVIRRNGADAACPYCGGP 29 (68)
Q Consensus 6 vcde~~kv~~~~~A~G~Cp~CGG~ 29 (68)
+|-.-+-.... .||+.||-||.+
T Consensus 136 vC~vCGy~~~g-e~P~~CPiCga~ 158 (166)
T COG1592 136 VCPVCGYTHEG-EAPEVCPICGAP 158 (166)
T ss_pred EcCCCCCcccC-CCCCcCCCCCCh
Confidence 33333444444 899999999975
No 52
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=74.07 E-value=3.4 Score=29.61 Aligned_cols=38 Identities=26% Similarity=0.529 Sum_probs=24.5
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeec-ceEEeeccccee
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVK-KKFYCTICSRRL 63 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~k-rk~~Ct~C~r~L 63 (68)
-||.||+......+.+.- ||.+.+.= -.|.|..||-+-
T Consensus 2 ~Cp~C~~~~~~~~~~~~~----IP~F~evii~sf~C~~CGyr~ 40 (192)
T TIGR00310 2 DCPSCGGECETVMKTVND----IPYFGEVLETSTICEHCGYRS 40 (192)
T ss_pred cCCCCCCCCEEEEEEEcC----CCCcceEEEEEEECCCCCCcc
Confidence 499999875544443331 66555543 478999999653
No 53
>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=73.56 E-value=4 Score=21.34 Aligned_cols=14 Identities=43% Similarity=0.971 Sum_probs=11.0
Q ss_pred cCCCCcCCCCCCce
Q 035300 17 NGADAACPYCGGPV 30 (68)
Q Consensus 17 ~~A~G~Cp~CGG~v 30 (68)
..++-.||-||.+-
T Consensus 14 ~~~~~~CP~Cg~~~ 27 (33)
T cd00350 14 EEAPWVCPVCGAPK 27 (33)
T ss_pred CcCCCcCcCCCCcH
Confidence 34889999999864
No 54
>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=72.57 E-value=2.8 Score=21.65 Aligned_cols=18 Identities=22% Similarity=0.746 Sum_probs=9.8
Q ss_pred cCCCCCCceEEEEeccee
Q 035300 22 ACPYCGGPVLAIDFDAHL 39 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~ 39 (68)
-||-||..+.-.+=|..+
T Consensus 1 ~CP~C~s~l~~~~~ev~~ 18 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDI 18 (28)
T ss_dssp B-TTT--BEEE-CCTTCE
T ss_pred CcCCCCCEeEcCCCCEeE
Confidence 399999999866655544
No 55
>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=72.31 E-value=5.8 Score=21.70 Aligned_cols=12 Identities=33% Similarity=0.980 Sum_probs=10.3
Q ss_pred cCCCCcCCCCCC
Q 035300 17 NGADAACPYCGG 28 (68)
Q Consensus 17 ~~A~G~Cp~CGG 28 (68)
+..+-.||.||+
T Consensus 23 ~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 23 EDDPVPCPECGS 34 (42)
T ss_pred CCCCCcCCCCCC
Confidence 367889999999
No 56
>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=71.30 E-value=5.9 Score=20.50 Aligned_cols=12 Identities=50% Similarity=1.104 Sum_probs=9.5
Q ss_pred CCCCcCCCCCCc
Q 035300 18 GADAACPYCGGP 29 (68)
Q Consensus 18 ~A~G~Cp~CGG~ 29 (68)
...-.||.||+.
T Consensus 24 ~~~~~CP~Cg~~ 35 (41)
T smart00834 24 DPLATCPECGGD 35 (41)
T ss_pred CCCCCCCCCCCc
Confidence 566789999984
No 57
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=70.34 E-value=5.9 Score=21.23 Aligned_cols=26 Identities=27% Similarity=0.661 Sum_probs=17.7
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR 62 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (68)
.|+.|||... .++.+--++|..||..
T Consensus 5 ~C~~C~~~~i---------------~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 5 KCSKCGGNGI---------------VNKEDDYEVCIFCGSS 30 (33)
T ss_pred EcCCCCCCeE---------------EEecCCeEEcccCCcE
Confidence 5888888763 2356666777777764
No 58
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=70.23 E-value=3.4 Score=24.32 Aligned_cols=11 Identities=55% Similarity=1.546 Sum_probs=9.2
Q ss_pred cCCCCCCceEE
Q 035300 22 ACPYCGGPVLA 32 (68)
Q Consensus 22 ~Cp~CGG~v~a 32 (68)
.|||||-.+..
T Consensus 2 ~CPyCge~~~~ 12 (52)
T PF14255_consen 2 QCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCeeEE
Confidence 59999998765
No 59
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=69.96 E-value=5.8 Score=22.35 Aligned_cols=27 Identities=19% Similarity=0.198 Sum_probs=14.1
Q ss_pred EEeCCceeeeee-cCCCCcCCCCCCceE
Q 035300 5 SIFDLREKVIRR-NGADAACPYCGGPVL 31 (68)
Q Consensus 5 ~vcde~~kv~~~-~~A~G~Cp~CGG~v~ 31 (68)
++|.+=+..+.. ...+-.||+||..+.
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~rIl 30 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGYRIL 30 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCceEE
Confidence 444443333332 345566777777654
No 60
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=69.36 E-value=1.5 Score=31.40 Aligned_cols=45 Identities=16% Similarity=0.411 Sum_probs=27.4
Q ss_pred cCCCCcCCCCCCceEEEEecceeeeEEee--eeeeecceEEeeccccee
Q 035300 17 NGADAACPYCGGPVLAIDFDAHLRFCFLP--ISHKVKKKFYCTICSRRL 63 (68)
Q Consensus 17 ~~A~G~Cp~CGG~v~a~Dves~~rfCflP--~~~k~krk~~Ct~C~r~L 63 (68)
++--..||+|+|.+..+.=|..-- =|| ++..+-.=+.|+.||+.+
T Consensus 94 ~~e~~RCp~CN~~L~~vs~eev~~--~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 94 FPEFSRCPECNGELEKVSREEVKE--KVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred ccccccCcccCCEeccCcHHHHhh--ccchhhhhcccceeECCCCcccc
Confidence 445678999999988765443110 033 333333334499999864
No 61
>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=68.27 E-value=5.1 Score=28.05 Aligned_cols=35 Identities=31% Similarity=0.790 Sum_probs=23.0
Q ss_pred CCCCCCc-eEEEEecceeeeEEeeeeeeec-ceEEeecccce
Q 035300 23 CPYCGGP-VLAIDFDAHLRFCFLPISHKVK-KKFYCTICSRR 62 (68)
Q Consensus 23 Cp~CGG~-v~a~Dves~~rfCflP~~~k~k-rk~~Ct~C~r~ 62 (68)
||.||+. +..+...+ =||.+.+.= -.|.|..||-+
T Consensus 1 CP~Cg~~~~~~~~~~~-----~IP~F~evii~sf~C~~CGyr 37 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDY-----DIPYFGKIMLSTYICEKCGYR 37 (163)
T ss_pred CCCCCCcceEeeeEec-----cCCCcceEEEEEEECCCCCCc
Confidence 9999996 44433322 267665543 37899999865
No 62
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=67.23 E-value=3.6 Score=22.97 Aligned_cols=38 Identities=24% Similarity=0.482 Sum_probs=21.1
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeec--ccceeeec
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTI--CSRRLVPA 66 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~--C~r~L~~~ 66 (68)
-||.||..+.+---+-.. |.. .+.-+.|+- ||...+..
T Consensus 1 ~CP~Cg~~a~ir~S~~~s-----~~~--~~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLS-----PLT--RELYCQCTNPECGHTFVAN 40 (47)
T ss_pred CcCCCCCeeEEEEchhhC-----cce--EEEEEEECCCcCCCEEEEE
Confidence 399999988765332221 111 123455666 77766543
No 63
>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=66.03 E-value=4.7 Score=28.41 Aligned_cols=39 Identities=18% Similarity=0.469 Sum_probs=26.8
Q ss_pred cCCCCCC-ceEEEEecceeeeEEeeeeeeecceEEeecccceeeec
Q 035300 22 ACPYCGG-PVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPA 66 (68)
Q Consensus 22 ~Cp~CGG-~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~ 66 (68)
-||+||. --.++|=+..- =-..++|+=.|..||+|..+|
T Consensus 2 ~CP~C~~~dtkViDSR~~~------dg~~IRRRReC~~C~~RFTTy 41 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVE------DGQSIRRRRECLECHERFTTF 41 (147)
T ss_pred CCCCCCCCCCEeeeccccC------CCCeeeecccCCccCCcccee
Confidence 4999998 45566644211 112467888999999998887
No 64
>PRK09401 reverse gyrase; Reviewed
Probab=65.83 E-value=2.4 Score=37.30 Aligned_cols=14 Identities=36% Similarity=0.975 Sum_probs=11.2
Q ss_pred CCcCCCCCCceEEE
Q 035300 20 DAACPYCGGPVLAI 33 (68)
Q Consensus 20 ~G~Cp~CGG~v~a~ 33 (68)
.++||+|||.++.-
T Consensus 7 ~~~cpnc~g~i~~~ 20 (1176)
T PRK09401 7 KNSCPNCGGDISDE 20 (1176)
T ss_pred cccCCCCCCcCcHh
Confidence 36899999998743
No 65
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=65.21 E-value=5.2 Score=26.90 Aligned_cols=14 Identities=36% Similarity=1.130 Sum_probs=11.9
Q ss_pred CCCCCCceEEEEec
Q 035300 23 CPYCGGPVLAIDFD 36 (68)
Q Consensus 23 Cp~CGG~v~a~Dve 36 (68)
||-|||.+.++.++
T Consensus 1 CPvCg~~l~vt~l~ 14 (113)
T PF09862_consen 1 CPVCGGELVVTRLK 14 (113)
T ss_pred CCCCCCceEEEEEE
Confidence 89999999988664
No 66
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=64.00 E-value=2.9 Score=18.60 Aligned_cols=13 Identities=31% Similarity=0.904 Sum_probs=7.8
Q ss_pred EEeecccceeeec
Q 035300 54 FYCTICSRRLVPA 66 (68)
Q Consensus 54 ~~Ct~C~r~L~~~ 66 (68)
|.|+.|+......
T Consensus 1 ~~C~~C~~~~~~~ 13 (24)
T PF13894_consen 1 FQCPICGKSFRSK 13 (24)
T ss_dssp EE-SSTS-EESSH
T ss_pred CCCcCCCCcCCcH
Confidence 6788888876653
No 67
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=63.53 E-value=3.2 Score=37.32 Aligned_cols=20 Identities=30% Similarity=0.833 Sum_probs=15.1
Q ss_pred CCcCCCCCCceEEEEeccee
Q 035300 20 DAACPYCGGPVLAIDFDAHL 39 (68)
Q Consensus 20 ~G~Cp~CGG~v~a~Dves~~ 39 (68)
-++||+|||.++.-..+...
T Consensus 8 ~~~CpNCGG~isseRL~~gl 27 (1187)
T COG1110 8 GSSCPNCGGDISSERLEKGL 27 (1187)
T ss_pred hccCCCCCCcCcHHHHhcCC
Confidence 37899999998876665544
No 68
>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=63.51 E-value=3.8 Score=24.65 Aligned_cols=24 Identities=33% Similarity=0.854 Sum_probs=17.5
Q ss_pred eeeeeecCC-CCcCCCCCCceEEEE
Q 035300 11 EKVIRRNGA-DAACPYCGGPVLAID 34 (68)
Q Consensus 11 ~kv~~~~~A-~G~Cp~CGG~v~a~D 34 (68)
+|++=.+.. -|.||.||.++.-.|
T Consensus 25 GkIiC~~Eg~~~pC~fCg~~l~~~~ 49 (57)
T PF06221_consen 25 GKIICEQEGPLGPCPFCGTPLLSSE 49 (57)
T ss_pred ChhhcccccCcCcCCCCCCcccCHH
Confidence 566777777 499999997775544
No 69
>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=63.37 E-value=5.2 Score=20.83 Aligned_cols=13 Identities=23% Similarity=0.447 Sum_probs=7.6
Q ss_pred ceEEeecccceee
Q 035300 52 KKFYCTICSRRLV 64 (68)
Q Consensus 52 rk~~Ct~C~r~L~ 64 (68)
.++.|+.|+..+.
T Consensus 24 ~~v~C~~C~~~~~ 36 (38)
T TIGR02098 24 GKVRCGKCGHVWY 36 (38)
T ss_pred CEEECCCCCCEEE
Confidence 3566666666554
No 70
>PRK11827 hypothetical protein; Provisional
Probab=63.16 E-value=6.3 Score=23.91 Aligned_cols=27 Identities=22% Similarity=0.668 Sum_probs=18.0
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccccee
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRL 63 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (68)
+||.|.|.+.- |-+.+ ...|+.|+..+
T Consensus 10 aCP~ckg~L~~-~~~~~--------------~Lic~~~~laY 36 (60)
T PRK11827 10 ACPVCNGKLWY-NQEKQ--------------ELICKLDNLAF 36 (60)
T ss_pred ECCCCCCcCeE-cCCCC--------------eEECCccCeec
Confidence 69999999864 32332 46677777654
No 71
>PF14353 CpXC: CpXC protein
Probab=63.16 E-value=6.7 Score=25.15 Aligned_cols=36 Identities=22% Similarity=0.433 Sum_probs=25.0
Q ss_pred eeeeeecCCCCcCCCCCCceE------EEEecceeeeEEeee
Q 035300 11 EKVIRRNGADAACPYCGGPVL------AIDFDAHLRFCFLPI 46 (68)
Q Consensus 11 ~kv~~~~~A~G~Cp~CGG~v~------a~Dves~~rfCflP~ 46 (68)
++++.-+=.--.||+||.... -.|.+-++.+-+.|-
T Consensus 29 e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~~~~~i~~~P~ 70 (128)
T PF14353_consen 29 EKILDGSLFSFTCPSCGHKFRLEYPLLYHDPEKKFMIYYFPD 70 (128)
T ss_pred HHHHcCCcCEEECCCCCCceecCCCEEEEcCCCCEEEEEcCC
Confidence 345544555668999998765 367777777777775
No 72
>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=63.01 E-value=4.8 Score=21.86 Aligned_cols=15 Identities=27% Similarity=0.857 Sum_probs=11.7
Q ss_pred cCCCCcCCCCCCceE
Q 035300 17 NGADAACPYCGGPVL 31 (68)
Q Consensus 17 ~~A~G~Cp~CGG~v~ 31 (68)
-+.+|.|..|||.+.
T Consensus 18 P~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 18 PKVEGVCDNCGGELV 32 (36)
T ss_dssp -SSTTBCTTTTEBEB
T ss_pred CCCCCccCCCCCeeE
Confidence 456799999999764
No 73
>PF07038 DUF1324: Protein of unknown function (DUF1324); InterPro: IPR009757 This family consists of several Circovirus proteins of around 60 residues in length. The function of this family is unknown.
Probab=62.81 E-value=6.1 Score=24.11 Aligned_cols=15 Identities=33% Similarity=0.824 Sum_probs=12.7
Q ss_pred ceeeeEEeeeeeeec
Q 035300 37 AHLRFCFLPISHKVK 51 (68)
Q Consensus 37 s~~rfCflP~~~k~k 51 (68)
-|.|||..|+-+|+.
T Consensus 7 fqsrfcifpltfkss 21 (59)
T PF07038_consen 7 FQSRFCIFPLTFKSS 21 (59)
T ss_pred EeeeeEEEEeeeccC
Confidence 478999999999863
No 74
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.12 E-value=6.8 Score=24.31 Aligned_cols=47 Identities=26% Similarity=0.437 Sum_probs=36.8
Q ss_pred eeeeeecCCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeeec
Q 035300 11 EKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPA 66 (68)
Q Consensus 11 ~kv~~~~~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~ 66 (68)
...+.....+-+||-=+++ -.+-|. |||+ ..+.-..|+-||+++++-
T Consensus 15 ~~~I~~~~~~l~C~g~~~p------~~HPrV-~L~m--g~~gev~CPYC~t~y~l~ 61 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPP------NDHPRV-FLDM--GDEGEVVCPYCSTRYRLN 61 (62)
T ss_pred ceEEEeCCeeEEcCCCCCC------CCCCEE-EEEc--CCCCcEecCccccEEEec
Confidence 5667777788888866665 456665 7999 888899999999999874
No 75
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=61.88 E-value=5.2 Score=23.56 Aligned_cols=15 Identities=40% Similarity=1.059 Sum_probs=11.1
Q ss_pred CCCcCCCCCCceEEE
Q 035300 19 ADAACPYCGGPVLAI 33 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~ 33 (68)
-.-.|||||..+-.-
T Consensus 23 ~~irCp~Cg~rIl~K 37 (49)
T COG1996 23 RGIRCPYCGSRILVK 37 (49)
T ss_pred CceeCCCCCcEEEEe
Confidence 345799999987653
No 76
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=61.86 E-value=1.4 Score=33.56 Aligned_cols=23 Identities=13% Similarity=0.007 Sum_probs=18.2
Q ss_pred eCCceeeeeecCCCCcCCCCCCc
Q 035300 7 FDLREKVIRRNGADAACPYCGGP 29 (68)
Q Consensus 7 cde~~kv~~~~~A~G~Cp~CGG~ 29 (68)
+|--++|+.+.+-|+.||+|||-
T Consensus 141 ~dva~~v~~~hfLpd~~gn~r~f 163 (253)
T COG1933 141 HDVAERVLNSHFIPDLRGNLRSF 163 (253)
T ss_pred HHHHHHhhccCCCcchhhhhhhh
Confidence 34557888889999999998875
No 77
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=61.47 E-value=3.7 Score=23.08 Aligned_cols=10 Identities=40% Similarity=1.042 Sum_probs=5.8
Q ss_pred CCcCCCCCCc
Q 035300 20 DAACPYCGGP 29 (68)
Q Consensus 20 ~G~Cp~CGG~ 29 (68)
++.||+||-+
T Consensus 2 ~~~CprC~kg 11 (36)
T PF14787_consen 2 PGLCPRCGKG 11 (36)
T ss_dssp --C-TTTSSS
T ss_pred CccCcccCCC
Confidence 6899999965
No 78
>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=61.44 E-value=4.6 Score=22.33 Aligned_cols=10 Identities=50% Similarity=1.464 Sum_probs=8.3
Q ss_pred CCcCCCCCCc
Q 035300 20 DAACPYCGGP 29 (68)
Q Consensus 20 ~G~Cp~CGG~ 29 (68)
.+.||.|||.
