Query 046214
Match_columns 66
No_of_seqs 48 out of 50
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 09:49:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046214.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046214hhsearch_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 95.2 0.044 9.5E-07 29.8 3.6 41 20-60 2-47 (47)
2 PF14690 zf-ISL3: zinc-finger 93.9 0.1 2.2E-06 28.1 3.2 38 20-59 2-47 (47)
3 PF04216 FdhE: Protein involve 93.3 0.037 8E-07 40.1 1.0 43 19-61 171-219 (290)
4 PF10601 zf-LITAF-like: LITAF- 93.3 0.05 1.1E-06 32.3 1.4 50 15-65 2-70 (73)
5 PF11672 DUF3268: Protein of u 93.3 0.077 1.7E-06 34.9 2.4 39 20-63 2-41 (102)
6 PF12760 Zn_Tnp_IS1595: Transp 92.7 0.15 3.2E-06 28.3 2.7 28 21-62 19-46 (46)
7 PRK00464 nrdR transcriptional 92.6 0.1 2.2E-06 36.1 2.3 37 22-64 2-39 (154)
8 PF06906 DUF1272: Protein of u 91.4 0.093 2E-06 32.0 0.9 13 20-32 41-53 (57)
9 COG3813 Uncharacterized protei 90.9 0.094 2E-06 34.0 0.6 18 19-36 40-57 (84)
10 COG1998 RPS31 Ribosomal protei 90.8 0.12 2.7E-06 30.8 1.1 36 9-62 11-46 (51)
11 TIGR03831 YgiT_finger YgiT-typ 89.7 0.82 1.8E-05 24.0 3.6 43 23-65 1-44 (46)
12 PF13240 zinc_ribbon_2: zinc-r 89.5 0.098 2.1E-06 26.0 -0.1 9 23-31 2-10 (23)
13 PF13248 zf-ribbon_3: zinc-rib 89.4 0.11 2.4E-06 26.1 0.0 9 22-30 4-12 (26)
14 TIGR03830 CxxCG_CxxCG_HTH puta 88.6 1.1 2.3E-05 27.9 4.1 41 23-64 1-42 (127)
15 TIGR03655 anti_R_Lar restricti 88.6 0.35 7.5E-06 27.5 1.7 35 22-64 3-37 (53)
16 PF07282 OrfB_Zn_ribbon: Putat 88.2 0.39 8.5E-06 27.7 1.9 30 19-63 27-56 (69)
17 PF01927 Mut7-C: Mut7-C RNAse 87.9 0.55 1.2E-05 31.2 2.6 44 20-63 91-134 (147)
18 smart00661 RPOL9 RNA polymeras 87.7 0.37 8.1E-06 26.3 1.5 29 22-63 2-30 (52)
19 PRK12775 putative trifunctiona 87.1 0.2 4.3E-06 42.5 0.2 28 7-34 824-852 (1006)
20 PRK00432 30S ribosomal protein 86.9 0.87 1.9E-05 26.2 2.8 37 7-63 11-47 (50)
21 COG0675 Transposase and inacti 86.1 0.46 9.9E-06 32.4 1.5 24 19-62 308-331 (364)
22 PRK10445 endonuclease VIII; Pr 85.7 0.94 2E-05 32.8 3.0 29 19-60 234-262 (263)
23 PRK14810 formamidopyrimidine-D 85.6 0.75 1.6E-05 33.5 2.5 26 22-60 246-271 (272)
24 PRK13945 formamidopyrimidine-D 84.7 0.86 1.9E-05 33.3 2.4 27 21-60 255-281 (282)
25 TIGR01562 FdhE formate dehydro 84.6 0.41 8.8E-06 36.3 0.8 45 18-62 182-233 (305)
26 PRK00420 hypothetical protein; 84.4 0.83 1.8E-05 30.5 2.1 30 19-64 22-51 (112)
27 smart00714 LITAF Possible memb 83.4 0.63 1.4E-05 27.2 1.1 47 18-65 1-64 (67)
28 PF14354 Lar_restr_allev: Rest 83.3 1.2 2.6E-05 25.1 2.2 33 22-61 5-37 (61)
29 PF12773 DZR: Double zinc ribb 83.0 0.32 7E-06 26.6 -0.3 14 50-63 26-39 (50)
30 TIGR00577 fpg formamidopyrimid 82.1 1.3 2.7E-05 32.3 2.4 26 21-59 246-271 (272)
31 PF14803 Nudix_N_2: Nudix N-te 81.9 1.1 2.3E-05 24.3 1.5 29 22-61 2-30 (34)
32 PRK03564 formate dehydrogenase 81.8 0.86 1.9E-05 34.7 1.6 43 19-61 186-234 (309)
33 PF14369 zf-RING_3: zinc-finge 81.5 1.1 2.4E-05 24.1 1.5 14 17-30 18-31 (35)
34 PF08271 TF_Zn_Ribbon: TFIIB z 81.2 1.7 3.6E-05 23.6 2.2 29 22-64 2-30 (43)
35 PRK00398 rpoP DNA-directed RNA 80.9 2.7 5.8E-05 23.0 3.0 13 20-32 21-33 (46)
36 PRK01103 formamidopyrimidine/5 80.9 1.6 3.5E-05 31.6 2.7 28 21-61 246-273 (274)
37 TIGR01206 lysW lysine biosynth 80.5 1.8 3.9E-05 25.5 2.3 32 21-65 3-34 (54)
38 PF09297 zf-NADH-PPase: NADH p 80.4 1.1 2.4E-05 23.0 1.3 16 21-36 4-19 (32)
39 cd00729 rubredoxin_SM Rubredox 80.1 2.5 5.4E-05 22.4 2.6 16 15-30 13-28 (34)
40 COG1645 Uncharacterized Zn-fin 80.1 1.5 3.4E-05 30.1 2.2 28 20-64 28-55 (131)
41 PRK14811 formamidopyrimidine-D 79.4 1.7 3.8E-05 31.6 2.4 28 21-61 236-263 (269)
42 PRK09678 DNA-binding transcrip 77.5 2.4 5.2E-05 26.3 2.3 37 22-65 3-41 (72)
43 PF01599 Ribosomal_S27: Riboso 77.4 3.2 6.8E-05 24.1 2.6 38 5-60 6-45 (47)
44 COG3464 Transposase and inacti 77.2 3.7 8.1E-05 31.7 3.7 46 18-63 36-87 (402)
45 PF05129 Elf1: Transcription e 76.2 3 6.6E-05 25.9 2.5 37 18-64 20-57 (81)
46 PF06827 zf-FPG_IleRS: Zinc fi 74.9 4.5 9.8E-05 20.3 2.6 14 22-35 3-16 (30)
47 TIGR00310 ZPR1_znf ZPR1 zinc f 74.6 3.1 6.8E-05 29.6 2.6 38 22-63 2-40 (192)
48 TIGR00622 ssl1 transcription f 73.6 1.6 3.4E-05 29.3 0.8 9 22-30 3-11 (112)
49 PF08792 A2L_zn_ribbon: A2L zi 71.8 5.4 0.00012 21.3 2.5 26 22-62 5-30 (33)
50 smart00531 TFIIE Transcription 71.1 2.2 4.8E-05 28.3 1.1 14 21-34 124-137 (147)
51 PF03119 DNA_ligase_ZBD: NAD-d 69.7 3.3 7.3E-05 21.2 1.3 18 22-39 1-18 (28)
52 PF14255 Cys_rich_CPXG: Cystei 69.4 3.7 8.1E-05 24.0 1.7 11 22-32 2-12 (52)
53 COG1656 Uncharacterized conser 69.2 1.5 3.3E-05 31.2 -0.0 45 17-63 94-140 (165)
54 TIGR00340 zpr1_rel ZPR1-relate 68.4 5.1 0.00011 27.9 2.4 35 23-62 1-37 (163)
55 PF09723 Zn-ribbon_8: Zinc rib 68.2 6.7 0.00014 21.3 2.4 12 17-28 23-34 (42)
56 smart00834 CxxC_CXXC_SSSS Puta 67.9 3.9 8.4E-05 21.1 1.4 12 18-29 24-35 (41)
57 TIGR00373 conserved hypothetic 67.8 3 6.5E-05 28.3 1.2 16 19-34 127-142 (158)
58 PF04606 Ogr_Delta: Ogr/Delta- 66.9 3.7 8.1E-05 22.8 1.3 13 22-34 1-13 (47)
59 PRK09401 reverse gyrase; Revie 66.2 2.3 5E-05 37.2 0.5 14 20-33 7-20 (1176)
60 PRK09710 lar restriction allev 65.5 9.4 0.0002 23.6 3.0 30 21-62 7-36 (64)
61 COG1592 Rubrerythrin [Energy p 65.5 5.5 0.00012 28.1 2.2 12 18-29 147-158 (166)
62 PF07038 DUF1324: Protein of u 65.4 5.2 0.00011 24.3 1.8 15 37-51 7-21 (59)
63 PF09862 DUF2089: Protein of u 64.9 5.1 0.00011 26.8 1.8 14 23-36 1-14 (113)
64 COG1110 Reverse gyrase [DNA re 64.2 3 6.6E-05 37.3 0.8 20 20-39 8-27 (1187)
65 PF06221 zf-C2HC5: Putative zi 64.0 3.7 8E-05 24.6 0.9 24 11-34 25-49 (57)
66 PF13894 zf-C2H2_4: C2H2-type 63.6 4 8.8E-05 18.0 0.8 11 54-64 1-11 (24)
67 PF05191 ADK_lid: Adenylate ki 62.9 4.9 0.00011 21.7 1.2 15 17-31 18-32 (36)
68 COG1996 RPC10 DNA-directed RNA 62.8 3.9 8.5E-05 23.9 0.9 14 19-32 23-36 (49)
69 TIGR02098 MJ0042_CXXC MJ0042 f 62.3 5.7 0.00012 20.6 1.4 13 52-64 24-36 (38)
70 PF14787 zf-CCHC_5: GAG-polypr 62.1 3.6 7.7E-05 23.0 0.6 10 20-29 2-11 (36)
71 COG1933 Archaeal DNA polymeras 62.1 1.5 3.3E-05 33.2 -1.2 24 7-30 141-164 (253)
72 PRK11827 hypothetical protein; 61.6 6.9 0.00015 23.6 1.8 27 22-63 10-36 (60)
73 PF14353 CpXC: CpXC protein 61.5 7.4 0.00016 24.8 2.1 36 11-46 29-70 (128)
74 cd00350 rubredoxin_like Rubred 61.4 9.9 0.00022 19.7 2.2 12 19-30 16-27 (33)
75 smart00778 Prim_Zn_Ribbon Zinc 61.0 4.7 0.0001 22.2 0.9 10 20-29 3-12 (37)
76 TIGR01054 rgy reverse gyrase. 60.5 3.7 7.9E-05 35.9 0.7 14 20-33 7-20 (1171)
77 TIGR01384 TFS_arch transcripti 59.9 5 0.00011 24.8 1.0 9 22-30 2-10 (104)
78 PF06677 Auto_anti-p27: Sjogre 59.9 4.9 0.00011 22.5 0.9 17 44-60 25-41 (41)
79 PF09947 DUF2180: Uncharacteri 59.7 1.7 3.7E-05 27.0 -1.1 57 4-63 3-66 (68)
80 PRK06266 transcription initiat 59.6 4.9 0.00011 28.0 1.1 16 19-34 135-150 (178)
81 PF01396 zf-C4_Topoisom: Topoi 59.4 6.9 0.00015 21.2 1.4 13 21-33 2-14 (39)
82 PF13465 zf-H2C2_2: Zinc-finge 58.1 5.9 0.00013 19.4 0.9 15 50-64 11-25 (26)
83 PF10263 SprT-like: SprT-like 58.0 9.5 0.00021 24.5 2.1 14 52-65 142-155 (157)
84 PF08273 Prim_Zn_Ribbon: Zinc- 57.9 3.9 8.5E-05 22.8 0.3 30 21-60 4-33 (40)
85 COG4391 Uncharacterized protei 57.4 9.1 0.0002 23.6 1.9 46 11-65 15-60 (62)
86 PRK12380 hydrogenase nickel in 56.6 6.7 0.00014 25.4 1.2 18 11-28 61-78 (113)
87 PF13453 zf-TFIIB: Transcripti 55.7 13 0.00027 19.9 2.1 12 23-34 2-13 (41)
88 PF12171 zf-C2H2_jaz: Zinc-fin 55.3 3.5 7.5E-05 20.1 -0.2 13 53-65 1-13 (27)
89 smart00709 Zpr1 Duplicated dom 55.2 16 0.00034 25.2 3.0 34 22-62 2-38 (160)
90 smart00659 RPOLCX RNA polymera 55.0 16 0.00034 20.5 2.4 14 18-31 17-30 (44)
91 PRK00241 nudC NADH pyrophospha 54.8 8.8 0.00019 27.8 1.7 13 20-32 99-111 (256)
92 PF04438 zf-HIT: HIT zinc fing 54.7 4.4 9.4E-05 21.1 0.1 16 47-63 8-23 (30)
93 PF04828 GFA: Glutathione-depe 54.5 8 0.00017 22.1 1.2 18 47-64 42-59 (92)
94 PF09538 FYDLN_acid: Protein o 53.3 6.5 0.00014 25.8 0.8 15 19-33 25-39 (108)
95 TIGR02605 CxxC_CxxC_SSSS putat 52.8 31 0.00068 18.7 3.4 11 18-28 24-34 (52)
96 TIGR00100 hypA hydrogenase nic 52.5 7.3 0.00016 25.2 0.9 18 11-28 61-78 (115)
97 PF07754 DUF1610: Domain of un 52.5 6.5 0.00014 20.0 0.5 10 18-27 14-23 (24)
98 PF02701 zf-Dof: Dof domain, z 52.5 6.4 0.00014 24.4 0.6 36 18-61 3-38 (63)
99 PRK05580 primosome assembly pr 52.0 12 0.00025 30.6 2.2 27 21-62 391-417 (679)
100 PRK14701 reverse gyrase; Provi 52.0 6.6 0.00014 35.8 0.9 17 20-36 6-22 (1638)
101 PF03966 Trm112p: Trm112p-like 51.1 19 0.00041 21.0 2.5 16 49-64 49-64 (68)
102 smart00132 LIM Zinc-binding do 50.7 6.8 0.00015 19.1 0.5 35 23-64 2-38 (39)
103 PRK14892 putative transcriptio 50.1 18 0.00039 23.5 2.5 33 18-62 19-51 (99)
104 PRK14873 primosome assembly pr 49.7 14 0.00029 30.7 2.3 12 21-32 393-404 (665)
105 PHA00626 hypothetical protein 49.1 21 0.00045 21.9 2.5 32 22-63 2-33 (59)
106 PF10571 UPF0547: Uncharacteri 48.7 9.2 0.0002 19.4 0.8 13 18-30 12-24 (26)
107 COG1571 Predicted DNA-binding 48.6 11 0.00023 30.3 1.5 34 16-65 346-379 (421)
108 PF00096 zf-C2H2: Zinc finger, 48.5 11 0.00023 17.2 0.9 11 54-64 1-11 (23)
109 PRK04351 hypothetical protein; 48.3 21 0.00045 24.4 2.6 16 50-65 129-144 (149)
110 COG2093 DNA-directed RNA polym 48.0 12 0.00025 23.3 1.3 16 22-37 20-44 (64)
111 PRK09521 exosome complex RNA-b 47.8 18 0.00039 24.8 2.3 26 22-63 151-176 (189)
112 PRK04023 DNA polymerase II lar 47.3 9.4 0.0002 34.1 1.0 20 45-64 655-674 (1121)
113 PF06689 zf-C4_ClpX: ClpX C4-t 46.3 6.7 0.00014 21.4 -0.0 10 54-63 2-11 (41)
114 PF05605 zf-Di19: Drought indu 46.2 9.7 0.00021 21.2 0.7 37 22-63 4-41 (54)
115 PRK03824 hypA hydrogenase nick 46.1 15 0.00032 24.4 1.7 50 11-62 61-116 (135)
116 COG1675 TFA1 Transcription ini 46.0 7.8 0.00017 27.6 0.3 14 21-34 133-146 (176)
117 PF13717 zinc_ribbon_4: zinc-r 45.8 11 0.00023 20.1 0.7 30 22-61 4-33 (36)
118 PRK00762 hypA hydrogenase nick 44.6 10 0.00022 24.9 0.7 9 21-29 93-101 (124)
119 TIGR00155 pqiA_fam integral me 44.5 12 0.00026 29.0 1.2 30 22-64 15-44 (403)
120 PF06750 DiS_P_DiS: Bacterial 44.0 3.7 8.1E-05 25.8 -1.4 37 19-63 32-68 (92)
121 PRK03681 hypA hydrogenase nick 43.7 16 0.00035 23.6 1.5 18 11-28 61-78 (114)
122 TIGR00244 transcriptional regu 43.7 18 0.00038 25.4 1.8 38 22-65 2-40 (147)
123 PF02150 RNA_POL_M_15KD: RNA p 43.6 22 0.00048 18.9 1.8 14 22-35 3-16 (35)
124 PF05280 FlhC: Flagellar trans 42.4 14 0.0003 26.0 1.1 26 22-60 136-161 (175)
125 PF07503 zf-HYPF: HypF finger; 42.4 7.6 0.00017 21.0 -0.1 18 17-34 18-35 (35)
126 cd04476 RPA1_DBD_C RPA1_DBD_C: 42.4 15 0.00032 24.2 1.2 11 52-62 50-60 (166)
127 COG1867 TRM1 N2,N2-dimethylgua 42.1 23 0.00049 28.3 2.4 30 3-32 239-269 (380)
128 PF01485 IBR: IBR domain; Int 41.9 5 0.00011 21.9 -1.0 26 14-39 12-39 (64)
129 PF12172 DUF35_N: Rubredoxin-l 41.5 9.9 0.00021 19.8 0.2 22 6-29 13-34 (37)
130 COG1779 C4-type Zn-finger prot 41.2 28 0.00061 25.6 2.6 42 17-63 11-53 (201)
131 PF03367 zf-ZPR1: ZPR1 zinc-fi 41.1 32 0.00068 23.6 2.7 37 22-63 3-40 (161)
132 PF09855 DUF2082: Nucleic-acid 40.9 58 0.0013 19.6 3.6 10 52-61 35-44 (64)
133 PRK00423 tfb transcription ini 40.8 25 0.00054 26.0 2.3 31 20-64 11-41 (310)
134 PF03604 DNA_RNApol_7kD: DNA d 40.4 18 0.00039 19.2 1.1 14 17-30 14-27 (32)
135 cd00730 rubredoxin Rubredoxin; 40.0 29 0.00063 19.9 2.1 13 18-30 32-44 (50)
136 COG2260 Predicted Zn-ribbon RN 39.8 12 0.00026 22.9 0.4 13 20-32 17-29 (59)
137 PF06054 CoiA: Competence prot 39.6 23 0.0005 27.1 2.0 16 18-33 28-43 (375)
138 COG5349 Uncharacterized protei 39.5 13 0.00027 25.8 0.5 12 18-29 19-30 (126)
139 PF12874 zf-met: Zinc-finger o 39.3 18 0.00038 16.7 0.9 12 54-65 1-12 (25)
140 smart00019 SF_P Pulmonary surf 39.0 15 0.00032 26.8 0.8 22 4-25 101-122 (191)
141 TIGR00354 polC DNA polymerase, 38.9 21 0.00046 31.9 1.9 20 14-33 1022-1041(1095)
142 PF04423 Rad50_zn_hook: Rad50 38.5 13 0.00028 20.8 0.4 13 18-30 18-30 (54)
143 PF06957 COPI_C: Coatomer (COP 38.3 25 0.00054 28.0 2.1 31 34-65 359-392 (422)
144 PRK04023 DNA polymerase II lar 38.2 23 0.00049 31.9 2.0 20 14-33 1047-1066(1121)
145 PF07213 DAP10: DAP10 membrane 38.0 14 0.00031 23.6 0.6 15 14-28 16-30 (79)
146 PRK05320 rhodanese superfamily 37.9 21 0.00045 25.9 1.5 28 4-31 226-255 (257)
147 COG1439 Predicted nucleic acid 37.6 36 0.00078 24.5 2.6 15 18-32 151-165 (177)
148 PF13395 HNH_4: HNH endonuclea 37.6 11 0.00024 21.2 0.0 13 23-35 1-13 (54)
149 PRK15103 paraquat-inducible me 37.4 21 0.00046 27.9 1.5 31 21-64 11-41 (419)
150 PF11793 FANCL_C: FANCL C-term 36.9 15 0.00033 21.8 0.6 16 17-32 52-67 (70)
151 PRK00564 hypA hydrogenase nick 36.8 15 0.00033 23.8 0.6 16 12-27 63-78 (117)
152 PF09889 DUF2116: Uncharacteri 36.7 16 0.00035 21.9 0.6 11 21-31 4-14 (59)
153 PRK14714 DNA polymerase II lar 36.3 24 0.00053 32.2 1.9 20 14-33 1263-1282(1337)
154 PF00301 Rubredoxin: Rubredoxi 36.3 25 0.00055 20.0 1.4 8 22-29 36-43 (47)
155 PRK05978 hypothetical protein; 36.2 18 0.0004 25.0 0.9 34 18-65 31-64 (148)
156 COG1405 SUA7 Transcription ini 36.2 31 0.00068 25.9 2.2 30 21-64 2-31 (285)
157 TIGR00375 conserved hypothetic 36.1 17 0.00038 28.3 0.9 11 20-31 259-269 (374)
158 PF12660 zf-TFIIIC: Putative z 35.9 17 0.00037 23.0 0.7 14 17-30 85-98 (99)
159 PRK06393 rpoE DNA-directed RNA 35.6 20 0.00043 22.0 0.9 9 21-29 18-26 (64)
160 COG1096 Predicted RNA-binding 35.2 34 0.00073 24.9 2.2 25 21-62 150-174 (188)
161 PRK14715 DNA polymerase II lar 35.0 26 0.00057 32.6 1.9 20 14-33 1551-1570(1627)
162 PRK08173 DNA topoisomerase III 34.9 37 0.00081 29.0 2.7 14 17-30 723-736 (862)
163 PHA02942 putative transposase; 34.7 24 0.00051 27.1 1.4 28 20-63 325-352 (383)
164 PF04879 Molybdop_Fe4S4: Molyb 34.7 10 0.00022 20.8 -0.4 13 17-29 2-14 (55)
165 PF01096 TFIIS_C: Transcriptio 34.6 26 0.00056 18.8 1.2 11 22-32 2-12 (39)
166 smart00507 HNHc HNH nucleases. 34.4 21 0.00045 17.9 0.8 11 21-31 11-21 (52)
167 PF08394 Arc_trans_TRASH: Arch 34.3 19 0.00041 19.9 0.6 30 23-63 1-33 (37)
168 PF08209 Sgf11: Sgf11 (transcr 33.8 17 0.00037 19.5 0.4 13 22-34 6-18 (33)
169 COG1594 RPB9 DNA-directed RNA 33.6 43 0.00094 21.8 2.3 11 22-32 4-14 (113)
170 PF14375 Cys_rich_CWC: Cystein 33.5 21 0.00045 20.0 0.7 11 23-33 1-11 (50)
171 KOG3456 NADH:ubiquinone oxidor 33.2 18 0.0004 24.8 0.5 12 17-28 101-112 (120)
172 PF09334 tRNA-synt_1g: tRNA sy 32.9 28 0.0006 26.6 1.5 22 6-27 122-143 (391)
173 KOG1598 Transcription initiati 32.9 25 0.00054 29.1 1.3 29 22-64 2-30 (521)
174 PF03884 DUF329: Domain of unk 32.3 10 0.00023 22.6 -0.7 13 22-34 4-16 (57)
175 PF02591 DUF164: Putative zinc 32.3 20 0.00044 20.1 0.6 35 20-63 22-56 (56)
176 TIGR00595 priA primosomal prot 31.6 27 0.00058 27.6 1.3 14 16-29 249-262 (505)
177 cd04467 S1_aIF5A S1_aIF5A: Arc 31.5 28 0.00061 20.6 1.1 15 27-41 13-27 (57)
178 PRK14559 putative protein seri 31.5 19 0.0004 30.0 0.4 9 55-63 43-51 (645)
179 PLN03086 PRLI-interacting fact 31.4 8.1 0.00018 31.9 -1.7 45 19-63 452-514 (567)
180 KOG4317 Predicted Zn-finger pr 31.3 20 0.00044 28.6 0.6 20 44-63 10-29 (383)
181 TIGR00308 TRM1 tRNA(guanine-26 31.3 35 0.00076 26.2 1.8 16 15-30 247-262 (374)
182 KOG0402 60S ribosomal protein 31.3 13 0.00027 24.6 -0.5 11 52-62 35-45 (92)
183 PF05741 zf-nanos: Nanos RNA b 30.9 15 0.00032 21.9 -0.2 10 52-61 32-41 (55)
184 PRK08351 DNA-directed RNA poly 30.7 22 0.00047 21.6 0.5 8 22-29 17-24 (61)
185 smart00647 IBR In Between Ring 29.7 51 0.0011 17.8 1.9 15 20-34 18-34 (64)
186 PRK12722 transcriptional activ 29.6 27 0.00059 25.1 0.9 14 21-34 135-148 (187)
187 PF13966 zf-RVT: zinc-binding 29.5 29 0.00062 20.6 0.9 15 17-31 56-70 (86)
188 smart00440 ZnF_C2C2 C2C2 Zinc 29.4 44 0.00095 18.0 1.6 11 22-32 2-12 (40)
189 COG3582 Predicted nucleic acid 28.9 29 0.00063 24.6 1.0 20 14-33 104-123 (162)
190 COG4888 Uncharacterized Zn rib 28.7 33 0.00072 23.0 1.2 16 50-65 19-34 (104)
191 PF03117 Herpes_UL49_1: UL49 f 28.5 41 0.00088 25.4 1.7 26 4-29 134-161 (245)
192 PF09845 DUF2072: Zn-ribbon co 28.4 24 0.00053 24.3 0.5 8 22-29 21-28 (131)
193 smart00064 FYVE Protein presen 28.4 36 0.00077 19.2 1.1 14 50-63 23-36 (68)
194 PF13912 zf-C2H2_6: C2H2-type 28.2 35 0.00075 16.0 0.9 11 54-64 2-12 (27)
195 PRK06260 threonine synthase; V 28.2 62 0.0014 24.4 2.7 23 11-33 10-32 (397)
196 PF01155 HypA: Hydrogenase exp 27.8 9.7 0.00021 24.4 -1.5 17 13-29 63-79 (113)
