Query 037013
Match_columns 128
No_of_seqs 215 out of 1056
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 07:41:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037013.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037013hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3791 Uncharacterized conser 100.0 2.4E-32 5.2E-37 184.8 9.7 115 8-127 4-124 (133)
2 TIGR02820 formald_GSH S-(hydro 100.0 2.7E-29 5.8E-34 176.5 9.8 112 6-120 15-141 (182)
3 PRK05417 glutathione-dependent 100.0 6.4E-29 1.4E-33 176.0 10.4 113 4-119 17-144 (191)
4 KOG4192 Uncharacterized conser 99.9 4.2E-24 9.2E-29 138.7 9.3 124 1-125 1-124 (134)
5 PF04828 GFA: Glutathione-depe 99.9 1.1E-24 2.4E-29 137.6 5.0 86 30-116 1-92 (92)
6 PF13240 zinc_ribbon_2: zinc-r 92.3 0.036 7.8E-07 26.0 -0.1 11 74-84 13-23 (23)
7 PF13248 zf-ribbon_3: zinc-rib 91.7 0.048 1E-06 26.3 -0.1 13 72-84 14-26 (26)
8 PF14803 Nudix_N_2: Nudix N-te 90.6 0.1 2.2E-06 26.9 0.5 14 75-88 1-14 (34)
9 PF09297 zf-NADH-PPase: NADH p 88.7 0.33 7.1E-06 24.4 1.5 16 74-89 3-18 (32)
10 PF02150 RNA_POL_M_15KD: RNA p 87.8 0.28 6.1E-06 25.3 0.9 15 75-89 2-16 (35)
11 smart00661 RPOL9 RNA polymeras 86.1 0.65 1.4E-05 25.6 1.9 11 74-84 20-30 (52)
12 PF03119 DNA_ligase_ZBD: NAD-d 81.4 1.2 2.6E-05 21.7 1.5 14 76-89 1-14 (28)
13 COG1998 RPS31 Ribosomal protei 81.0 1.7 3.6E-05 24.3 2.1 16 73-88 18-33 (51)
14 PRK00432 30S ribosomal protein 80.8 1.5 3.3E-05 24.5 2.0 22 62-83 6-29 (50)
15 PF08772 NOB1_Zn_bind: Nin one 80.7 0.48 1E-05 28.7 -0.1 16 70-85 20-35 (73)
16 COG1645 Uncharacterized Zn-fin 76.3 1.2 2.6E-05 30.0 0.8 19 69-87 23-41 (131)
17 TIGR00357 methionine-R-sulfoxi 75.4 5.1 0.00011 27.1 3.6 29 75-103 90-122 (134)
18 PF06677 Auto_anti-p27: Sjogre 74.3 1.9 4.2E-05 23.1 1.1 13 74-86 17-29 (41)
19 PRK00222 methionine sulfoxide 72.7 5.8 0.00013 27.1 3.4 42 62-103 78-125 (142)
20 PF04032 Rpr2: RNAse P Rpr2/Rp 71.5 1.1 2.4E-05 27.3 -0.3 17 69-85 41-57 (85)
21 PRK00398 rpoP DNA-directed RNA 67.4 5.8 0.00013 21.3 2.1 16 74-89 21-36 (46)
22 smart00659 RPOLCX RNA polymera 67.2 8.8 0.00019 20.7 2.8 16 75-90 20-35 (44)
23 COG1594 RPB9 DNA-directed RNA 65.7 6.1 0.00013 25.8 2.3 11 76-86 4-14 (113)
24 PRK05508 methionine sulfoxide 64.3 13 0.00028 24.7 3.6 31 73-103 78-113 (119)
25 COG4469 CoiA Competence protei 64.2 3.5 7.5E-05 32.1 1.0 15 74-88 25-39 (342)
26 PF12773 DZR: Double zinc ribb 63.7 2.2 4.8E-05 23.3 -0.1 13 73-85 11-23 (50)
27 PRK00420 hypothetical protein; 63.2 3.5 7.7E-05 27.0 0.8 14 74-87 23-36 (112)
28 KOG2906 RNA polymerase III sub 62.2 5.8 0.00013 25.4 1.6 15 75-89 2-16 (105)
29 PF09151 DUF1936: Domain of un 61.4 7.1 0.00015 19.6 1.5 12 75-86 2-13 (36)
30 PF13408 Zn_ribbon_recom: Reco 61.1 5.4 0.00012 22.1 1.3 16 74-89 5-20 (58)
31 TIGR02098 MJ0042_CXXC MJ0042 f 60.7 9.4 0.0002 19.5 2.1 13 74-86 25-37 (38)