T Consensus 3 ~~pCP~CGG~ 12 (37)
T smart00778 3 HGPCPNCGGS 12 (37)
T ss_pred ccCCCCCCCc
Confidence 4789999994
No 79
>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=60.38 E-value=4.9 Score=24.98 Aligned_cols=9 Identities=44% Similarity=1.202 Sum_probs=6.9
Q ss_pred cCCCCCCce
Q 035300 22 ACPYCGGPV 30 (68)
Q Consensus 22 ~Cp~CGG~v 30 (68)
-||.||+.+
T Consensus 2 fC~~Cg~~l 10 (104)
T TIGR01384 2 FCPKCGSLM 10 (104)
T ss_pred CCcccCccc
Confidence 488888877
No 80
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=60.38 E-value=14 Score=22.99 Aligned_cols=30 Identities=27% Similarity=0.713 Sum_probs=20.8
Q ss_pred CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300 21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR 62 (68)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (68)
-.||.||..+.-+..... |=.+.|--|++.
T Consensus 7 KPCPFCG~~~~~v~~~~g------------~~~v~C~~CgA~ 36 (64)
T PRK09710 7 KPCPFCGCPSVTVKAISG------------YYRAKCNGCESR 36 (64)
T ss_pred cCCCCCCCceeEEEecCc------------eEEEEcCCCCcC
Confidence 469999998776654322 225788888875
No 81
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=60.36 E-value=3.7 Score=36.10 Aligned_cols=13 Identities=38% Similarity=1.101 Sum_probs=11.1
Q ss_pred CCcCCCCCCceEE
Q 035300 20 DAACPYCGGPVLA 32 (68)
Q Consensus 20 ~G~Cp~CGG~v~a 32 (68)
.+.||+|||.+..
T Consensus 7 ~~~CPnCgg~i~~ 19 (1171)
T TIGR01054 7 SNLCPNCGGEISS 19 (1171)
T ss_pred cCCCCCCCCccch
Confidence 5789999999865
No 82
>PRK04023 DNA polymerase II large subunit; Validated
Probab=60.10 E-value=4.7 Score=36.16 Aligned_cols=39 Identities=26% Similarity=0.602 Sum_probs=21.8
Q ss_pred CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeeecc
Q 035300 21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPAT 67 (68)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~~ 67 (68)
-.||.||.. ....+|| |-|.+.-..+.|..||..+..++
T Consensus 639 frCP~CG~~------Te~i~fC--P~CG~~~~~y~CPKCG~El~~~s 677 (1121)
T PRK04023 639 RRCPFCGTH------TEPVYRC--PRCGIEVEEDECEKCGREPTPYS 677 (1121)
T ss_pred ccCCCCCCC------CCcceeC--ccccCcCCCCcCCCCCCCCCccc
Confidence 456666655 1223444 55555555566777777666543
No 83
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=59.77 E-value=6.5 Score=25.59 Aligned_cols=18 Identities=28% Similarity=0.274 Sum_probs=12.7
Q ss_pred eeeeeecCCCCcCCCCCC
Q 035300 11 EKVIRRNGADAACPYCGG 28 (68)
Q Consensus 11 ~kv~~~~~A~G~Cp~CGG 28 (68)
+=++-..|+.+.|+.||.
T Consensus 61 ~L~I~~vp~~~~C~~Cg~ 78 (113)
T PRK12380 61 DLHIVYKPAQAWCWDCSQ 78 (113)
T ss_pred EEEEEeeCcEEEcccCCC
Confidence 445666777788888883
No 84
>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=59.51 E-value=6.7 Score=21.33 Aligned_cols=13 Identities=46% Similarity=1.252 Sum_probs=9.6
Q ss_pred CcCCCCCCceEEE
Q 035300 21 AACPYCGGPVLAI 33 (68)
Q Consensus 21 G~Cp~CGG~v~a~ 33 (68)
..||.|||.++.-
T Consensus 2 ~~CP~Cg~~lv~r 14 (39)
T PF01396_consen 2 EKCPKCGGPLVLR 14 (39)
T ss_pred cCCCCCCceeEEE
Confidence 4799999876543
No 85
>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=58.86 E-value=25 Score=19.19 Aligned_cols=11 Identities=55% Similarity=1.226 Sum_probs=8.5
Q ss_pred CCCCcCCCCCC
Q 035300 18 GADAACPYCGG 28 (68)
Q Consensus 18 ~A~G~Cp~CGG 28 (68)
..+-.||.||+
T Consensus 24 ~~~~~CP~Cg~ 34 (52)
T TIGR02605 24 DPLATCPECGG 34 (52)
T ss_pred CCCCCCCCCCC
Confidence 34557999998
No 86
>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=58.50 E-value=5.4 Score=22.43 Aligned_cols=17 Identities=29% Similarity=0.786 Sum_probs=10.9
Q ss_pred eeeeeeecceEEeeccc
Q 035300 44 LPISHKVKKKFYCTICS 60 (68)
Q Consensus 44 lP~~~k~krk~~Ct~C~ 60 (68)
.|+......+.+|..|+
T Consensus 25 ~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 25 TPLMRDKDGKIYCVSCG 41 (41)
T ss_pred CeeEEecCCCEECCCCC
Confidence 45666455567888775
No 87
>PF09947 DUF2180: Uncharacterized protein conserved in archaea (DUF2180); InterPro: IPR017211 This group represents a predicted zinc finger protein, AF1427 type.
Probab=57.93 E-value=1.8 Score=27.03 Aligned_cols=57 Identities=19% Similarity=0.193 Sum_probs=35.8
Q ss_pred EEEeCCceeeeeecCCCCcCCCCCCceEEE---EecceeeeEEeeee----eeecceEEeeccccee
Q 035300 4 LSIFDLREKVIRRNGADAACPYCGGPVLAI---DFDAHLRFCFLPIS----HKVKKKFYCTICSRRL 63 (68)
Q Consensus 4 ~~vcde~~kv~~~~~A~G~Cp~CGG~v~a~---Dves~~rfCflP~~----~k~krk~~Ct~C~r~L 63 (68)
++.|.+++|. ..|-|+|-.||-++=.- ..|....=---|+- .+.-+|+.|+-|...+
T Consensus 3 CY~Ca~~gkd---t~AVavCivCG~GlC~~H~~~e~~~~~~g~yp~~~~~~~~~l~RilC~~C~~a~ 66 (68)
T PF09947_consen 3 CYDCAEEGKD---TDAVAVCIVCGAGLCMDHSKREEIPVWEGGYPFPSKKLKKPLPRILCPECHAAL 66 (68)
T ss_pred chhhhhcCCC---ccceehHHhcCchhhHHHHhhhheeeeccCCCCccccccCCCCeeecHHHHHHh
Confidence 5677788874 38999999999887321 11111111234544 4455889999887654
No 88
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=57.70 E-value=4 Score=22.87 Aligned_cols=31 Identities=29% Similarity=0.814 Sum_probs=12.9
Q ss_pred CCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccc
Q 035300 20 DAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60 (68)
Q Consensus 20 ~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~ 60 (68)
.+.||.|||. -||-..+ =.+..-.++|..|+
T Consensus 3 h~pCP~CGG~---------DrFri~~-d~~~~G~~~C~~C~ 33 (40)
T PF08273_consen 3 HGPCPICGGK---------DRFRIFD-DKDGRGTWICRQCG 33 (40)
T ss_dssp EE--TTTT-T---------TTEEEET-T----S-EEETTTT
T ss_pred CCCCCCCcCc---------cccccCc-CcccCCCEECCCCC
Confidence 3679999993 2443111 11233567777773
No 89
>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=56.73 E-value=10 Score=24.49 Aligned_cols=14 Identities=36% Similarity=0.819 Sum_probs=11.2
Q ss_pred ceEEeecccceeee
Q 035300 52 KKFYCTICSRRLVP 65 (68)
Q Consensus 52 rk~~Ct~C~r~L~~ 65 (68)
.+|.|..|+..|+.
T Consensus 142 ~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 142 KRYRCGRCGGPLVQ 155 (157)
T ss_pred hhEECCCCCCEEEE
Confidence 45889999988874
No 90
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=56.37 E-value=12 Score=20.03 Aligned_cols=13 Identities=31% Similarity=0.971 Sum_probs=7.5
Q ss_pred CCCCCCceEEEEe
Q 035300 23 CPYCGGPVLAIDF 35 (68)
Q Consensus 23 Cp~CGG~v~a~Dv 35 (68)
||.|+..+....+
T Consensus 2 CP~C~~~l~~~~~ 14 (41)
T PF13453_consen 2 CPRCGTELEPVRL 14 (41)
T ss_pred cCCCCcccceEEE
Confidence 7777765544333
No 91
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=56.10 E-value=8 Score=28.21 Aligned_cols=13 Identities=38% Similarity=1.012 Sum_probs=9.3
Q ss_pred CCcCCCCCCceEE
Q 035300 20 DAACPYCGGPVLA 32 (68)
Q Consensus 20 ~G~Cp~CGG~v~a 32 (68)
.--||+||.+...
T Consensus 99 ~~fC~~CG~~~~~ 111 (256)
T PRK00241 99 HRFCGYCGHPMHP 111 (256)
T ss_pred CccccccCCCCee
Confidence 3468888887664
No 92
>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=55.92 E-value=6.4 Score=25.96 Aligned_cols=16 Identities=25% Similarity=0.544 Sum_probs=11.7
Q ss_pred CCCCcCCCCCCceEEE
Q 035300 18 GADAACPYCGGPVLAI 33 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~a~ 33 (68)
+-|-+||+||--....
T Consensus 24 k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 24 KDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCCccCCCCCCccCcc
Confidence 3577899999766544
No 93
>PRK05580 primosome assembly protein PriA; Validated
Probab=55.70 E-value=9.2 Score=31.39 Aligned_cols=27 Identities=26% Similarity=0.823 Sum_probs=16.6
Q ss_pred CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300 21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR 62 (68)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (68)
..||+|++++. ++|..+...|..||..
T Consensus 391 ~~C~~C~~~l~---------------~h~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 391 AECPHCDASLT---------------LHRFQRRLRCHHCGYQ 417 (679)
T ss_pred cCCCCCCCcee---------------EECCCCeEECCCCcCC
Confidence 46888888763 3455555566666544
No 94
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=55.64 E-value=6.9 Score=19.26 Aligned_cols=14 Identities=21% Similarity=0.733 Sum_probs=10.9
Q ss_pred ecceEEeeccccee
Q 035300 50 VKKKFYCTICSRRL 63 (68)
Q Consensus 50 ~krk~~Ct~C~r~L 63 (68)
..++|.|+.|++..
T Consensus 11 ~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 11 GEKPYKCPYCGKSF 24 (26)
T ss_dssp SSSSEEESSSSEEE
T ss_pred CCCCCCCCCCcCee
Confidence 35779999998864
No 95
>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=54.79 E-value=6 Score=20.28 Aligned_cols=10 Identities=40% Similarity=1.122 Sum_probs=8.1
Q ss_pred CCCCcCCCCC
Q 035300 18 GADAACPYCG 27 (68)
Q Consensus 18 ~A~G~Cp~CG 27 (68)
-++=.||+||
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 6677899998
No 96
>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=53.65 E-value=5.2 Score=20.97 Aligned_cols=23 Identities=22% Similarity=0.664 Sum_probs=12.6
Q ss_pred eeEEeeeeeeecceEEeecccceeee
Q 035300 40 RFCFLPISHKVKKKFYCTICSRRLVP 65 (68)
Q Consensus 40 rfCflP~~~k~krk~~Ct~C~r~L~~ 65 (68)
.+|-| |-. +.+|.|+.|+.++=|
T Consensus 3 ~~C~v--C~~-~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 3 KLCSV--CGN-PAKYRCPRCGARYCS 25 (30)
T ss_dssp EEETS--SSS-EESEE-TTT--EESS
T ss_pred CCCcc--CcC-CCEEECCCcCCceeC
Confidence 34444 444 888889988877533
No 97
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=53.42 E-value=4.1 Score=19.93 Aligned_cols=13 Identities=31% Similarity=1.058 Sum_probs=9.6
Q ss_pred eEEeecccceeee
Q 035300 53 KFYCTICSRRLVP 65 (68)
Q Consensus 53 k~~Ct~C~r~L~~ 65 (68)
+|+|..|++.+.+
T Consensus 1 q~~C~~C~k~f~~ 13 (27)
T PF12171_consen 1 QFYCDACDKYFSS 13 (27)
T ss_dssp -CBBTTTTBBBSS
T ss_pred CCCcccCCCCcCC
Confidence 4789999987653
No 98
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=53.33 E-value=16 Score=25.41 Aligned_cols=34 Identities=35% Similarity=0.764 Sum_probs=24.5
Q ss_pred cCCCCCCceEEEEecceeeeEE--eeeeeeecc-eEEeecccce
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCF--LPISHKVKK-KFYCTICSRR 62 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCf--lP~~~k~kr-k~~Ct~C~r~ 62 (68)
.||.||+... +|++. ||.+.+.== .|.|..||-+
T Consensus 2 ~Cp~C~~~~~-------~~~~~~~IP~F~evii~sf~C~~CGyk 38 (160)
T smart00709 2 DCPSCGGNGT-------TRMLLTSIPYFREVIIMSFECEHCGYR 38 (160)
T ss_pred cCCCCCCCCE-------EEEEEecCCCcceEEEEEEECCCCCCc
Confidence 5999998743 44443 787766654 8999999965
No 99
>PRK14873 primosome assembly protein PriA; Provisional
Probab=53.03 E-value=11 Score=31.40 Aligned_cols=12 Identities=42% Similarity=0.861 Sum_probs=8.0
Q ss_pred CcCCCCCCceEE
Q 035300 21 AACPYCGGPVLA 32 (68)
Q Consensus 21 G~Cp~CGG~v~a 32 (68)
-.||+|++++.-
T Consensus 393 ~~C~~C~~~L~~ 404 (665)
T PRK14873 393 ARCRHCTGPLGL 404 (665)
T ss_pred eECCCCCCceeE
Confidence 357777777664
No 100
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=52.02 E-value=15 Score=23.98 Aligned_cols=33 Identities=18% Similarity=0.403 Sum_probs=21.9
Q ss_pred CCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300 18 GADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR 62 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (68)
+.--.||+||-....+++.- .+-...|..||-.
T Consensus 19 pt~f~CP~Cge~~v~v~~~k------------~~~h~~C~~CG~y 51 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKK------------NIAIITCGNCGLY 51 (99)
T ss_pred CcEeECCCCCCeEeeeecCC------------CcceEECCCCCCc
Confidence 44557999996554444442 3667789988853
No 101
>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=51.65 E-value=15 Score=19.59 Aligned_cols=14 Identities=36% Similarity=0.918 Sum_probs=8.8
Q ss_pred cCCCCcCCCCCCce
Q 035300 17 NGADAACPYCGGPV 30 (68)
Q Consensus 17 ~~A~G~Cp~CGG~v 30 (68)
...+-.||+||.-+
T Consensus 14 ~~~~irC~~CG~RI 27 (32)
T PF03604_consen 14 PGDPIRCPECGHRI 27 (32)
T ss_dssp TSSTSSBSSSS-SE
T ss_pred CCCcEECCcCCCeE
Confidence 34456788888765
No 102
>PRK14701 reverse gyrase; Provisional
Probab=51.48 E-value=6.9 Score=35.88 Aligned_cols=17 Identities=29% Similarity=0.817 Sum_probs=12.7
Q ss_pred CCcCCCCCCceEEEEec
Q 035300 20 DAACPYCGGPVLAIDFD 36 (68)
Q Consensus 20 ~G~Cp~CGG~v~a~Dve 36 (68)
.++||+|||.++.-..+
T Consensus 6 ~~~cpnc~g~~~~~rl~ 22 (1638)
T PRK14701 6 KEMCPNCGGDITDERLA 22 (1638)
T ss_pred cccCCCCCCccchhHHh
Confidence 36899999988765444
No 103
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=51.26 E-value=7 Score=19.13 Aligned_cols=35 Identities=31% Similarity=0.581 Sum_probs=20.3
Q ss_pred CCCCCCceEEEEecceeeeEEeeeeeeecc--eEEeecccceee
Q 035300 23 CPYCGGPVLAIDFDAHLRFCFLPISHKVKK--KFYCTICSRRLV 64 (68)
Q Consensus 23 Cp~CGG~v~a~Dves~~rfCflP~~~k~kr--k~~Ct~C~r~L~ 64 (68)
|+.|+-.+...+.. +..-.+.|- =|.|+.|++.|.
T Consensus 2 C~~C~~~i~~~~~~-------~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGELV-------LRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcEE-------EEeCCccccccCCCCcccCCcCc
Confidence 77777766543111 122233343 388999999875
No 104
>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=51.13 E-value=21 Score=20.91 Aligned_cols=16 Identities=25% Similarity=0.584 Sum_probs=11.1
Q ss_pred eecceEEeecccceee
Q 035300 49 KVKKKFYCTICSRRLV 64 (68)
Q Consensus 49 k~krk~~Ct~C~r~L~ 64 (68)
-..-...|+.|+|.+.
T Consensus 49 i~eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 49 IVEGELICPECGREYP 64 (68)
T ss_dssp TTTTEEEETTTTEEEE
T ss_pred ccCCEEEcCCCCCEEe
Confidence 3456677888888764
No 105
>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=50.85 E-value=9.3 Score=21.97 Aligned_cols=19 Identities=26% Similarity=0.691 Sum_probs=13.1
Q ss_pred eeeecceEEeecccceeee
Q 035300 47 SHKVKKKFYCTICSRRLVP 65 (68)
Q Consensus 47 ~~k~krk~~Ct~C~r~L~~ 65 (68)
.-+..++++|..||..|-.