197 TIGR03031 cas_csx12 CRISPR-ass 27.7 28 0.0006 30.2 0.8 13 18-30 758-770 (802)
198 PRK01343 zinc-binding protein; 27.6 21 0.00046 21.4 0.1 13 19-31 8-20 (57)
199 COG4311 SoxD Sarcosine oxidase 27.4 27 0.00059 23.2 0.6 7 22-28 5-11 (97)
200 COG1885 Uncharacterized protei 27.1 1.1E+02 0.0023 21.0 3.4 30 20-49 49-78 (115)
201 COG1198 PriA Primosomal protei 26.9 48 0.0011 28.2 2.1 13 17-29 472-484 (730)
202 cd01407 SIR2-fam SIR2 family o 26.8 30 0.00066 23.9 0.8 11 20-30 133-143 (218)
203 COG2888 Predicted Zn-ribbon RN 26.7 26 0.00056 21.6 0.4 12 16-27 46-57 (61)
204 TIGR02159 PA_CoA_Oxy4 phenylac 26.6 29 0.00064 23.6 0.7 10 20-29 105-114 (146)
205 TIGR02300 FYDLN_acid conserved 26.6 35 0.00075 23.6 1.0 14 18-31 24-37 (129)
206 PF14447 Prok-RING_4: Prokaryo 26.6 25 0.00054 21.1 0.3 16 20-35 39-54 (55)
207 PRK12860 transcriptional activ 26.5 32 0.0007 24.8 0.9 13 21-33 135-147 (189)
208 PF09856 DUF2083: Predicted tr 26.2 71 0.0015 22.2 2.5 25 2-26 12-44 (156)
209 PRK00481 NAD-dependent deacety 26.1 31 0.00067 24.3 0.7 9 22-30 144-152 (242)
210 KOG2906 RNA polymerase III sub 26.0 39 0.00085 22.8 1.2 22 8-29 53-74 (105)
211 cd04482 RPA2_OBF_like RPA2_OBF 26.0 37 0.00081 20.9 1.0 10 18-27 82-91 (91)
212 PF06044 DRP: Dam-replacing fa 26.0 61 0.0013 24.7 2.3 34 20-65 31-65 (254)
213 PF13408 Zn_ribbon_recom: Reco 25.9 41 0.00089 18.0 1.1 11 22-32 7-17 (58)
214 cd01412 SIRT5_Af1_CobB SIRT5_A 25.5 33 0.00072 23.7 0.8 10 21-30 131-140 (224)
215 PF11023 DUF2614: Protein of u 25.4 26 0.00056 23.8 0.2 21 7-30 75-95 (114)
216 TIGR02443 conserved hypothetic 25.3 42 0.0009 20.4 1.1 17 15-31 4-20 (59)
217 PF05015 Plasmid_killer: Plasm 25.2 70 0.0015 19.6 2.1 19 28-46 62-80 (93)
218 PF13913 zf-C2HC_2: zinc-finge 25.2 34 0.00074 16.8 0.6 10 22-31 4-13 (25)
219 KOG3799 Rab3 effector RIM1 and 25.1 24 0.00051 25.4 -0.0 26 22-62 91-116 (169)
220 PF15616 TerY-C: TerY-C metal 25.0 53 0.0011 22.5 1.7 37 21-63 78-115 (131)
221 PRK13130 H/ACA RNA-protein com 24.8 25 0.00055 20.8 0.1 12 20-31 17-28 (56)
222 PF01363 FYVE: FYVE zinc finge 24.7 45 0.00097 18.8 1.1 14 50-63 22-35 (69)
223 PRK14724 DNA topoisomerase III 24.6 45 0.00098 29.0 1.6 14 17-30 752-765 (987)
224 PRK14138 NAD-dependent deacety 24.6 37 0.0008 24.3 0.9 11 20-30 143-153 (244)
225 PF02176 zf-TRAF: TRAF-type zi 24.5 12 0.00026 20.5 -1.3 39 19-64 8-53 (60)
226 KOG3362 Predicted BBOX Zn-fing 24.4 22 0.00049 25.3 -0.2 16 50-65 126-141 (156)
227 COG3809 Uncharacterized protei 24.4 35 0.00075 22.4 0.7 8 23-30 4-11 (88)
228 smart00451 ZnF_U1 U1-like zinc 24.3 33 0.00071 16.8 0.4 12 53-64 3-14 (35)
229 KOG2807 RNA polymerase II tran 24.2 42 0.00091 26.9 1.2 28 19-65 275-302 (378)
230 PF04400 DUF539: Protein of un 23.9 22 0.00048 20.5 -0.3 22 13-38 2-23 (45)
231 PF07295 DUF1451: Protein of u 23.5 88 0.0019 21.4 2.5 7 22-28 132-138 (146)
232 PRK06450 threonine synthase; V 23.5 83 0.0018 23.5 2.6 16 18-33 16-31 (338)
233 PF08772 NOB1_Zn_bind: Nin one 23.5 32 0.00069 21.3 0.3 10 20-29 24-33 (73)
234 COG2835 Uncharacterized conser 23.4 90 0.0019 19.0 2.3 27 22-63 10-36 (60)
235 TIGR01374 soxD sarcosine oxida 23.4 37 0.00079 21.7 0.6 6 22-27 3-8 (84)
236 TIGR02646 conserved hypothetic 23.3 27 0.00059 23.0 -0.0 17 17-33 21-37 (144)
237 PF01780 Ribosomal_L37ae: Ribo 23.2 30 0.00066 22.4 0.2 13 51-63 33-45 (90)
238 PRK00415 rps27e 30S ribosomal 23.2 61 0.0013 19.6 1.5 21 45-65 22-42 (59)
239 cd07973 Spt4 Transcription elo 23.2 39 0.00085 21.9 0.7 9 19-27 19-27 (98)
240 PF00130 C1_1: Phorbol esters/ 23.2 1.3E+02 0.0029 15.9 2.9 31 16-62 7-37 (53)
241 COG3024 Uncharacterized protei 23.1 31 0.00067 21.5 0.2 15 20-34 7-21 (65)
242 PF11682 DUF3279: Protein of u 22.6 64 0.0014 22.0 1.7 15 52-66 27-41 (128)
243 PRK07956 ligA NAD-dependent DN 22.4 75 0.0016 26.4 2.4 15 19-33 403-417 (665)
244 PRK05333 NAD-dependent deacety 22.4 41 0.00089 24.5 0.8 11 21-31 180-190 (285)
245 cd01411 SIR2H SIR2H: Uncharact 22.4 43 0.00093 23.6 0.9 11 20-30 136-146 (225)
246 PF13719 zinc_ribbon_5: zinc-r 22.3 37 0.00081 17.9 0.4 31 22-62 4-34 (37)
247 PF01258 zf-dskA_traR: Prokary 22.1 66 0.0014 16.6 1.4 14 20-33 3-16 (36)
248 smart00532 LIGANc Ligase N fam 22.1 81 0.0017 25.0 2.4 16 19-34 398-413 (441)
249 PF08063 PADR1: PADR1 (NUC008) 22.0 44 0.00095 19.4 0.7 17 18-34 12-28 (55)
250 PF04194 PDCD2_C: Programmed c 21.9 43 0.00093 22.7 0.8 11 20-30 97-107 (164)
251 PRK04338 N(2),N(2)-dimethylgua 21.8 67 0.0014 24.7 1.8 13 18-30 259-271 (382)
252 PF10825 DUF2752: Protein of u 21.8 38 0.00082 19.2 0.4 8 22-29 11-18 (52)
253 TIGR00575 dnlj DNA ligase, NAD 21.7 81 0.0017 26.1 2.4 15 19-33 391-405 (652)
254 PF00571 CBS: CBS domain CBS d 21.5 89 0.0019 16.1 1.8 14 3-16 32-45 (57)
255 PF04135 Nop10p: Nucleolar RNA 21.5 45 0.00097 19.7 0.7 12 21-32 18-29 (53)
256 PF14206 Cys_rich_CPCC: Cystei 21.4 47 0.001 20.9 0.8 11 22-32 3-13 (78)
257 PF09526 DUF2387: Probable met 21.4 54 0.0012 20.1 1.0 14 17-30 5-18 (71)
258 COG0266 Nei Formamidopyrimidin 21.2 76 0.0017 24.0 2.0 17 20-36 245-261 (273)
259 KOG0373 Serine/threonine speci 21.1 84 0.0018 24.4 2.2 26 13-38 253-278 (306)
260 COG4049 Uncharacterized protei 21.1 37 0.00081 21.1 0.3 8 21-28 18-25 (65)
261 cd01413 SIR2_Af2 SIR2_Af2: Arc 20.8 46 0.001 23.3 0.7 10 21-30 137-146 (222)
262 PF07191 zinc-ribbons_6: zinc- 20.7 90 0.0019 19.4 2.0 9 22-30 3-11 (70)
263 PF02146 SIR2: Sir2 family; I 20.7 69 0.0015 21.2 1.6 14 18-31 127-140 (178)
264 COG3043 NapB Nitrate reductase 20.7 45 0.00099 23.8 0.7 13 48-60 121-133 (155)
265 PF09151 DUF1936: Domain of un 20.4 53 0.0011 18.2 0.8 10 22-31 3-12 (36)
266 PRK14351 ligA NAD-dependent DN 20.1 83 0.0018 26.4 2.2 15 18-32 421-435 (689)
267 PF08646 Rep_fac-A_C: Replicat 20.1 74 0.0016 20.5 1.6 16 18-33 16-33 (146)
268 PRK11586 napB nitrate reductas 20.0 46 0.001 23.6 0.6 12 50-61 117-128 (149)
269 PRK09783 copper/silver efflux 20.0 57 0.0012 24.8 1.1 17 16-32 54-70 (409)
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=95.15 E-value=0.044 Score=29.84 Aligned_cols=41 Identities=27% Similarity=0.647 Sum_probs=29.3
Q ss_pred CCcCCCCCCceEEEEec-eeeEEEEEeeeeeec----cEEEeeccc
Q 046214 20 PGACPFCGGMIRAMDVQ-SEWRFCFLPLYFKTK----RKFYCTVCA 60 (66)
Q Consensus 20 pG~Cp~CGG~v~a~Dve-s~~rfCflP~~~k~k----rk~~Ct~C~ 60 (66)
+.+||.||+.+.-+-.+ .+-.|=++|.-++.. -+|.|+-|+
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 56899999999866555 556666788766543 367777775
No 2
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=93.90 E-value=0.1 Score=28.11 Aligned_cols=38 Identities=34% Similarity=0.826 Sum_probs=23.3
Q ss_pred CCcCCCCCCceEEE--EeceeeEEEEEee-----eee-eccEEEeecc
Q 046214 20 PGACPFCGGMIRAM--DVQSEWRFCFLPL-----YFK-TKRKFYCTVC 59 (66)
Q Consensus 20 pG~Cp~CGG~v~a~--Dves~~rfCflP~-----~~k-~krk~~Ct~C 59 (66)
|-.||+||..-..- -.+..|+ .+|+ +.+ .+++|.|..|
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 2334444 4444 433 3678988876
No 3
>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=93.30 E-value=0.037 Score=40.12 Aligned_cols=43 Identities=23% Similarity=0.458 Sum_probs=24.2
Q ss_pred CCCcCCCCCCceEEEEecee----eEEEEEeeeeeecc--EEEeecccc
Q 046214 19 APGACPFCGGMIRAMDVQSE----WRFCFLPLYFKTKR--KFYCTVCAR 61 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~Dves~----~rfCflP~~~k~kr--k~~Ct~C~r 61 (66)
..|.||-||+.-++.-+... .|+.+=.+|.-.|+ +..|+.||.
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 35999999999888887764 58888788765553 457888885
No 4
>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=93.29 E-value=0.05 Score=32.33 Aligned_cols=50 Identities=24% Similarity=0.670 Sum_probs=36.6
Q ss_pred eeccCCCcCCCCCCceEEEEecee-----------------eEEEEEeeeeee--ccEEEeecccceeee
Q 046214 15 GTQTAPGACPFCGGMIRAMDVQSE-----------------WRFCFLPLYFKT--KRKFYCTVCARRLVV 65 (66)
Q Consensus 15 ~~~~ApG~Cp~CGG~v~a~Dves~-----------------~rfCflP~~~k~--krk~~Ct~C~r~L~~ 65 (66)
+++|..-.||+||-.+. +.++.+ |-+|+||++.+. ...++|+.|++.|-.
T Consensus 2 ~~~p~~~~CP~C~~~~~-T~v~~~~g~~t~~~~~~l~~~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~ 70 (73)
T PF10601_consen 2 GPEPVRIYCPYCQQQVQ-TRVEYKSGTMTYICAALLCLFGCWPCCCIPFCCDSCKDVYHYCPNCGAFLGT 70 (73)
T ss_pred CCCceeeECCCCCCEEE-EEEEEEeChHHHHHHHHHHHHHHHHHhhHhhccccccCceEECCCCCCEeEE
Confidence 56788889999998764 334422 345789999854 457899999998854
No 5
>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=93.29 E-value=0.077 Score=34.90 Aligned_cols=39 Identities=31% Similarity=0.660 Sum_probs=24.6
Q ss_pred CCcCCCCCCceEEEEeceeeEEEEEeeeeeecc-EEEeeccccee
Q 046214 20 PGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKR-KFYCTVCARRL 63 (66)
Q Consensus 20 pG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr-k~~Ct~C~r~L 63 (66)
|-.||||||.+.-+|= +.. -|--...+. -|.|+.|++-.
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 39999998754
No 6
>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=92.72 E-value=0.15 Score=28.26 Aligned_cols=28 Identities=21% Similarity=0.863 Sum_probs=20.6
Q ss_pred CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccce
Q 046214 21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARR 62 (66)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (66)
-.||+||.. .+.-+.+ ...|.|..|+++
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 5555554 677888888764
No 7
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=92.58 E-value=0.1 Score=36.09 Aligned_cols=37 Identities=30% Similarity=0.640 Sum_probs=24.3
Q ss_pred cCCCCCCce-EEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214 22 ACPFCGGMI-RAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV 64 (66)
Q Consensus 22 ~Cp~CGG~v-~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (66)
.|||||++. .|.|=+. ++==.-.+|++.|..||++..
T Consensus 2 ~cp~c~~~~~~~~~s~~------~~~~~~~~~~~~c~~c~~~f~ 39 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRP------AEDGNAIRRRRECLACGKRFT 39 (154)
T ss_pred cCCCCCCCCCEeEeccc------cCCCCceeeeeeccccCCcce
Confidence 499999976 5555331 111123667799999998754
No 8
>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=91.41 E-value=0.093 Score=31.95 Aligned_cols=13 Identities=46% Similarity=1.145 Sum_probs=11.1
Q ss_pred CCcCCCCCCceEE
Q 046214 20 PGACPFCGGMIRA 32 (66)
Q Consensus 20 pG~Cp~CGG~v~a 32 (66)
.|.||+|||.++.
T Consensus 41 ~~~CPNCgGelv~ 53 (57)
T PF06906_consen 41 NGVCPNCGGELVR 53 (57)
T ss_pred cCcCcCCCCcccc
Confidence 6999999998753
No 9
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.86 E-value=0.094 Score=33.95 Aligned_cols=18 Identities=39% Similarity=0.874 Sum_probs=14.5
Q ss_pred CCCcCCCCCCceEEEEec
Q 046214 19 APGACPFCGGMIRAMDVQ 36 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~Dve 36 (66)
-.|.||+|||.+++--++
T Consensus 40 l~g~CPnCGGelv~RP~R 57 (84)
T COG3813 40 LHGLCPNCGGELVARPIR 57 (84)
T ss_pred hcCcCCCCCchhhcCcCC
Confidence 469999999999876554
No 10
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=90.83 E-value=0.12 Score=30.84 Aligned_cols=36 Identities=31% Similarity=0.647 Sum_probs=25.4
Q ss_pred CcceeeeeccCCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccce
Q 046214 9 EDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARR 62 (66)
Q Consensus 9 e~~kv~~~~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (66)
+.+||+...+ .||+||-++-.+| ++.++.|-.||-.
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 4455666554 6999998877666 4457888888754
No 11
>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=89.68 E-value=0.82 Score=23.98 Aligned_cols=43 Identities=19% Similarity=0.343 Sum_probs=25.7
Q ss_pred CCCCCCceEEEEeceeeEEEE-EeeeeeeccEEEeecccceeee
Q 046214 23 CPFCGGMIRAMDVQSEWRFCF-LPLYFKTKRKFYCTVCARRLVV 65 (66)
Q Consensus 23 Cp~CGG~v~a~Dves~~rfCf-lP~~~k~krk~~Ct~C~r~L~~ 65 (66)
||-|||....-++++.+.--- -=+..+.=..+.|+.||..+-+
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~~~~~~i~~vp~~~C~~CGE~~~~ 44 (46)
T TIGR03831 1 CPICGGEELEGKTTTETYEYGGELIVIENVPALVCPQCGEEYLD 44 (46)
T ss_pred CCCCCCceecceEEEEEEEeCCEEEEEeCCCccccccCCCEeeC
Confidence 889988877777654432111 1223344456679999877643
No 12
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=89.48 E-value=0.098 Score=26.03 Aligned_cols=9 Identities=56% Similarity=1.368 Sum_probs=6.5
Q ss_pred CCCCCCceE
Q 046214 23 CPFCGGMIR 31 (66)
Q Consensus 23 Cp~CGG~v~ 31 (66)
||+||-.+.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 778877664
No 13
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=89.41 E-value=0.11 Score=26.08 Aligned_cols=9 Identities=56% Similarity=1.269 Sum_probs=6.7
Q ss_pred cCCCCCCce
Q 046214 22 ACPFCGGMI 30 (66)
Q Consensus 22 ~Cp~CGG~v 30 (66)
.||+||-.+
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 588898743
No 14
>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=88.63 E-value=1.1 Score=27.88 Aligned_cols=41 Identities=27% Similarity=0.648 Sum_probs=30.8
Q ss_pred CCCCCCceEEEEecee-eEEEEEeeeeeeccEEEeecccceee
Q 046214 23 CPFCGGMIRAMDVQSE-WRFCFLPLYFKTKRKFYCTVCARRLV 64 (66)
Q Consensus 23 Cp~CGG~v~a~Dves~-~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (66)
||.||++....++++. +.+.-.-+-+ .-..+.|+.||..+.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v-~~~~~~C~~CGe~~~ 42 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITI-GVPGWYCPACGEELL 42 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEE-eeeeeECCCCCCEEE
Confidence 8999976666777764 4677777777 667788999998764
No 15
>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=88.57 E-value=0.35 Score=27.45 Aligned_cols=35 Identities=29% Similarity=0.609 Sum_probs=19.1
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV 64 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (66)
-||.|||......-. + - -...+.-|.|+.||....
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 499999987733200 0 0 011122336888987643
No 16
>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=88.25 E-value=0.39 Score=27.69 Aligned_cols=30 Identities=27% Similarity=0.671 Sum_probs=23.0
Q ss_pred CCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214 19 APGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL 63 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (66)
..-.||.||..... ..+.|.|.|+.||...
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 34579999987765 4577889999998753
No 17
>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=87.87 E-value=0.55 Score=31.18 Aligned_cols=44 Identities=18% Similarity=0.333 Sum_probs=30.9
Q ss_pred CCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214 20 PGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL 63 (66)
Q Consensus 20 pG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (66)
...|+.|+|.++.++-|....----.++..+..=+.|+.||+.+
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 48999999999888766544442223334455678899999865
No 18
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=87.70 E-value=0.37 Score=26.28 Aligned_cols=29 Identities=34% Similarity=0.811 Sum_probs=17.9
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL 63 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (66)
-||.||..+..-+.+. ...+.|+.||...
T Consensus 2 FCp~Cg~~l~~~~~~~-------------~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCPKCGNMLIPKEGKE-------------KRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCccccccCCC-------------CCEEECCcCCCeE
Confidence 4899998664443331 2367788887543
No 19
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=87.07 E-value=0.2 Score=42.47 Aligned_cols=28 Identities=43% Similarity=0.958 Sum_probs=20.3
Q ss_pred ecCcceeeeeccCC-CcCCCCCCceEEEE
Q 046214 7 CDEDERVLGTQTAP-GACPFCGGMIRAMD 34 (66)
Q Consensus 7 cde~~kv~~~~~Ap-G~Cp~CGG~v~a~D 34 (66)
||.=+||----.+| |.||+|||.+++.|
T Consensus 824 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 852 (1006)
T PRK12775 824 CDDCGKVSEGFAFPYGMCPACGGKLQALD 852 (1006)
T ss_pred hhhhccccccccCCcCcCcccccchhhhh
Confidence 55445554444566 99999999998876
No 20
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=86.92 E-value=0.87 Score=26.20 Aligned_cols=37 Identities=24% Similarity=0.483 Sum_probs=23.4
Q ss_pred ecCcceeeeeccCCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214 7 CDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL 63 (66)
Q Consensus 7 cde~~kv~~~~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (66)
+|.+ +|....+ -||+||..+.+. ++.++.|..||...
T Consensus 11 v~~~-~v~~~~~---fCP~Cg~~~m~~----------------~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 11 VDGG-KVKRKNK---FCPRCGSGFMAE----------------HLDRWHCGKCGYTE 47 (50)
T ss_pred ECCC-EEEEccC---cCcCCCcchhec----------------cCCcEECCCcCCEE
Confidence 3543 6664443 899999752222 23688899998654
No 21
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=86.06 E-value=0.46 Score=32.42 Aligned_cols=24 Identities=33% Similarity=0.801 Sum_probs=19.2
Q ss_pred CCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccce
Q 046214 19 APGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARR 62 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (66)
..-.||.||. .+.|.|.|+.||-.
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 45789999999964
No 22
>PRK10445 endonuclease VIII; Provisional
Probab=85.67 E-value=0.94 Score=32.84 Aligned_cols=29 Identities=31% Similarity=0.800 Sum_probs=21.3
Q ss_pred CCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccc
Q 046214 19 APGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~ 60 (66)
+...||+||+.+.-..+-. ...|+|+.|-
T Consensus 234 ~g~~Cp~Cg~~I~~~~~~g-------------R~t~~CP~CQ 262 (263)
T PRK10445 234 DGEACERCGGIIEKTTLSS-------------RPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCCEeEEEEECC-------------CCcEECCCCc
Confidence 3456999999999887763 5567777663
No 23
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=85.60 E-value=0.75 Score=33.50 Aligned_cols=26 Identities=31% Similarity=0.704 Sum_probs=20.1
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccc
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~ 60 (66)
.||+||+.+.-..+.. ...|+|+.|-
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 24
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=84.66 E-value=0.86 Score=33.30 Aligned_cols=27 Identities=22% Similarity=0.706 Sum_probs=20.5
Q ss_pred CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccc
Q 046214 21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60 (66)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~ 60 (66)
..||+||+.+.-.-|.. ...|+|+.|-
T Consensus 255 ~pC~~Cg~~I~~~~~~g-------------R~t~~CP~CQ 281 (282)
T PRK13945 255 KPCRKCGTPIERIKLAG-------------RSTHWCPNCQ 281 (282)
T ss_pred CCCCcCCCeeEEEEECC-------------CccEECCCCc
Confidence 46999999998877754 5667777773
No 25
>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=84.60 E-value=0.41 Score=36.33 Aligned_cols=45 Identities=22% Similarity=0.411 Sum_probs=34.1
Q ss_pred cCCCcCCCCCCceEEEEe-----ceeeEEEEEeeeeeecc--EEEeecccce
Q 046214 18 TAPGACPFCGGMIRAMDV-----QSEWRFCFLPLYFKTKR--KFYCTVCARR 62 (66)
Q Consensus 18 ~ApG~Cp~CGG~v~a~Dv-----es~~rfCflP~~~k~kr--k~~Ct~C~r~ 62 (66)
...|.||-||+.-++.-+ +...|+..=++|.--|+ +..|+.||..
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 457799999999766555 34578888888876664 7889999853
No 26
>PRK00420 hypothetical protein; Validated
Probab=84.40 E-value=0.83 Score=30.47 Aligned_cols=30 Identities=27% Similarity=0.652 Sum_probs=22.3
Q ss_pred CCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214 19 APGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV 64 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (66)
....||.||. |++.=...+.+|..||..+.
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 4578999985 44443667889999998764
No 27
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=83.40 E-value=0.63 Score=27.20 Aligned_cols=47 Identities=26% Similarity=0.496 Sum_probs=30.1
Q ss_pred cCCCcCCCCCCceEEEEeceee---------------EEEEEeeeeee--ccEEEeecccceeee
Q 046214 18 TAPGACPFCGGMIRAMDVQSEW---------------RFCFLPLYFKT--KRKFYCTVCARRLVV 65 (66)
Q Consensus 18 ~ApG~Cp~CGG~v~a~Dves~~---------------rfCflP~~~k~--krk~~Ct~C~r~L~~ 65 (66)
|+.-.||+||.-+. +.||.+. =+|+||++.+. ...++|+.|++.|-.
T Consensus 1 p~~i~Cp~C~~~~~-T~v~~~~g~~t~~~~~ll~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~ 64 (67)
T smart00714 1 PYQLFCPRCQNNVT-TRVETETGVCAWLICCLLFLLCFCCCLPCCLDSFKDVNHYCPNCGAFLGT 64 (67)
T ss_pred CcceECCCCCCEEE-EEEEEEeChHHHHHHHHHHHHHHHHHHHHhcccccCccEECCCCCCEeEE
Confidence 34557999987543 4454322 24568985443 346899999998754
No 28
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=83.33 E-value=1.2 Score=25.15 Aligned_cols=33 Identities=24% Similarity=0.629 Sum_probs=19.2
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccc
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCAR 61 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r 61 (66)
-||.||.+....+-+..+.---. -.+.|+.||.
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~-------~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMY-------YYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCE-------EEEEcCCCCC
Confidence 39999777766665433210000 3466888886
No 29
>PF12773 DZR: Double zinc ribbon
Probab=83.02 E-value=0.32 Score=26.57 Aligned_cols=14 Identities=21% Similarity=0.446 Sum_probs=7.4
Q ss_pred eccEEEeeccccee
Q 046214 50 TKRKFYCTVCARRL 63 (66)
Q Consensus 50 ~krk~~Ct~C~r~L 63 (66)
.....+|+.||+.+
T Consensus 26 ~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 26 DQSKKICPNCGAEN 39 (50)
T ss_pred cCCCCCCcCCcCCC
Confidence 33445566666543
No 30
>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=82.13 E-value=1.3 Score=32.27 Aligned_cols=26 Identities=27% Similarity=0.765 Sum_probs=19.8
Q ss_pred CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecc
Q 046214 21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVC 59 (66)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C 59 (66)
-.||+||+.+.-.-+.. ...|+|+.|
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 36999999998877753 566777766
No 31
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=81.87 E-value=1.1 Score=24.27 Aligned_cols=29 Identities=24% Similarity=0.708 Sum_probs=13.6
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccc
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCAR 61 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r 61 (66)
-||.||++++-.=.+- -...++.|+.||.
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 3999999987653311 1334567787775
No 32
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=81.84 E-value=0.86 Score=34.74 Aligned_cols=43 Identities=21% Similarity=0.485 Sum_probs=32.1
Q ss_pred CCCcCCCCCCceEEE--Ee--ceeeEEEEEeeeeeecc--EEEeecccc
Q 046214 19 APGACPFCGGMIRAM--DV--QSEWRFCFLPLYFKTKR--KFYCTVCAR 61 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~--Dv--es~~rfCflP~~~k~kr--k~~Ct~C~r 61 (66)
..|.||-||+.-++. +. +...|++.=++|.--|+ +..|+.||.
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 579999999985433 33 34578888888877664 788999985
No 33
>PF14369 zf-RING_3: zinc-finger
Probab=81.52 E-value=1.1 Score=24.12 Aligned_cols=14 Identities=36% Similarity=0.700 Sum_probs=10.1
Q ss_pred ccCCCcCCCCCCce
Q 046214 17 QTAPGACPFCGGMI 30 (66)
Q Consensus 17 ~~ApG~Cp~CGG~v 30 (66)
....-+||+|+|+-
T Consensus 18 ~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 18 PDSDVACPRCHGGF 31 (35)
T ss_pred CCCCcCCcCCCCcE
Confidence 34444699999975
No 34
>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=81.21 E-value=1.7 Score=23.56 Aligned_cols=29 Identities=28% Similarity=0.655 Sum_probs=20.1
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV 64 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (66)
.||+||..-...|-+ .-.++|+.||..|.
T Consensus 2 ~Cp~Cg~~~~~~D~~--------------~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPE--------------RGELVCPNCGLVLE 30 (43)
T ss_dssp SBTTTSSSEEEEETT--------------TTEEEETTT-BBEE
T ss_pred CCcCCcCCceEEcCC--------------CCeEECCCCCCEee
Confidence 599999987655533 34677889988775
No 35
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=80.94 E-value=2.7 Score=22.98 Aligned_cols=13 Identities=38% Similarity=0.784 Sum_probs=8.3
Q ss_pred CCcCCCCCCceEE
Q 046214 20 PGACPFCGGMIRA 32 (66)
Q Consensus 20 pG~Cp~CGG~v~a 32 (66)
+..||+||+.+..
T Consensus 21 ~~~Cp~CG~~~~~ 33 (46)
T PRK00398 21 GVRCPYCGYRILF 33 (46)
T ss_pred ceECCCCCCeEEE
Confidence 5667777766553
No 36
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=80.91 E-value=1.6 Score=31.59 Aligned_cols=28 Identities=25% Similarity=0.770 Sum_probs=20.6
Q ss_pred CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccc
Q 046214 21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCAR 61 (66)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r 61 (66)
-.||+||+.+.-..+.. ...|+|+.|-+
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 36999999998777653 56677777753
No 37
>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=80.54 E-value=1.8 Score=25.50 Aligned_cols=32 Identities=28% Similarity=0.532 Sum_probs=20.9
Q ss_pred CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceeee
Q 046214 21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLVV 65 (66)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~ 65 (66)
..||.||..+..-|.... --+.|..||+.|..
T Consensus 3 ~~CP~CG~~iev~~~~~G-------------eiV~Cp~CGaeleV 34 (54)
T TIGR01206 3 FECPDCGAEIELENPELG-------------ELVICDECGAELEV 34 (54)
T ss_pred cCCCCCCCEEecCCCccC-------------CEEeCCCCCCEEEE
Confidence 479999987766443211 13478888888753
No 38
>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=80.39 E-value=1.1 Score=23.02 Aligned_cols=16 Identities=19% Similarity=0.341 Sum_probs=9.1
Q ss_pred CcCCCCCCceEEEEec
Q 046214 21 GACPFCGGMIRAMDVQ 36 (66)
Q Consensus 21 G~Cp~CGG~v~a~Dve 36 (66)
.-||+||++...++=+
T Consensus 4 rfC~~CG~~t~~~~~g 19 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGG 19 (32)
T ss_dssp SB-TTT--BEEE-SSS
T ss_pred cccCcCCccccCCCCc
Confidence 5699999998876654
No 39
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=80.13 E-value=2.5 Score=22.43 Aligned_cols=16 Identities=38% Similarity=0.889 Sum_probs=12.3
Q ss_pred eeccCCCcCCCCCCce
Q 046214 15 GTQTAPGACPFCGGMI 30 (66)
Q Consensus 15 ~~~~ApG~Cp~CGG~v 30 (66)
....+|..||-||.+-
T Consensus 13 ~g~~~p~~CP~Cg~~~ 28 (34)
T cd00729 13 EGEEAPEKCPICGAPK 28 (34)
T ss_pred ECCcCCCcCcCCCCch
Confidence 3345899999999864
No 40
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=80.05 E-value=1.5 Score=30.11 Aligned_cols=28 Identities=39% Similarity=0.963 Sum_probs=21.2
Q ss_pred CCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214 20 PGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV 64 (66)
Q Consensus 20 pG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (66)
.-.||.|| .||+. .--.++|+.|+.+-+
T Consensus 28 ~~hCp~Cg----------------~PLF~-KdG~v~CPvC~~~~~ 55 (131)
T COG1645 28 AKHCPKCG----------------TPLFR-KDGEVFCPVCGYREV 55 (131)
T ss_pred HhhCcccC----------------Cccee-eCCeEECCCCCceEE
Confidence 34688888 67877 667899999996543
No 41
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=79.37 E-value=1.7 Score=31.62 Aligned_cols=28 Identities=29% Similarity=0.756 Sum_probs=21.0
Q ss_pred CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccc
Q 046214 21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCAR 61 (66)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r 61 (66)
-.||+||+.+.-.-+-. ...|+|+.|-+
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 36999999998877653 56677777754
No 42
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=77.47 E-value=2.4 Score=26.30 Aligned_cols=37 Identities=19% Similarity=0.433 Sum_probs=25.0
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEee--cccceeee
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCT--VCARRLVV 65 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct--~C~r~L~~ 65 (66)
-||.||..+.+.|=+-.. +. -..+.+.|+ .||.+.++
T Consensus 3 ~CP~Cg~~a~irtSr~~s-----~~--~~~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 3 HCPLCQHAAHARTSRYIT-----DT--TKERYHQCQNVNCSATFIT 41 (72)
T ss_pred cCCCCCCccEEEEChhcC-----hh--hheeeeecCCCCCCCEEEE
Confidence 499999998665543222 22 245667898 99988765
No 43
>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=77.35 E-value=3.2 Score=24.13 Aligned_cols=38 Identities=29% Similarity=0.648 Sum_probs=25.6
Q ss_pred EEecCcceeeeeccCCCcCC--CCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccc
Q 046214 5 CVCDEDERVLGTQTAPGACP--FCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60 (66)
Q Consensus 5 ~vcde~~kv~~~~~ApG~Cp--~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~ 60 (66)
+=+|+++||.+.+ -.|| +||.+|-.++- +.+++|-.||
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 4567777775
No 44
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=77.17 E-value=3.7 Score=31.67 Aligned_cols=46 Identities=26% Similarity=0.489 Sum_probs=30.6
Q ss_pred cCCCcCCCCCCceEEEEeceeeEEEEEeeee------eeccEEEeeccccee
Q 046214 18 TAPGACPFCGGMIRAMDVQSEWRFCFLPLYF------KTKRKFYCTVCARRL 63 (66)
Q Consensus 18 ~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~------k~krk~~Ct~C~r~L 63 (66)
+....||.||++----+=---..+++||+.- =.+|+|.|+.|+..-
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 3348999999997111111245677886543 357899999999763
No 45
>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=76.20 E-value=3 Score=25.92 Aligned_cols=37 Identities=19% Similarity=0.499 Sum_probs=20.2
Q ss_pred cCCCcCCCCC-CceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214 18 TAPGACPFCG-GMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV 64 (66)
Q Consensus 18 ~ApG~Cp~CG-G~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (66)
+.-=.||.|| ...+.++++.. ...-...|..||....
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 3445799999 77777787655 3344678999987654
No 46
>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=74.86 E-value=4.5 Score=20.29 Aligned_cols=14 Identities=29% Similarity=0.785 Sum_probs=8.5
Q ss_pred cCCCCCCceEEEEe
Q 046214 22 ACPFCGGMIRAMDV 35 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dv 35 (66)
.||+||..+.-+.+
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 59999999876665
No 47
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=74.56 E-value=3.1 Score=29.58 Aligned_cols=38 Identities=24% Similarity=0.517 Sum_probs=24.4
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeec-cEEEeeccccee
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTK-RKFYCTVCARRL 63 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~k-rk~~Ct~C~r~L 63 (66)
-||.||+......+.++- ||.+.+.= -.|.|..||-+-
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 48
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=73.64 E-value=1.6 Score=29.30 Aligned_cols=9 Identities=33% Similarity=0.995 Sum_probs=6.0
Q ss_pred cCCCCCCce
Q 046214 22 ACPFCGGMI 30 (66)
Q Consensus 22 ~Cp~CGG~v 30 (66)
.||+|+.+|
T Consensus 3 ~CPrC~skv 11 (112)
T TIGR00622 3 FCPQCRAKV 11 (112)
T ss_pred cCCCCCCCc
Confidence 477777665
No 49
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=71.77 E-value=5.4 Score=21.25 Aligned_cols=26 Identities=27% Similarity=0.493 Sum_probs=18.1
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccce
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARR 62 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (66)
.|+.|||... .++.+--++|.+|+..
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 3366667777777764
No 50
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=71.15 E-value=2.2 Score=28.33 Aligned_cols=14 Identities=36% Similarity=0.750 Sum_probs=12.0
Q ss_pred CcCCCCCCceEEEE
Q 046214 21 GACPFCGGMIRAMD 34 (66)
Q Consensus 21 G~Cp~CGG~v~a~D 34 (66)
-.||+||+.+.-.|
T Consensus 124 f~Cp~Cg~~l~~~d 137 (147)
T smart00531 124 FTCPRCGEELEEDD 137 (147)
T ss_pred EECCCCCCEEEEcC
Confidence 68999999998766
No 51
>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=69.68 E-value=3.3 Score=21.23 Aligned_cols=18 Identities=22% Similarity=0.669 Sum_probs=9.6
Q ss_pred cCCCCCCceEEEEeceee
Q 046214 22 ACPFCGGMIRAMDVQSEW 39 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~ 39 (66)
-||-||..+.-.+=|..+
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 399999999865555443
No 52
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=69.39 E-value=3.7 Score=24.01 Aligned_cols=11 Identities=45% Similarity=1.286 Sum_probs=9.2
Q ss_pred cCCCCCCceEE
Q 046214 22 ACPFCGGMIRA 32 (66)
Q Consensus 22 ~Cp~CGG~v~a 32 (66)
.|||||-.+..
T Consensus 2 ~CPyCge~~~~ 12 (52)
T PF14255_consen 2 QCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCeeEE
Confidence 59999998765
No 53
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=69.15 E-value=1.5 Score=31.20 Aligned_cols=45 Identities=18% Similarity=0.447 Sum_probs=27.3
Q ss_pred ccCCCcCCCCCCceEEEEeceeeEEEEEe--eeeeeccEEEeeccccee
Q 046214 17 QTAPGACPFCGGMIRAMDVQSEWRFCFLP--LYFKTKRKFYCTVCARRL 63 (66)
Q Consensus 17 ~~ApG~Cp~CGG~v~a~Dves~~rfCflP--~~~k~krk~~Ct~C~r~L 63 (66)
++--..||.|+|.+..+.=|..-- =|| ++..+-.=+.|+.||+.+
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 344678999999988765443110 033 333333344499999864
No 54
>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=68.44 E-value=5.1 Score=27.90 Aligned_cols=35 Identities=29% Similarity=0.755 Sum_probs=22.8
Q ss_pred CCCCCCc-eEEEEeceeeEEEEEeeeeeec-cEEEeecccce
Q 046214 23 CPFCGGM-IRAMDVQSEWRFCFLPLYFKTK-RKFYCTVCARR 62 (66)
Q Consensus 23 Cp~CGG~-v~a~Dves~~rfCflP~~~k~k-rk~~Ct~C~r~ 62 (66)
||.||+. +......+ =||.+.+.= -.|.|..||-+
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 44433222 267665543 47889999865
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=68.24 E-value=6.7 Score=21.32 Aligned_cols=12 Identities=42% Similarity=1.102 Sum_probs=10.3
Q ss_pred ccCCCcCCCCCC
Q 046214 17 QTAPGACPFCGG 28 (66)
Q Consensus 17 ~~ApG~Cp~CGG 28 (66)
+..+-.||.||+
T Consensus 23 ~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 23 EDDPVPCPECGS 34 (42)
T ss_pred CCCCCcCCCCCC
Confidence 467889999999
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=67.91 E-value=3.9 Score=21.08 Aligned_cols=12 Identities=42% Similarity=0.999 Sum_probs=9.8
Q ss_pred cCCCcCCCCCCc
Q 046214 18 TAPGACPFCGGM 29 (66)
Q Consensus 18 ~ApG~Cp~CGG~ 29 (66)
...-.||.||+.
T Consensus 24 ~~~~~CP~Cg~~ 35 (41)
T smart00834 24 DPLATCPECGGD 35 (41)
T ss_pred CCCCCCCCCCCc
Confidence 567789999994
No 57
>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=67.78 E-value=3 Score=28.35 Aligned_cols=16 Identities=38% Similarity=0.831 Sum_probs=13.3
Q ss_pred CCCcCCCCCCceEEEE
Q 046214 19 APGACPFCGGMIRAMD 34 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~D 34 (66)
..-.||.|||.+.-.|
T Consensus 127 ~~F~Cp~Cg~~L~~~d 142 (158)
T TIGR00373 127 LNFTCPRCGAMLDYLD 142 (158)
T ss_pred cCCcCCCCCCEeeecc
Confidence 3678999999988766
No 58
>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=66.94 E-value=3.7 Score=22.79 Aligned_cols=13 Identities=38% Similarity=0.945 Sum_probs=10.1
Q ss_pred cCCCCCCceEEEE
Q 046214 22 ACPFCGGMIRAMD 34 (66)
Q Consensus 22 ~Cp~CGG~v~a~D 34 (66)
-||.||..+.+--
T Consensus 1 ~CP~Cg~~a~ir~ 13 (47)
T PF04606_consen 1 RCPHCGSKARIRT 13 (47)
T ss_pred CcCCCCCeeEEEE
Confidence 3999999887653
No 59
>PRK09401 reverse gyrase; Reviewed
Probab=66.22 E-value=2.3 Score=37.17 Aligned_cols=14 Identities=43% Similarity=0.954 Sum_probs=11.3
Q ss_pred CCcCCCCCCceEEE
Q 046214 20 PGACPFCGGMIRAM 33 (66)
Q Consensus 20 pG~Cp~CGG~v~a~ 33 (66)
.++||+|||.++.-
T Consensus 7 ~~~cpnc~g~i~~~ 20 (1176)
T PRK09401 7 KNSCPNCGGDISDE 20 (1176)
T ss_pred cccCCCCCCcCcHh
Confidence 47899999998743
No 60
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=65.48 E-value=9.4 Score=23.56 Aligned_cols=30 Identities=30% Similarity=0.629 Sum_probs=20.5
Q ss_pred CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccce
Q 046214 21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARR 62 (66)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (66)
-.||.||..+.-+..... |=.+.|--|++.
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 224778888764
No 61
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=65.46 E-value=5.5 Score=28.12 Aligned_cols=12 Identities=50% Similarity=1.262 Sum_probs=10.9
Q ss_pred cCCCcCCCCCCc
Q 046214 18 TAPGACPFCGGM 29 (66)
Q Consensus 18 ~ApG~Cp~CGG~ 29 (66)
.||+.||-||.+
T Consensus 147 e~P~~CPiCga~ 158 (166)
T COG1592 147 EAPEVCPICGAP 158 (166)
T ss_pred CCCCcCCCCCCh
Confidence 899999999975
No 62
>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=65.39 E-value=5.2 Score=24.27 Aligned_cols=15 Identities=47% Similarity=0.961 Sum_probs=12.8
Q ss_pred eeeEEEEEeeeeeec
Q 046214 37 SEWRFCFLPLYFKTK 51 (66)
Q Consensus 37 s~~rfCflP~~~k~k 51 (66)
-|.|||..|+-||+.
T Consensus 7 fqsrfcifpltfkss 21 (59)
T PF07038_consen 7 FQSRFCIFPLTFKSS 21 (59)
T ss_pred EeeeeEEEEeeeccC
Confidence 478999999999864
No 63
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=64.88 E-value=5.1 Score=26.79 Aligned_cols=14 Identities=36% Similarity=1.075 Sum_probs=11.9
Q ss_pred CCCCCCceEEEEec
Q 046214 23 CPFCGGMIRAMDVQ 36 (66)
Q Consensus 23 Cp~CGG~v~a~Dve 36 (66)
||-|||.+.++.++
T Consensus 1 CPvCg~~l~vt~l~ 14 (113)
T PF09862_consen 1 CPVCGGELVVTRLK 14 (113)
T ss_pred CCCCCCceEEEEEE
Confidence 89999999988664
No 64
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=64.19 E-value=3 Score=37.26 Aligned_cols=20 Identities=30% Similarity=0.705 Sum_probs=15.0
Q ss_pred CCcCCCCCCceEEEEeceee
Q 046214 20 PGACPFCGGMIRAMDVQSEW 39 (66)
Q Consensus 20 pG~Cp~CGG~v~a~Dves~~ 39 (66)
-++||+|||.++.-..++..