T Consensus 42 s~~~~~r~FC~~CGs~l~~ 60 (92)
T PF04828_consen 42 SGKGVERYFCPTCGSPLFS 60 (92)
T ss_dssp TTSSCEEEEETTT--EEEE
T ss_pred CCCcCcCcccCCCCCeeec
Confidence 3456688999999998864
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=50.60 E-value=12 Score=24.28 Aligned_cols=18 Identities=17% Similarity=0.425 Sum_probs=13.2
Q ss_pred eeeeeecCCCCcCCCCCC
Q 035300 11 EKVIRRNGADAACPYCGG 28 (68)
Q Consensus 11 ~kv~~~~~A~G~Cp~CGG 28 (68)
+=.+-..|+.+.|+.||-
T Consensus 61 ~L~I~~~p~~~~C~~Cg~ 78 (115)
T TIGR00100 61 KLNIEDEPVECECEDCSE 78 (115)
T ss_pred EEEEEeeCcEEEcccCCC
Confidence 445667788888888883
No 107
>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=50.28 E-value=22 Score=21.64 Aligned_cols=12 Identities=25% Similarity=0.451 Sum_probs=8.5
Q ss_pred cceEEeecccce
Q 035300 51 KKKFYCTICSRR 62 (68)
Q Consensus 51 krk~~Ct~C~r~ 62 (68)
-..++|+.||-.
T Consensus 34 f~~v~C~~CGYT 45 (64)
T PF09855_consen 34 FTTVSCTNCGYT 45 (64)
T ss_pred EEEEECCCCCCE
Confidence 345689999854
No 108
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=50.27 E-value=11 Score=23.62 Aligned_cols=16 Identities=38% Similarity=0.974 Sum_probs=11.8
Q ss_pred cCCCCCCc---------eEEEEecc
Q 035300 22 ACPYCGGP---------VLAIDFDA 37 (68)
Q Consensus 22 ~Cp~CGG~---------v~a~Dves 37 (68)
.||.||.. +..+|-|+
T Consensus 20 ~CP~Cgs~~~te~W~G~~iIidpe~ 44 (64)
T COG2093 20 ICPVCGSTDLTEEWFGLLIIIDPEK 44 (64)
T ss_pred cCCCCCCcccchhhccEEEEEcCcH
Confidence 59999965 66677664
No 109
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=49.53 E-value=18 Score=26.10 Aligned_cols=25 Identities=20% Similarity=0.517 Sum_probs=16.0
Q ss_pred EeCCceeeeeecCCCCcCCCCCCceEE
Q 035300 6 IFDLREKVIRRNGADAACPYCGGPVLA 32 (68)
Q Consensus 6 vcde~~kv~~~~~A~G~Cp~CGG~v~a 32 (68)
+|---.++.- +--+.||.|||.+.-
T Consensus 141 rC~GC~~~f~--~~~~~Cp~CG~~~~~ 165 (177)
T COG1439 141 RCHGCKRIFP--EPKDFCPICGSPLKR 165 (177)
T ss_pred EEecCceecC--CCCCcCCCCCCceEE
Confidence 3333344444 556899999999654
No 110
>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=49.23 E-value=14 Score=29.36 Aligned_cols=26 Identities=31% Similarity=0.751 Sum_probs=16.1
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR 62 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (68)
.||+|++++. ++|..+...|..||..
T Consensus 224 ~C~~C~~~l~---------------~h~~~~~l~Ch~Cg~~ 249 (505)
T TIGR00595 224 CCPNCDVSLT---------------YHKKEGKLRCHYCGYQ 249 (505)
T ss_pred CCCCCCCceE---------------EecCCCeEEcCCCcCc
Confidence 3777777654 3455666666666654
No 111
>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=48.84 E-value=9.1 Score=19.54 Aligned_cols=13 Identities=31% Similarity=0.710 Sum_probs=9.2
Q ss_pred CCCCcCCCCCCce
Q 035300 18 GADAACPYCGGPV 30 (68)
Q Consensus 18 ~A~G~Cp~CGG~v 30 (68)
.+.-.||+||-.-
T Consensus 12 ~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 12 ESAKFCPHCGYDF 24 (26)
T ss_pred hhcCcCCCCCCCC
Confidence 3566899999643
No 112
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=48.63 E-value=7.7 Score=24.14 Aligned_cols=36 Identities=22% Similarity=0.792 Sum_probs=28.8
Q ss_pred CCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccc
Q 035300 18 GADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSR 61 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r 61 (68)
+.+-.||+|+- +.++||+.==+.-+--+|+|--|.|
T Consensus 3 ~~~~~CPRC~S--------~nTKFcYyNNy~~~QPR~~Ck~C~r 38 (63)
T PF02701_consen 3 EQPLPCPRCDS--------TNTKFCYYNNYNLSQPRYFCKSCRR 38 (63)
T ss_pred ccCCCCCCcCC--------CCCEEEeecCCCCCCcchhhHHHHH
Confidence 44567999984 4689999888888888999988865
No 113
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=48.51 E-value=16 Score=25.14 Aligned_cols=25 Identities=24% Similarity=0.680 Sum_probs=19.1
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR 62 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (68)
.|+.||++. +| .+|+...|+.||.+
T Consensus 151 ~~~~~g~~~-------------~~---~~~~~~~c~~~~~~ 175 (189)
T PRK09521 151 MCSRCRTPL-------------VK---KGENELKCPNCGNI 175 (189)
T ss_pred EccccCCce-------------EE---CCCCEEECCCCCCE
Confidence 588888766 56 45677999999965
No 114
>PHA00626 hypothetical protein
Probab=48.28 E-value=21 Score=22.01 Aligned_cols=32 Identities=22% Similarity=0.508 Sum_probs=22.0
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccccee
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRL 63 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (68)
.||.||-.-.+ . -.++.+...+|.|..||-..
T Consensus 2 ~CP~CGS~~Iv---r-------cg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIA---K-------EKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceee---e-------eceecccCcceEcCCCCCee
Confidence 59999974221 1 24566777899999998653
No 115
>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=47.50 E-value=3.3 Score=26.23 Aligned_cols=38 Identities=26% Similarity=0.595 Sum_probs=30.8
Q ss_pred CCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300 19 ADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV 64 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (68)
.+..||+||-++..-|. ||+..=..-|=.|..|++++-
T Consensus 32 ~rS~C~~C~~~L~~~~l--------IPi~S~l~lrGrCr~C~~~I~ 69 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWWDL--------IPILSYLLLRGRCRYCGAPIP 69 (92)
T ss_pred CCCcCcCCCCcCccccc--------chHHHHHHhCCCCcccCCCCC
Confidence 46889999999998886 788777777778888887764
No 116
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=47.07 E-value=16 Score=24.43 Aligned_cols=50 Identities=20% Similarity=0.372 Sum_probs=30.6
Q ss_pred eeeeeecCCCCcCCCCCCceEEEE------ecceeeeEEeeeeeeecceEEeecccce
Q 035300 11 EKVIRRNGADAACPYCGGPVLAID------FDAHLRFCFLPISHKVKKKFYCTICSRR 62 (68)
Q Consensus 11 ~kv~~~~~A~G~Cp~CGG~v~a~D------ves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (68)
+=++-..|+.+.|+.||--....| =+...-+=|+|---. .-+.|+.||..
T Consensus 61 ~L~i~~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~CP~Cgs~ 116 (135)
T PRK03824 61 EIIFEEEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVH--AFLKCPKCGSR 116 (135)
T ss_pred EEEEEecceEEECCCCCCEEecccccccccccccccccccccccc--cCcCCcCCCCC
Confidence 445668889999999995554432 223344445664221 22569999865
No 117
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=47.04 E-value=12 Score=30.19 Aligned_cols=34 Identities=26% Similarity=0.694 Sum_probs=22.0
Q ss_pred ecCCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeee
Q 035300 16 RNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVP 65 (68)
Q Consensus 16 ~~~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~ 65 (68)
.....-.||+|||-. +|. =+.-|-|..||++...
T Consensus 346 ~~~~~p~Cp~Cg~~m-----~S~-----------G~~g~rC~kCg~~~~~ 379 (421)
T COG1571 346 YERVNPVCPRCGGRM-----KSA-----------GRNGFRCKKCGTRARE 379 (421)
T ss_pred eEEcCCCCCccCCch-----hhc-----------CCCCcccccccccCCc
Confidence 344456899999963 221 1225889999988653
No 118
>PRK05320 rhodanese superfamily protein; Provisional
Probab=47.00 E-value=13 Score=27.09 Aligned_cols=28 Identities=25% Similarity=0.362 Sum_probs=19.7
Q ss_pred EEEeCCceeeeee--cCCCCcCCCCCCceE
Q 035300 4 LSIFDLREKVIRR--NGADAACPYCGGPVL 31 (68)
Q Consensus 4 ~~vcde~~kv~~~--~~A~G~Cp~CGG~v~ 31 (68)
+||+|++--|--. ..+.+.|..||-+++
T Consensus 226 ~fVFD~R~~~~~~~~~~~~~~c~~c~~~~~ 255 (257)
T PRK05320 226 CFVFDYRTALDPQLAPLVDVTCFACRAVVT 255 (257)
T ss_pred eeeecCeeecCCCCccCccceecCCCCcCC
Confidence 7999998754332 234577999998875
No 119
>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=46.98 E-value=9.2 Score=21.46 Aligned_cols=37 Identities=35% Similarity=0.770 Sum_probs=21.1
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeee-cceEEeeccccee
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKV-KKKFYCTICSRRL 63 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~-krk~~Ct~C~r~L 63 (68)
.||+||-.....++-.. +--.++. .+.+.|++|..++
T Consensus 4 ~CP~C~~~~~~~~L~~H-----~~~~H~~~~~~v~CPiC~~~~ 41 (54)
T PF05605_consen 4 TCPYCGKGFSESSLVEH-----CEDEHRSESKNVVCPICSSRV 41 (54)
T ss_pred CCCCCCCccCHHHHHHH-----HHhHCcCCCCCccCCCchhhh
Confidence 69999985443332221 2222332 3468999998754
No 120
>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=46.48 E-value=22 Score=18.47 Aligned_cols=23 Identities=22% Similarity=0.403 Sum_probs=10.1
Q ss_pred EEeCCceeeeeecCCCCcCCCCCCc
Q 035300 5 SIFDLREKVIRRNGADAACPYCGGP 29 (68)
Q Consensus 5 ~vcde~~kv~~~~~A~G~Cp~CGG~ 29 (68)
.-|+.-+++ .-|....||+||+.
T Consensus 12 ~rC~~Cg~~--~~pPr~~Cp~C~s~ 34 (37)
T PF12172_consen 12 QRCRDCGRV--QFPPRPVCPHCGSD 34 (37)
T ss_dssp EE-TTT--E--EES--SEETTTT--
T ss_pred EEcCCCCCE--ecCCCcCCCCcCcc
Confidence 344444444 34566889999753
No 121
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=45.86 E-value=7.9 Score=27.70 Aligned_cols=14 Identities=36% Similarity=0.831 Sum_probs=12.4
Q ss_pred CcCCCCCCceEEEE
Q 035300 21 AACPYCGGPVLAID 34 (68)
Q Consensus 21 G~Cp~CGG~v~a~D 34 (68)
..||.||+.++-+|
T Consensus 133 F~Cp~Cg~~L~~~d 146 (176)
T COG1675 133 FTCPKCGEDLEEYD 146 (176)
T ss_pred CCCCCCCchhhhcc
Confidence 78999999998776
No 122
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.74 E-value=9.7 Score=25.13 Aligned_cols=10 Identities=40% Similarity=1.102 Sum_probs=7.8
Q ss_pred CcCCCCCCce
Q 035300 21 AACPYCGGPV 30 (68)
Q Consensus 21 G~Cp~CGG~v 30 (68)
..||.||+.-
T Consensus 93 ~~CP~Cgs~~ 102 (124)
T PRK00762 93 IECPVCGNKR 102 (124)
T ss_pred CcCcCCCCCC
Confidence 5799999753
No 123
>PRK04351 hypothetical protein; Provisional
Probab=45.50 E-value=23 Score=24.34 Aligned_cols=17 Identities=24% Similarity=0.542 Sum_probs=14.3
Q ss_pred ecceEEeecccceeeec
Q 035300 50 VKKKFYCTICSRRLVPA 66 (68)
Q Consensus 50 ~krk~~Ct~C~r~L~~~ 66 (68)
+.++|.|-.|+.+|+..
T Consensus 129 n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 129 NTKRYRCGKCRGKLKLI 145 (149)
T ss_pred CCCcEEeCCCCcEeeec
Confidence 46899999999999764
No 124
>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=45.08 E-value=13 Score=28.98 Aligned_cols=31 Identities=23% Similarity=0.425 Sum_probs=18.0
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeee
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVP 65 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~ 65 (68)
+||.||--++..+.+.. .+-.|++||..|..
T Consensus 15 ~C~~Cd~l~~~~~l~~g-------------~~a~CpRCg~~L~~ 45 (403)
T TIGR00155 15 LCSQCDMLVALPRIESG-------------QKAACPRCGTTLTV 45 (403)
T ss_pred eCCCCCCcccccCCCCC-------------CeeECCCCCCCCcC
Confidence 47777766555444332 24557777777643
No 125
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=45.05 E-value=7.1 Score=21.45 Aligned_cols=10 Identities=30% Similarity=0.727 Sum_probs=4.5
Q ss_pred EEeeccccee
Q 035300 54 FYCTICSRRL 63 (68)
Q Consensus 54 ~~Ct~C~r~L 63 (68)
-.|+||||..
T Consensus 2 ~~CSFCgr~~ 11 (41)
T PF06689_consen 2 KRCSFCGRPE 11 (41)
T ss_dssp -B-TTT--BT
T ss_pred CCccCCCCCH
Confidence 4699999864
No 126
>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=44.85 E-value=22 Score=18.95 Aligned_cols=15 Identities=27% Similarity=0.645 Sum_probs=9.9
Q ss_pred cCCCCCCceEEEEec
Q 035300 22 ACPYCGGPVLAIDFD 36 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dve 36 (68)
-||.||..+..-+-+
T Consensus 3 FCp~C~nlL~p~~~~ 17 (35)
T PF02150_consen 3 FCPECGNLLYPKEDK 17 (35)
T ss_dssp BETTTTSBEEEEEET
T ss_pred eCCCCCccceEcCCC
Confidence 388888887654433
No 127
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=44.83 E-value=20 Score=28.77 Aligned_cols=30 Identities=23% Similarity=0.460 Sum_probs=20.2
Q ss_pred EEEEeCCceeee-eecCCCCcCCCCCCceEE
Q 035300 3 VLSIFDLREKVI-RRNGADAACPYCGGPVLA 32 (68)
Q Consensus 3 ~~~vcde~~kv~-~~~~A~G~Cp~CGG~v~a 32 (68)
..+.|.+.+++. +-.+...-||+|||.+..
T Consensus 239 ~~~~c~~cg~~~~~~~~~~~~c~~Cg~~~~~ 269 (380)
T COG1867 239 YIYHCSRCGEIVGSFREVDEKCPHCGGKVHL 269 (380)
T ss_pred cEEEcccccceecccccccccCCccccccee
Confidence 456677775444 446777889999975443
No 128
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=44.27 E-value=13 Score=16.97 Aligned_cols=12 Identities=25% Similarity=0.955 Sum_probs=8.5
Q ss_pred EEeecccceeee
Q 035300 54 FYCTICSRRLVP 65 (68)
Q Consensus 54 ~~Ct~C~r~L~~ 65 (68)
|.|..|++....
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 678888877643
No 129
>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=43.01 E-value=4.4 Score=22.19 Aligned_cols=26 Identities=15% Similarity=0.088 Sum_probs=10.7
Q ss_pred eeecCCCCcCCC--CCCceEEEEeccee
Q 035300 14 IRRNGADAACPY--CGGPVLAIDFDAHL 39 (68)
Q Consensus 14 ~~~~~A~G~Cp~--CGG~v~a~Dves~~ 39 (68)
+...+..--||+ |++.+...+-....
T Consensus 12 ~~~~~~~~~Cp~~~C~~~~~~~~~~~~~ 39 (64)
T PF01485_consen 12 LESDPNIRWCPNPDCEYIIEKDDGCNSP 39 (64)
T ss_dssp --S---CC--TTSST---ECS-SSTTS-
T ss_pred HHCCCCccCCCCCCCcccEEecCCCCCC
Confidence 344445558988 99999988887664
No 130
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=42.72 E-value=11 Score=21.24 Aligned_cols=13 Identities=46% Similarity=1.247 Sum_probs=6.1
Q ss_pred CCCCcCCCCCCce
Q 035300 18 GADAACPYCGGPV 30 (68)
Q Consensus 18 ~A~G~Cp~CGG~v 30 (68)
.+.|.||=||.++
T Consensus 18 ~~~~~CPlC~r~l 30 (54)
T PF04423_consen 18 EAKGCCPLCGRPL 30 (54)
T ss_dssp T-SEE-TTT--EE
T ss_pred cCCCcCCCCCCCC
Confidence 4556888888765
No 131
>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=42.68 E-value=7.8 Score=21.09 Aligned_cols=18 Identities=28% Similarity=0.432 Sum_probs=10.1
Q ss_pred cCCCCcCCCCCCceEEEE
Q 035300 17 NGADAACPYCGGPVLAID 34 (68)
Q Consensus 17 ~~A~G~Cp~CGG~v~a~D 34 (68)
.-.+-+|+.||-.++.+|
T Consensus 18 ~~~~isC~~CGPr~~i~~ 35 (35)
T PF07503_consen 18 HYQFISCTNCGPRYSIID 35 (35)
T ss_dssp T-TT--BTTCC-SCCCES
T ss_pred cCcCccCCCCCCCEEEeC
Confidence 445668999998776554
No 132
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=42.32 E-value=23 Score=22.99 Aligned_cols=19 Identities=16% Similarity=0.335 Sum_probs=14.4
Q ss_pred ceeeeeecCCCCcCCCCCC
Q 035300 10 REKVIRRNGADAACPYCGG 28 (68)
Q Consensus 10 ~~kv~~~~~A~G~Cp~CGG 28 (68)
-+=++-..|+.+.|+.||-
T Consensus 60 A~L~i~~~p~~~~C~~Cg~ 78 (114)
T PRK03681 60 CKLHLEEQEAECWCETCQQ 78 (114)
T ss_pred CEEEEEeeCcEEEcccCCC
Confidence 3446677888899999994
No 133
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=42.19 E-value=23 Score=26.30 Aligned_cols=31 Identities=26% Similarity=0.677 Sum_probs=21.3
Q ss_pred CCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300 20 DAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV 64 (68)
Q Consensus 20 ~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (68)
...||.||+.-.+.|.++- -.+|+.||-.|.