T Consensus 8 ~~~CpNCGG~isseRL~~gl 27 (1187)
T COG1110 8 GSSCPNCGGDISSERLEKGL 27 (1187)
T ss_pred hccCCCCCCcCcHHHHhcCC
Confidence 37899999998876665543
No 65
>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=64.02 E-value=3.7 Score=24.55 Aligned_cols=24 Identities=29% Similarity=0.793 Sum_probs=16.7
Q ss_pred ceeeeeccC-CCcCCCCCCceEEEE
Q 046214 11 ERVLGTQTA-PGACPFCGGMIRAMD 34 (66)
Q Consensus 11 ~kv~~~~~A-pG~Cp~CGG~v~a~D 34 (66)
+|++=.+.. -|.||.||..+.-.|
T Consensus 25 GkIiC~~Eg~~~pC~fCg~~l~~~~ 49 (57)
T PF06221_consen 25 GKIICEQEGPLGPCPFCGTPLLSSE 49 (57)
T ss_pred ChhhcccccCcCcCCCCCCcccCHH
Confidence 456666777 489999997765443
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=63.64 E-value=4 Score=18.02 Aligned_cols=11 Identities=27% Similarity=1.044 Sum_probs=6.4
Q ss_pred EEeecccceee
Q 046214 54 FYCTVCARRLV 64 (66)
Q Consensus 54 ~~Ct~C~r~L~ 64 (66)
|.|+.|+....
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 57888887664
No 67
>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=62.92 E-value=4.9 Score=21.72 Aligned_cols=15 Identities=33% Similarity=0.831 Sum_probs=11.7
Q ss_pred ccCCCcCCCCCCceE
Q 046214 17 QTAPGACPFCGGMIR 31 (66)
Q Consensus 17 ~~ApG~Cp~CGG~v~ 31 (66)
-+.+|.|..|||.+.
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 68
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=62.77 E-value=3.9 Score=23.95 Aligned_cols=14 Identities=36% Similarity=0.847 Sum_probs=10.6
Q ss_pred CCCcCCCCCCceEE
Q 046214 19 APGACPFCGGMIRA 32 (66)
Q Consensus 19 ApG~Cp~CGG~v~a 32 (66)
-.-.|||||..+-.
T Consensus 23 ~~irCp~Cg~rIl~ 36 (49)
T COG1996 23 RGIRCPYCGSRILV 36 (49)
T ss_pred CceeCCCCCcEEEE
Confidence 34569999998754
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=62.34 E-value=5.7 Score=20.56 Aligned_cols=13 Identities=23% Similarity=0.462 Sum_probs=7.7
Q ss_pred cEEEeecccceee
Q 046214 52 RKFYCTVCARRLV 64 (66)
Q Consensus 52 rk~~Ct~C~r~L~ 64 (66)
.++.|+.|+..+.
T Consensus 24 ~~v~C~~C~~~~~ 36 (38)
T TIGR02098 24 GKVRCGKCGHVWY 36 (38)
T ss_pred CEEECCCCCCEEE
Confidence 3566666666553
No 70
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=62.06 E-value=3.6 Score=23.00 Aligned_cols=10 Identities=60% Similarity=1.411 Sum_probs=5.8
Q ss_pred CCcCCCCCCc
Q 046214 20 PGACPFCGGM 29 (66)
Q Consensus 20 pG~Cp~CGG~ 29 (66)
++.||+||-+
T Consensus 2 ~~~CprC~kg 11 (36)
T PF14787_consen 2 PGLCPRCGKG 11 (36)
T ss_dssp --C-TTTSSS
T ss_pred CccCcccCCC
Confidence 6899999854
No 71
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=62.05 E-value=1.5 Score=33.22 Aligned_cols=24 Identities=25% Similarity=0.217 Sum_probs=18.5
Q ss_pred ecCcceeeeeccCCCcCCCCCCce
Q 046214 7 CDEDERVLGTQTAPGACPFCGGMI 30 (66)
Q Consensus 7 cde~~kv~~~~~ApG~Cp~CGG~v 30 (66)
+|--++|+.+++-|+.||+|||-.
T Consensus 141 ~dva~~v~~~hfLpd~~gn~r~f~ 164 (253)
T COG1933 141 HDVAERVLNSHFIPDLRGNLRSFT 164 (253)
T ss_pred HHHHHHhhccCCCcchhhhhhhhh
Confidence 344578888889999999888753
No 72
>PRK11827 hypothetical protein; Provisional
Probab=61.56 E-value=6.9 Score=23.60 Aligned_cols=27 Identities=22% Similarity=0.661 Sum_probs=17.8
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL 63 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (66)
+||.|.|.+.- |-+.+ ...|+.|+..+
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 69999999874 32322 46677776554
No 73
>PF14353 CpXC: CpXC protein
Probab=61.48 E-value=7.4 Score=24.80 Aligned_cols=36 Identities=25% Similarity=0.543 Sum_probs=24.5
Q ss_pred ceeeeeccCCCcCCCCCCceEE------EEeceeeEEEEEee
Q 046214 11 ERVLGTQTAPGACPFCGGMIRA------MDVQSEWRFCFLPL 46 (66)
Q Consensus 11 ~kv~~~~~ApG~Cp~CGG~v~a------~Dves~~rfCflP~ 46 (66)
++++.-+=.--.||+||....+ .|.+-++.+-+.|-
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 3445444455689999987653 57777777777775
No 74
>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=61.38 E-value=9.9 Score=19.67 Aligned_cols=12 Identities=50% Similarity=1.093 Sum_probs=10.2
Q ss_pred CCCcCCCCCCce
Q 046214 19 APGACPFCGGMI 30 (66)
Q Consensus 19 ApG~Cp~CGG~v 30 (66)
++-.||-||.+-
T Consensus 16 ~~~~CP~Cg~~~ 27 (33)
T cd00350 16 APWVCPVCGAPK 27 (33)
T ss_pred CCCcCcCCCCcH
Confidence 888999999764
No 75
>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=61.04 E-value=4.7 Score=22.15 Aligned_cols=10 Identities=60% Similarity=1.501 Sum_probs=8.3
Q ss_pred CCcCCCCCCc
Q 046214 20 PGACPFCGGM 29 (66)
Q Consensus 20 pG~Cp~CGG~ 29 (66)
.+.||.|||.
T Consensus 3 ~~pCP~CGG~ 12 (37)
T smart00778 3 HGPCPNCGGS 12 (37)
T ss_pred ccCCCCCCCc
Confidence 4789999994
No 76
>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=60.51 E-value=3.7 Score=35.93 Aligned_cols=14 Identities=43% Similarity=0.980 Sum_probs=11.4
Q ss_pred CCcCCCCCCceEEE
Q 046214 20 PGACPFCGGMIRAM 33 (66)
Q Consensus 20 pG~Cp~CGG~v~a~ 33 (66)
.+.||+|||.+..-
T Consensus 7 ~~~CPnCgg~i~~~ 20 (1171)
T TIGR01054 7 SNLCPNCGGEISSE 20 (1171)
T ss_pred cCCCCCCCCccchh
Confidence 57899999998653
No 77
>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=59.95 E-value=5 Score=24.80 Aligned_cols=9 Identities=44% Similarity=1.379 Sum_probs=6.6
Q ss_pred cCCCCCCce
Q 046214 22 ACPFCGGMI 30 (66)
Q Consensus 22 ~Cp~CGG~v 30 (66)
-||.||+.+
T Consensus 2 fC~~Cg~~l 10 (104)
T TIGR01384 2 FCPKCGSLM 10 (104)
T ss_pred CCcccCccc
Confidence 478888776
No 78
>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=59.89 E-value=4.9 Score=22.46 Aligned_cols=17 Identities=35% Similarity=0.813 Sum_probs=11.1
Q ss_pred EeeeeeeccEEEeeccc
Q 046214 44 LPLYFKTKRKFYCTVCA 60 (66)
Q Consensus 44 lP~~~k~krk~~Ct~C~ 60 (66)
.|+......+.+|..|+
T Consensus 25 ~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 25 TPLMRDKDGKIYCVSCG 41 (41)
T ss_pred CeeEEecCCCEECCCCC
Confidence 46666455567888775
No 79
>PF09947 DUF2180: Uncharacterized protein conserved in archaea (DUF2180); InterPro: IPR017211 This group represents a predicted zinc finger protein, AF1427 type.
Probab=59.68 E-value=1.7 Score=27.02 Aligned_cols=57 Identities=19% Similarity=0.272 Sum_probs=36.2
Q ss_pred EEEecCcceeeeeccCCCcCCCCCCceEEE---EeceeeEEEEEeee----eeeccEEEeeccccee
Q 046214 4 VCVCDEDERVLGTQTAPGACPFCGGMIRAM---DVQSEWRFCFLPLY----FKTKRKFYCTVCARRL 63 (66)
Q Consensus 4 ~~vcde~~kv~~~~~ApG~Cp~CGG~v~a~---Dves~~rfCflP~~----~k~krk~~Ct~C~r~L 63 (66)
+|.|.+++|.. .|-|+|-.||-++=.- ..|....=---|+- .+.-+|+.|+-|...+
T Consensus 3 CY~Ca~~gkdt---~AVavCivCG~GlC~~H~~~e~~~~~~g~yp~~~~~~~~~l~RilC~~C~~a~ 66 (68)
T PF09947_consen 3 CYDCAEEGKDT---DAVAVCIVCGAGLCMDHSKREEIPVWEGGYPFPSKKLKKPLPRILCPECHAAL 66 (68)
T ss_pred chhhhhcCCCc---cceehHHhcCchhhHHHHhhhheeeeccCCCCccccccCCCCeeecHHHHHHh
Confidence 56777888743 8999999999887321 11111111234544 4456889999887654
No 80
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=59.59 E-value=4.9 Score=27.96 Aligned_cols=16 Identities=38% Similarity=0.754 Sum_probs=13.4
Q ss_pred CCCcCCCCCCceEEEE
Q 046214 19 APGACPFCGGMIRAMD 34 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~D 34 (66)
..-.||.|||.+.-.|
T Consensus 135 ~~F~Cp~Cg~~L~~~d 150 (178)
T PRK06266 135 YGFRCPQCGEMLEEYD 150 (178)
T ss_pred cCCcCCCCCCCCeecc
Confidence 3678999999998766
No 81
>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=59.42 E-value=6.9 Score=21.16 Aligned_cols=13 Identities=38% Similarity=0.892 Sum_probs=9.6
Q ss_pred CcCCCCCCceEEE
Q 046214 21 GACPFCGGMIRAM 33 (66)
Q Consensus 21 G~Cp~CGG~v~a~ 33 (66)
..||.|||.++.-
T Consensus 2 ~~CP~Cg~~lv~r 14 (39)
T PF01396_consen 2 EKCPKCGGPLVLR 14 (39)
T ss_pred cCCCCCCceeEEE
Confidence 4799999876543
No 82
>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=58.12 E-value=5.9 Score=19.41 Aligned_cols=15 Identities=13% Similarity=0.693 Sum_probs=11.2
Q ss_pred eccEEEeecccceee
Q 046214 50 TKRKFYCTVCARRLV 64 (66)
Q Consensus 50 ~krk~~Ct~C~r~L~ 64 (66)
..++|.|+.|++...
T Consensus 11 ~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 11 GEKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSSEEESSSSEEES
T ss_pred CCCCCCCCCCcCeeC
Confidence 356799999988653
No 83
>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=58.00 E-value=9.5 Score=24.47 Aligned_cols=14 Identities=29% Similarity=0.788 Sum_probs=11.3
Q ss_pred cEEEeecccceeee
Q 046214 52 RKFYCTVCARRLVV 65 (66)
Q Consensus 52 rk~~Ct~C~r~L~~ 65 (66)
.+|.|..|+..|+.
T Consensus 142 ~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 142 KRYRCGRCGGPLVQ 155 (157)
T ss_pred hhEECCCCCCEEEE
Confidence 45899999988874
No 84
>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=57.85 E-value=3.9 Score=22.78 Aligned_cols=30 Identities=33% Similarity=0.852 Sum_probs=12.5
Q ss_pred CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccc
Q 046214 21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60 (66)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~ 60 (66)
+.||.|||. -||-..+ =....-.++|..|+
T Consensus 4 ~pCP~CGG~---------DrFri~~-d~~~~G~~~C~~C~ 33 (40)
T PF08273_consen 4 GPCPICGGK---------DRFRIFD-DKDGRGTWICRQCG 33 (40)
T ss_dssp E--TTTT-T---------TTEEEET-T----S-EEETTTT
T ss_pred CCCCCCcCc---------cccccCc-CcccCCCEECCCCC
Confidence 679999993 2333111 11233567777773
No 85
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.43 E-value=9.1 Score=23.62 Aligned_cols=46 Identities=20% Similarity=0.361 Sum_probs=35.1
Q ss_pred ceeeeeccCCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceeee
Q 046214 11 ERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLVV 65 (66)
Q Consensus 11 ~kv~~~~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~ 65 (66)
...+...-.+-+||-=+++ -..-|. |||+ ..+.-..|+-||+++++
T Consensus 15 ~~~I~~~~~~l~C~g~~~p------~~HPrV-~L~m--g~~gev~CPYC~t~y~l 60 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPP------NDHPRV-FLDM--GDEGEVVCPYCSTRYRL 60 (62)
T ss_pred ceEEEeCCeeEEcCCCCCC------CCCCEE-EEEc--CCCCcEecCccccEEEe
Confidence 5567777777788765555 455565 7898 88888999999999875
No 86
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=56.57 E-value=6.7 Score=25.38 Aligned_cols=18 Identities=17% Similarity=0.181 Sum_probs=11.7
Q ss_pred ceeeeeccCCCcCCCCCC
Q 046214 11 ERVLGTQTAPGACPFCGG 28 (66)
Q Consensus 11 ~kv~~~~~ApG~Cp~CGG 28 (66)
+=++-..|+.+.|+.||.
T Consensus 61 ~L~I~~vp~~~~C~~Cg~ 78 (113)
T PRK12380 61 DLHIVYKPAQAWCWDCSQ 78 (113)
T ss_pred EEEEEeeCcEEEcccCCC
Confidence 344556677777777773
No 87
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=55.71 E-value=13 Score=19.90 Aligned_cols=12 Identities=33% Similarity=0.991 Sum_probs=7.0
Q ss_pred CCCCCCceEEEE
Q 046214 23 CPFCGGMIRAMD 34 (66)
Q Consensus 23 Cp~CGG~v~a~D 34 (66)
||.|+..+....
T Consensus 2 CP~C~~~l~~~~ 13 (41)
T PF13453_consen 2 CPRCGTELEPVR 13 (41)
T ss_pred cCCCCcccceEE
Confidence 777776544333
No 88
>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=55.32 E-value=3.5 Score=20.07 Aligned_cols=13 Identities=31% Similarity=1.024 Sum_probs=9.7
Q ss_pred EEEeecccceeee
Q 046214 53 KFYCTVCARRLVV 65 (66)
Q Consensus 53 k~~Ct~C~r~L~~ 65 (66)
+|+|..|++.+.+
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 4789999987754
No 89
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=55.17 E-value=16 Score=25.22 Aligned_cols=34 Identities=32% Similarity=0.686 Sum_probs=24.2
Q ss_pred cCCCCCCceEEEEeceeeEEE--EEeeeeeecc-EEEeecccce
Q 046214 22 ACPFCGGMIRAMDVQSEWRFC--FLPLYFKTKR-KFYCTVCARR 62 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfC--flP~~~k~kr-k~~Ct~C~r~ 62 (66)
.||.||+... +|++ =||.+.+.== .|.|..||-+
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 5999998643 3444 3787766554 8899999865
No 90
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=54.98 E-value=16 Score=20.46 Aligned_cols=14 Identities=29% Similarity=0.358 Sum_probs=8.3
Q ss_pred cCCCcCCCCCCceE
Q 046214 18 TAPGACPFCGGMIR 31 (66)
Q Consensus 18 ~ApG~Cp~CGG~v~ 31 (66)
..+-.||+||..+-
T Consensus 17 ~~~irC~~CG~rIl 30 (44)
T smart00659 17 KDVVRCRECGYRIL 30 (44)
T ss_pred CCceECCCCCceEE
Confidence 45556777776553
No 91
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=54.84 E-value=8.8 Score=27.84 Aligned_cols=13 Identities=23% Similarity=0.725 Sum_probs=9.3
Q ss_pred CCcCCCCCCceEE
Q 046214 20 PGACPFCGGMIRA 32 (66)
Q Consensus 20 pG~Cp~CGG~v~a 32 (66)
.--||+||.....
T Consensus 99 ~~fC~~CG~~~~~ 111 (256)
T PRK00241 99 HRFCGYCGHPMHP 111 (256)
T ss_pred CccccccCCCCee
Confidence 4468888887664
No 92
>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=54.66 E-value=4.4 Score=21.15 Aligned_cols=16 Identities=25% Similarity=0.544 Sum_probs=9.3
Q ss_pred eeeeccEEEeeccccee
Q 046214 47 YFKTKRKFYCTVCARRL 63 (66)
Q Consensus 47 ~~k~krk~~Ct~C~r~L 63 (66)
|-. +.+|.|+.|+.++
T Consensus 8 C~~-~~kY~Cp~C~~~~ 23 (30)
T PF04438_consen 8 CGN-PAKYRCPRCGARY 23 (30)
T ss_dssp SSS-EESEE-TTT--EE
T ss_pred CcC-CCEEECCCcCCce
Confidence 444 7788888888765
No 93
>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=54.55 E-value=8 Score=22.13 Aligned_cols=18 Identities=22% Similarity=0.615 Sum_probs=12.3
Q ss_pred eeeeccEEEeecccceee
Q 046214 47 YFKTKRKFYCTVCARRLV 64 (66)
Q Consensus 47 ~~k~krk~~Ct~C~r~L~ 64 (66)
.-+..++++|..||..|-
T Consensus 42 s~~~~~r~FC~~CGs~l~ 59 (92)
T PF04828_consen 42 SGKGVERYFCPTCGSPLF 59 (92)
T ss_dssp TTSSCEEEEETTT--EEE
T ss_pred CCCcCcCcccCCCCCeee
Confidence 345668899999998875
No 94
>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=53.34 E-value=6.5 Score=25.78 Aligned_cols=15 Identities=33% Similarity=0.713 Sum_probs=11.3
Q ss_pred CCCcCCCCCCceEEE
Q 046214 19 APGACPFCGGMIRAM 33 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~ 33 (66)
-|-+||+||--....
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 567899999766544
No 95
>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=52.81 E-value=31 Score=18.70 Aligned_cols=11 Identities=45% Similarity=1.180 Sum_probs=8.5
Q ss_pred cCCCcCCCCCC
Q 046214 18 TAPGACPFCGG 28 (66)
Q Consensus 18 ~ApG~Cp~CGG 28 (66)
..+-.||.||+
T Consensus 24 ~~~~~CP~Cg~ 34 (52)
T TIGR02605 24 DPLATCPECGG 34 (52)
T ss_pred CCCCCCCCCCC
Confidence 34557999998
No 96
>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=52.55 E-value=7.3 Score=25.21 Aligned_cols=18 Identities=11% Similarity=0.294 Sum_probs=12.4
Q ss_pred ceeeeeccCCCcCCCCCC
Q 046214 11 ERVLGTQTAPGACPFCGG 28 (66)
Q Consensus 11 ~kv~~~~~ApG~Cp~CGG 28 (66)
+=.+-..|+.+.|+.||-
T Consensus 61 ~L~I~~~p~~~~C~~Cg~ 78 (115)
T TIGR00100 61 KLNIEDEPVECECEDCSE 78 (115)
T ss_pred EEEEEeeCcEEEcccCCC
Confidence 344566777788888883
No 97
>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=52.54 E-value=6.5 Score=20.03 Aligned_cols=10 Identities=50% Similarity=1.248 Sum_probs=8.0
Q ss_pred cCCCcCCCCC
Q 046214 18 TAPGACPFCG 27 (66)
Q Consensus 18 ~ApG~Cp~CG 27 (66)
-++-.||+||
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 5667899998
No 98
>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=52.51 E-value=6.4 Score=24.36 Aligned_cols=36 Identities=28% Similarity=0.890 Sum_probs=28.9
Q ss_pred cCCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccc
Q 046214 18 TAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCAR 61 (66)
Q Consensus 18 ~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r 61 (66)
+.+-.||+|+- +.++|||.==+.-+--+|+|--|.|
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 99
>PRK05580 primosome assembly protein PriA; Validated
Probab=52.00 E-value=12 Score=30.62 Aligned_cols=27 Identities=22% Similarity=0.780 Sum_probs=16.6
Q ss_pred CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccce
Q 046214 21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARR 62 (66)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (66)
..||+|++++. ++|..+...|..||..
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 46888887764 3355556666666554
No 100
>PRK14701 reverse gyrase; Provisional
Probab=51.96 E-value=6.6 Score=35.77 Aligned_cols=17 Identities=35% Similarity=0.753 Sum_probs=12.7
Q ss_pred CCcCCCCCCceEEEEec
Q 046214 20 PGACPFCGGMIRAMDVQ 36 (66)
Q Consensus 20 pG~Cp~CGG~v~a~Dve 36 (66)
.++||+|||.++.-..+
T Consensus 6 ~~~cpnc~g~~~~~rl~ 22 (1638)
T PRK14701 6 KEMCPNCGGDITDERLA 22 (1638)
T ss_pred cccCCCCCCccchhHHh
Confidence 37899999988765444
No 101
>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=51.12 E-value=19 Score=21.01 Aligned_cols=16 Identities=19% Similarity=0.534 Sum_probs=10.8
Q ss_pred eeccEEEeecccceee
Q 046214 49 KTKRKFYCTVCARRLV 64 (66)
Q Consensus 49 k~krk~~Ct~C~r~L~ 64 (66)
-..-...|+.|+|.+.
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 3455677888887764
No 102
>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=50.72 E-value=6.8 Score=19.06 Aligned_cols=35 Identities=31% Similarity=0.523 Sum_probs=20.2
Q ss_pred CCCCCCceEEEEeceeeEEEEEeeeeeecc--EEEeecccceee
Q 046214 23 CPFCGGMIRAMDVQSEWRFCFLPLYFKTKR--KFYCTVCARRLV 64 (66)
Q Consensus 23 Cp~CGG~v~a~Dves~~rfCflP~~~k~kr--k~~Ct~C~r~L~ 64 (66)
|+.|+-.+...+.. +..-.+.|- =|.|+.|++.|.
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 67777766543111 112233343 388999999885
No 103
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=50.06 E-value=18 Score=23.54 Aligned_cols=33 Identities=18% Similarity=0.416 Sum_probs=21.4
Q ss_pred cCCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccce
Q 046214 18 TAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARR 62 (66)
Q Consensus 18 ~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (66)
+.--.||+||-....+++.- .+-...|..||-.
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 34457999996544444432 3667788888854
No 104
>PRK14873 primosome assembly protein PriA; Provisional
Probab=49.75 E-value=14 Score=30.66 Aligned_cols=12 Identities=25% Similarity=0.711 Sum_probs=7.9
Q ss_pred CcCCCCCCceEE
Q 046214 21 GACPFCGGMIRA 32 (66)
Q Consensus 21 G~Cp~CGG~v~a 32 (66)
-.||+|++++.-
T Consensus 393 ~~C~~C~~~L~~ 404 (665)
T PRK14873 393 ARCRHCTGPLGL 404 (665)
T ss_pred eECCCCCCceeE
Confidence 357777777654
No 105
>PHA00626 hypothetical protein
Probab=49.08 E-value=21 Score=21.90 Aligned_cols=32 Identities=22% Similarity=0.384 Sum_probs=22.0
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL 63 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (66)
.||.||-.-.+ . -..+.+....|.|..||-..
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 69999974221 1 24566777899999998654
No 106
>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=48.75 E-value=9.2 Score=19.41 Aligned_cols=13 Identities=31% Similarity=0.743 Sum_probs=9.1
Q ss_pred cCCCcCCCCCCce
Q 046214 18 TAPGACPFCGGMI 30 (66)
Q Consensus 18 ~ApG~Cp~CGG~v 30 (66)
.+.-.||+||-..
T Consensus 12 ~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 12 ESAKFCPHCGYDF 24 (26)
T ss_pred hhcCcCCCCCCCC
Confidence 3556899999643
No 107
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=48.61 E-value=11 Score=30.30 Aligned_cols=34 Identities=29% Similarity=0.683 Sum_probs=22.2
Q ss_pred eccCCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceeee
Q 046214 16 TQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLVV 65 (66)
Q Consensus 16 ~~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~ 65 (66)
.....-.||+|||-. +|. =+.-|-|..||++..+
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 344556899999963 222 1225889999988653
No 108
>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=48.50 E-value=11 Score=17.17 Aligned_cols=11 Identities=18% Similarity=1.005 Sum_probs=8.1
Q ss_pred EEeecccceee
Q 046214 54 FYCTVCARRLV 64 (66)
Q Consensus 54 ~~Ct~C~r~L~ 64 (66)
|.|..|++...
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 67888887764
No 109
>PRK04351 hypothetical protein; Provisional
Probab=48.27 E-value=21 Score=24.40 Aligned_cols=16 Identities=19% Similarity=0.723 Sum_probs=13.6
Q ss_pred eccEEEeecccceeee
Q 046214 50 TKRKFYCTVCARRLVV 65 (66)
Q Consensus 50 ~krk~~Ct~C~r~L~~ 65 (66)
+.++|.|..|+..|+.
T Consensus 129 n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 129 NTKRYRCGKCRGKLKL 144 (149)
T ss_pred CCCcEEeCCCCcEeee
Confidence 5689999999999875
No 110
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=48.03 E-value=12 Score=23.31 Aligned_cols=16 Identities=31% Similarity=0.897 Sum_probs=11.8
Q ss_pred cCCCCCCc---------eEEEEece
Q 046214 22 ACPFCGGM---------IRAMDVQS 37 (66)
Q Consensus 22 ~Cp~CGG~---------v~a~Dves 37 (66)
.||.||.. +..+|-|+
T Consensus 20 ~CP~Cgs~~~te~W~G~~iIidpe~ 44 (64)
T COG2093 20 ICPVCGSTDLTEEWFGLLIIIDPEK 44 (64)
T ss_pred cCCCCCCcccchhhccEEEEEcCcH
Confidence 59999964 66677664
No 111
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=47.77 E-value=18 Score=24.77 Aligned_cols=26 Identities=19% Similarity=0.516 Sum_probs=19.4
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL 63 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (66)
.|+.||++. +| .+|+...|+.||.+-
T Consensus 151 ~~~~~g~~~-------------~~---~~~~~~~c~~~~~~e 176 (189)
T PRK09521 151 MCSRCRTPL-------------VK---KGENELKCPNCGNIE 176 (189)
T ss_pred EccccCCce-------------EE---CCCCEEECCCCCCEE
Confidence 578888765 55 456789999999653
No 112
>PRK04023 DNA polymerase II large subunit; Validated
Probab=47.32 E-value=9.4 Score=34.15 Aligned_cols=20 Identities=20% Similarity=0.247 Sum_probs=11.3
Q ss_pred eeeeeeccEEEeecccceee
Q 046214 45 PLYFKTKRKFYCTVCARRLV 64 (66)
Q Consensus 45 P~~~k~krk~~Ct~C~r~L~ 64 (66)
|-|.+.-..+.|..||..+.
T Consensus 655 P~CG~~~~~y~CPKCG~El~ 674 (1121)
T PRK04023 655 PRCGIEVEEDECEKCGREPT 674 (1121)
T ss_pred ccccCcCCCCcCCCCCCCCC
Confidence 55555444566666666543
No 113
>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=46.25 E-value=6.7 Score=21.44 Aligned_cols=10 Identities=30% Similarity=0.700 Sum_probs=4.4
Q ss_pred EEeeccccee
Q 046214 54 FYCTVCARRL 63 (66)
Q Consensus 54 ~~Ct~C~r~L 63 (66)
-.||||||..
T Consensus 2 ~~CSFCgr~~ 11 (41)
T PF06689_consen 2 KRCSFCGRPE 11 (41)
T ss_dssp -B-TTT--BT
T ss_pred CCccCCCCCH
Confidence 3699999863
No 114
>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=46.20 E-value=9.7 Score=21.24 Aligned_cols=37 Identities=19% Similarity=0.623 Sum_probs=20.2
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeee-eccEEEeeccccee
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFK-TKRKFYCTVCARRL 63 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k-~krk~~Ct~C~r~L 63 (66)
.||+||-.....++-.. +--..+ ..+.+.|++|+.++
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 69999985433322211 122222 23468898888754
No 115
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.12 E-value=15 Score=24.44 Aligned_cols=50 Identities=20% Similarity=0.366 Sum_probs=30.2
Q ss_pred ceeeeeccCCCcCCCCCCceEEEE------eceeeEEEEEeeeeeeccEEEeecccce
Q 046214 11 ERVLGTQTAPGACPFCGGMIRAMD------VQSEWRFCFLPLYFKTKRKFYCTVCARR 62 (66)
Q Consensus 11 ~kv~~~~~ApG~Cp~CGG~v~a~D------ves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (66)
+=++-..|+.+.|+.||--....| =+...-+=|+|---. .-+.|+.||..
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 345557889999999996554442 233344445664221 22569999864
No 116
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=46.02 E-value=7.8 Score=27.57 Aligned_cols=14 Identities=36% Similarity=0.790 Sum_probs=12.6
Q ss_pred CcCCCCCCceEEEE
Q 046214 21 GACPFCGGMIRAMD 34 (66)
Q Consensus 21 G~Cp~CGG~v~a~D 34 (66)
..||.||+.++-+|
T Consensus 133 F~Cp~Cg~~L~~~d 146 (176)
T COG1675 133 FTCPKCGEDLEEYD 146 (176)
T ss_pred CCCCCCCchhhhcc
Confidence 78999999998877
No 117
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=45.76 E-value=11 Score=20.13 Aligned_cols=30 Identities=30% Similarity=0.726 Sum_probs=14.7
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccc
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCAR 61 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r 61 (66)
.||+|+..-.+-|=. || ..-++..|+.|+.
T Consensus 4 ~Cp~C~~~y~i~d~~-------ip---~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEK-------IP---PKGRKVRCSKCGH 33 (36)
T ss_pred ECCCCCCEEeCCHHH-------CC---CCCcEEECCCCCC
Confidence 366666554444322 22 2344556666654
No 118
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.63 E-value=10 Score=24.89 Aligned_cols=9 Identities=44% Similarity=1.176 Sum_probs=7.5
Q ss_pred CcCCCCCCc
Q 046214 21 GACPFCGGM 29 (66)
Q Consensus 21 G~Cp~CGG~ 29 (66)
..||.||+.
T Consensus 93 ~~CP~Cgs~ 101 (124)
T PRK00762 93 IECPVCGNK 101 (124)
T ss_pred CcCcCCCCC
Confidence 579999974
No 119
>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=44.45 E-value=12 Score=28.99 Aligned_cols=30 Identities=23% Similarity=0.547 Sum_probs=16.8
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV 64 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (66)
+||.||--++..+.+.. .+-.|++||..|.
T Consensus 15 ~C~~Cd~l~~~~~l~~g-------------~~a~CpRCg~~L~ 44 (403)
T TIGR00155 15 LCSQCDMLVALPRIESG-------------QKAACPRCGTTLT 44 (403)
T ss_pred eCCCCCCcccccCCCCC-------------CeeECCCCCCCCc
Confidence 47777765554443322 2445777776664
No 120
>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=43.99 E-value=3.7 Score=25.85 Aligned_cols=37 Identities=22% Similarity=0.529 Sum_probs=29.0
Q ss_pred CCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214 19 APGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL 63 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (66)
.+..||+||-++..-|. ||+..=..-|=.|..|++++
T Consensus 32 ~rS~C~~C~~~L~~~~l--------IPi~S~l~lrGrCr~C~~~I 68 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWWDL--------IPILSYLLLRGRCRYCGAPI 68 (92)
T ss_pred CCCcCcCCCCcCccccc--------chHHHHHHhCCCCcccCCCC
Confidence 46889999999998886 78777666777777777664
No 121
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=43.69 E-value=16 Score=23.61 Aligned_cols=18 Identities=28% Similarity=0.322 Sum_probs=13.3
Q ss_pred ceeeeeccCCCcCCCCCC
Q 046214 11 ERVLGTQTAPGACPFCGG 28 (66)
Q Consensus 11 ~kv~~~~~ApG~Cp~CGG 28 (66)
+=++-..|+.+.|+.||-
T Consensus 61 ~L~i~~~p~~~~C~~Cg~ 78 (114)
T PRK03681 61 KLHLEEQEAECWCETCQQ 78 (114)
T ss_pred EEEEEeeCcEEEcccCCC
Confidence 345667788888888884
No 122
>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=43.68 E-value=18 Score=25.37 Aligned_cols=38 Identities=26% Similarity=0.486 Sum_probs=23.4
Q ss_pred cCCCCCC-ceEEEEeceeeEEEEEeeeeeeccEEEeecccceeee
Q 046214 22 ACPFCGG-MIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLVV 65 (66)
Q Consensus 22 ~Cp~CGG-~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~ 65 (66)
-||+||. --.++|=+..- =-..++|+=.|..||+|..+
T Consensus 2 ~CP~C~~~dtkViDSR~~~------dg~~IRRRReC~~C~~RFTT 40 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVE------DGQSIRRRRECLECHERFTT 40 (147)
T ss_pred CCCCCCCCCCEeeeccccC------CCCeeeecccCCccCCccce
Confidence 4888987 44555543211 11246777888888888653
No 123
>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=43.57 E-value=22 Score=18.86 Aligned_cols=14 Identities=29% Similarity=0.807 Sum_probs=9.5
Q ss_pred cCCCCCCceEEEEe
Q 046214 22 ACPFCGGMIRAMDV 35 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dv 35 (66)
-||.||..+..-+-
T Consensus 3 FCp~C~nlL~p~~~ 16 (35)
T PF02150_consen 3 FCPECGNLLYPKED 16 (35)
T ss_dssp BETTTTSBEEEEEE
T ss_pred eCCCCCccceEcCC
Confidence 38888887765443
No 124
>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=42.44 E-value=14 Score=25.95 Aligned_cols=26 Identities=27% Similarity=0.774 Sum_probs=10.9
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccc
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~ 60 (66)
.|++|||.-.+..-+ ....|.|++|.
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 599999998876433 34566777775
No 125
>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=42.38 E-value=7.6 Score=20.99 Aligned_cols=18 Identities=22% Similarity=0.385 Sum_probs=10.2
Q ss_pred ccCCCcCCCCCCceEEEE
Q 046214 17 QTAPGACPFCGGMIRAMD 34 (66)
Q Consensus 17 ~~ApG~Cp~CGG~v~a~D 34 (66)
+-.+-+|+.||-.++.+|
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 455678999998776554
No 126
>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=42.37 E-value=15 Score=24.21 Aligned_cols=11 Identities=18% Similarity=0.782 Sum_probs=7.7
Q ss_pred cEEEeecccce
Q 046214 52 RKFYCTVCARR 62 (66)
Q Consensus 52 rk~~Ct~C~r~ 62 (66)
..|.|..|+..
T Consensus 50 ~~~~C~~C~~~ 60 (166)
T cd04476 50 GTYRCEKCNKS 60 (166)
T ss_pred CcEECCCCCCc
Confidence 56778777764
No 127
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=42.07 E-value=23 Score=28.26 Aligned_cols=30 Identities=20% Similarity=0.564 Sum_probs=20.2
Q ss_pred EEEEecCccee-eeeccCCCcCCCCCCceEE
Q 046214 3 LVCVCDEDERV-LGTQTAPGACPFCGGMIRA 32 (66)
Q Consensus 3 ~~~vcde~~kv-~~~~~ApG~Cp~CGG~v~a 32 (66)
..+.|.+-+++ .+-.+...-||+|||.+..
T Consensus 239 ~~~~c~~cg~~~~~~~~~~~~c~~Cg~~~~~ 269 (380)
T COG1867 239 YIYHCSRCGEIVGSFREVDEKCPHCGGKVHL 269 (380)
T ss_pred cEEEcccccceecccccccccCCccccccee
Confidence 45667777544 4446777889999975544
No 128
>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=41.86 E-value=5 Score=21.86 Aligned_cols=26 Identities=23% Similarity=0.252 Sum_probs=10.6
Q ss_pred eeeccCCCcCCC--CCCceEEEEeceee
Q 046214 14 LGTQTAPGACPF--CGGMIRAMDVQSEW 39 (66)
Q Consensus 14 ~~~~~ApG~Cp~--CGG~v~a~Dves~~ 39 (66)
+...+..--||+ |++.+...+-....
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 344445458988 99999988877664
No 129
>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=41.46 E-value=9.9 Score=19.76 Aligned_cols=22 Identities=32% Similarity=0.696 Sum_probs=9.9
Q ss_pred EecCcceeeeeccCCCcCCCCCCc
Q 046214 6 VCDEDERVLGTQTAPGACPFCGGM 29 (66)
Q Consensus 6 vcde~~kv~~~~~ApG~Cp~CGG~ 29 (66)
-|++-+++ .-|....||+||+.
T Consensus 13 rC~~Cg~~--~~pPr~~Cp~C~s~ 34 (37)
T PF12172_consen 13 RCRDCGRV--QFPPRPVCPHCGSD 34 (37)
T ss_dssp E-TTT--E--EES--SEETTTT--
T ss_pred EcCCCCCE--ecCCCcCCCCcCcc
Confidence 34444443 34666899999853
No 130
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=41.15 E-value=28 Score=25.62 Aligned_cols=42 Identities=21% Similarity=0.479 Sum_probs=29.3
Q ss_pred ccCCCcCCCCCCceEEEEeceeeEEEEEeeeeee-ccEEEeeccccee
Q 046214 17 QTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKT-KRKFYCTVCARRL 63 (66)
Q Consensus 17 ~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~-krk~~Ct~C~r~L 63 (66)
+.-...||-||| ++...++.==+|.+-+. -.-++|..||-|.
T Consensus 11 ~~~~~~CPvCg~-----~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~ 53 (201)
T COG1779 11 FETRIDCPVCGG-----TLKAHMYLYDIPYFGEVLISTGVCERCGYRS 53 (201)
T ss_pred eeeeecCCcccc-----eeeEEEeeecCCccceEEEEEEEccccCCcc
Confidence 334578999999 55556666667876553 3457899999765
No 131
>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=41.09 E-value=32 Score=23.62 Aligned_cols=37 Identities=22% Similarity=0.474 Sum_probs=20.2
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeee-ccEEEeeccccee
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKT-KRKFYCTVCARRL 63 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~-krk~~Ct~C~r~L 63 (66)
.||.||....- .+-.=-+|.+.+. =-.|.|..||-+-
T Consensus 3 ~Cp~C~~~~~~-----~~~~~~IP~F~evii~sf~C~~CGyk~ 40 (161)
T PF03367_consen 3 LCPNCGENGTT-----RILLTDIPYFKEVIIMSFECEHCGYKN 40 (161)
T ss_dssp E-TTTSSCCEE-----EEEEEEETTTEEEEEEEEE-TTT--EE
T ss_pred cCCCCCCCcEE-----EEEEEcCCCCceEEEEEeECCCCCCEe
Confidence 59999987532 1122236776664 3578899998653
No 132
>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=40.91 E-value=58 Score=19.64 Aligned_cols=10 Identities=30% Similarity=0.670 Sum_probs=7.2
Q ss_pred cEEEeecccc
Q 046214 52 RKFYCTVCAR 61 (66)
Q Consensus 52 rk~~Ct~C~r 61 (66)
..++|+.||-
T Consensus 35 ~~v~C~~CGY 44 (64)
T PF09855_consen 35 TTVSCTNCGY 44 (64)
T ss_pred EEEECCCCCC
Confidence 3568999984
No 133
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=40.85 E-value=25 Score=26.00 Aligned_cols=31 Identities=23% Similarity=0.472 Sum_probs=21.4
Q ss_pred CCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214 20 PGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV 64 (66)
Q Consensus 20 pG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (66)
...||.||+.-.+.|.++- -++|+.||-.|.
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 3579999987666775443 456777877654
No 134
>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=40.39 E-value=18 Score=19.21 Aligned_cols=14 Identities=43% Similarity=0.835 Sum_probs=9.8
Q ss_pred ccCCCcCCCCCCce
Q 046214 17 QTAPGACPFCGGMI 30 (66)
Q Consensus 17 ~~ApG~Cp~CGG~v 30 (66)
...+-.||+||.-+
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 34566899999876
No 135
>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=40.00 E-value=29 Score=19.92 Aligned_cols=13 Identities=31% Similarity=0.703 Sum_probs=8.9
Q ss_pred cCCCcCCCCCCce
Q 046214 18 TAPGACPFCGGMI 30 (66)
Q Consensus 18 ~ApG~Cp~CGG~v 30 (66)
|+.-.||-||.+-
T Consensus 32 p~~w~CP~C~a~K 44 (50)
T cd00730 32 PDDWVCPVCGAGK 44 (50)
T ss_pred CCCCCCCCCCCcH
Confidence 3344899998753
No 136
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=39.80 E-value=12 Score=22.85 Aligned_cols=13 Identities=38% Similarity=1.058 Sum_probs=10.0
Q ss_pred CCcCCCCCCceEE
Q 046214 20 PGACPFCGGMIRA 32 (66)
Q Consensus 20 pG~Cp~CGG~v~a 32 (66)
--.||.|||....
T Consensus 17 ke~Cp~CG~~t~~ 29 (59)
T COG2260 17 KEKCPVCGGDTKV 29 (59)
T ss_pred cccCCCCCCcccc
Confidence 3589999997654
No 137
>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=39.64 E-value=23 Score=27.09 Aligned_cols=16 Identities=25% Similarity=0.430 Sum_probs=13.0
Q ss_pred cCCCcCCCCCCceEEE
Q 046214 18 TAPGACPFCGGMIRAM 33 (66)
Q Consensus 18 ~ApG~Cp~CGG~v~a~ 33 (66)
.-.-.||.||+.|..-
T Consensus 28 ~~~~~CP~C~~~v~lk 43 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILK 43 (375)
T ss_pred CCcEECCCCCCeeEEE
Confidence 5567899999999873
No 138
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.52 E-value=13 Score=25.75 Aligned_cols=12 Identities=42% Similarity=0.902 Sum_probs=9.4
Q ss_pred cCCCcCCCCCCc
Q 046214 18 TAPGACPFCGGM 29 (66)
Q Consensus 18 ~ApG~Cp~CGG~ 29 (66)
...|.||+||-+
T Consensus 19 Gl~grCP~CGeG 30 (126)
T COG5349 19 GLRGRCPRCGEG 30 (126)
T ss_pred HhcCCCCCCCCc
Confidence 456899999954
No 139
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=39.34 E-value=18 Score=16.71 Aligned_cols=12 Identities=33% Similarity=1.196 Sum_probs=9.2
Q ss_pred EEeecccceeee
Q 046214 54 FYCTVCARRLVV 65 (66)
Q Consensus 54 ~~Ct~C~r~L~~ 65 (66)
|.|..|.+...+
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 689999887653
No 140
>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=38.95 E-value=15 Score=26.81 Aligned_cols=22 Identities=27% Similarity=0.646 Sum_probs=19.0
Q ss_pred EEEecCcceeeeeccCCCcCCC
Q 046214 4 VCVCDEDERVLGTQTAPGACPF 25 (66)
Q Consensus 4 ~~vcde~~kv~~~~~ApG~Cp~ 25 (66)
..|+|-++-.++-+||||.|=|
T Consensus 101 ~VvyDYqrLLiaykPaPGtcCY 122 (191)
T smart00019 101 IVVYDYQRLLIAYKPAPGTCCY 122 (191)
T ss_pred EEEEEhhhhheeccCCCCceEE
Confidence 3578989999999999999854
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=38.94 E-value=21 Score=31.94 Aligned_cols=20 Identities=20% Similarity=0.388 Sum_probs=16.5
Q ss_pred eeeccCCCcCCCCCCceEEE
Q 046214 14 LGTQTAPGACPFCGGMIRAM 33 (66)
Q Consensus 14 ~~~~~ApG~Cp~CGG~v~a~ 33 (66)
-+|-|-.|.||.|||.+.-+
T Consensus 1022 YRR~PL~G~C~kCGg~lilT 1041 (1095)
T TIGR00354 1022 YRRIPLVGKCLKCGNNLTLT 1041 (1095)
T ss_pred cccCCCCCcccccCCeEEEE
Confidence 35678899999999998754
No 142
>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=38.48 E-value=13 Score=20.79 Aligned_cols=13 Identities=46% Similarity=1.214 Sum_probs=5.8
Q ss_pred cCCCcCCCCCCce
Q 046214 18 TAPGACPFCGGMI 30 (66)
Q Consensus 18 ~ApG~Cp~CGG~v 30 (66)
.+.|.||=||.++
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 3455788887664
No 143
>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=38.25 E-value=25 Score=28.03 Aligned_cols=31 Identities=19% Similarity=0.669 Sum_probs=17.4
Q ss_pred EeceeeEEE---EEeeeeeeccEEEeecccceeee
Q 046214 34 DVQSEWRFC---FLPLYFKTKRKFYCTVCARRLVV 65 (66)
Q Consensus 34 Dves~~rfC---flP~~~k~krk~~Ct~C~r~L~~ 65 (66)
|-....-+| |.|+| |-+....|++||+++..
T Consensus 359 D~~npF~ICa~s~tPIY-~G~~~v~CP~cgA~y~~ 392 (422)
T PF06957_consen 359 DERNPFDICAASYTPIY-RGSPSVKCPYCGAKYHP 392 (422)
T ss_dssp -TTS-EEEBTTT--EEE-TTS-EEE-TTT--EEEG
T ss_pred CCCCCceeeeccccccc-CCCCCeeCCCCCCccCh
Confidence 334566778 67998 66677999999998763
No 144
>PRK04023 DNA polymerase II large subunit; Validated
Probab=38.18 E-value=23 Score=31.89 Aligned_cols=20 Identities=30% Similarity=0.684 Sum_probs=16.7
Q ss_pred eeeccCCCcCCCCCCceEEE
Q 046214 14 LGTQTAPGACPFCGGMIRAM 33 (66)
Q Consensus 14 ~~~~~ApG~Cp~CGG~v~a~ 33 (66)
-+|-|-.|.||.|||.+.-+
T Consensus 1047 YRR~PL~G~C~kCGg~lilT 1066 (1121)
T PRK04023 1047 YRRPPLSGKCPKCGGNLILT 1066 (1121)
T ss_pred cccCCCCCcCccCCCeEEEE
Confidence 35678899999999998755
No 145
>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=38.03 E-value=14 Score=23.57 Aligned_cols=15 Identities=40% Similarity=0.729 Sum_probs=12.2
Q ss_pred eeeccCCCcCCCCCC
Q 046214 14 LGTQTAPGACPFCGG 28 (66)
Q Consensus 14 ~~~~~ApG~Cp~CGG 28 (66)
-+.|..+|+|+.||.