T Consensus 11 ~~~Cp~Cg~~~iv~d~~~G--------------e~vC~~CG~Vl~ 41 (310)
T PRK00423 11 KLVCPECGSDKLIYDYERG--------------EIVCADCGLVIE 41 (310)
T ss_pred CCcCcCCCCCCeeEECCCC--------------eEeecccCCccc
Confidence 3579999987777775443 456777776553
No 134
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.18 E-value=16 Score=23.91 Aligned_cols=18 Identities=17% Similarity=0.276 Sum_probs=12.1
Q ss_pred ceeeeeecCCCCcCCCCC
Q 035300 10 REKVIRRNGADAACPYCG 27 (68)
Q Consensus 10 ~~kv~~~~~A~G~Cp~CG 27 (68)
.+=.+-..|+-+.|..||
T Consensus 61 a~L~Ie~vp~~~~C~~Cg 78 (117)
T PRK00564 61 AILDIVDEKVELECKDCS 78 (117)
T ss_pred CEEEEEecCCEEEhhhCC
Confidence 344556677777777777
No 135
>PF06054 CoiA: Competence protein CoiA-like family; InterPro: IPR010330 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein.
Probab=42.11 E-value=20 Score=27.60 Aligned_cols=16 Identities=38% Similarity=0.798 Sum_probs=13.1
Q ss_pred CCCCcCCCCCCceEEE
Q 035300 18 GADAACPYCGGPVLAI 33 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~a~ 33 (68)
.-.-.||.||++|..-
T Consensus 28 ~~~~~CP~C~~~v~lk 43 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILK 43 (375)
T ss_pred CCcEECCCCCCeeEEE
Confidence 5567899999999873
No 136
>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=41.47 E-value=15 Score=24.26 Aligned_cols=11 Identities=18% Similarity=0.803 Sum_probs=7.9
Q ss_pred ceEEeecccce
Q 035300 52 KKFYCTICSRR 62 (68)
Q Consensus 52 rk~~Ct~C~r~ 62 (68)
..|.|..|+..
T Consensus 50 ~~~~C~~C~~~ 60 (166)
T cd04476 50 GTYRCEKCNKS 60 (166)
T ss_pred CcEECCCCCCc
Confidence 56778888764
No 137
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=41.27 E-value=11 Score=23.09 Aligned_cols=12 Identities=42% Similarity=1.099 Sum_probs=9.6
Q ss_pred CcCCCCCCceEE
Q 035300 21 AACPYCGGPVLA 32 (68)
Q Consensus 21 G~Cp~CGG~v~a 32 (68)
-.||.|||....
T Consensus 18 e~Cp~CG~~t~~ 29 (59)
T COG2260 18 EKCPVCGGDTKV 29 (59)
T ss_pred ccCCCCCCcccc
Confidence 579999997654
No 138
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=40.94 E-value=28 Score=25.80 Aligned_cols=41 Identities=29% Similarity=0.599 Sum_probs=29.5
Q ss_pred CCCCcCCCCCCceEEEEecceeeeEEeeeeeee-cceEEeeccccee
Q 035300 18 GADAACPYCGGPVLAIDFDAHLRFCFLPISHKV-KKKFYCTICSRRL 63 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~-krk~~Ct~C~r~L 63 (68)
.-...||-||| ++...++.==+|.+-+. -.-.+|..||-|.
T Consensus 12 ~~~~~CPvCg~-----~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~ 53 (201)
T COG1779 12 ETRIDCPVCGG-----TLKAHMYLYDIPYFGEVLISTGVCERCGYRS 53 (201)
T ss_pred eeeecCCcccc-----eeeEEEeeecCCccceEEEEEEEccccCCcc
Confidence 34578999999 55666666668876654 3457899999764
No 139
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=40.62 E-value=14 Score=26.13 Aligned_cols=26 Identities=31% Similarity=0.885 Sum_probs=10.8
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccc
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~ 60 (68)
.|++|||.-.+..-+ ....|.|++|.
T Consensus 136 ~C~~C~~~fv~~~~~-------------~~~~~~Cp~C~ 161 (175)
T PF05280_consen 136 PCRRCGGHFVTHAHD-------------PRHSFVCPFCQ 161 (175)
T ss_dssp E-TTT--EEEEESS---------------SS----TT--
T ss_pred CCCCCCCCeECcCCC-------------CCcCcCCCCCC
Confidence 599999998876432 34566777775
No 140
>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=40.01 E-value=29 Score=20.04 Aligned_cols=13 Identities=38% Similarity=0.836 Sum_probs=9.0
Q ss_pred CCCCcCCCCCCce
Q 035300 18 GADAACPYCGGPV 30 (68)
Q Consensus 18 ~A~G~Cp~CGG~v 30 (68)
|+.-.||-||.+-
T Consensus 32 p~~w~CP~C~a~K 44 (50)
T cd00730 32 PDDWVCPVCGAGK 44 (50)
T ss_pred CCCCCCCCCCCcH
Confidence 4444899998753
No 141
>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=39.79 E-value=21 Score=32.21 Aligned_cols=20 Identities=25% Similarity=0.396 Sum_probs=16.8
Q ss_pred eeecCCCCcCCCCCCceEEE
Q 035300 14 IRRNGADAACPYCGGPVLAI 33 (68)
Q Consensus 14 ~~~~~A~G~Cp~CGG~v~a~ 33 (68)
-+|-|-.|.||.|||.+.-+
T Consensus 1022 YRR~PL~G~C~kCGg~lilT 1041 (1095)
T TIGR00354 1022 YRRIPLVGKCLKCGNNLTLT 1041 (1095)
T ss_pred cccCCCCCcccccCCeEEEE
Confidence 46778999999999988754
No 142
>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=39.75 E-value=5.6 Score=25.71 Aligned_cols=21 Identities=33% Similarity=0.411 Sum_probs=10.3
Q ss_pred eeeeeecCCCCcCCCCCCceE
Q 035300 11 EKVIRRNGADAACPYCGGPVL 31 (68)
Q Consensus 11 ~kv~~~~~A~G~Cp~CGG~v~ 31 (68)
+=.+-..|+-+.|..||.-..
T Consensus 61 ~L~Ie~~p~~~~C~~Cg~~~~ 81 (113)
T PF01155_consen 61 ELEIEEVPARARCRDCGHEFE 81 (113)
T ss_dssp EEEEEEE--EEEETTTS-EEE
T ss_pred EEEEEecCCcEECCCCCCEEe
Confidence 344555666666666665443
No 143
>PF13395 HNH_4: HNH endonuclease
Probab=39.70 E-value=10 Score=21.47 Aligned_cols=13 Identities=46% Similarity=1.362 Sum_probs=11.0
Q ss_pred CCCCCCceEEEEe
Q 035300 23 CPYCGGPVLAIDF 35 (68)
Q Consensus 23 Cp~CGG~v~a~Dv 35 (68)
|+|||-.+...++
T Consensus 1 C~Y~g~~i~~~~l 13 (54)
T PF13395_consen 1 CPYCGKPISIENL 13 (54)
T ss_pred CCCCCCCCChhhc
Confidence 8999999887764
No 144
>PLN03086 PRLI-interacting factor K; Provisional
Probab=39.54 E-value=5.4 Score=33.11 Aligned_cols=45 Identities=16% Similarity=0.448 Sum_probs=29.1
Q ss_pred CCCcCCCCCCceEEEEecceeeeEEeeeee------------------eecceEEeeccccee
Q 035300 19 ADAACPYCGGPVLAIDFDAHLRFCFLPISH------------------KVKKKFYCTICSRRL 63 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~------------------k~krk~~Ct~C~r~L 63 (68)
..-.|++||......+++.+.+.|--|+-+ --+|.+.|.+|+...
T Consensus 452 ~H~~C~~Cgk~f~~s~LekH~~~~Hkpv~CpCg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v 514 (567)
T PLN03086 452 NHVHCEKCGQAFQQGEMEKHMKVFHEPLQCPCGVVLEKEQMVQHQASTCPLRLITCRFCGDMV 514 (567)
T ss_pred cCccCCCCCCccchHHHHHHHHhcCCCccCCCCCCcchhHHHhhhhccCCCCceeCCCCCCcc
Confidence 345788888888777777777764333311 125777888887654
No 145
>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=39.40 E-value=33 Score=23.65 Aligned_cols=37 Identities=24% Similarity=0.506 Sum_probs=20.2
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeee-cceEEeeccccee
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKV-KKKFYCTICSRRL 63 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~-krk~~Ct~C~r~L 63 (68)
.||.||....-. +-.=-+|.+.+. =-.|.|..||-+-
T Consensus 3 ~Cp~C~~~~~~~-----~~~~~IP~F~evii~sf~C~~CGyk~ 40 (161)
T PF03367_consen 3 LCPNCGENGTTR-----ILLTDIPYFKEVIIMSFECEHCGYKN 40 (161)
T ss_dssp E-TTTSSCCEEE-----EEEEEETTTEEEEEEEEE-TTT--EE
T ss_pred cCCCCCCCcEEE-----EEEEcCCCCceEEEEEeECCCCCCEe
Confidence 599999875321 111136776664 3578899998664
No 146
>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=39.39 E-value=14 Score=22.28 Aligned_cols=11 Identities=45% Similarity=1.277 Sum_probs=8.6
Q ss_pred CcCCCCCCceE
Q 035300 21 AACPYCGGPVL 31 (68)
Q Consensus 21 G~Cp~CGG~v~ 31 (68)
.-||+||.++-
T Consensus 4 kHC~~CG~~Ip 14 (59)
T PF09889_consen 4 KHCPVCGKPIP 14 (59)
T ss_pred CcCCcCCCcCC
Confidence 56999997764
No 147
>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=39.30 E-value=8.4 Score=23.14 Aligned_cols=14 Identities=43% Similarity=0.790 Sum_probs=7.2
Q ss_pred cCCCCCCceEEEEe
Q 035300 22 ACPYCGGPVLAIDF 35 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dv 35 (68)
.||.||..+...+-
T Consensus 4 ~CP~C~k~~~~~~~ 17 (57)
T PF03884_consen 4 KCPICGKPVEWSPE 17 (57)
T ss_dssp E-TTT--EEE-SSS
T ss_pred cCCCCCCeecccCC
Confidence 59999998877543
No 148
>PRK04023 DNA polymerase II large subunit; Validated
Probab=38.92 E-value=22 Score=32.15 Aligned_cols=20 Identities=35% Similarity=0.820 Sum_probs=16.9
Q ss_pred eeecCCCCcCCCCCCceEEE
Q 035300 14 IRRNGADAACPYCGGPVLAI 33 (68)
Q Consensus 14 ~~~~~A~G~Cp~CGG~v~a~ 33 (68)
-+|-|-.|.||.|||.+.-+
T Consensus 1047 YRR~PL~G~C~kCGg~lilT 1066 (1121)
T PRK04023 1047 YRRPPLSGKCPKCGGNLILT 1066 (1121)
T ss_pred cccCCCCCcCccCCCeEEEE
Confidence 46778999999999998755
No 149
>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=38.02 E-value=22 Score=19.17 Aligned_cols=11 Identities=36% Similarity=0.890 Sum_probs=5.8
Q ss_pred cCCCCCCceEE
Q 035300 22 ACPYCGGPVLA 32 (68)
Q Consensus 22 ~Cp~CGG~v~a 32 (68)
.||.||..-.+
T Consensus 2 ~Cp~Cg~~~a~ 12 (39)
T PF01096_consen 2 KCPKCGHNEAV 12 (39)
T ss_dssp --SSS-SSEEE
T ss_pred CCcCCCCCeEE
Confidence 49999987543
No 150
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=37.37 E-value=28 Score=25.47 Aligned_cols=25 Identities=24% Similarity=0.680 Sum_probs=18.3
Q ss_pred CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300 21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR 62 (68)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (68)
..|++||+.+.- .++..+|+.||+.
T Consensus 150 A~CsrC~~~L~~-----------------~~~~l~Cp~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK-----------------KGNMLKCPNCGNT 174 (188)
T ss_pred EEccCCCcceEE-----------------cCcEEECCCCCCE
Confidence 469999987642 5667788888864
No 151
>PRK05978 hypothetical protein; Provisional
Probab=37.35 E-value=17 Score=25.31 Aligned_cols=35 Identities=26% Similarity=0.471 Sum_probs=21.9
Q ss_pred CCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeeec
Q 035300 18 GADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPA 66 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~ 66 (68)
...|.||+||-+=.=- .=.|=+-.|+.||-.+...
T Consensus 31 Gl~grCP~CG~G~LF~--------------g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 31 GFRGRCPACGEGKLFR--------------AFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred HHcCcCCCCCCCcccc--------------cccccCCCccccCCccccC
Confidence 4568999999663210 1123445688898877644
No 152
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.27 E-value=14 Score=25.64 Aligned_cols=12 Identities=42% Similarity=1.054 Sum_probs=9.5
Q ss_pred CCCCcCCCCCCc
Q 035300 18 GADAACPYCGGP 29 (68)
Q Consensus 18 ~A~G~Cp~CGG~ 29 (68)
...|.||+||-+
T Consensus 19 Gl~grCP~CGeG 30 (126)
T COG5349 19 GLRGRCPRCGEG 30 (126)
T ss_pred HhcCCCCCCCCc
Confidence 456899999954
No 153
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=37.09 E-value=24 Score=32.48 Aligned_cols=20 Identities=30% Similarity=0.665 Sum_probs=16.8
Q ss_pred eeecCCCCcCCCCCCceEEE
Q 035300 14 IRRNGADAACPYCGGPVLAI 33 (68)
Q Consensus 14 ~~~~~A~G~Cp~CGG~v~a~ 33 (68)
-+|-|-.|.||.|||.+.-+
T Consensus 1263 yRR~PL~G~C~kCGg~iilT 1282 (1337)
T PRK14714 1263 YRRMPLAGKCRKCGGRIILT 1282 (1337)
T ss_pred cccCCCCCcccccCCeEEEE
Confidence 46779999999999998754
No 154
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=36.58 E-value=9.3 Score=27.56 Aligned_cols=30 Identities=27% Similarity=0.619 Sum_probs=19.8
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeeec
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPA 66 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~ 66 (68)
.|-+|||.|+- ..+|-...|+.|..+-.++
T Consensus 91 ~CARCGGrv~l---------------rsNKv~wvcnlc~k~q~il 120 (169)
T KOG3799|consen 91 FCARCGGRVSL---------------RSNKVMWVCNLCRKQQEIL 120 (169)
T ss_pred HHHhcCCeeee---------------ccCceEEeccCCcHHHHHH
Confidence 47788998763 2366677788887665443
No 155
>KOG3456 consensus NADH:ubiquinone oxidoreductase, NDUFS6/13 kDa subunit [Energy production and conversion]
Probab=36.40 E-value=16 Score=25.24 Aligned_cols=12 Identities=33% Similarity=0.800 Sum_probs=10.2
Q ss_pred cCCCCcCCCCCC
Q 035300 17 NGADAACPYCGG 28 (68)
Q Consensus 17 ~~A~G~Cp~CGG 28 (68)
+|.+++|.|||=
T Consensus 101 k~~~~~CgYCGl 112 (120)
T KOG3456|consen 101 KPGPHICGYCGL 112 (120)
T ss_pred CCCCcccccchh
Confidence 677899999994
No 156
>PRK08173 DNA topoisomerase III; Validated
Probab=36.36 E-value=34 Score=29.42 Aligned_cols=14 Identities=50% Similarity=1.056 Sum_probs=11.8
Q ss_pred cCCCCcCCCCCCce
Q 035300 17 NGADAACPYCGGPV 30 (68)
Q Consensus 17 ~~A~G~Cp~CGG~v 30 (68)
+...|.||.||+.+
T Consensus 723 ~~~~g~CPkCg~~v 736 (862)
T PRK08173 723 QEPVGACPKCGGRV 736 (862)
T ss_pred cccccCCCCCCCee
Confidence 56789999999964
No 157
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=36.27 E-value=17 Score=20.19 Aligned_cols=30 Identities=37% Similarity=1.043 Sum_probs=17.4
Q ss_pred CCCCCCceEEEEecceeeeEEeeeeeeecce--EEe-eccccee
Q 035300 23 CPYCGGPVLAIDFDAHLRFCFLPISHKVKKK--FYC-TICSRRL 63 (68)
Q Consensus 23 Cp~CGG~v~a~Dves~~rfCflP~~~k~krk--~~C-t~C~r~L 63 (68)
|.+|||.+.- =|+-.|+.++ |+| ..|-+++
T Consensus 1 Cd~CG~~I~~-----------eP~~~k~~~~~y~fCC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEITG-----------EPIVVKIGNKVYYFCCPTCLSQF 33 (37)
T ss_pred CCccCCcccC-----------CEEEEEECCeEEEEECHHHHHHH
Confidence 7889998753 2555555444 344 5665544
No 158
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=36.10 E-value=14 Score=22.10 Aligned_cols=16 Identities=31% Similarity=0.729 Sum_probs=9.4
Q ss_pred cCCCCcCCCCCCceEE
Q 035300 17 NGADAACPYCGGPVLA 32 (68)
Q Consensus 17 ~~A~G~Cp~CGG~v~a 32 (68)
.+..|.||+|.-+++.