T Consensus 16 aAaq~~~gscs~C~~ 30 (79)
T PF07213_consen 16 AAAQTQPGSCSGCYP 30 (79)
T ss_pred hhhcCCCCCCCCccc
Confidence 356788999999985
No 146
>PRK05320 rhodanese superfamily protein; Provisional
Probab=37.88 E-value=21 Score=25.92 Aligned_cols=28 Identities=14% Similarity=0.182 Sum_probs=19.3
Q ss_pred EEEecCcceeeee--ccCCCcCCCCCCceE
Q 046214 4 VCVCDEDERVLGT--QTAPGACPFCGGMIR 31 (66)
Q Consensus 4 ~~vcde~~kv~~~--~~ApG~Cp~CGG~v~ 31 (66)
+||+|++--|--. ..+.+.|..||-+++
T Consensus 226 ~fVFD~R~~~~~~~~~~~~~~c~~c~~~~~ 255 (257)
T PRK05320 226 CFVFDYRTALDPQLAPLVDVTCFACRAVVT 255 (257)
T ss_pred eeeecCeeecCCCCccCccceecCCCCcCC
Confidence 7999987644332 234577999998764
No 147
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=37.64 E-value=36 Score=24.46 Aligned_cols=15 Identities=27% Similarity=0.855 Sum_probs=11.6
Q ss_pred cCCCcCCCCCCceEE
Q 046214 18 TAPGACPFCGGMIRA 32 (66)
Q Consensus 18 ~ApG~Cp~CGG~v~a 32 (66)
+--+.||.|||.+.-
T Consensus 151 ~~~~~Cp~CG~~~~~ 165 (177)
T COG1439 151 EPKDFCPICGSPLKR 165 (177)
T ss_pred CCCCcCCCCCCceEE
Confidence 456889999998654
No 148
>PF13395 HNH_4: HNH endonuclease
Probab=37.63 E-value=11 Score=21.18 Aligned_cols=13 Identities=38% Similarity=1.122 Sum_probs=11.0
Q ss_pred CCCCCCceEEEEe
Q 046214 23 CPFCGGMIRAMDV 35 (66)
Q Consensus 23 Cp~CGG~v~a~Dv 35 (66)
|+|||-.+...++
T Consensus 1 C~Y~g~~i~~~~l 13 (54)
T PF13395_consen 1 CPYCGKPISIENL 13 (54)
T ss_pred CCCCCCCCChhhc
Confidence 8999999887764
No 149
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=37.35 E-value=21 Score=27.89 Aligned_cols=31 Identities=23% Similarity=0.474 Sum_probs=17.2
Q ss_pred CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214 21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV 64 (66)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (66)
-+||.||--++..+++..- +-.|++||..|.
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 4477777655544443222 345777777664
No 150
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=36.91 E-value=15 Score=21.79 Aligned_cols=16 Identities=31% Similarity=0.719 Sum_probs=9.3
Q ss_pred ccCCCcCCCCCCceEE
Q 046214 17 QTAPGACPFCGGMIRA 32 (66)
Q Consensus 17 ~~ApG~Cp~CGG~v~a 32 (66)
.+.-|.||+|.-.++.
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 151
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.79 E-value=15 Score=23.83 Aligned_cols=16 Identities=13% Similarity=0.204 Sum_probs=9.7
Q ss_pred eeeeeccCCCcCCCCC
Q 046214 12 RVLGTQTAPGACPFCG 27 (66)
Q Consensus 12 kv~~~~~ApG~Cp~CG 27 (66)
=.+-..|+.+.|..||
T Consensus 63 L~Ie~vp~~~~C~~Cg 78 (117)
T PRK00564 63 LDIVDEKVELECKDCS 78 (117)
T ss_pred EEEEecCCEEEhhhCC
Confidence 3445566666666666
No 152
>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=36.71 E-value=16 Score=21.89 Aligned_cols=11 Identities=45% Similarity=1.059 Sum_probs=8.6
Q ss_pred CcCCCCCCceE
Q 046214 21 GACPFCGGMIR 31 (66)
Q Consensus 21 G~Cp~CGG~v~ 31 (66)
.-||+||.++-
T Consensus 4 kHC~~CG~~Ip 14 (59)
T PF09889_consen 4 KHCPVCGKPIP 14 (59)
T ss_pred CcCCcCCCcCC
Confidence 46999997764
No 153
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=36.33 E-value=24 Score=32.22 Aligned_cols=20 Identities=30% Similarity=0.556 Sum_probs=16.5
Q ss_pred eeeccCCCcCCCCCCceEEE
Q 046214 14 LGTQTAPGACPFCGGMIRAM 33 (66)
Q Consensus 14 ~~~~~ApG~Cp~CGG~v~a~ 33 (66)
-+|-|-.|.||.|||.+.-+
T Consensus 1263 yRR~PL~G~C~kCGg~iilT 1282 (1337)
T PRK14714 1263 YRRMPLAGKCRKCGGRIILT 1282 (1337)
T ss_pred cccCCCCCcccccCCeEEEE
Confidence 35678999999999998754
No 154
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=36.26 E-value=25 Score=19.99 Aligned_cols=8 Identities=50% Similarity=1.476 Sum_probs=5.5
Q ss_pred cCCCCCCc
Q 046214 22 ACPFCGGM 29 (66)
Q Consensus 22 ~Cp~CGG~ 29 (66)
.||-||.+
T Consensus 36 ~CP~C~a~ 43 (47)
T PF00301_consen 36 VCPVCGAP 43 (47)
T ss_dssp B-TTTSSB
T ss_pred cCcCCCCc
Confidence 79988865
No 155
>PRK05978 hypothetical protein; Provisional
Probab=36.24 E-value=18 Score=25.04 Aligned_cols=34 Identities=24% Similarity=0.347 Sum_probs=20.9
Q ss_pred cCCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceeee
Q 046214 18 TAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLVV 65 (66)
Q Consensus 18 ~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~ 65 (66)
...|.||+||-+=-=- .=.|=+-.|+.||-.+..
T Consensus 31 Gl~grCP~CG~G~LF~--------------g~Lkv~~~C~~CG~~~~~ 64 (148)
T PRK05978 31 GFRGRCPACGEGKLFR--------------AFLKPVDHCAACGEDFTH 64 (148)
T ss_pred HHcCcCCCCCCCcccc--------------cccccCCCccccCCcccc
Confidence 4568999999653210 112344568888877653
No 156
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=36.18 E-value=31 Score=25.89 Aligned_cols=30 Identities=27% Similarity=0.538 Sum_probs=21.6
Q ss_pred CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214 21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV 64 (66)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (66)
..||.||+.....|++. -.+.|.-||-.+.
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 4566777776553
No 157
>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=36.05 E-value=17 Score=28.31 Aligned_cols=11 Identities=55% Similarity=1.389 Sum_probs=9.0
Q ss_pred CCcCCCCCCceE
Q 046214 20 PGACPFCGGMIR 31 (66)
Q Consensus 20 pG~Cp~CGG~v~ 31 (66)
.+.|| ||+.+.
T Consensus 259 ~~~Cp-CG~~i~ 269 (374)
T TIGR00375 259 CANCP-CGGRIK 269 (374)
T ss_pred CCCCC-CCCcce
Confidence 49999 999953
No 158
>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=35.86 E-value=17 Score=23.04 Aligned_cols=14 Identities=29% Similarity=0.812 Sum_probs=7.8
Q ss_pred ccCCCcCCCCCCce
Q 046214 17 QTAPGACPFCGGMI 30 (66)
Q Consensus 17 ~~ApG~Cp~CGG~v 30 (66)
..+...|.||||+.
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 45678999999975
No 159
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=35.58 E-value=20 Score=22.03 Aligned_cols=9 Identities=33% Similarity=0.818 Sum_probs=7.3
Q ss_pred CcCCCCCCc
Q 046214 21 GACPFCGGM 29 (66)
Q Consensus 21 G~Cp~CGG~ 29 (66)
..||.||+.
T Consensus 18 ~~Cp~Cgs~ 26 (64)
T PRK06393 18 KTCPVHGDE 26 (64)
T ss_pred CcCCCCCCC
Confidence 389999973
No 160
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=35.22 E-value=34 Score=24.93 Aligned_cols=25 Identities=16% Similarity=0.493 Sum_probs=18.1
Q ss_pred CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccce
Q 046214 21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARR 62 (66)
Q Consensus 21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (66)
..|++||+.+.- .++...|+.||+.
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 369999987542 5667788888865
No 161
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=34.98 E-value=26 Score=32.57 Aligned_cols=20 Identities=25% Similarity=0.556 Sum_probs=16.7
Q ss_pred eeeccCCCcCCCCCCceEEE
Q 046214 14 LGTQTAPGACPFCGGMIRAM 33 (66)
Q Consensus 14 ~~~~~ApG~Cp~CGG~v~a~ 33 (66)
-+|-|-.|.||.|||.+.-+
T Consensus 1551 yRR~PL~G~C~kCGg~~ilT 1570 (1627)
T PRK14715 1551 YRRVPLKGKCPKCGSKLILT 1570 (1627)
T ss_pred cccCCCCCcCcccCCeEEEE
Confidence 35678999999999998754
No 162
>PRK08173 DNA topoisomerase III; Validated
Probab=34.92 E-value=37 Score=28.98 Aligned_cols=14 Identities=57% Similarity=1.236 Sum_probs=11.8
Q ss_pred ccCCCcCCCCCCce
Q 046214 17 QTAPGACPFCGGMI 30 (66)
Q Consensus 17 ~~ApG~Cp~CGG~v 30 (66)
+...|.||.||+.+
T Consensus 723 ~~~~g~CPkCg~~v 736 (862)
T PRK08173 723 QEPVGACPKCGGRV 736 (862)
T ss_pred cccccCCCCCCCee
Confidence 56789999999964
No 163
>PHA02942 putative transposase; Provisional
Probab=34.72 E-value=24 Score=27.14 Aligned_cols=28 Identities=29% Similarity=0.739 Sum_probs=19.4
Q ss_pred CCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214 20 PGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL 63 (66)
Q Consensus 20 pG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (66)
.-.||.||.... + + +.|.|.|..||-..
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 34689999999653
No 164
>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=34.66 E-value=10 Score=20.84 Aligned_cols=13 Identities=38% Similarity=1.119 Sum_probs=8.4
Q ss_pred ccCCCcCCCCCCc
Q 046214 17 QTAPGACPFCGGM 29 (66)
Q Consensus 17 ~~ApG~Cp~CGG~ 29 (66)
|.++.+||+|+.+
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 4567789999865
No 165
>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=34.63 E-value=26 Score=18.81 Aligned_cols=11 Identities=36% Similarity=0.809 Sum_probs=5.8
Q ss_pred cCCCCCCceEE
Q 046214 22 ACPFCGGMIRA 32 (66)
Q Consensus 22 ~Cp~CGG~v~a 32 (66)
.||.||..-.+
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 49999986543
No 166
>smart00507 HNHc HNH nucleases.
Probab=34.42 E-value=21 Score=17.94 Aligned_cols=11 Identities=36% Similarity=1.126 Sum_probs=9.6
Q ss_pred CcCCCCCCceE
Q 046214 21 GACPFCGGMIR 31 (66)
Q Consensus 21 G~Cp~CGG~v~ 31 (66)
+.|++||....
T Consensus 11 ~~C~~C~~~~~ 21 (52)
T smart00507 11 GVCAYCGKPAS 21 (52)
T ss_pred CCCcCCcCCCC
Confidence 89999998875
No 167
>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=34.34 E-value=19 Score=19.90 Aligned_cols=30 Identities=33% Similarity=0.998 Sum_probs=17.5
Q ss_pred CCCCCCceEEEEeceeeEEEEEeeeeeeccE--EEe-eccccee
Q 046214 23 CPFCGGMIRAMDVQSEWRFCFLPLYFKTKRK--FYC-TVCARRL 63 (66)
Q Consensus 23 Cp~CGG~v~a~Dves~~rfCflP~~~k~krk--~~C-t~C~r~L 63 (66)
|.+|||.+.- =|+-.|+.++ |+| ..|-+++
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 2555554443 444 6665554
No 168
>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=33.79 E-value=17 Score=19.54 Aligned_cols=13 Identities=38% Similarity=0.869 Sum_probs=9.5
Q ss_pred cCCCCCCceEEEE
Q 046214 22 ACPFCGGMIRAMD 34 (66)
Q Consensus 22 ~Cp~CGG~v~a~D 34 (66)
.||+||-.|.|.-
T Consensus 6 ~C~nC~R~v~a~R 18 (33)
T PF08209_consen 6 ECPNCGRPVAASR 18 (33)
T ss_dssp E-TTTSSEEEGGG
T ss_pred ECCCCcCCcchhh
Confidence 5999999887653
No 169
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=33.63 E-value=43 Score=21.81 Aligned_cols=11 Identities=36% Similarity=1.093 Sum_probs=8.1
Q ss_pred cCCCCCCceEE
Q 046214 22 ACPFCGGMIRA 32 (66)
Q Consensus 22 ~Cp~CGG~v~a 32 (66)
-||.||+.+.+
T Consensus 4 FCp~Cgsll~p 14 (113)
T COG1594 4 FCPKCGSLLYP 14 (113)
T ss_pred ccCCccCeeEE
Confidence 48888887765
No 170
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=33.50 E-value=21 Score=20.00 Aligned_cols=11 Identities=36% Similarity=0.923 Sum_probs=7.8
Q ss_pred CCCCCCceEEE
Q 046214 23 CPFCGGMIRAM 33 (66)
Q Consensus 23 Cp~CGG~v~a~ 33 (66)
||+||+...=.
T Consensus 1 CP~Cg~~f~C~ 11 (50)
T PF14375_consen 1 CPRCGAPFECG 11 (50)
T ss_pred CCCCCCcCCCC
Confidence 78888876543
No 171
>KOG3456 consensus NADH:ubiquinone oxidoreductase, NDUFS6/13 kDa subunit [Energy production and conversion]
Probab=33.23 E-value=18 Score=24.80 Aligned_cols=12 Identities=33% Similarity=1.004 Sum_probs=10.1
Q ss_pred ccCCCcCCCCCC
Q 046214 17 QTAPGACPFCGG 28 (66)
Q Consensus 17 ~~ApG~Cp~CGG 28 (66)
++-+++|.|||=
T Consensus 101 k~~~~~CgYCGl 112 (120)
T KOG3456|consen 101 KPGPHICGYCGL 112 (120)
T ss_pred CCCCcccccchh
Confidence 677899999994
No 172
>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=32.87 E-value=28 Score=26.61 Aligned_cols=22 Identities=41% Similarity=0.976 Sum_probs=13.9
Q ss_pred EecCcceeeeeccCCCcCCCCC
Q 046214 6 VCDEDERVLGTQTAPGACPFCG 27 (66)
Q Consensus 6 vcde~~kv~~~~~ApG~Cp~CG 27 (66)
-|...|+-+.-..+.|.||+||
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 3556666777777778888666
No 173
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=32.86 E-value=25 Score=29.09 Aligned_cols=29 Identities=34% Similarity=0.720 Sum_probs=21.7
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV 64 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~ 64 (66)
.|++|||..-.-|- .--.-+||.||..|+
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 334668999998875
No 174
>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=32.31 E-value=10 Score=22.59 Aligned_cols=13 Identities=31% Similarity=0.823 Sum_probs=6.7
Q ss_pred cCCCCCCceEEEE
Q 046214 22 ACPFCGGMIRAMD 34 (66)
Q Consensus 22 ~Cp~CGG~v~a~D 34 (66)
.||.||..+...+
T Consensus 4 ~CP~C~k~~~~~~ 16 (57)
T PF03884_consen 4 KCPICGKPVEWSP 16 (57)
T ss_dssp E-TTT--EEE-SS
T ss_pred cCCCCCCeecccC
Confidence 5999999887643
No 175
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=32.26 E-value=20 Score=20.09 Aligned_cols=35 Identities=23% Similarity=0.490 Sum_probs=20.6
Q ss_pred CCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214 20 PGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL 63 (66)
Q Consensus 20 pG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (66)
.|+|.-|+=.+...++..- .+...-++|+.|||.|
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 4677777655544433321 1224568899999875
No 176
>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=31.55 E-value=27 Score=27.62 Aligned_cols=14 Identities=36% Similarity=0.978 Sum_probs=11.6
Q ss_pred eccCCCcCCCCCCc
Q 046214 16 TQTAPGACPFCGGM 29 (66)
Q Consensus 16 ~~~ApG~Cp~CGG~ 29 (66)
+++.|-.||.||+.
T Consensus 249 ~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 249 QEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCCCCCCC
Confidence 46779999999985
No 177
>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=31.51 E-value=28 Score=20.65 Aligned_cols=15 Identities=27% Similarity=0.567 Sum_probs=11.5
Q ss_pred CCceEEEEeceeeEE
Q 046214 27 GGMIRAMDVQSEWRF 41 (66)
Q Consensus 27 GG~v~a~Dves~~rf 41 (66)
|+.|+.||+||---|
T Consensus 13 g~~vQlMD~eTYeT~ 27 (57)
T cd04467 13 GDVVQLMDLETYETF 27 (57)
T ss_pred CCEEEEeccccceeE
Confidence 668999999965543
No 178
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=31.47 E-value=19 Score=29.99 Aligned_cols=9 Identities=22% Similarity=0.656 Sum_probs=5.3
Q ss_pred Eeeccccee
Q 046214 55 YCTVCARRL 63 (66)
Q Consensus 55 ~Ct~C~r~L 63 (66)
+|..||..+
T Consensus 43 fC~~CG~~~ 51 (645)
T PRK14559 43 HCPNCGAET 51 (645)
T ss_pred cccccCCcc
Confidence 566666554
No 179
>PLN03086 PRLI-interacting factor K; Provisional
Probab=31.37 E-value=8.1 Score=31.91 Aligned_cols=45 Identities=18% Similarity=0.379 Sum_probs=26.7
Q ss_pred CCCcCCCCCCceEEEEeceeeEEEEEee---e---------------eeeccEEEeeccccee
Q 046214 19 APGACPFCGGMIRAMDVQSEWRFCFLPL---Y---------------FKTKRKFYCTVCARRL 63 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~Dves~~rfCflP~---~---------------~k~krk~~Ct~C~r~L 63 (66)
..-.|++||......+++.+.+.|--|+ | .--+|.+.|.+|+...
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 3447888887777666666666543222 2 0125677777777643
No 180
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=31.33 E-value=20 Score=28.60 Aligned_cols=20 Identities=20% Similarity=0.351 Sum_probs=11.4
Q ss_pred EeeeeeeccEEEeeccccee
Q 046214 44 LPLYFKTKRKFYCTVCARRL 63 (66)
Q Consensus 44 lP~~~k~krk~~Ct~C~r~L 63 (66)
-|+|-+-||.|.|++|..++
T Consensus 10 C~ic~vq~~~YtCPRCn~~Y 29 (383)
T KOG4317|consen 10 CGICGVQKREYTCPRCNLLY 29 (383)
T ss_pred ccccccccccccCCCCCccc
Confidence 35555666666666665543
No 181
>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=31.29 E-value=35 Score=26.24 Aligned_cols=16 Identities=38% Similarity=0.833 Sum_probs=11.1
Q ss_pred eeccCCCcCCCCCCce
Q 046214 15 GTQTAPGACPFCGGMI 30 (66)
Q Consensus 15 ~~~~ApG~Cp~CGG~v 30 (66)
+.++.++.||+||+..
T Consensus 247 ~~~~~~~~C~~c~~~~ 262 (374)
T TIGR00308 247 GISQRKGRCKECGGEY 262 (374)
T ss_pred cccCCCCCCCCCCCcc
Confidence 3455667899998754
No 182
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=31.27 E-value=13 Score=24.59 Aligned_cols=11 Identities=27% Similarity=1.099 Sum_probs=7.9
Q ss_pred cEEEeecccce
Q 046214 52 RKFYCTVCARR 62 (66)
Q Consensus 52 rk~~Ct~C~r~ 62 (66)
.+|.|++||+.
T Consensus 35 aky~CsfCGK~ 45 (92)
T KOG0402|consen 35 AKYTCSFCGKK 45 (92)
T ss_pred hhhhhhhcchh
Confidence 46788888763
No 183
>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=30.93 E-value=15 Score=21.90 Aligned_cols=10 Identities=40% Similarity=1.265 Sum_probs=3.3
Q ss_pred cEEEeecccc
Q 046214 52 RKFYCTVCAR 61 (66)
Q Consensus 52 rk~~Ct~C~r 61 (66)
|+|.|.+||+
T Consensus 32 r~y~Cp~CgA 41 (55)
T PF05741_consen 32 RKYVCPICGA 41 (55)
T ss_dssp GG---TTT--
T ss_pred hcCcCCCCcC
Confidence 5567777765
No 184
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=30.74 E-value=22 Score=21.57 Aligned_cols=8 Identities=50% Similarity=1.472 Sum_probs=6.6
Q ss_pred cCCCCCCc
Q 046214 22 ACPFCGGM 29 (66)
Q Consensus 22 ~Cp~CGG~ 29 (66)
.||.||+.
T Consensus 17 ~CP~Cgs~ 24 (61)
T PRK08351 17 RCPVCGSR 24 (61)
T ss_pred cCCCCcCC
Confidence 59999973
No 185
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=29.73 E-value=51 Score=17.78 Aligned_cols=15 Identities=27% Similarity=0.514 Sum_probs=11.0
Q ss_pred CCcCC--CCCCceEEEE
Q 046214 20 PGACP--FCGGMIRAMD 34 (66)
Q Consensus 20 pG~Cp--~CGG~v~a~D 34 (66)
---|| .|+..+...|
T Consensus 18 ~~~CP~~~C~~~~~~~~ 34 (64)
T smart00647 18 LKWCPAPDCSAAIIVTE 34 (64)
T ss_pred ccCCCCCCCcceEEecC
Confidence 34588 9988887763
No 186
>PRK12722 transcriptional activator FlhC; Provisional
Probab=29.57 E-value=27 Score=25.13 Aligned_cols=14 Identities=29% Similarity=0.778 Sum_probs=10.4
Q ss_pred CcCCCCCCceEEEE
Q 046214 21 GACPFCGGMIRAMD 34 (66)
Q Consensus 21 G~Cp~CGG~v~a~D 34 (66)
-.|.+|||.-.+.-
T Consensus 135 ~~C~~Cgg~fv~~~ 148 (187)
T PRK12722 135 SSCNCCGGHFVTHA 148 (187)
T ss_pred ccCCCCCCCeeccc
Confidence 36999999976443
No 187
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=29.50 E-value=29 Score=20.57 Aligned_cols=15 Identities=27% Similarity=0.676 Sum_probs=11.5
Q ss_pred ccCCCcCCCCCCceE
Q 046214 17 QTAPGACPFCGGMIR 31 (66)
Q Consensus 17 ~~ApG~Cp~CGG~v~ 31 (66)
-..+..|+.||+..+
T Consensus 56 ~~~~~~C~~C~~~~E 70 (86)
T PF13966_consen 56 IQVDPICPLCGNEEE 70 (86)
T ss_pred CccCCccccCCCccc
Confidence 467799999998543
No 188
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=29.40 E-value=44 Score=18.02 Aligned_cols=11 Identities=36% Similarity=0.914 Sum_probs=7.7
Q ss_pred cCCCCCCceEE
Q 046214 22 ACPFCGGMIRA 32 (66)
Q Consensus 22 ~Cp~CGG~v~a 32 (66)
.||.||+.-.+
T Consensus 2 ~Cp~C~~~~a~ 12 (40)
T smart00440 2 PCPKCGNREAT 12 (40)
T ss_pred cCCCCCCCeEE
Confidence 59999865433
No 189
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=28.89 E-value=29 Score=24.57 Aligned_cols=20 Identities=30% Similarity=0.552 Sum_probs=15.2
Q ss_pred eeeccCCCcCCCCCCceEEE
Q 046214 14 LGTQTAPGACPFCGGMIRAM 33 (66)
Q Consensus 14 ~~~~~ApG~Cp~CGG~v~a~ 33 (66)
.++-++++.|++|||---+.