T Consensus 52 ~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 52 IPIFGECPYCSSPISW 67 (70)
T ss_dssp T--EEE-TTT-SEEEG
T ss_pred cccccCCcCCCCeeeE
Confidence 4667999999988763
No 159
>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=35.94 E-value=26 Score=28.15 Aligned_cols=30 Identities=20% Similarity=0.552 Sum_probs=17.4
Q ss_pred ecceeeeE---EeeeeeeecceEEeecccceeee
Q 035300 35 FDAHLRFC---FLPISHKVKKKFYCTICSRRLVP 65 (68)
Q Consensus 35 ves~~rfC---flP~~~k~krk~~Ct~C~r~L~~ 65 (68)
-....-+| |.||| |-+....|++||+++..
T Consensus 360 ~~npF~ICa~s~tPIY-~G~~~v~CP~cgA~y~~ 392 (422)
T PF06957_consen 360 ERNPFDICAASYTPIY-RGSPSVKCPYCGAKYHP 392 (422)
T ss_dssp TTS-EEEBTTT--EEE-TTS-EEE-TTT--EEEG
T ss_pred CCCCceeeeccccccc-CCCCCeeCCCCCCccCh
Confidence 34566777 67998 66677999999998864
No 160
>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=35.70 E-value=17 Score=28.57 Aligned_cols=11 Identities=55% Similarity=1.295 Sum_probs=9.0
Q ss_pred CCcCCCCCCceE
Q 035300 20 DAACPYCGGPVL 31 (68)
Q Consensus 20 ~G~Cp~CGG~v~ 31 (68)
.+.|| ||+.+.
T Consensus 259 ~~~Cp-CG~~i~ 269 (374)
T TIGR00375 259 CANCP-CGGRIK 269 (374)
T ss_pred CCCCC-CCCcce
Confidence 39999 999953
No 161
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=35.68 E-value=21 Score=16.55 Aligned_cols=12 Identities=42% Similarity=1.292 Sum_probs=9.5
Q ss_pred EEeecccceeee
Q 035300 54 FYCTICSRRLVP 65 (68)
Q Consensus 54 ~~Ct~C~r~L~~ 65 (68)
|.|..|.+...+
T Consensus 1 ~~C~~C~~~f~s 12 (25)
T PF12874_consen 1 FYCDICNKSFSS 12 (25)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCCcCC
Confidence 689999887654
No 162
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=35.65 E-value=26 Score=32.83 Aligned_cols=20 Identities=30% Similarity=0.700 Sum_probs=16.9
Q ss_pred eeecCCCCcCCCCCCceEEE
Q 035300 14 IRRNGADAACPYCGGPVLAI 33 (68)
Q Consensus 14 ~~~~~A~G~Cp~CGG~v~a~ 33 (68)
-+|-|-.|.||.|||.+.-+
T Consensus 1551 yRR~PL~G~C~kCGg~~ilT 1570 (1627)
T PRK14715 1551 YRRVPLKGKCPKCGSKLILT 1570 (1627)
T ss_pred cccCCCCCcCcccCCeEEEE
Confidence 46779999999999998754
No 163
>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=35.29 E-value=20 Score=22.83 Aligned_cols=14 Identities=36% Similarity=0.797 Sum_probs=7.5
Q ss_pred cCCCCcCCCCCCce
Q 035300 17 NGADAACPYCGGPV 30 (68)
Q Consensus 17 ~~A~G~Cp~CGG~v 30 (68)
..+...|.||||+.
T Consensus 85 l~~~d~CiyCGgkf 98 (99)
T PF12660_consen 85 LESFDVCIYCGGKF 98 (99)
T ss_dssp HHTSSB-TTT--B-
T ss_pred HhCCCEEeCCCCCc
Confidence 34567999999975
No 164
>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=35.24 E-value=15 Score=19.85 Aligned_cols=15 Identities=53% Similarity=1.145 Sum_probs=10.7
Q ss_pred cCCCCCCceEEEEec
Q 035300 22 ACPYCGGPVLAIDFD 36 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dve 36 (68)
.||+||-.|.|.-+.
T Consensus 6 ~C~nC~R~v~a~RfA 20 (33)
T PF08209_consen 6 ECPNCGRPVAASRFA 20 (33)
T ss_dssp E-TTTSSEEEGGGHH
T ss_pred ECCCCcCCcchhhhH
Confidence 699999998876443
No 165
>smart00019 SF_P Pulmonary surfactant proteins. Pulmonary surfactant associated proteins promote alveolar stability by lowering the surface tension at the air-liquid interface in the peripheral air spaces. SP-C, a component of surfactant, is a highly hydrophobic peptide of 35 amino acid residues which is processed from a larger precursor protein. SP-C is post-translationally modified by the covalent attachment of two palmitoyl groups on two adjacent cysteines
Probab=35.05 E-value=15 Score=26.94 Aligned_cols=21 Identities=24% Similarity=0.529 Sum_probs=18.6
Q ss_pred EEeCCceeeeeecCCCCcCCC
Q 035300 5 SIFDLREKVIRRNGADAACPY 25 (68)
Q Consensus 5 ~vcde~~kv~~~~~A~G~Cp~ 25 (68)
.++|-++-.++-+||||.|=|
T Consensus 102 VvyDYqrLLiaykPaPGtcCY 122 (191)
T smart00019 102 VVYDYQRLLIAYKPAPGTCCY 122 (191)
T ss_pred EEEEhhhhheeccCCCCceEE
Confidence 578989999999999999855
No 166
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=35.02 E-value=22 Score=21.90 Aligned_cols=9 Identities=33% Similarity=0.855 Sum_probs=7.3
Q ss_pred CcCCCCCCc
Q 035300 21 AACPYCGGP 29 (68)
Q Consensus 21 G~Cp~CGG~ 29 (68)
..||.||+.
T Consensus 18 ~~Cp~Cgs~ 26 (64)
T PRK06393 18 KTCPVHGDE 26 (64)
T ss_pred CcCCCCCCC
Confidence 389999974
No 167
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=34.66 E-value=27 Score=27.46 Aligned_cols=31 Identities=26% Similarity=0.470 Sum_probs=17.1
Q ss_pred CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300 21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV 64 (68)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (68)
-+||.||--++..+++..- +-.|++||..|.
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~-------------~a~CpRCg~~L~ 41 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQ-------------KAACPRCGTTLT 41 (419)
T ss_pred ccCCCCCceeecCCCCCCC-------------eeECCCCCCCCc
Confidence 4477777655544443322 345777777664
No 168
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=34.57 E-value=20 Score=20.21 Aligned_cols=11 Identities=45% Similarity=1.114 Sum_probs=7.8
Q ss_pred CCCCCCceEEE
Q 035300 23 CPYCGGPVLAI 33 (68)
Q Consensus 23 Cp~CGG~v~a~ 33 (68)
||+||++..=.
T Consensus 1 CP~Cg~~f~C~ 11 (50)
T PF14375_consen 1 CPRCGAPFECG 11 (50)
T ss_pred CCCCCCcCCCC
Confidence 78888876543
No 169
>PF07213 DAP10: DAP10 membrane protein; InterPro: IPR009861 This family consists of several mammalian DAP10 membrane proteins. In activated mouse natural killer (NK) cells, the NKG2D receptor associates with two intracellular adaptors, DAP10 and DAP12, which trigger phosphatidyl inositol 3 kinase (PI3K) and Syk family protein tyrosine kinases, respectively. It has been suggested that the DAP10-PI3K pathway is sufficient to initiate NKG2D-mediated killing of target cells [].
Probab=34.48 E-value=18 Score=23.32 Aligned_cols=15 Identities=13% Similarity=0.270 Sum_probs=12.1
Q ss_pred eeecCCCCcCCCCCC
Q 035300 14 IRRNGADAACPYCGG 28 (68)
Q Consensus 14 ~~~~~A~G~Cp~CGG 28 (68)
-+.|..+|+|+.||.
T Consensus 16 aAaq~~~gscs~C~~ 30 (79)
T PF07213_consen 16 AAAQTQPGSCSGCYP 30 (79)
T ss_pred hhhcCCCCCCCCccc
Confidence 346788999999985
No 170
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=34.37 E-value=35 Score=25.81 Aligned_cols=30 Identities=27% Similarity=0.718 Sum_probs=21.4
Q ss_pred CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300 21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV 64 (68)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (68)
..||.||+.....|++. -.+.|.-||-.+.
T Consensus 2 ~~CpeCg~~~~~~d~~~--------------ge~VC~~CG~Vi~ 31 (285)
T COG1405 2 MSCPECGSTNIITDYER--------------GEIVCADCGLVLE 31 (285)
T ss_pred CCCCCCCCccceeeccC--------------CeEEeccCCEEec
Confidence 57999999977777663 4566777776543
No 171
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=33.98 E-value=24 Score=29.41 Aligned_cols=29 Identities=34% Similarity=0.777 Sum_probs=22.1
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV 64 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (68)
.|++|||-.-.-|- .--.-+||.||..|+
T Consensus 2 ~C~~C~~s~fe~d~--------------a~g~~~C~~CG~v~E 30 (521)
T KOG1598|consen 2 VCKNCGGSNFERDE--------------ATGNLYCTACGTVLE 30 (521)
T ss_pred cCCCCCCCCccccc--------------ccCCceeccccceee
Confidence 69999998766664 334678999998875
No 172
>PHA02942 putative transposase; Provisional
Probab=33.96 E-value=24 Score=27.28 Aligned_cols=28 Identities=29% Similarity=0.813 Sum_probs=19.3
Q ss_pred CCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccccee
Q 035300 20 DAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRL 63 (68)
Q Consensus 20 ~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (68)
.-.||.||.... + + +.|.|.|..||-..
T Consensus 325 Sq~Cs~CG~~~~--~-----------l---~~r~f~C~~CG~~~ 352 (383)
T PHA02942 325 SVSCPKCGHKMV--E-----------I---AHRYFHCPSCGYEN 352 (383)
T ss_pred CccCCCCCCccC--c-----------C---CCCEEECCCCCCEe
Confidence 356999998542 1 1 34679999999653
No 173
>PRK06260 threonine synthase; Validated
Probab=33.40 E-value=43 Score=25.41 Aligned_cols=28 Identities=25% Similarity=0.287 Sum_probs=17.5
Q ss_pred EeCCceeeeeecCCCCcCCCCCCceEEE
Q 035300 6 IFDLREKVIRRNGADAACPYCGGPVLAI 33 (68)
Q Consensus 6 vcde~~kv~~~~~A~G~Cp~CGG~v~a~ 33 (68)
.|-.-++...-....-.||.|||.+.+.
T Consensus 5 ~C~~cg~~~~~~~~~~~Cp~cg~~l~~~ 32 (397)
T PRK06260 5 KCIECGKEYDPDEIIYTCPECGGLLEVI 32 (397)
T ss_pred EECCCCCCCCCCCccccCCCCCCeEEEE
Confidence 3444444444444556799999987655
No 174
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=32.90 E-value=18 Score=33.27 Aligned_cols=13 Identities=31% Similarity=0.674 Sum_probs=8.3
Q ss_pred Eeecccceeeecc
Q 035300 55 YCTICSRRLVPAT 67 (68)
Q Consensus 55 ~Ct~C~r~L~~~~ 67 (68)
.|..|+..++.+.
T Consensus 711 ~CP~CGtplv~~~ 723 (1337)
T PRK14714 711 ECPRCDVELTPYQ 723 (1337)
T ss_pred cCCCCCCcccccc
Confidence 5677776666553
No 175
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=32.50 E-value=9.1 Score=21.13 Aligned_cols=39 Identities=28% Similarity=0.674 Sum_probs=25.1
Q ss_pred CCCcCCC--CCCceEEEEecceee-eEEeeeeeeecceEEeec----ccceee
Q 035300 19 ADAACPY--CGGPVLAIDFDAHLR-FCFLPISHKVKKKFYCTI----CSRRLV 64 (68)
Q Consensus 19 A~G~Cp~--CGG~v~a~Dves~~r-fCflP~~~k~krk~~Ct~----C~r~L~ 64 (68)
++-.||+ |...+..-+++.+.. -| -++.+.|++ |+.+..
T Consensus 8 ~~v~C~~~cc~~~i~r~~l~~H~~~~C-------~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIPRKELDDHLENEC-------PKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp SEEE-TT--S-BEEECCCHHHHHHTTS-------TTSEEE-SS----S--EEE
T ss_pred CEeeCCCCCcccceeHHHHHHHHHccC-------CCCcEECCCCCCCCCCccc
Confidence 4567998 556688888888887 66 457788888 877653
No 176
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=32.47 E-value=33 Score=26.55 Aligned_cols=16 Identities=25% Similarity=0.576 Sum_probs=10.7
Q ss_pred eecCCCCcCCCCCCce
Q 035300 15 RRNGADAACPYCGGPV 30 (68)
Q Consensus 15 ~~~~A~G~Cp~CGG~v 30 (68)
+.++.++.||+||+..
T Consensus 247 ~~~~~~~~C~~c~~~~ 262 (374)
T TIGR00308 247 GISQRKGRCKECGGEY 262 (374)
T ss_pred cccCCCCCCCCCCCcc
Confidence 3355667888888753
No 177
>smart00507 HNHc HNH nucleases.
Probab=32.43 E-value=25 Score=17.73 Aligned_cols=11 Identities=45% Similarity=1.295 Sum_probs=9.6
Q ss_pred CcCCCCCCceE
Q 035300 21 AACPYCGGPVL 31 (68)
Q Consensus 21 G~Cp~CGG~v~ 31 (68)
+.|++||....
T Consensus 11 ~~C~~C~~~~~ 21 (52)
T smart00507 11 GVCAYCGKPAS 21 (52)
T ss_pred CCCcCCcCCCC
Confidence 89999999875
No 178
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=32.29 E-value=18 Score=30.21 Aligned_cols=10 Identities=20% Similarity=0.458 Sum_probs=6.0
Q ss_pred Eeecccceee
Q 035300 55 YCTICSRRLV 64 (68)
Q Consensus 55 ~Ct~C~r~L~ 64 (68)
+|..||..+.
T Consensus 43 fC~~CG~~~~ 52 (645)
T PRK14559 43 HCPNCGAETG 52 (645)
T ss_pred cccccCCccc
Confidence 5666666553
No 179
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=32.26 E-value=20 Score=21.79 Aligned_cols=8 Identities=50% Similarity=1.456 Sum_probs=6.7
Q ss_pred cCCCCCCc
Q 035300 22 ACPYCGGP 29 (68)
Q Consensus 22 ~Cp~CGG~ 29 (68)
.||.||+.
T Consensus 17 ~CP~Cgs~ 24 (61)
T PRK08351 17 RCPVCGSR 24 (61)
T ss_pred cCCCCcCC
Confidence 59999973
No 180
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=32.04 E-value=21 Score=20.17 Aligned_cols=35 Identities=20% Similarity=0.478 Sum_probs=20.2
Q ss_pred CCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccccee
Q 035300 20 DAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRL 63 (68)
Q Consensus 20 ~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (68)
.|+|.-|+=.+...++..- .+...-++|+.|||.|
T Consensus 22 ~~~C~gC~~~l~~~~~~~i---------~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEI---------RKGDEIVFCPNCGRIL 56 (56)
T ss_pred CCccCCCCEEcCHHHHHHH---------HcCCCeEECcCCCccC
Confidence 3567777655544433321 1224568899999875
No 181
>PF04879 Molybdop_Fe4S4: Molybdopterin oxidoreductase Fe4S4 domain; InterPro: IPR006963 The molybdopterin oxidoreductase Fe4S4 domain is found in a number of reductase/dehydrogenase families, which include the periplasmic nitrate reductase precursor and the formate dehydrogenase alpha chain [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 2VPZ_A 2VPY_A 2VPW_A 2VPX_A 2NYA_A 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 ....
Probab=32.03 E-value=11 Score=20.80 Aligned_cols=13 Identities=31% Similarity=0.958 Sum_probs=8.1
Q ss_pred cCCCCcCCCCCCc
Q 035300 17 NGADAACPYCGGP 29 (68)
Q Consensus 17 ~~A~G~Cp~CGG~ 29 (68)
|.++.+||+|+.+
T Consensus 2 k~~~t~C~~C~~g 14 (55)
T PF04879_consen 2 KTVPTVCPYCSSG 14 (55)
T ss_dssp EEEEEE-SSCTT-
T ss_pred eEEeeECcCCcCC
Confidence 3457789999864
No 182
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=31.99 E-value=48 Score=21.76 Aligned_cols=11 Identities=36% Similarity=0.999 Sum_probs=8.1
Q ss_pred cCCCCCCceEE
Q 035300 22 ACPYCGGPVLA 32 (68)
Q Consensus 22 ~Cp~CGG~v~a 32 (68)
-||.||+.+.+
T Consensus 4 FCp~Cgsll~p 14 (113)
T COG1594 4 FCPKCGSLLYP 14 (113)
T ss_pred ccCCccCeeEE
Confidence 48888887765
No 183
>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=31.71 E-value=26 Score=24.37 Aligned_cols=15 Identities=33% Similarity=0.499 Sum_probs=11.4
Q ss_pred cCCCCcCCCCCCceE
Q 035300 17 NGADAACPYCGGPVL 31 (68)
Q Consensus 17 ~~A~G~Cp~CGG~v~ 31 (68)
++-|-.||+||--..
T Consensus 23 nk~p~vcP~cg~~~~ 37 (129)
T TIGR02300 23 NRRPAVSPYTGEQFP 37 (129)
T ss_pred CCCCccCCCcCCccC
Confidence 347889999997654
No 184
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=31.40 E-value=21 Score=28.74 Aligned_cols=22 Identities=18% Similarity=0.328 Sum_probs=13.6
Q ss_pred EeeeeeeecceEEeecccceee
Q 035300 43 FLPISHKVKKKFYCTICSRRLV 64 (68)
Q Consensus 43 flP~~~k~krk~~Ct~C~r~L~ 64 (68)
+-|+|-+-||.|.|++|..++-
T Consensus 9 ~C~ic~vq~~~YtCPRCn~~YC 30 (383)
T KOG4317|consen 9 ACGICGVQKREYTCPRCNLLYC 30 (383)
T ss_pred eccccccccccccCCCCCccce
Confidence 3466666666666666666543
No 185
>cd04467 S1_aIF5A S1_aIF5A: Archaeal translation Initiation Factor 5A (aIF5A), S1-like RNA-binding domain. aIF5A is a homolog of eukaryotic eIF5A. IF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is a post-translationally modified lysine and is essential for IF5A function. In yeast, eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the cold-shock domain which binds RNA. Moreover, IF5A prefers binding to the actively translating ribosome. This evidence suggests that IF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=30.94 E-value=29 Score=20.74 Aligned_cols=15 Identities=27% Similarity=0.441 Sum_probs=11.4
Q ss_pred CCceEEEEecceeee
Q 035300 27 GGPVLAIDFDAHLRF 41 (68)
Q Consensus 27 GG~v~a~Dves~~rf 41 (68)
|+.|+.||+||---|
T Consensus 13 g~~vQlMD~eTYeT~ 27 (57)
T cd04467 13 GDVVQLMDLETYETF 27 (57)
T ss_pred CCEEEEeccccceeE
Confidence 568999999965433
No 186
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=30.86 E-value=16 Score=21.89 Aligned_cols=11 Identities=36% Similarity=1.108 Sum_probs=3.5
Q ss_pred ceEEeecccce
Q 035300 52 KKFYCTICSRR 62 (68)
Q Consensus 52 rk~~Ct~C~r~ 62 (68)
|+|.|.+||+.
T Consensus 32 r~y~Cp~CgAt 42 (55)
T PF05741_consen 32 RKYVCPICGAT 42 (55)
T ss_dssp GG---TTT---
T ss_pred hcCcCCCCcCc
Confidence 56777777763
No 187
>PRK01343 zinc-binding protein; Provisional
Probab=30.61 E-value=18 Score=21.82 Aligned_cols=13 Identities=38% Similarity=0.991 Sum_probs=9.9
Q ss_pred CCCcCCCCCCceE
Q 035300 19 ADAACPYCGGPVL 31 (68)
Q Consensus 19 A~G~Cp~CGG~v~ 31 (68)
..-.||-||-++.
T Consensus 8 p~~~CP~C~k~~~ 20 (57)
T PRK01343 8 PTRPCPECGKPST 20 (57)
T ss_pred CCCcCCCCCCcCc
Confidence 3467999999864
No 188
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.37 E-value=26 Score=23.05 Aligned_cols=8 Identities=50% Similarity=1.327 Sum_probs=4.1
Q ss_pred CcCCCCCC
Q 035300 21 AACPYCGG 28 (68)
Q Consensus 21 G~Cp~CGG 28 (68)
--||+|+|
T Consensus 22 D~CPrCrG 29 (88)
T COG3809 22 DYCPRCRG 29 (88)
T ss_pred eeCCcccc
Confidence 34555554
No 189
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=30.35 E-value=87 Score=21.50 Aligned_cols=32 Identities=31% Similarity=0.471 Sum_probs=23.1
Q ss_pred CCCcCCCCCCceEEEEecceeeeEEeeeeeee
Q 035300 19 ADAACPYCGGPVLAIDFDAHLRFCFLPISHKV 50 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~ 50 (68)
-.-+||.||-++.++=|-..+-+=-|=|.-|.
T Consensus 48 G~t~CP~Cg~~~e~~fvva~~aLVgl~l~mkV 79 (115)
T COG1885 48 GSTSCPKCGEPFESAFVVANTALVGLILSMKV 79 (115)
T ss_pred ccccCCCCCCccceeEEEecceeEEEEEEEEE
Confidence 34689999999988887777766555555443
No 190
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=30.35 E-value=41 Score=18.24 Aligned_cols=11 Identities=36% Similarity=0.981 Sum_probs=7.8
Q ss_pred cCCCCCCceEE
Q 035300 22 ACPYCGGPVLA 32 (68)
Q Consensus 22 ~Cp~CGG~v~a 32 (68)
.||.||+.-.+
T Consensus 2 ~Cp~C~~~~a~ 12 (40)
T smart00440 2 PCPKCGNREAT 12 (40)
T ss_pred cCCCCCCCeEE
Confidence 59999865443
No 191
>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 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=29.92 E-value=30 Score=26.62 Aligned_cols=22 Identities=27% Similarity=0.709 Sum_probs=13.4
Q ss_pred EeCCceeeeeecCCCCcCCCCC
Q 035300 6 IFDLREKVIRRNGADAACPYCG 27 (68)
Q Consensus 6 vcde~~kv~~~~~A~G~Cp~CG 27 (68)
-|...|+-+.-..+.|.||+||
T Consensus 122 Yc~~~e~fl~e~~v~g~CP~C~ 143 (391)
T PF09334_consen 122 YCPSCERFLPESFVEGTCPYCG 143 (391)
T ss_dssp EETTTTEEE-GGGETCEETTT-
T ss_pred EecCcCcccccceeeccccCcC
Confidence 3455666666666778888666
No 193
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=29.92 E-value=29 Score=20.67 Aligned_cols=15 Identities=33% Similarity=0.731 Sum_probs=11.6
Q ss_pred cCCCCcCCCCCCceE
Q 035300 17 NGADAACPYCGGPVL 31 (68)
Q Consensus 17 ~~A~G~Cp~CGG~v~ 31 (68)
-..+..|+.||+..+
T Consensus 56 ~~~~~~C~~C~~~~E 70 (86)
T PF13966_consen 56 IQVDPICPLCGNEEE 70 (86)
T ss_pred CccCCccccCCCccc
Confidence 467799999998544
No 194
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=29.54 E-value=22 Score=21.99 Aligned_cols=12 Identities=42% Similarity=1.043 Sum_probs=8.3
Q ss_pred ecCCCCcCCCCC
Q 035300 16 RNGADAACPYCG 27 (68)
Q Consensus 16 ~~~A~G~Cp~CG 27 (68)
++.++-.||.||
T Consensus 46 k~g~~Y~Cp~CG 57 (61)
T COG2888 46 KLGNPYRCPKCG 57 (61)
T ss_pred HcCCceECCCcC
Confidence 456677777776
No 195
>TIGR03031 cas_csx12 CRISPR-associated protein, Csx12 family. Members of this family of CRISPR-associated (cas) protein are found, so far, in CRISPR/cas loci in Wolinella succinogenes DSM 1740, Legionella pneumophila str. Paris, and Francisella tularensis, where the last probably is an example of a degenerate CRISPR locus, having neither repeats nor a functional Cas1. The characteristic repeat length is 37 base pairs and period is about 72. One region of this large protein shows sequence similarity to PFAM model pfam01844, HNH endonuclease.
Probab=29.53 E-value=25 Score=30.60 Aligned_cols=13 Identities=31% Similarity=0.700 Sum_probs=11.0
Q ss_pred CCCCcCCCCCCce
Q 035300 18 GADAACPYCGGPV 30 (68)
Q Consensus 18 ~A~G~Cp~CGG~v 30 (68)
-+-|+|||||..+
T Consensus 758 fs~gIcpY~Ga~i 770 (802)
T TIGR03031 758 FSMGICPYKGASI 770 (802)
T ss_pred HhccCCCCCCCCC
Confidence 3679999999877
No 196
>PRK12722 transcriptional activator FlhC; Provisional
Probab=29.46 E-value=27 Score=25.29 Aligned_cols=14 Identities=29% Similarity=0.854 Sum_probs=10.5
Q ss_pred CcCCCCCCceEEEE
Q 035300 21 AACPYCGGPVLAID 34 (68)
Q Consensus 21 G~Cp~CGG~v~a~D 34 (68)
-.|.+|||.-.+.-
T Consensus 135 ~~C~~Cgg~fv~~~ 148 (187)
T PRK12722 135 SSCNCCGGHFVTHA 148 (187)
T ss_pred ccCCCCCCCeeccc
Confidence 46999999976443
No 197
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=29.33 E-value=17 Score=17.23 Aligned_cols=13 Identities=23% Similarity=0.710 Sum_probs=10.1
Q ss_pred EEeecccceeeec
Q 035300 54 FYCTICSRRLVPA 66 (68)
Q Consensus 54 ~~Ct~C~r~L~~~ 66 (68)
|.|..|++...+.
T Consensus 2 ~~C~~C~~~F~~~ 14 (27)
T PF13912_consen 2 FECDECGKTFSSL 14 (27)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCccCCccCCh
Confidence 7899999877654
No 198
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=29.18 E-value=49 Score=17.94 Aligned_cols=17 Identities=18% Similarity=0.534 Sum_probs=11.7
Q ss_pred CCCCcCC--CCCCceEEEE
Q 035300 18 GADAACP--YCGGPVLAID 34 (68)
Q Consensus 18 ~A~G~Cp--~CGG~v~a~D 34 (68)
+.---|| .|+..+...|
T Consensus 16 ~~~~~CP~~~C~~~~~~~~ 34 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVTE 34 (64)
T ss_pred CCccCCCCCCCcceEEecC
Confidence 3334588 9988887763
No 199
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=28.65 E-value=30 Score=23.40 Aligned_cols=15 Identities=33% Similarity=0.702 Sum_probs=6.6
Q ss_pred cceEEeecccceeee
Q 035300 51 KKKFYCTICSRRLVP 65 (68)
Q Consensus 51 krk~~Ct~C~r~L~~ 65 (68)
.+.|.|.+|+...++
T Consensus 20 ~k~FtCp~Cghe~vs 34 (104)
T COG4888 20 PKTFTCPRCGHEKVS 34 (104)
T ss_pred CceEecCccCCeeee
Confidence 344444444444433
No 200
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=28.59 E-value=30 Score=27.84 Aligned_cols=30 Identities=43% Similarity=0.904 Sum_probs=21.8
Q ss_pred CCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeeecc
Q 035300 19 ADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPAT 67 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~~ 67 (68)
+.-.||+|+.+ .|=||+ .|+.|+-.|++-+
T Consensus 275 ~Gy~CP~Ckak-----------vCsLP~--------eCpiC~ltLVss~ 304 (378)
T KOG2807|consen 275 GGYFCPQCKAK-----------VCSLPI--------ECPICSLTLVSSP 304 (378)
T ss_pred CceeCCcccCe-----------eecCCc--------cCCccceeEecch
Confidence 34468888764 577875 6889998888753
No 201
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=28.52 E-value=25 Score=24.45 Aligned_cols=8 Identities=63% Similarity=1.693 Sum_probs=6.8
Q ss_pred cCCCCCCc
Q 035300 22 ACPYCGGP 29 (68)
Q Consensus 22 ~Cp~CGG~ 29 (68)
-||.|||.
T Consensus 21 GCP~CGg~ 28 (131)
T PF09845_consen 21 GCPECGGN 28 (131)
T ss_pred cCcccCCc
Confidence 49999996
No 202
>PRK06450 threonine synthase; Validated
Probab=28.48 E-value=56 Score=24.57 Aligned_cols=16 Identities=31% Similarity=0.729 Sum_probs=11.7
Q ss_pred CCCCcCCCCCCceEEE
Q 035300 18 GADAACPYCGGPVLAI 33 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~a~ 33 (68)
...-.||.|||.+...
T Consensus 16 ~~~~~C~~cg~~l~~~ 31 (338)
T PRK06450 16 IYEIRCKKCGGPFEIL 31 (338)
T ss_pred cccccCCcCCCEeEEe
Confidence 3346899999987654
No 203
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.45 E-value=23 Score=22.16 Aligned_cols=17 Identities=35% Similarity=0.757 Sum_probs=11.7
Q ss_pred CCcCCCCCCceEEEEec
Q 035300 20 DAACPYCGGPVLAIDFD 36 (68)
Q Consensus 20 ~G~Cp~CGG~v~a~Dve 36 (68)
---||.||-+|.=.+-.
T Consensus 7 ~v~CP~Cgkpv~w~~~s 23 (65)
T COG3024 7 TVPCPTCGKPVVWGEES 23 (65)
T ss_pred cccCCCCCCcccccccC
Confidence 34599999887654433
No 204
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=28.30 E-value=26 Score=23.44 Aligned_cols=7 Identities=71% Similarity=2.114 Sum_probs=5.6
Q ss_pred cCCCCCC
Q 035300 22 ACPYCGG 28 (68)
Q Consensus 22 ~Cp~CGG 28 (68)
.|||||-
T Consensus 5 ~CP~Cg~ 11 (97)
T COG4311 5 PCPYCGE 11 (97)
T ss_pred cCCCCCC
Confidence 5999984
No 205
>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=28.08 E-value=28 Score=24.20 Aligned_cols=11 Identities=45% Similarity=1.150 Sum_probs=8.6
Q ss_pred CCcCCCCCCce
Q 035300 20 DAACPYCGGPV 30 (68)
Q Consensus 20 ~G~Cp~CGG~v 30 (68)
.-.||.|||.+
T Consensus 133 ~p~C~~Cg~~l 143 (218)
T cd01407 133 VPRCPKCGGLL 143 (218)
T ss_pred CCcCCCCCCcc
Confidence 34799999974
No 206
>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=27.92 E-value=32 Score=21.02 Aligned_cols=18 Identities=33% Similarity=0.512 Sum_probs=12.6
Q ss_pred eeecCCCCcCCCCCCceE
Q 035300 14 IRRNGADAACPYCGGPVL 31 (68)
Q Consensus 14 ~~~~~A~G~Cp~CGG~v~ 31 (68)
.+|=-|...||.|+-+=.
T Consensus 3 kKRFIAGA~CP~C~~~Dt 20 (59)
T TIGR02443 3 KKRFIAGAVCPACSAQDT 20 (59)
T ss_pred cceEeccccCCCCcCccE
Confidence 344557889999986533
No 207
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=27.84 E-value=31 Score=24.56 Aligned_cols=20 Identities=25% Similarity=0.438 Sum_probs=15.2
Q ss_pred eeecCCCCcCCCCCCceEEE
Q 035300 14 IRRNGADAACPYCGGPVLAI 33 (68)
Q Consensus 14 ~~~~~A~G~Cp~CGG~v~a~ 33 (68)
..+-++++.|++|||.--+.
T Consensus 104 g~~s~l~~~c~~c~g~fc~~ 123 (162)
T COG3582 104 GKGSTLAGKCNYCTGYFCAE 123 (162)
T ss_pred cCCccccccccCCCCcceec
Confidence 34568899999999975543
No 208
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=27.77 E-value=16 Score=24.27 Aligned_cols=11 Identities=27% Similarity=1.129 Sum_probs=8.2
Q ss_pred ceEEeecccce
Q 035300 52 KKFYCTICSRR 62 (68)
Q Consensus 52 rk~~Ct~C~r~ 62 (68)
.+|.|++||+.
T Consensus 35 aky~CsfCGK~ 45 (92)
T KOG0402|consen 35 AKYTCSFCGKK 45 (92)
T ss_pred hhhhhhhcchh
Confidence 46888888864
No 209
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=27.71 E-value=27 Score=23.86 Aligned_cols=10 Identities=40% Similarity=1.215 Sum_probs=8.1
Q ss_pred CCcCCCCCCc
Q 035300 20 DAACPYCGGP 29 (68)
Q Consensus 20 ~G~Cp~CGG~ 29 (68)
+-.|||||..
T Consensus 105 ~~~cp~c~s~ 114 (146)
T TIGR02159 105 SVQCPRCGSA 114 (146)
T ss_pred CCcCCCCCCC
Confidence 4589999975
No 210
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=27.64 E-value=28 Score=24.64 Aligned_cols=9 Identities=56% Similarity=1.490 Sum_probs=7.5
Q ss_pred cCCCCCCce
Q 035300 22 ACPYCGGPV 30 (68)
Q Consensus 22 ~Cp~CGG~v 30 (68)
.||.|||.+
T Consensus 144 ~C~~Cgg~l 152 (242)
T PRK00481 144 RCPKCGGIL 152 (242)
T ss_pred CCCCCCCcc
Confidence 399999974
No 211
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=27.55 E-value=35 Score=23.11 Aligned_cols=22 Identities=27% Similarity=0.493 Sum_probs=14.8
Q ss_pred CCceeeeeecCCCCcCCCCCCc
Q 035300 8 DLREKVIRRNGADAACPYCGGP 29 (68)
Q Consensus 8 de~~kv~~~~~A~G~Cp~CGG~ 29 (68)
|+++-.-.-++....||.||+.
T Consensus 53 gg~~a~~nv~~t~~~Cp~Cgh~ 74 (105)
T KOG2906|consen 53 GGDEAWENVDQTEATCPTCGHE 74 (105)
T ss_pred CCcccccchhhccCcCCCCCCC
Confidence 3334444446777899999986
No 212
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=27.54 E-value=6.1 Score=19.67 Aligned_cols=10 Identities=40% Similarity=1.075 Sum_probs=6.7
Q ss_pred cCCCCCCceE
Q 035300 22 ACPYCGGPVL 31 (68)
Q Consensus 22 ~Cp~CGG~v~ 31 (68)
.||.||-.-.
T Consensus 4 ~C~~CgR~F~ 13 (25)
T PF13913_consen 4 PCPICGRKFN 13 (25)
T ss_pred cCCCCCCEEC
Confidence 4788876653
No 213
>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=27.17 E-value=21 Score=24.36 Aligned_cols=21 Identities=29% Similarity=0.574 Sum_probs=12.1
Q ss_pred eCCceeeeeecCCCCcCCCCCCce
Q 035300 7 FDLREKVIRRNGADAACPYCGGPV 30 (68)
Q Consensus 7 cde~~kv~~~~~A~G~Cp~CGG~v 30 (68)
||..=|++|+.. .|+||+-++
T Consensus 75 C~K~TKmLGr~D---~CM~C~~pL 95 (114)
T PF11023_consen 75 CGKQTKMLGRVD---ACMHCKEPL 95 (114)
T ss_pred CCChHhhhchhh---ccCcCCCcC
Confidence 344445566653 677777654
No 214
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=26.66 E-value=31 Score=23.94 Aligned_cols=11 Identities=45% Similarity=1.117 Sum_probs=8.4
Q ss_pred CCcCCCCCCce
Q 035300 20 DAACPYCGGPV 30 (68)
Q Consensus 20 ~G~Cp~CGG~v 30 (68)
.-.||.|||.+
T Consensus 130 ~p~C~~Cgg~l 140 (224)
T cd01412 130 LPRCPKCGGLL 140 (224)
T ss_pred CCCCCCCCCcc
Confidence 34699999964
No 215
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=26.62 E-value=24 Score=21.11 Aligned_cols=12 Identities=42% Similarity=1.101 Sum_probs=9.4
Q ss_pred CCcCCCCCCceE
Q 035300 20 DAACPYCGGPVL 31 (68)
Q Consensus 20 ~G~Cp~CGG~v~ 31 (68)
...||.||+...