T Consensus 104 g~~s~l~~~c~~c~g~fc~~ 123 (162)
T COG3582 104 GKGSTLAGKCNYCTGYFCAE 123 (162)
T ss_pred cCCccccccccCCCCcceec
Confidence 34568999999999965543
No 190
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=28.66 E-value=33 Score=23.03 Aligned_cols=16 Identities=25% Similarity=0.602 Sum_probs=10.3
Q ss_pred eccEEEeecccceeee
Q 046214 50 TKRKFYCTVCARRLVV 65 (66)
Q Consensus 50 ~krk~~Ct~C~r~L~~ 65 (66)
..+.|.|.+|+...++
T Consensus 19 L~k~FtCp~Cghe~vs 34 (104)
T COG4888 19 LPKTFTCPRCGHEKVS 34 (104)
T ss_pred CCceEecCccCCeeee
Confidence 4566777777766554
No 191
>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=28.47 E-value=41 Score=25.40 Aligned_cols=26 Identities=23% Similarity=0.489 Sum_probs=19.1
Q ss_pred EEEecCcceeeeeccCCC--cCCCCCCc
Q 046214 4 VCVCDEDERVLGTQTAPG--ACPFCGGM 29 (66)
Q Consensus 4 ~~vcde~~kv~~~~~ApG--~Cp~CGG~ 29 (66)
++-=||+||-+---...| -|++||..
T Consensus 134 FY~RDqkEK~v~~c~~tgriyCS~CGS~ 161 (245)
T PF03117_consen 134 FYYRDQKEKQVIYCATTGRIYCSLCGSQ 161 (245)
T ss_pred eEeccccceeEEEeccCCCEEEccCCCC
Confidence 455688888776655555 59999986
No 192
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=28.44 E-value=24 Score=24.32 Aligned_cols=8 Identities=63% Similarity=1.589 Sum_probs=6.9
Q ss_pred cCCCCCCc
Q 046214 22 ACPFCGGM 29 (66)
Q Consensus 22 ~Cp~CGG~ 29 (66)
-||.|||.
T Consensus 21 GCP~CGg~ 28 (131)
T PF09845_consen 21 GCPECGGN 28 (131)
T ss_pred cCcccCCc
Confidence 49999996
No 193
>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 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=28.20 E-value=35 Score=15.96 Aligned_cols=11 Identities=27% Similarity=0.890 Sum_probs=8.7
Q ss_pred EEeecccceee
Q 046214 54 FYCTVCARRLV 64 (66)
Q Consensus 54 ~~Ct~C~r~L~ 64 (66)
|.|..|++...
T Consensus 2 ~~C~~C~~~F~ 12 (27)
T PF13912_consen 2 FECDECGKTFS 12 (27)
T ss_dssp EEETTTTEEES
T ss_pred CCCCccCCccC
Confidence 78999988764
No 195
>PRK06260 threonine synthase; Validated
Probab=28.19 E-value=62 Score=24.39 Aligned_cols=23 Identities=22% Similarity=0.619 Sum_probs=15.0
Q ss_pred ceeeeeccCCCcCCCCCCceEEE
Q 046214 11 ERVLGTQTAPGACPFCGGMIRAM 33 (66)
Q Consensus 11 ~kv~~~~~ApG~Cp~CGG~v~a~ 33 (66)
++........-.||.|||.+.+.
T Consensus 10 g~~~~~~~~~~~Cp~cg~~l~~~ 32 (397)
T PRK06260 10 GKEYDPDEIIYTCPECGGLLEVI 32 (397)
T ss_pred CCCCCCCCccccCCCCCCeEEEE
Confidence 33333344456799999987765
No 196
>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=27.78 E-value=9.7 Score=24.45 Aligned_cols=17 Identities=24% Similarity=0.409 Sum_probs=6.7
Q ss_pred eeeeccCCCcCCCCCCc
Q 046214 13 VLGTQTAPGACPFCGGM 29 (66)
Q Consensus 13 v~~~~~ApG~Cp~CGG~ 29 (66)
.+-..|+-+.|..||.-
T Consensus 63 ~Ie~~p~~~~C~~Cg~~ 79 (113)
T PF01155_consen 63 EIEEVPARARCRDCGHE 79 (113)
T ss_dssp EEEEE--EEEETTTS-E
T ss_pred EEEecCCcEECCCCCCE
Confidence 33444555555555543
No 197
>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=27.68 E-value=28 Score=30.17 Aligned_cols=13 Identities=38% Similarity=0.856 Sum_probs=11.0
Q ss_pred cCCCcCCCCCCce
Q 046214 18 TAPGACPFCGGMI 30 (66)
Q Consensus 18 ~ApG~Cp~CGG~v 30 (66)
-+-|+|||||..+
T Consensus 758 fs~gIcpY~Ga~i 770 (802)
T TIGR03031 758 FSMGICPYKGASI 770 (802)
T ss_pred HhccCCCCCCCCC
Confidence 3679999999877
No 198
>PRK01343 zinc-binding protein; Provisional
Probab=27.58 E-value=21 Score=21.42 Aligned_cols=13 Identities=31% Similarity=0.705 Sum_probs=9.9
Q ss_pred CCCcCCCCCCceE
Q 046214 19 APGACPFCGGMIR 31 (66)
Q Consensus 19 ApG~Cp~CGG~v~ 31 (66)
..-.||-||-.+.
T Consensus 8 p~~~CP~C~k~~~ 20 (57)
T PRK01343 8 PTRPCPECGKPST 20 (57)
T ss_pred CCCcCCCCCCcCc
Confidence 3467999998864
No 199
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=27.37 E-value=27 Score=23.18 Aligned_cols=7 Identities=57% Similarity=1.986 Sum_probs=5.6
Q ss_pred cCCCCCC
Q 046214 22 ACPFCGG 28 (66)
Q Consensus 22 ~Cp~CGG 28 (66)
.|||||-
T Consensus 5 ~CP~Cg~ 11 (97)
T COG4311 5 PCPYCGE 11 (97)
T ss_pred cCCCCCC
Confidence 5999984
No 200
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.05 E-value=1.1e+02 Score=20.98 Aligned_cols=30 Identities=27% Similarity=0.371 Sum_probs=22.0
Q ss_pred CCcCCCCCCceEEEEeceeeEEEEEeeeee
Q 046214 20 PGACPFCGGMIRAMDVQSEWRFCFLPLYFK 49 (66)
Q Consensus 20 pG~Cp~CGG~v~a~Dves~~rfCflP~~~k 49 (66)
.-+||.||-.+.++=|-..+-+=-|=|.-|
T Consensus 49 ~t~CP~Cg~~~e~~fvva~~aLVgl~l~mk 78 (115)
T COG1885 49 STSCPKCGEPFESAFVVANTALVGLILSMK 78 (115)
T ss_pred cccCCCCCCccceeEEEecceeEEEEEEEE
Confidence 458999999998887777666655554444
No 201
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=26.91 E-value=48 Score=28.18 Aligned_cols=13 Identities=38% Similarity=1.035 Sum_probs=11.8
Q ss_pred ccCCCcCCCCCCc
Q 046214 17 QTAPGACPFCGGM 29 (66)
Q Consensus 17 ~~ApG~Cp~CGG~ 29 (66)
++-|..||.||+.
T Consensus 472 ~~~p~~Cp~Cgs~ 484 (730)
T COG1198 472 EPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCC
Confidence 5889999999997
No 202
>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=26.79 E-value=30 Score=23.89 Aligned_cols=11 Identities=45% Similarity=1.274 Sum_probs=8.6
Q ss_pred CCcCCCCCCce
Q 046214 20 PGACPFCGGMI 30 (66)
Q Consensus 20 pG~Cp~CGG~v 30 (66)
.-.||.|||.+
T Consensus 133 ~p~C~~Cg~~l 143 (218)
T cd01407 133 VPRCPKCGGLL 143 (218)
T ss_pred CCcCCCCCCcc
Confidence 34799999974
No 203
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=26.73 E-value=26 Score=21.56 Aligned_cols=12 Identities=42% Similarity=0.944 Sum_probs=7.6
Q ss_pred eccCCCcCCCCC
Q 046214 16 TQTAPGACPFCG 27 (66)
Q Consensus 16 ~~~ApG~Cp~CG 27 (66)
++.++-.||.||
T Consensus 46 k~g~~Y~Cp~CG 57 (61)
T COG2888 46 KLGNPYRCPKCG 57 (61)
T ss_pred HcCCceECCCcC
Confidence 355666677776
No 204
>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=26.64 E-value=29 Score=23.57 Aligned_cols=10 Identities=40% Similarity=1.019 Sum_probs=8.0
Q ss_pred CCcCCCCCCc
Q 046214 20 PGACPFCGGM 29 (66)
Q Consensus 20 pG~Cp~CGG~ 29 (66)
+-.|||||..
T Consensus 105 ~~~cp~c~s~ 114 (146)
T TIGR02159 105 SVQCPRCGSA 114 (146)
T ss_pred CCcCCCCCCC
Confidence 3589999974
No 205
>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=26.61 E-value=35 Score=23.62 Aligned_cols=14 Identities=21% Similarity=0.586 Sum_probs=11.0
Q ss_pred cCCCcCCCCCCceE
Q 046214 18 TAPGACPFCGGMIR 31 (66)
Q Consensus 18 ~ApG~Cp~CGG~v~ 31 (66)
+-|-+||+||--..
T Consensus 24 k~p~vcP~cg~~~~ 37 (129)
T TIGR02300 24 RRPAVSPYTGEQFP 37 (129)
T ss_pred CCCccCCCcCCccC
Confidence 46889999997654
No 206
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=26.61 E-value=25 Score=21.09 Aligned_cols=16 Identities=38% Similarity=0.781 Sum_probs=12.1
Q ss_pred CCcCCCCCCceEEEEe
Q 046214 20 PGACPFCGGMIRAMDV 35 (66)
Q Consensus 20 pG~Cp~CGG~v~a~Dv 35 (66)
...||-||.+++-.|.
T Consensus 39 YngCPfC~~~~~~~~~ 54 (55)
T PF14447_consen 39 YNGCPFCGTPFEFDDP 54 (55)
T ss_pred ccCCCCCCCcccCCCC
Confidence 3579999998876654
No 207
>PRK12860 transcriptional activator FlhC; Provisional
Probab=26.48 E-value=32 Score=24.80 Aligned_cols=13 Identities=31% Similarity=0.685 Sum_probs=10.2
Q ss_pred CcCCCCCCceEEE
Q 046214 21 GACPFCGGMIRAM 33 (66)
Q Consensus 21 G~Cp~CGG~v~a~ 33 (66)
-.|.+|||.-.+.
T Consensus 135 ~~C~~Cgg~fv~~ 147 (189)
T PRK12860 135 ARCCRCGGKFVTH 147 (189)
T ss_pred ccCCCCCCCeecc
Confidence 4699999997644
No 208
>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=26.16 E-value=71 Score=22.22 Aligned_cols=25 Identities=28% Similarity=0.604 Sum_probs=21.0
Q ss_pred eEEEEecCcceeeeeccCCC--------cCCCC
Q 046214 2 CLVCVCDEDERVLGTQTAPG--------ACPFC 26 (66)
Q Consensus 2 ~~~~vcde~~kv~~~~~ApG--------~Cp~C 26 (66)
+|+..||..+.++.+++|+| +||.=
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 67754
No 209
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=26.14 E-value=31 Score=24.31 Aligned_cols=9 Identities=56% Similarity=1.671 Sum_probs=7.5
Q ss_pred cCCCCCCce
Q 046214 22 ACPFCGGMI 30 (66)
Q Consensus 22 ~Cp~CGG~v 30 (66)
.||.|||.+
T Consensus 144 ~C~~Cgg~l 152 (242)
T PRK00481 144 RCPKCGGIL 152 (242)
T ss_pred CCCCCCCcc
Confidence 399999975
No 210
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=26.05 E-value=39 Score=22.75 Aligned_cols=22 Identities=27% Similarity=0.542 Sum_probs=14.7
Q ss_pred cCcceeeeeccCCCcCCCCCCc
Q 046214 8 DEDERVLGTQTAPGACPFCGGM 29 (66)
Q Consensus 8 de~~kv~~~~~ApG~Cp~CGG~ 29 (66)
|+++-.-.-++..-.||.||+.
T Consensus 53 gg~~a~~nv~~t~~~Cp~Cgh~ 74 (105)
T KOG2906|consen 53 GGDEAWENVDQTEATCPTCGHE 74 (105)
T ss_pred CCcccccchhhccCcCCCCCCC
Confidence 3344444446777899999986
No 211
>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=26.00 E-value=37 Score=20.86 Aligned_cols=10 Identities=40% Similarity=1.042 Sum_probs=8.1
Q ss_pred cCCCcCCCCC
Q 046214 18 TAPGACPFCG 27 (66)
Q Consensus 18 ~ApG~Cp~CG 27 (66)
.++..||+||
T Consensus 82 ~~np~C~~C~ 91 (91)
T cd04482 82 RENPVCPKCG 91 (91)
T ss_pred EcCCcCCCCC
Confidence 3678899997
No 212
>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=25.96 E-value=61 Score=24.72 Aligned_cols=34 Identities=24% Similarity=0.661 Sum_probs=12.2
Q ss_pred CCcCCCCCCc-eEEEEeceeeEEEEEeeeeeeccEEEeecccceeee
Q 046214 20 PGACPFCGGM-IRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLVV 65 (66)
Q Consensus 20 pG~Cp~CGG~-v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~ 65 (66)
.+.||+||-. ++.. +..... .-|+|+-|+-.+++
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 4679999987 5543 333322 25788888876654
No 213
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=25.90 E-value=41 Score=17.99 Aligned_cols=11 Identities=27% Similarity=0.848 Sum_probs=9.2
Q ss_pred cCCCCCCceEE
Q 046214 22 ACPFCGGMIRA 32 (66)
Q Consensus 22 ~Cp~CGG~v~a 32 (66)
.|+.||.....
T Consensus 7 ~C~~CG~~m~~ 17 (58)
T PF13408_consen 7 RCGHCGSKMTR 17 (58)
T ss_pred EcccCCcEeEE
Confidence 59999998776
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=25.54 E-value=33 Score=23.66 Aligned_cols=10 Identities=50% Similarity=1.461 Sum_probs=8.1
Q ss_pred CcCCCCCCce
Q 046214 21 GACPFCGGMI 30 (66)
Q Consensus 21 G~Cp~CGG~v 30 (66)
-.||.|||.+
T Consensus 131 p~C~~Cgg~l 140 (224)
T cd01412 131 PRCPKCGGLL 140 (224)
T ss_pred CCCCCCCCcc
Confidence 4699999964
No 215
>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=25.40 E-value=26 Score=23.85 Aligned_cols=21 Identities=29% Similarity=0.765 Sum_probs=12.5
Q ss_pred ecCcceeeeeccCCCcCCCCCCce
Q 046214 7 CDEDERVLGTQTAPGACPFCGGMI 30 (66)
Q Consensus 7 cde~~kv~~~~~ApG~Cp~CGG~v 30 (66)
|+..=|++|+.. .|+||+-++
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 444556666663 677777654
No 216
>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=25.32 E-value=42 Score=20.41 Aligned_cols=17 Identities=24% Similarity=0.415 Sum_probs=12.2
Q ss_pred eeccCCCcCCCCCCceE
Q 046214 15 GTQTAPGACPFCGGMIR 31 (66)
Q Consensus 15 ~~~~ApG~Cp~CGG~v~ 31 (66)
.|=-|...||.|+-+=.
T Consensus 4 KRFIAGA~CP~C~~~Dt 20 (59)
T TIGR02443 4 KRFIAGAVCPACSAQDT 20 (59)
T ss_pred ceEeccccCCCCcCccE
Confidence 44557889999986533
No 217
>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=25.23 E-value=70 Score=19.65 Aligned_cols=19 Identities=16% Similarity=0.323 Sum_probs=15.6
Q ss_pred CceEEEEeceeeEEEEEee
Q 046214 28 GMIRAMDVQSEWRFCFLPL 46 (66)
Q Consensus 28 G~v~a~Dves~~rfCflP~ 46 (66)
.+--++||.-+||++|-+.
T Consensus 62 ~g~~Si~i~~~~RliF~~~ 80 (93)
T PF05015_consen 62 KGQWSIRINGNWRLIFRFE 80 (93)
T ss_pred CCcEEEEeCCCEEEEEEEe
Confidence 3567899999999999653
No 218
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=25.15 E-value=34 Score=16.77 Aligned_cols=10 Identities=40% Similarity=1.245 Sum_probs=6.7
Q ss_pred cCCCCCCceE
Q 046214 22 ACPFCGGMIR 31 (66)
Q Consensus 22 ~Cp~CGG~v~ 31 (66)
.||.||-...
T Consensus 4 ~C~~CgR~F~ 13 (25)
T PF13913_consen 4 PCPICGRKFN 13 (25)
T ss_pred cCCCCCCEEC
Confidence 4788886653
No 219
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.14 E-value=24 Score=25.35 Aligned_cols=26 Identities=27% Similarity=0.764 Sum_probs=17.1
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccce
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARR 62 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (66)
.|-+|||.|+- ..+|-...|+.|..+
T Consensus 91 ~CARCGGrv~l---------------rsNKv~wvcnlc~k~ 116 (169)
T KOG3799|consen 91 FCARCGGRVSL---------------RSNKVMWVCNLCRKQ 116 (169)
T ss_pred HHHhcCCeeee---------------ccCceEEeccCCcHH
Confidence 57889999863 235556667666543
No 220
>PF15616 TerY-C: TerY-C metal binding domain
Probab=25.01 E-value=53 Score=22.45 Aligned_cols=37 Identities=24% Similarity=0.547 Sum_probs=21.3
Q ss_pred CcCCCCCCc-eEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214 21 GACPFCGGM-IRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL 63 (66)
Q Consensus 21 G~Cp~CGG~-v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (66)
..||+||-. .-|+= ..---|| +.---...|+-|++..
T Consensus 78 PgCP~CGn~~~fa~C-~CGkl~C-----i~g~~~~~CPwCg~~g 115 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVC-GCGKLFC-----IDGEGEVTCPWCGNEG 115 (131)
T ss_pred CCCCCCcChhcEEEe-cCCCEEE-----eCCCCCEECCCCCCee
Confidence 569999987 33332 3333333 3334467777777654
No 221
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=24.82 E-value=25 Score=20.85 Aligned_cols=12 Identities=42% Similarity=1.176 Sum_probs=9.5
Q ss_pred CCcCCCCCCceE
Q 046214 20 PGACPFCGGMIR 31 (66)
Q Consensus 20 pG~Cp~CGG~v~ 31 (66)
...||.||+...
T Consensus 17 k~~CP~CG~~t~ 28 (56)
T PRK13130 17 KEICPVCGGKTK 28 (56)
T ss_pred cccCcCCCCCCC
Confidence 568999998754
No 222
>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=24.68 E-value=45 Score=18.84 Aligned_cols=14 Identities=29% Similarity=0.743 Sum_probs=8.1
Q ss_pred eccEEEeeccccee
Q 046214 50 TKRKFYCTVCARRL 63 (66)
Q Consensus 50 ~krk~~Ct~C~r~L 63 (66)
..||+.|..||+..
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 58999999999764
No 223
>PRK14724 DNA topoisomerase III; Provisional
Probab=24.64 E-value=45 Score=28.98 Aligned_cols=14 Identities=43% Similarity=1.032 Sum_probs=11.8
Q ss_pred ccCCCcCCCCCCce
Q 046214 17 QTAPGACPFCGGMI 30 (66)
Q Consensus 17 ~~ApG~Cp~CGG~v 30 (66)
+.+-|.||.||+.+
T Consensus 752 ~~~~g~CPkCg~~v 765 (987)
T PRK14724 752 QESLGPCPKCGAPV 765 (987)
T ss_pred cccccCCCCCCCce
Confidence 56779999999985
No 224
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=24.64 E-value=37 Score=24.28 Aligned_cols=11 Identities=36% Similarity=0.836 Sum_probs=8.5
Q ss_pred CCcCCCCCCce
Q 046214 20 PGACPFCGGMI 30 (66)
Q Consensus 20 pG~Cp~CGG~v 30 (66)
.-.||.|||.+
T Consensus 143 ~p~Cp~Cgg~l 153 (244)
T PRK14138 143 VPRCDDCSGLI 153 (244)
T ss_pred CCCCCCCCCeE
Confidence 34699999864
No 225
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=24.53 E-value=12 Score=20.52 Aligned_cols=39 Identities=31% Similarity=0.694 Sum_probs=23.8
Q ss_pred CCCcCCC--CCCceEEEEeceeeE-EEEEeeeeeeccEEEeec----ccceee
Q 046214 19 APGACPF--CGGMIRAMDVQSEWR-FCFLPLYFKTKRKFYCTV----CARRLV 64 (66)
Q Consensus 19 ApG~Cp~--CGG~v~a~Dves~~r-fCflP~~~k~krk~~Ct~----C~r~L~ 64 (66)
++-.||+ |...+..-+++.... -| -++.+.|++ |+.+..
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 4557888 555688888887776 55 457788888 876653
No 226
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=24.42 E-value=22 Score=25.34 Aligned_cols=16 Identities=19% Similarity=0.575 Sum_probs=13.4
Q ss_pred eccEEEeecccceeee
Q 046214 50 TKRKFYCTVCARRLVV 65 (66)
Q Consensus 50 ~krk~~Ct~C~r~L~~ 65 (66)
++.+|+|+.||.++=|
T Consensus 126 ~~S~ysC~~CG~kyCs 141 (156)
T KOG3362|consen 126 YDSKYSCVNCGTKYCS 141 (156)
T ss_pred CCchhHHHhcCCceee
Confidence 7889999999988744
No 227
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.42 E-value=35 Score=22.36 Aligned_cols=8 Identities=50% Similarity=1.485 Sum_probs=3.8
Q ss_pred CCCCCCce
Q 046214 23 CPFCGGMI 30 (66)
Q Consensus 23 Cp~CGG~v 30 (66)
||.||-.+
T Consensus 4 CP~C~v~l 11 (88)
T COG3809 4 CPICGVEL 11 (88)
T ss_pred cCcCCcee
Confidence 45554443
No 228
>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=24.33 E-value=33 Score=16.79 Aligned_cols=12 Identities=33% Similarity=1.057 Sum_probs=9.6
Q ss_pred EEEeecccceee
Q 046214 53 KFYCTVCARRLV 64 (66)
Q Consensus 53 k~~Ct~C~r~L~ 64 (66)
+|+|..|...+.
T Consensus 3 ~~~C~~C~~~~~ 14 (35)
T smart00451 3 GFYCKLCNVTFT 14 (35)
T ss_pred CeEccccCCccC
Confidence 588999988764
No 229
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=24.25 E-value=42 Score=26.89 Aligned_cols=28 Identities=36% Similarity=0.838 Sum_probs=19.8
Q ss_pred CCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceeee
Q 046214 19 APGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLVV 65 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~ 65 (66)
+.-.||+|+.+ .|=||+ .|+.|+-.|++
T Consensus 275 ~Gy~CP~Ckak-----------vCsLP~--------eCpiC~ltLVs 302 (378)
T KOG2807|consen 275 GGYFCPQCKAK-----------VCSLPI--------ECPICSLTLVS 302 (378)
T ss_pred CceeCCcccCe-----------eecCCc--------cCCccceeEec
Confidence 34468888754 577775 68888888875
No 230
>PF04400 DUF539: Protein of unknown function (DUF539); InterPro: IPR007495 This is a family of putative periplasmic proteins.
Probab=23.92 E-value=22 Score=20.51 Aligned_cols=22 Identities=27% Similarity=0.739 Sum_probs=15.6
Q ss_pred eeeeccCCCcCCCCCCceEEEEecee
Q 046214 13 VLGTQTAPGACPFCGGMIRAMDVQSE 38 (66)
Q Consensus 13 v~~~~~ApG~Cp~CGG~v~a~Dves~ 38 (66)
++++++..||| |++.++.++..
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 46788999997 45666776654
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=23.54 E-value=88 Score=21.42 Aligned_cols=7 Identities=57% Similarity=1.559 Sum_probs=3.6
Q ss_pred cCCCCCC
Q 046214 22 ACPFCGG 28 (66)
Q Consensus 22 ~Cp~CGG 28 (66)
.||.|||
T Consensus 132 ~Cp~C~~ 138 (146)
T PF07295_consen 132 PCPKCGH 138 (146)
T ss_pred CCCCCCC
Confidence 4555554
No 232
>PRK06450 threonine synthase; Validated
Probab=23.51 E-value=83 Score=23.53 Aligned_cols=16 Identities=25% Similarity=0.519 Sum_probs=11.8
Q ss_pred cCCCcCCCCCCceEEE
Q 046214 18 TAPGACPFCGGMIRAM 33 (66)
Q Consensus 18 ~ApG~Cp~CGG~v~a~ 33 (66)
...-.||.|||.+...
T Consensus 16 ~~~~~C~~cg~~l~~~ 31 (338)
T PRK06450 16 IYEIRCKKCGGPFEIL 31 (338)
T ss_pred cccccCCcCCCEeEEe
Confidence 3346899999987654
No 233
>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=23.46 E-value=32 Score=21.32 Aligned_cols=10 Identities=40% Similarity=0.989 Sum_probs=4.3
Q ss_pred CCcCCCCCCc
Q 046214 20 PGACPFCGGM 29 (66)
Q Consensus 20 pG~Cp~CGG~ 29 (66)
---||.||.+
T Consensus 24 k~FCp~CGn~ 33 (73)
T PF08772_consen 24 KQFCPKCGNA 33 (73)
T ss_dssp --S-SSS--S
T ss_pred ceeCcccCCC
Confidence 3469999986
No 234
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=23.42 E-value=90 Score=19.00 Aligned_cols=27 Identities=30% Similarity=0.716 Sum_probs=18.3
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL 63 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L 63 (66)
+||-|-|+++.. +.+...+|..|++-+
T Consensus 10 aCP~~kg~L~~~---------------~~~~~L~c~~~~~aY 36 (60)
T COG2835 10 ACPVCKGPLVYD---------------EEKQELICPRCKLAY 36 (60)
T ss_pred eccCcCCcceEe---------------ccCCEEEecccCcee
Confidence 699999995543 334477777777654
No 235
>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=23.39 E-value=37 Score=21.75 Aligned_cols=6 Identities=67% Similarity=2.361 Sum_probs=5.0
Q ss_pred cCCCCC
Q 046214 22 ACPFCG 27 (66)
Q Consensus 22 ~Cp~CG 27 (66)
.||+||
T Consensus 3 ~CP~CG 8 (84)
T TIGR01374 3 PCPYCG 8 (84)
T ss_pred cCCCCC
Confidence 599998
No 236
>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=23.28 E-value=27 Score=22.98 Aligned_cols=17 Identities=29% Similarity=0.698 Sum_probs=12.8
Q ss_pred ccCCCcCCCCCCceEEE
Q 046214 17 QTAPGACPFCGGMIRAM 33 (66)
Q Consensus 17 ~~ApG~Cp~CGG~v~a~ 33 (66)
+-+.|.|+||+-.+...
T Consensus 21 ~~~~~~C~YC~~~~~~~ 37 (144)
T TIGR02646 21 QLQGGLCAYCEREIELL 37 (144)
T ss_pred HHhCCCcCccCCCcCCC
Confidence 34589999999966643
No 237
>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=23.22 E-value=30 Score=22.40 Aligned_cols=13 Identities=23% Similarity=0.782 Sum_probs=8.5
Q ss_pred ccEEEeeccccee
Q 046214 51 KRKFYCTVCARRL 63 (66)
Q Consensus 51 krk~~Ct~C~r~L 63 (66)
..+|.|++||+.-
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 4578888888653
No 238
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=23.17 E-value=61 Score=19.61 Aligned_cols=21 Identities=19% Similarity=0.482 Sum_probs=16.8
Q ss_pred eeeeeeccEEEeecccceeee
Q 046214 45 PLYFKTKRKFYCTVCARRLVV 65 (66)
Q Consensus 45 P~~~k~krk~~Ct~C~r~L~~ 65 (66)
.++.+.-....|..||+.|..
T Consensus 22 ~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 22 VVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EEEecCCcEEECcccCCCccc
Confidence 466778888999999998853
No 239
>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=23.16 E-value=39 Score=21.92 Aligned_cols=9 Identities=33% Similarity=0.977 Sum_probs=7.0
Q ss_pred CCCcCCCCC
Q 046214 19 APGACPFCG 27 (66)
Q Consensus 19 ApG~Cp~CG 27 (66)
..--||+||
T Consensus 19 ~~~gCpnC~ 27 (98)
T cd07973 19 ERDGCPNCE 27 (98)
T ss_pred cCCCCCCCc
Confidence 446799997
No 240
>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=23.15 E-value=1.3e+02 Score=15.93 Aligned_cols=31 Identities=29% Similarity=0.641 Sum_probs=20.2
Q ss_pred eccCCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccce
Q 046214 16 TQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARR 62 (66)
Q Consensus 16 ~~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (66)
+-..|..|..|+..+ ....+..|.|+.|+..
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 346778888888876 1245677888888754
No 241
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.10 E-value=31 Score=21.45 Aligned_cols=15 Identities=27% Similarity=0.563 Sum_probs=10.7
Q ss_pred CCcCCCCCCceEEEE
Q 046214 20 PGACPFCGGMIRAMD 34 (66)
Q Consensus 20 pG~Cp~CGG~v~a~D 34 (66)
---||.||-+|.=.+
T Consensus 7 ~v~CP~Cgkpv~w~~ 21 (65)
T COG3024 7 TVPCPTCGKPVVWGE 21 (65)
T ss_pred cccCCCCCCcccccc
Confidence 345999998876544
No 242
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=22.60 E-value=64 Score=22.01 Aligned_cols=15 Identities=20% Similarity=0.693 Sum_probs=8.7
Q ss_pred cEEEeecccceeeeC
Q 046214 52 RKFYCTVCARRLVVQ 66 (66)
Q Consensus 52 rk~~Ct~C~r~L~~~ 66 (66)
..++|..||-+|..|
T Consensus 27 ~~~tC~~Cg~~L~lh 41 (128)
T PF11682_consen 27 DHWTCHSCGCPLILH 41 (128)
T ss_pred CeEEEecCCceEEEe
Confidence 455666666666554
No 243
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=22.44 E-value=75 Score=26.44 Aligned_cols=15 Identities=33% Similarity=0.944 Sum_probs=12.9
Q ss_pred CCCcCCCCCCceEEE
Q 046214 19 APGACPFCGGMIRAM 33 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~ 33 (66)
.|-.||.||+.++..
T Consensus 403 ~P~~CP~Cgs~l~~~ 417 (665)
T PRK07956 403 MPTHCPVCGSELVRV 417 (665)
T ss_pred CCCCCCCCCCEeEec
Confidence 688999999999753
No 244
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=22.41 E-value=41 Score=24.50 Aligned_cols=11 Identities=55% Similarity=1.521 Sum_probs=8.5
Q ss_pred CcCCCCCCceE
Q 046214 21 GACPFCGGMIR 31 (66)
Q Consensus 21 G~Cp~CGG~v~ 31 (66)
-.||.|||.+.
T Consensus 180 P~C~~Cgg~lr 190 (285)
T PRK05333 180 PACPACGGILK 190 (285)
T ss_pred CCCCCCCCccc
Confidence 46999999753
No 245
>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=22.38 E-value=43 Score=23.56 Aligned_cols=11 Identities=36% Similarity=0.685 Sum_probs=8.6
Q ss_pred CCcCCCCCCce
Q 046214 20 PGACPFCGGMI 30 (66)
Q Consensus 20 pG~Cp~CGG~v 30 (66)
.-.||.|||.+
T Consensus 136 ~p~C~~Cgg~l 146 (225)
T cd01411 136 SPYHAKCGGVI 146 (225)
T ss_pred CCCCCCCCCEe
Confidence 35799999864
No 246
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=22.33 E-value=37 Score=17.92 Aligned_cols=31 Identities=35% Similarity=0.717 Sum_probs=21.2
Q ss_pred cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccce
Q 046214 22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARR 62 (66)
Q Consensus 22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~ 62 (66)
.||+|+..-...|=+ || ...++.-|+.|+-.
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 247
>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=22.10 E-value=66 Score=16.58 Aligned_cols=14 Identities=36% Similarity=0.600 Sum_probs=9.5
Q ss_pred CCcCCCCCCceEEE
Q 046214 20 PGACPFCGGMIRAM 33 (66)
Q Consensus 20 pG~Cp~CGG~v~a~ 33 (66)
.|.|..||..+...
T Consensus 3 yg~C~~CGe~I~~~ 16 (36)
T PF01258_consen 3 YGICEDCGEPIPEE 16 (36)
T ss_dssp -SB-TTTSSBEEHH
T ss_pred CCCccccCChHHHH
Confidence 57899999988644
No 248
>smart00532 LIGANc Ligase N family.
Probab=22.08 E-value=81 Score=25.02 Aligned_cols=16 Identities=31% Similarity=0.806 Sum_probs=13.5
Q ss_pred CCCcCCCCCCceEEEE
Q 046214 19 APGACPFCGGMIRAMD 34 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~D 34 (66)
.|-.||.||..++-.+
T Consensus 398 ~P~~CP~C~s~l~~~~ 413 (441)
T smart00532 398 MPTHCPSCGSELVREE 413 (441)
T ss_pred CCCCCCCCCCEeEecC
Confidence 7999999999997543
No 249
>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=21.99 E-value=44 Score=19.39 Aligned_cols=17 Identities=35% Similarity=0.546 Sum_probs=8.9
Q ss_pred cCCCcCCCCCCceEEEE
Q 046214 18 TAPGACPFCGGMIRAMD 34 (66)
Q Consensus 18 ~ApG~Cp~CGG~v~a~D 34 (66)
.|.+.||-|+|+--.-|
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 36788999999754443
No 250
>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=21.92 E-value=43 Score=22.66 Aligned_cols=11 Identities=27% Similarity=0.516 Sum_probs=8.7
Q ss_pred CCcCCCCCCce
Q 046214 20 PGACPFCGGMI 30 (66)
Q Consensus 20 pG~Cp~CGG~v 30 (66)
.-.|++|||.-
T Consensus 97 ip~C~~Cg~~R 107 (164)
T PF04194_consen 97 IPKCENCGSPR 107 (164)
T ss_pred CCCCccCCCcc
Confidence 45799999864
No 251
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=21.77 E-value=67 Score=24.66 Aligned_cols=13 Identities=46% Similarity=1.262 Sum_probs=8.9
Q ss_pred cCCCcCCCCCCce
Q 046214 18 TAPGACPFCGGMI 30 (66)
Q Consensus 18 ~ApG~Cp~CGG~v 30 (66)
+.+..||+||+..
T Consensus 259 ~~~~~C~~c~~~~ 271 (382)
T PRK04338 259 LPPEECPVCGGKF 271 (382)
T ss_pred CCCCCCCCCCCcc
Confidence 4566788887753
No 252
>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=21.77 E-value=38 Score=19.22 Aligned_cols=8 Identities=50% Similarity=1.173 Sum_probs=6.4
Q ss_pred cCCCCCCc
Q 046214 22 ACPFCGGM 29 (66)
Q Consensus 22 ~Cp~CGG~ 29 (66)
-||-||+-
T Consensus 11 ~CPgCG~t 18 (52)
T PF10825_consen 11 PCPGCGMT 18 (52)
T ss_pred CCCCCcHH
Confidence 59999974
No 253
>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=21.66 E-value=81 Score=26.15 Aligned_cols=15 Identities=33% Similarity=0.859 Sum_probs=12.9
Q ss_pred CCCcCCCCCCceEEE
Q 046214 19 APGACPFCGGMIRAM 33 (66)
Q Consensus 19 ApG~Cp~CGG~v~a~ 33 (66)
.|-.||.||..++--
T Consensus 391 ~P~~CP~C~s~l~~~ 405 (652)
T TIGR00575 391 FPTHCPSCGSPLVKI 405 (652)
T ss_pred CCCCCCCCCCEeEec
Confidence 689999999999763
No 254
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=21.54 E-value=89 Score=16.11 Aligned_cols=14 Identities=36% Similarity=0.581 Sum_probs=10.7
Q ss_pred EEEEecCcceeeee
Q 046214 3 LVCVCDEDERVLGT 16 (66)
Q Consensus 3 ~~~vcde~~kv~~~ 16 (66)
...|+|++++++|-
T Consensus 32 ~~~V~d~~~~~~G~ 45 (57)
T PF00571_consen 32 RLPVVDEDGKLVGI 45 (57)
T ss_dssp EEEEESTTSBEEEE
T ss_pred EEEEEecCCEEEEE
Confidence 35788988888874
No 255
>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=21.49 E-value=45 Score=19.65 Aligned_cols=12 Identities=42% Similarity=1.060 Sum_probs=9.7
Q ss_pred CcCCCCCCceEE
Q 046214 21 GACPFCGGMIRA 32 (66)
Q Consensus 21 G~Cp~CGG~v~a 32 (66)
-.||.|||....
T Consensus 18 ~~cp~cG~~T~~ 29 (53)
T PF04135_consen 18 DKCPPCGGPTES 29 (53)
T ss_dssp SBBTTTSSBSEE
T ss_pred CccCCCCCCCcC
Confidence 589999997654
No 256
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=21.40 E-value=47 Score=20.85 Aligned_cols=11 Identities=36% Similarity=0.899 Sum_probs=6.4
Q ss_pred cCCCCCCceEE
Q 046214 22 ACPFCGGMIRA 32 (66)
Q Consensus 22 ~Cp~CGG~v~a 32 (66)
.||.||=-.-.
T Consensus 3 ~CPCCg~~Tl~ 13 (78)
T PF14206_consen 3 PCPCCGYYTLE 13 (78)
T ss_pred cCCCCCcEEec
Confidence 47777755443
No 257
>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=21.37 E-value=54 Score=20.07 Aligned_cols=14 Identities=36% Similarity=0.608 Sum_probs=10.5
Q ss_pred ccCCCcCCCCCCce
Q 046214 17 QTAPGACPFCGGMI 30 (66)
Q Consensus 17 ~~ApG~Cp~CGG~v 30 (66)
=-|...||.|+.+=
T Consensus 5 FIAGa~CP~C~~~D 18 (71)
T PF09526_consen 5 FIAGAVCPKCQAMD 18 (71)
T ss_pred EecCccCCCCcCcc
Confidence 34778999998653
No 258
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=21.22 E-value=76 Score=24.03 Aligned_cols=17 Identities=24% Similarity=0.544 Sum_probs=13.1
Q ss_pred CCcCCCCCCceEEEEec
Q 046214 20 PGACPFCGGMIRAMDVQ 36 (66)
Q Consensus 20 pG~Cp~CGG~v~a~Dve 36 (66)
.--|++||+.++-.-+.
T Consensus 245 GepC~~CGt~I~k~~~~ 261 (273)
T COG0266 245 GEPCRRCGTPIEKIKLG 261 (273)
T ss_pred CCCCCccCCEeEEEEEc
Confidence 34699999999876554
No 259
>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=21.09 E-value=84 Score=24.44 Aligned_cols=26 Identities=23% Similarity=0.516 Sum_probs=22.5
Q ss_pred eeeeccCCCcCCCCCCceEEEEecee
Q 046214 13 VLGTQTAPGACPFCGGMIRAMDVQSE 38 (66)
Q Consensus 13 v~~~~~ApG~Cp~CGG~v~a~Dves~ 38 (66)
++---.||.-|-|||-.++++.++..
T Consensus 253 lvTVWSAPNYCYRCGNvAsi~~~d~~ 278 (306)
T KOG0373|consen 253 LVTVWSAPNYCYRCGNVASIMSFDDN 278 (306)
T ss_pred EEEEecCCchhhhccCeeeEEEeccc
Confidence 66677899999999999999988754
No 260
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=21.08 E-value=37 Score=21.06 Aligned_cols=8 Identities=50% Similarity=1.061 Sum_probs=6.3
Q ss_pred CcCCCCCC
Q 046214 21 GACPFCGG 28 (66)
Q Consensus 21 G~Cp~CGG 28 (66)
-.||+||-
T Consensus 18 lrCPRC~~ 25 (65)
T COG4049 18 LRCPRCGM 25 (65)
T ss_pred eeCCchhH
Confidence 46999984
No 261
>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=20.78 E-value=46 Score=23.29 Aligned_cols=10 Identities=60% Similarity=1.491 Sum_probs=8.1
Q ss_pred CcCCCCCCce
Q 046214 21 GACPFCGGMI 30 (66)
Q Consensus 21 G~Cp~CGG~v 30 (66)
-.||.|||.+
T Consensus 137 p~C~~Cgg~l 146 (222)
T cd01413 137 PRCPKCGGII 146 (222)
T ss_pred CcCCCCCCcc
Confidence 4699999864
No 262
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=20.73 E-value=90 Score=19.42 Aligned_cols=9 Identities=33% Similarity=0.988 Sum_probs=4.4
Q ss_pred cCCCCCCce
Q 046214 22 ACPFCGGMI 30 (66)
Q Consensus 22 ~Cp~CGG~v 30 (66)
.||.|+..+
T Consensus 3 ~CP~C~~~L 11 (70)
T PF07191_consen 3 TCPKCQQEL 11 (70)
T ss_dssp B-SSS-SBE
T ss_pred cCCCCCCcc
Confidence 577777653
No 263
>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=20.72 E-value=69 Score=21.23 Aligned_cols=14 Identities=50% Similarity=1.334 Sum_probs=10.3
Q ss_pred cCCCcCCCCCCceE
Q 046214 18 TAPGACPFCGGMIR 31 (66)
Q Consensus 18 ~ApG~Cp~CGG~v~ 31 (66)
+.+..||.|||.+.
T Consensus 127 ~~~~~C~~C~~~lr 140 (178)
T PF02146_consen 127 EEPPRCPKCGGLLR 140 (178)
T ss_dssp TSSCBCTTTSCBEE
T ss_pred cccccccccCccCC
Confidence 44569999999543
No 264
>COG3043 NapB Nitrate reductase cytochrome c-type subunit [Energy production and conversion]
Probab=20.66 E-value=45 Score=23.77 Aligned_cols=13 Identities=23% Similarity=0.812 Sum_probs=10.2
Q ss_pred eeeccEEEeeccc
Q 046214 48 FKTKRKFYCTVCA 60 (66)
Q Consensus 48 ~k~krk~~Ct~C~ 60 (66)
--+-|||+|+.|.
T Consensus 121 ~vSPRRYFClQCH 133 (155)
T COG3043 121 DVSPRRYFCLQCH 133 (155)
T ss_pred ccCccceeeeecc
Confidence 3467999999995
No 265
>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=20.43 E-value=53 Score=18.25 Aligned_cols=10 Identities=40% Similarity=0.893 Sum_probs=7.4
Q ss_pred cCCCCCCceE
Q 046214 22 ACPFCGGMIR 31 (66)
Q Consensus 22 ~Cp~CGG~v~ 31 (66)
.||.||-+|-
T Consensus 3 lcpkcgvgvl 12 (36)
T PF09151_consen 3 LCPKCGVGVL 12 (36)
T ss_dssp B-TTTSSSBE
T ss_pred cCCccCceEE
Confidence 6999998874
No 266
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=20.13 E-value=83 Score=26.43 Aligned_cols=15 Identities=27% Similarity=0.873 Sum_probs=12.8
Q ss_pred cCCCcCCCCCCceEE
Q 046214 18 TAPGACPFCGGMIRA 32 (66)
Q Consensus 18 ~ApG~Cp~CGG~v~a 32 (66)
..|-.||.||..++-
T Consensus 421 ~~P~~CP~C~~~l~~ 435 (689)
T PRK14351 421 EFPDTCPVCDSAVER 435 (689)
T ss_pred cCCCCCCCCCCEeee
Confidence 478999999999863
No 267
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=20.05 E-value=74 Score=20.47 Aligned_cols=16 Identities=25% Similarity=0.374 Sum_probs=7.7
Q ss_pred cCCCcCC--CCCCceEEE
Q 046214 18 TAPGACP--FCGGMIRAM 33 (66)
Q Consensus 18 ~ApG~Cp--~CGG~v~a~ 33 (66)
.-.-+|| .|+.+|.--
T Consensus 16 ~~Y~aC~~~~C~kKv~~~ 33 (146)
T PF08646_consen 16 WYYPACPNEKCNKKVTEN 33 (146)
T ss_dssp TEEEE-TSTTTS-B-EEE
T ss_pred cEECCCCCccCCCEeecC
Confidence 3445677 777775543
No 268
>PRK11586 napB nitrate reductase cytochrome C550 subunit; Provisional
Probab=20.04 E-value=46 Score=23.56 Aligned_cols=12 Identities=25% Similarity=0.971 Sum_probs=9.9
Q ss_pred eccEEEeecccc
Q 046214 50 TKRKFYCTVCAR 61 (66)
Q Consensus 50 ~krk~~Ct~C~r 61 (66)
+-|+|+|+.|.-
T Consensus 117 sprRYfCtQCHV 128 (149)
T PRK11586 117 APRRYFCLQCHV 128 (149)
T ss_pred CccceeeccccC
Confidence 668999999963
No 269
>PRK09783 copper/silver efflux system membrane fusion protein CusB; Provisional
Probab=20.03 E-value=57 Score=24.83 Aligned_cols=17 Identities=24% Similarity=0.376 Sum_probs=13.5
Q ss_pred eccCCCcCCCCCCceEE
Q 046214 16 TQTAPGACPFCGGMIRA 32 (66)
Q Consensus 16 ~~~ApG~Cp~CGG~v~a 32 (66)
+++.||.||-||=.+..
T Consensus 54 ~~~~pg~~p~~~m~lvp 70 (409)
T PRK09783 54 RFDKPGKSPFMDMDLVP 70 (409)
T ss_pred CCCCCCCCCCCCCeeeE
Confidence 56889999999866554
Done!