T Consensus 17 k~~CP~CG~~t~ 28 (56)
T PRK13130 17 KEICPVCGGKTK 28 (56)
T ss_pred cccCcCCCCCCC
Confidence 567999998754
No 216
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=26.57 E-value=46 Score=25.52 Aligned_cols=23 Identities=35% Similarity=0.817 Sum_probs=18.3
Q ss_pred eeeeeecCCCCcCCCCCCceEEE
Q 035300 11 EKVIRRNGADAACPYCGGPVLAI 33 (68)
Q Consensus 11 ~kv~~~~~A~G~Cp~CGG~v~a~ 33 (68)
++-.++-|--|.||.|||.++-+
T Consensus 174 ~~k~rr~pl~g~c~kcg~~~~lt 196 (253)
T COG1933 174 NTKFRRPPLDGKCPICGGKIVLT 196 (253)
T ss_pred hhhhcCCCccccccccCCeEEEE
Confidence 45567889999999999977643
No 217
>PF09856 DUF2083: Predicted transcriptional regulator (DUF2083); InterPro: IPR018653 This domain is found in various prokaryotic transcriptional regulatory proteins belonging to the XRE family. Its exact function is, as yet, unknown.
Probab=26.44 E-value=72 Score=22.32 Aligned_cols=25 Identities=24% Similarity=0.353 Sum_probs=21.0
Q ss_pred eEEEEeCCceeeeeecCCCC--------cCCCC
Q 035300 2 SVLSIFDLREKVIRRNGADA--------ACPYC 26 (68)
Q Consensus 2 ~~~~vcde~~kv~~~~~A~G--------~Cp~C 26 (68)
+|+..||..+.++.+++|+| +||.-
T Consensus 12 ff~~r~D~AGniskR~~a~gf~~~R~GgaCPlW 44 (156)
T PF09856_consen 12 FFFVRCDRAGNISKRFSATGFPFPRFGGACPLW 44 (156)
T ss_pred EEEEEEcCCCCEEeeccCCCCccCCCCCcCcCc
Confidence 57889999999999999875 67764
No 218
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=26.37 E-value=80 Score=19.33 Aligned_cols=28 Identities=32% Similarity=0.777 Sum_probs=18.9
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV 64 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (68)
+||-|-|+++.. +.+...+|..|++-+.
T Consensus 10 aCP~~kg~L~~~---------------~~~~~L~c~~~~~aYp 37 (60)
T COG2835 10 ACPVCKGPLVYD---------------EEKQELICPRCKLAYP 37 (60)
T ss_pred eccCcCCcceEe---------------ccCCEEEecccCceee
Confidence 699999995543 3333777887776553
No 219
>cd01230 PH_EFA6 EFA6 Pleckstrin Homology (PH) domain. EFA6 Pleckstrin Homology (PH) domain. EFA6 is an guanine nucleotide exchange factor for ARF6, which is involved in membrane recycling. It consists of a SEC7 domain followed by a PH domain. The EFA6 PH domain regulates its association with the plasma membrane. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=26.29 E-value=44 Score=21.97 Aligned_cols=23 Identities=22% Similarity=0.278 Sum_probs=19.3
Q ss_pred eeeeeecceEEeecccceeeecc
Q 035300 45 PISHKVKKKFYCTICSRRLVPAT 67 (68)
Q Consensus 45 P~~~k~krk~~Ct~C~r~L~~~~ 67 (68)
|.-.+.|++++|+..|-.|..|-
T Consensus 20 ~~~~R~Wk~~y~vL~g~~L~~yK 42 (117)
T cd01230 20 PFGKRSWKMFYGILRGLVLYLQK 42 (117)
T ss_pred CCCCCcceEEEEEEECCEEEEEc
Confidence 45568999999999999998874
No 220
>PRK12860 transcriptional activator FlhC; Provisional
Probab=26.26 E-value=33 Score=24.94 Aligned_cols=13 Identities=38% Similarity=0.841 Sum_probs=10.3
Q ss_pred CcCCCCCCceEEE
Q 035300 21 AACPYCGGPVLAI 33 (68)
Q Consensus 21 G~Cp~CGG~v~a~ 33 (68)
-.|.+|||.-.+.
T Consensus 135 ~~C~~Cgg~fv~~ 147 (189)
T PRK12860 135 ARCCRCGGKFVTH 147 (189)
T ss_pred ccCCCCCCCeecc
Confidence 4699999997644
No 221
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=26.16 E-value=53 Score=28.15 Aligned_cols=13 Identities=31% Similarity=0.848 Sum_probs=11.8
Q ss_pred cCCCCcCCCCCCc
Q 035300 17 NGADAACPYCGGP 29 (68)
Q Consensus 17 ~~A~G~Cp~CGG~ 29 (68)
++-|-.||.||+.
T Consensus 472 ~~~p~~Cp~Cgs~ 484 (730)
T COG1198 472 EPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCC
Confidence 5889999999998
No 222
>PRK14724 DNA topoisomerase III; Provisional
Probab=26.06 E-value=42 Score=29.35 Aligned_cols=14 Identities=43% Similarity=1.056 Sum_probs=11.8
Q ss_pred cCCCCcCCCCCCce
Q 035300 17 NGADAACPYCGGPV 30 (68)
Q Consensus 17 ~~A~G~Cp~CGG~v 30 (68)
+.+-|.||.||+++
T Consensus 752 ~~~~g~CPkCg~~v 765 (987)
T PRK14724 752 QESLGPCPKCGAPV 765 (987)
T ss_pred cccccCCCCCCCce
Confidence 56679999999985
No 223
>PF15616 TerY-C: TerY-C metal binding domain
Probab=25.96 E-value=49 Score=22.74 Aligned_cols=38 Identities=24% Similarity=0.573 Sum_probs=21.9
Q ss_pred CcCCCCCCc-eEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300 21 AACPYCGGP-VLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV 64 (68)
Q Consensus 21 G~Cp~CGG~-v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (68)
..|||||-. ..|+= ..-=-|| +.---...|+-|++...
T Consensus 78 PgCP~CGn~~~fa~C-~CGkl~C-----i~g~~~~~CPwCg~~g~ 116 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVC-GCGKLFC-----IDGEGEVTCPWCGNEGS 116 (131)
T ss_pred CCCCCCcChhcEEEe-cCCCEEE-----eCCCCCEECCCCCCeee
Confidence 569999987 33332 3333333 33344677788877643
No 224
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=25.72 E-value=34 Score=24.63 Aligned_cols=11 Identities=27% Similarity=0.730 Sum_probs=8.5
Q ss_pred CCcCCCCCCce
Q 035300 20 DAACPYCGGPV 30 (68)
Q Consensus 20 ~G~Cp~CGG~v 30 (68)
.-.||.|||.+
T Consensus 143 ~p~Cp~Cgg~l 153 (244)
T PRK14138 143 VPRCDDCSGLI 153 (244)
T ss_pred CCCCCCCCCeE
Confidence 34699999864
No 225
>PF05015 Plasmid_killer: Plasmid maintenance system killer protein; InterPro: IPR007711 Several plasmids with proteic killer gene systems have been reported. All of them encode a stable toxin and an unstable antidote. Upon loss of the plasmid, the less stable inhibitor is inactivated more rapidly than the toxin, allowing the toxin to be activated. The activation of those systems result in cell filamentation and cessation of viable cell production. It has been verified that both the stable killer and the unstable inhibitor of the systems are short polypeptides. This family corresponds to the toxin.
Probab=25.47 E-value=70 Score=19.77 Aligned_cols=19 Identities=16% Similarity=0.142 Sum_probs=15.7
Q ss_pred CceEEEEecceeeeEEeee
Q 035300 28 GPVLAIDFDAHLRFCFLPI 46 (68)
Q Consensus 28 G~v~a~Dves~~rfCflP~ 46 (68)
.+--++||.-+||++|-+.
T Consensus 62 ~g~~Si~i~~~~RliF~~~ 80 (93)
T PF05015_consen 62 KGQWSIRINGNWRLIFRFE 80 (93)
T ss_pred CCcEEEEeCCCEEEEEEEe
Confidence 3677899999999999653
No 226
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=25.18 E-value=28 Score=20.99 Aligned_cols=16 Identities=38% Similarity=0.798 Sum_probs=12.0
Q ss_pred CCcCCCCCCceEEEEe
Q 035300 20 DAACPYCGGPVLAIDF 35 (68)
Q Consensus 20 ~G~Cp~CGG~v~a~Dv 35 (68)
...||-||.+++-.|.
T Consensus 39 YngCPfC~~~~~~~~~ 54 (55)
T PF14447_consen 39 YNGCPFCGTPFEFDDP 54 (55)
T ss_pred ccCCCCCCCcccCCCC
Confidence 3579999998876654
No 227
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a 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). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=24.81 E-value=40 Score=20.86 Aligned_cols=9 Identities=44% Similarity=1.394 Sum_probs=7.5
Q ss_pred CCCcCCCCC
Q 035300 19 ADAACPYCG 27 (68)
Q Consensus 19 A~G~Cp~CG 27 (68)
++..||+||
T Consensus 83 ~np~C~~C~ 91 (91)
T cd04482 83 ENPVCPKCG 91 (91)
T ss_pred cCCcCCCCC
Confidence 677899997
No 228
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=24.69 E-value=39 Score=19.75 Aligned_cols=17 Identities=47% Similarity=0.856 Sum_probs=9.1
Q ss_pred CCCCcCCCCCCceEEEE
Q 035300 18 GADAACPYCGGPVLAID 34 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~a~D 34 (68)
.|.+.||-|+|+-..-|
T Consensus 12 Gal~~Cp~C~~~~l~~~ 28 (55)
T PF08063_consen 12 GALEPCPKCKGGQLYFD 28 (55)
T ss_dssp TEE---SSSSE-EEEEE
T ss_pred cCCCCCCCCCCCeEEec
Confidence 46788999999755443
No 229
>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=24.44 E-value=30 Score=21.55 Aligned_cols=11 Identities=36% Similarity=1.041 Sum_probs=4.7
Q ss_pred CCCcCCCCCCc
Q 035300 19 ADAACPYCGGP 29 (68)
Q Consensus 19 A~G~Cp~CGG~ 29 (68)
.---||.||.+
T Consensus 23 ~k~FCp~CGn~ 33 (73)
T PF08772_consen 23 TKQFCPKCGNA 33 (73)
T ss_dssp S--S-SSS--S
T ss_pred CceeCcccCCC
Confidence 34469999987
No 230
>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=24.27 E-value=67 Score=24.64 Aligned_cols=34 Identities=24% Similarity=0.672 Sum_probs=11.9
Q ss_pred CCcCCCCCCc-eEEEEecceeeeEEeeeeeeecceEEeecccceeee
Q 035300 20 DAACPYCGGP-VLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVP 65 (68)
Q Consensus 20 ~G~Cp~CGG~-v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~ 65 (68)
.+.||+||-. ++.. +..... .-|+|+-|+-.+++
T Consensus 31 n~yCP~Cg~~~L~~f--~NN~PV----------aDF~C~~C~eeyEL 65 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKF--ENNRPV----------ADFYCPNCNEEYEL 65 (254)
T ss_dssp H---TTT--SS-EE--------------------EEE-TTT--EEEE
T ss_pred CCcCCCCCChhHhhc--cCCCcc----------ceeECCCCchHHhh
Confidence 3679999987 5543 333222 24788888876653
No 231
>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=24.14 E-value=92 Score=21.45 Aligned_cols=8 Identities=50% Similarity=1.427 Sum_probs=4.6
Q ss_pred CcCCCCCC
Q 035300 21 AACPYCGG 28 (68)
Q Consensus 21 G~Cp~CGG 28 (68)
..||.|||
T Consensus 131 ~~Cp~C~~ 138 (146)
T PF07295_consen 131 PPCPKCGH 138 (146)
T ss_pred CCCCCCCC
Confidence 34666665
No 232
>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=24.09 E-value=40 Score=19.99 Aligned_cols=12 Identities=50% Similarity=1.273 Sum_probs=9.7
Q ss_pred CcCCCCCCceEE
Q 035300 21 AACPYCGGPVLA 32 (68)
Q Consensus 21 G~Cp~CGG~v~a 32 (68)
-.||.|||....
T Consensus 18 ~~cp~cG~~T~~ 29 (53)
T PF04135_consen 18 DKCPPCGGPTES 29 (53)
T ss_dssp SBBTTTSSBSEE
T ss_pred CccCCCCCCCcC
Confidence 589999998654
No 233
>TIGR01374 soxD sarcosine oxidase, delta subunit family, heterotetrameric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form
Probab=24.06 E-value=35 Score=21.98 Aligned_cols=6 Identities=83% Similarity=2.510 Sum_probs=5.0
Q ss_pred cCCCCC
Q 035300 22 ACPYCG 27 (68)
Q Consensus 22 ~Cp~CG 27 (68)
.||+||
T Consensus 3 ~CP~CG 8 (84)
T TIGR01374 3 PCPYCG 8 (84)
T ss_pred cCCCCC
Confidence 599998
No 234
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=23.67 E-value=38 Score=24.82 Aligned_cols=10 Identities=60% Similarity=1.448 Sum_probs=8.1
Q ss_pred CcCCCCCCce
Q 035300 21 AACPYCGGPV 30 (68)
Q Consensus 21 G~Cp~CGG~v 30 (68)
-.||.|||.+
T Consensus 180 P~C~~Cgg~l 189 (285)
T PRK05333 180 PACPACGGIL 189 (285)
T ss_pred CCCCCCCCcc
Confidence 4699999975
No 235
>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=23.50 E-value=46 Score=20.49 Aligned_cols=14 Identities=36% Similarity=0.479 Sum_probs=10.5
Q ss_pred cCCCCcCCCCCCce
Q 035300 17 NGADAACPYCGGPV 30 (68)
Q Consensus 17 ~~A~G~Cp~CGG~v 30 (68)
=-|...||.|+.+=
T Consensus 5 FIAGa~CP~C~~~D 18 (71)
T PF09526_consen 5 FIAGAVCPKCQAMD 18 (71)
T ss_pred EecCccCCCCcCcc
Confidence 34778999998653
No 236
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=23.47 E-value=56 Score=17.53 Aligned_cols=9 Identities=33% Similarity=0.984 Sum_probs=5.0
Q ss_pred cCCCCCCce
Q 035300 22 ACPYCGGPV 30 (68)
Q Consensus 22 ~Cp~CGG~v 30 (68)
.|+.||...
T Consensus 7 ~C~~CG~~m 15 (58)
T PF13408_consen 7 RCGHCGSKM 15 (58)
T ss_pred EcccCCcEe
Confidence 366666543
No 237
>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=23.46 E-value=39 Score=23.91 Aligned_cols=11 Identities=27% Similarity=0.652 Sum_probs=8.6
Q ss_pred CCcCCCCCCce
Q 035300 20 DAACPYCGGPV 30 (68)
Q Consensus 20 ~G~Cp~CGG~v 30 (68)
.-.||.|||.+
T Consensus 136 ~p~C~~Cgg~l 146 (225)
T cd01411 136 SPYHAKCGGVI 146 (225)
T ss_pred CCCCCCCCCEe
Confidence 35799999864
No 238
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=23.38 E-value=64 Score=24.88 Aligned_cols=13 Identities=38% Similarity=0.958 Sum_probs=8.5
Q ss_pred CCCCcCCCCCCce
Q 035300 18 GADAACPYCGGPV 30 (68)
Q Consensus 18 ~A~G~Cp~CGG~v 30 (68)
+.+..||+||+..
T Consensus 259 ~~~~~C~~c~~~~ 271 (382)
T PRK04338 259 LPPEECPVCGGKF 271 (382)
T ss_pred CCCCCCCCCCCcc
Confidence 4566788887643
No 239
>PF04194 PDCD2_C: Programmed cell death protein 2, C-terminal putative domain ; InterPro: IPR007320 PDCD2 is localized predominantly in the cytosol of cells situated at the opposite pole of the germinal centre from the centroblasts as well as in cells in the mantle zone. It has been shown to interact with BCL6, an evolutionarily conserved Kruppel-type zinc finger protein that functions as a strong transcriptional repressor and is required for germinal centre development. The rat homologue, Rp8, is associated with programmed cell death in thymocytes.; GO: 0005737 cytoplasm
Probab=23.30 E-value=39 Score=23.01 Aligned_cols=11 Identities=36% Similarity=0.903 Sum_probs=8.7
Q ss_pred CCcCCCCCCce
Q 035300 20 DAACPYCGGPV 30 (68)
Q Consensus 20 ~G~Cp~CGG~v 30 (68)
.-.|++|||.-
T Consensus 97 ip~C~~Cg~~R 107 (164)
T PF04194_consen 97 IPKCENCGSPR 107 (164)
T ss_pred CCCCccCCCcc
Confidence 45799999864
No 240
>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=22.90 E-value=33 Score=22.39 Aligned_cols=13 Identities=23% Similarity=0.807 Sum_probs=9.0
Q ss_pred cceEEeeccccee
Q 035300 51 KKKFYCTICSRRL 63 (68)
Q Consensus 51 krk~~Ct~C~r~L 63 (68)
+.+|.|++||+.-
T Consensus 33 ~~ky~Cp~Cgk~~ 45 (90)
T PF01780_consen 33 HAKYTCPFCGKTS 45 (90)
T ss_dssp HS-BEESSSSSSE
T ss_pred hCCCcCCCCCCce
Confidence 4678888888754
No 241
>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=22.75 E-value=64 Score=26.11 Aligned_cols=37 Identities=19% Similarity=0.713 Sum_probs=21.7
Q ss_pred cCCCCCCceEEEEecceeeeEEeeee-eeecceEEeeccccee
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPIS-HKVKKKFYCTICSRRL 63 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~-~k~krk~~Ct~C~r~L 63 (68)
.||+||..-. .+.+. .++ |-= ....-.|.|..||...
T Consensus 202 pCPhCg~~~~-l~~~~-l~w---~~~~~~~~a~y~C~~Cg~~i 239 (557)
T PF05876_consen 202 PCPHCGEEQV-LEWEN-LKW---DKGEAPETARYVCPHCGCEI 239 (557)
T ss_pred cCCCCCCCcc-ccccc-eee---cCCCCccceEEECCCCcCCC
Confidence 5999998765 33332 111 110 2334578899998754
No 242
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=22.68 E-value=22 Score=25.51 Aligned_cols=16 Identities=19% Similarity=0.613 Sum_probs=13.4
Q ss_pred ecceEEeecccceeee
Q 035300 50 VKKKFYCTICSRRLVP 65 (68)
Q Consensus 50 ~krk~~Ct~C~r~L~~ 65 (68)
++.+|.|+.||.++=+
T Consensus 126 ~~S~ysC~~CG~kyCs 141 (156)
T KOG3362|consen 126 YDSKYSCVNCGTKYCS 141 (156)
T ss_pred CCchhHHHhcCCceee
Confidence 7889999999988754
No 243
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=22.58 E-value=39 Score=16.60 Aligned_cols=12 Identities=33% Similarity=1.118 Sum_probs=9.8
Q ss_pred eEEeecccceee
Q 035300 53 KFYCTICSRRLV 64 (68)
Q Consensus 53 k~~Ct~C~r~L~ 64 (68)
+|+|..|...+.
T Consensus 3 ~~~C~~C~~~~~ 14 (35)
T smart00451 3 GFYCKLCNVTFT 14 (35)
T ss_pred CeEccccCCccC
Confidence 688999998765
No 244
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=22.32 E-value=70 Score=26.76 Aligned_cols=15 Identities=27% Similarity=0.899 Sum_probs=12.9
Q ss_pred CCCcCCCCCCceEEE
Q 035300 19 ADAACPYCGGPVLAI 33 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~ 33 (68)
.|-.||.||+.++..
T Consensus 403 ~P~~CP~Cgs~l~~~ 417 (665)
T PRK07956 403 MPTHCPVCGSELVRV 417 (665)
T ss_pred CCCCCCCCCCEeEec
Confidence 688999999999753
No 245
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=22.27 E-value=64 Score=18.01 Aligned_cols=10 Identities=60% Similarity=1.212 Sum_probs=7.5
Q ss_pred cCCCCCCceE
Q 035300 22 ACPYCGGPVL 31 (68)
Q Consensus 22 ~Cp~CGG~v~ 31 (68)
.||.||-+|.
T Consensus 3 lcpkcgvgvl 12 (36)
T PF09151_consen 3 LCPKCGVGVL 12 (36)
T ss_dssp B-TTTSSSBE
T ss_pred cCCccCceEE
Confidence 6999998875
No 246
>smart00532 LIGANc Ligase N family.
Probab=22.06 E-value=75 Score=25.34 Aligned_cols=16 Identities=25% Similarity=0.762 Sum_probs=13.5
Q ss_pred CCCcCCCCCCceEEEE
Q 035300 19 ADAACPYCGGPVLAID 34 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~D 34 (68)
.|-.||.||..++-.+
T Consensus 398 ~P~~CP~C~s~l~~~~ 413 (441)
T smart00532 398 MPTHCPSCGSELVREE 413 (441)
T ss_pred CCCCCCCCCCEeEecC
Confidence 6899999999997543
No 247
>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=21.99 E-value=42 Score=23.62 Aligned_cols=10 Identities=50% Similarity=1.394 Sum_probs=8.1
Q ss_pred CcCCCCCCce
Q 035300 21 AACPYCGGPV 30 (68)
Q Consensus 21 G~Cp~CGG~v 30 (68)
-.||.|||.+
T Consensus 137 p~C~~Cgg~l 146 (222)
T cd01413 137 PRCPKCGGII 146 (222)
T ss_pred CcCCCCCCcc
Confidence 4699999864
No 248
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=21.97 E-value=74 Score=26.52 Aligned_cols=15 Identities=40% Similarity=1.050 Sum_probs=12.9
Q ss_pred CCCcCCCCCCceEEE
Q 035300 19 ADAACPYCGGPVLAI 33 (68)
Q Consensus 19 A~G~Cp~CGG~v~a~ 33 (68)
.|-.||.||..++--
T Consensus 391 ~P~~CP~C~s~l~~~ 405 (652)
T TIGR00575 391 FPTHCPSCGSPLVKI 405 (652)
T ss_pred CCCCCCCCCCEeEec
Confidence 689999999999763
No 249
>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=21.90 E-value=67 Score=16.65 Aligned_cols=15 Identities=27% Similarity=0.618 Sum_probs=9.9
Q ss_pred CCcCCCCCCceEEEE
Q 035300 20 DAACPYCGGPVLAID 34 (68)
Q Consensus 20 ~G~Cp~CGG~v~a~D 34 (68)
.|.|..||.++....
T Consensus 3 yg~C~~CGe~I~~~R 17 (36)
T PF01258_consen 3 YGICEDCGEPIPEER 17 (36)
T ss_dssp -SB-TTTSSBEEHHH
T ss_pred CCCccccCChHHHHH
Confidence 578999999886543
No 250
>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=21.90 E-value=43 Score=21.85 Aligned_cols=9 Identities=33% Similarity=1.047 Sum_probs=7.0
Q ss_pred CCCcCCCCC
Q 035300 19 ADAACPYCG 27 (68)
Q Consensus 19 A~G~Cp~CG 27 (68)
..--||+||
T Consensus 19 ~~~gCpnC~ 27 (98)
T cd07973 19 ERDGCPNCE 27 (98)
T ss_pred cCCCCCCCc
Confidence 446799997
No 251
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=21.85 E-value=40 Score=17.91 Aligned_cols=31 Identities=29% Similarity=0.580 Sum_probs=21.0
Q ss_pred cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300 22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR 62 (68)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (68)
.||+|+..-...|=+ || ...++.-|+.|+-.
T Consensus 4 ~CP~C~~~f~v~~~~-------l~---~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDK-------LP---AGGRKVRCPKCGHV 34 (37)
T ss_pred ECCCCCceEEcCHHH-------cc---cCCcEEECCCCCcE
Confidence 599999877665532 22 45668888888764
No 252
>TIGR02646 conserved hypothetical protein TIGR02646. Members of this uncharacterized protein family are found exclusively in bacteria. Neighboring genes in various genomes are also uncharacterized or may annotated as similar to restriction system proteins.
Probab=21.82 E-value=26 Score=23.23 Aligned_cols=16 Identities=19% Similarity=0.532 Sum_probs=12.3
Q ss_pred CCCCcCCCCCCceEEE
Q 035300 18 GADAACPYCGGPVLAI 33 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~a~ 33 (68)
-+.|.|+||+-.+...
T Consensus 22 ~~~~~C~YC~~~~~~~ 37 (144)
T TIGR02646 22 LQGGLCAYCEREIELL 37 (144)
T ss_pred HhCCCcCccCCCcCCC
Confidence 3579999999966643
No 253
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=21.76 E-value=35 Score=21.28 Aligned_cols=8 Identities=50% Similarity=1.252 Sum_probs=6.3
Q ss_pred CcCCCCCC
Q 035300 21 AACPYCGG 28 (68)
Q Consensus 21 G~Cp~CGG 28 (68)
-.||+||.
T Consensus 18 lrCPRC~~ 25 (65)
T COG4049 18 LRCPRCGM 25 (65)
T ss_pred eeCCchhH
Confidence 46999984
No 254
>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=21.67 E-value=69 Score=21.38 Aligned_cols=14 Identities=36% Similarity=0.885 Sum_probs=10.4
Q ss_pred CCCCcCCCCCCceE
Q 035300 18 GADAACPYCGGPVL 31 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~ 31 (68)
+.+..||.|||.+.
T Consensus 127 ~~~~~C~~C~~~lr 140 (178)
T PF02146_consen 127 EEPPRCPKCGGLLR 140 (178)
T ss_dssp TSSCBCTTTSCBEE
T ss_pred cccccccccCccCC
Confidence 45569999999543
No 255
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=21.49 E-value=38 Score=19.31 Aligned_cols=8 Identities=50% Similarity=1.252 Sum_probs=6.4
Q ss_pred cCCCCCCc
Q 035300 22 ACPYCGGP 29 (68)
Q Consensus 22 ~Cp~CGG~ 29 (68)
-||-||+-
T Consensus 11 ~CPgCG~t 18 (52)
T PF10825_consen 11 PCPGCGMT 18 (52)
T ss_pred CCCCCcHH
Confidence 49999974
No 256
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=21.24 E-value=46 Score=21.02 Aligned_cols=11 Identities=45% Similarity=1.026 Sum_probs=6.5
Q ss_pred cCCCCCCceEE
Q 035300 22 ACPYCGGPVLA 32 (68)
Q Consensus 22 ~Cp~CGG~v~a 32 (68)
.||.||--.-.
T Consensus 3 ~CPCCg~~Tl~ 13 (78)
T PF14206_consen 3 PCPCCGYYTLE 13 (78)
T ss_pred cCCCCCcEEec
Confidence 47777755443
No 257
>KOG0373 consensus Serine/threonine specific protein phosphatase involved in cell cycle control, PP2A-related [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=21.08 E-value=86 Score=24.51 Aligned_cols=26 Identities=23% Similarity=0.447 Sum_probs=22.6
Q ss_pred eeeecCCCCcCCCCCCceEEEEecce
Q 035300 13 VIRRNGADAACPYCGGPVLAIDFDAH 38 (68)
Q Consensus 13 v~~~~~A~G~Cp~CGG~v~a~Dves~ 38 (68)
++---.||.-|-|||-.++++.++..
T Consensus 253 lvTVWSAPNYCYRCGNvAsi~~~d~~ 278 (306)
T KOG0373|consen 253 LVTVWSAPNYCYRCGNVASIMSFDDN 278 (306)
T ss_pred EEEEecCCchhhhccCeeeEEEeccc
Confidence 66677899999999999999988754
No 258
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=20.95 E-value=78 Score=24.12 Aligned_cols=17 Identities=29% Similarity=0.790 Sum_probs=13.1
Q ss_pred CCcCCCCCCceEEEEec
Q 035300 20 DAACPYCGGPVLAIDFD 36 (68)
Q Consensus 20 ~G~Cp~CGG~v~a~Dve 36 (68)
.--|++||+.++-.-+.
T Consensus 245 GepC~~CGt~I~k~~~~ 261 (273)
T COG0266 245 GEPCRRCGTPIEKIKLG 261 (273)
T ss_pred CCCCCccCCEeEEEEEc
Confidence 34599999999876654
No 259
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=20.78 E-value=43 Score=20.46 Aligned_cols=12 Identities=33% Similarity=1.007 Sum_probs=8.0
Q ss_pred ecCCCCcCCCCC
Q 035300 16 RNGADAACPYCG 27 (68)
Q Consensus 16 ~~~A~G~Cp~CG 27 (68)
.|..+-.||.||
T Consensus 44 k~~~~Y~CP~CG 55 (59)
T PRK14890 44 KQSNPYTCPKCG 55 (59)
T ss_pred hcCCceECCCCC
Confidence 355666777776
No 260
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=20.73 E-value=1.6e+02 Score=15.76 Aligned_cols=31 Identities=19% Similarity=0.389 Sum_probs=19.8
Q ss_pred ecCCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300 16 RNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR 62 (68)
Q Consensus 16 ~~~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (68)
+-..|..|..|+..+ ....+..|.|+.|+..
T Consensus 7 ~~~~~~~C~~C~~~i----------------~g~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 7 TFSKPTYCDVCGKFI----------------WGLGKQGYRCSWCGLV 37 (53)
T ss_dssp ESSSTEB-TTSSSBE----------------CSSSSCEEEETTTT-E
T ss_pred cCCCCCCCcccCccc----------------CCCCCCeEEECCCCCh
Confidence 446778888888876 1145667788888754
No 261
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=20.52 E-value=1e+02 Score=17.73 Aligned_cols=14 Identities=21% Similarity=0.570 Sum_probs=7.1
Q ss_pred CCCCcCCCCCCceE
Q 035300 18 GADAACPYCGGPVL 31 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~ 31 (68)
...|.|..|++.-.
T Consensus 52 ~~~~~C~~C~~~~~ 65 (69)
T PF09012_consen 52 CCGGSCSSCGPASK 65 (69)
T ss_dssp -SSSSSSS-SS---
T ss_pred CCCCCCCCCCCccc
Confidence 33688999987643
No 262
>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=20.52 E-value=48 Score=18.85 Aligned_cols=14 Identities=21% Similarity=0.733 Sum_probs=7.8
Q ss_pred ecceEEeeccccee
Q 035300 50 VKKKFYCTICSRRL 63 (68)
Q Consensus 50 ~krk~~Ct~C~r~L 63 (68)
..||+.|..||+..
T Consensus 22 ~~rrhhCr~CG~~v 35 (69)
T PF01363_consen 22 FRRRHHCRNCGRVV 35 (69)
T ss_dssp SS-EEE-TTT--EE
T ss_pred ceeeEccCCCCCEE
Confidence 58899999998754
No 263
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=20.45 E-value=43 Score=17.31 Aligned_cols=9 Identities=56% Similarity=1.416 Sum_probs=3.0
Q ss_pred CCCCCCceE
Q 035300 23 CPYCGGPVL 31 (68)
Q Consensus 23 Cp~CGG~v~ 31 (68)
|++||-...
T Consensus 1 C~~C~~~~~ 9 (47)
T PF01844_consen 1 CQYCGKPGS 9 (47)
T ss_dssp -TTT--B--
T ss_pred CCCCCCcCc
Confidence 677777653
No 264
>PF04400 DUF539: Protein of unknown function (DUF539); InterPro: IPR007495 This is a family of putative periplasmic proteins.
Probab=20.43 E-value=30 Score=20.08 Aligned_cols=22 Identities=23% Similarity=0.504 Sum_probs=15.5
Q ss_pred eeeecCCCCcCCCCCCceEEEEecce
Q 035300 13 VIRRNGADAACPYCGGPVLAIDFDAH 38 (68)
Q Consensus 13 v~~~~~A~G~Cp~CGG~v~a~Dves~ 38 (68)
++++++-.||| |++.++.++..
T Consensus 2 i~~rk~I~GSC----GGl~~lGi~~~ 23 (45)
T PF04400_consen 2 IFGRKPIKGSC----GGLGALGIDKE 23 (45)
T ss_pred cccCCcccccc----hhhhhcCCCcc
Confidence 35788999997 45666777654
No 265
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=20.38 E-value=70 Score=19.46 Aligned_cols=21 Identities=14% Similarity=0.431 Sum_probs=16.9
Q ss_pred eeeeeecceEEeecccceeee
Q 035300 45 PISHKVKKKFYCTICSRRLVP 65 (68)
Q Consensus 45 P~~~k~krk~~Ct~C~r~L~~ 65 (68)
.++.+.-....|..||+.|.-
T Consensus 22 ~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 22 VVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EEEecCCcEEECcccCCCccc
Confidence 467778888999999998853
No 266
>cd00296 SIR2 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic
Probab=20.35 E-value=45 Score=22.59 Aligned_cols=14 Identities=36% Similarity=0.876 Sum_probs=10.5
Q ss_pred CCCCcCCCCCCceE
Q 035300 18 GADAACPYCGGPVL 31 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~ 31 (68)
.....||.|||.+.
T Consensus 132 ~~~p~C~~C~~~l~ 145 (222)
T cd00296 132 EKPPRCPKCGGLLR 145 (222)
T ss_pred cCCCCCCCCCCccc
Confidence 34677999999754
No 267
>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=20.17 E-value=1.1e+02 Score=23.27 Aligned_cols=26 Identities=23% Similarity=0.437 Sum_probs=19.2
Q ss_pred EEEeCCceeeeeecCCCC--cCCCCCCc
Q 035300 4 LSIFDLREKVIRRNGADA--ACPYCGGP 29 (68)
Q Consensus 4 ~~vcde~~kv~~~~~A~G--~Cp~CGG~ 29 (68)
++==||+||-+----..| -|++||..
T Consensus 134 FY~RDqkEK~v~~c~~tgriyCS~CGS~ 161 (245)
T PF03117_consen 134 FYYRDQKEKQVIYCATTGRIYCSLCGSQ 161 (245)
T ss_pred eEeccccceeEEEeccCCCEEEccCCCC
Confidence 455688888777655555 59999986
No 268
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=20.09 E-value=60 Score=26.45 Aligned_cols=12 Identities=42% Similarity=1.115 Sum_probs=9.6
Q ss_pred CCCcCCCCCCce
Q 035300 19 ADAACPYCGGPV 30 (68)
Q Consensus 19 A~G~Cp~CGG~v 30 (68)
..|.||.|||.+
T Consensus 588 ~~~~CPkCg~~l 599 (618)
T TIGR01057 588 VVGKCPKCGGKL 599 (618)
T ss_pred ccCCCCcCCCee
Confidence 458899999863
No 269
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=20.00 E-value=82 Score=26.61 Aligned_cols=15 Identities=27% Similarity=0.596 Sum_probs=12.8
Q ss_pred CCCCcCCCCCCceEE
Q 035300 18 GADAACPYCGGPVLA 32 (68)
Q Consensus 18 ~A~G~Cp~CGG~v~a 32 (68)
..|-.||.||..++-
T Consensus 421 ~~P~~CP~C~~~l~~ 435 (689)
T PRK14351 421 EFPDTCPVCDSAVER 435 (689)
T ss_pred cCCCCCCCCCCEeee
Confidence 468999999999863
Done!