32 TIGR01384 TFS_arch transcripti 58.5 3.9 8.4E-05 26.0 0.4 12 76-87 2-13 (104)
33 PF08271 TF_Zn_Ribbon: TFIIB z 58.3 8.8 0.00019 20.3 1.7 9 76-84 21-29 (43)
34 PRK12496 hypothetical protein; 57.4 4.2 9E-05 28.4 0.4 16 73-88 142-157 (164)
35 PF05191 ADK_lid: Adenylate ki 57.4 8.7 0.00019 19.8 1.5 13 74-87 1-13 (36)
36 PRK06393 rpoE DNA-directed RNA 56.5 9.9 0.00021 22.4 1.8 21 76-98 19-39 (64)
37 PF07754 DUF1610: Domain of un 56.4 6.7 0.00015 18.5 0.9 10 72-81 14-23 (24)
38 COG1996 RPC10 DNA-directed RNA 55.9 17 0.00038 20.2 2.7 17 74-90 24-40 (49)
39 PF01396 zf-C4_Topoisom: Topoi 54.9 15 0.00033 19.1 2.3 15 76-90 3-17 (39)
40 COG2816 NPY1 NTP pyrophosphohy 54.8 5.1 0.00011 30.5 0.5 17 72-88 109-125 (279)
41 PF01641 SelR: SelR domain; I 54.6 30 0.00066 23.1 4.1 33 71-103 83-120 (124)
42 COG0229 Conserved domain frequ 52.0 23 0.00051 24.1 3.3 42 62-103 77-125 (140)
43 PF10955 DUF2757: Protein of u 51.6 7.9 0.00017 23.6 0.9 17 73-89 3-19 (76)
44 PF13842 Tnp_zf-ribbon_2: DDE_ 50.8 12 0.00026 18.7 1.4 13 73-85 15-27 (32)
45 COG1439 Predicted nucleic acid 49.9 7.9 0.00017 27.5 0.8 15 73-87 152-166 (177)
46 smart00714 LITAF Possible memb 49.7 14 0.00031 21.5 1.8 16 72-87 50-65 (67)
47 PRK08351 DNA-directed RNA poly 49.4 14 0.0003 21.6 1.6 20 76-97 17-36 (61)
48 PRK00241 nudC NADH pyrophospha 47.6 6.8 0.00015 29.2 0.2 15 73-87 98-112 (256)
49 PF08882 Acetone_carb_G: Aceto 47.6 16 0.00035 23.9 1.9 17 72-88 72-88 (112)
50 PRK14890 putative Zn-ribbon RN 46.9 17 0.00037 21.0 1.8 16 72-87 23-38 (59)
51 PRK14018 trifunctional thiored 46.8 23 0.00049 29.4 3.1 29 75-103 468-501 (521)
52 PF01599 Ribosomal_S27: Riboso 46.3 17 0.00038 20.0 1.7 17 73-89 17-35 (47)
53 PF11682 DUF3279: Protein of u 45.3 16 0.00036 24.5 1.8 19 70-88 24-42 (128)
54 PRK12495 hypothetical protein; 44.6 7.5 0.00016 28.5 0.0 19 69-87 37-55 (226)
55 KOG3084 NADH pyrophosphatase I 44.3 9.2 0.0002 29.7 0.5 17 73-89 149-165 (345)
56 PF07191 zinc-ribbons_6: zinc- 43.1 19 0.0004 21.6 1.6 17 70-86 26-42 (70)
57 COG3024 Uncharacterized protei 42.6 12 0.00025 22.1 0.6 13 75-87 8-20 (65)
58 PF03811 Zn_Tnp_IS1: InsA N-te 42.4 18 0.00039 18.7 1.3 19 62-80 17-35 (36)
59 PF13005 zf-IS66: zinc-finger 42.0 24 0.00051 18.8 1.8 12 75-86 3-14 (47)
60 PF11062 DUF2863: Protein of u 41.4 11 0.00024 30.0 0.6 16 74-89 364-379 (398)
61 PF10601 zf-LITAF-like: LITAF- 40.9 26 0.00056 20.7 2.0 15 72-86 56-70 (73)
62 PF10571 UPF0547: Uncharacteri 40.0 13 0.00029 17.7 0.5 9 74-82 14-22 (26)
63 COG2023 RPR2 RNase P subunit R 37.5 5.1 0.00011 25.9 -1.5 18 69-86 51-68 (105)
64 PF09889 DUF2116: Uncharacteri 37.3 15 0.00032 21.3 0.5 12 75-86 4-15 (59)
65 COG2093 DNA-directed RNA polym 37.0 29 0.00063 20.4 1.7 21 75-97 19-39 (64)
66 KOG2907 RNA polymerase I trans 36.8 7.7 0.00017 25.5 -0.8 16 73-88 6-21 (116)
67 PF00643 zf-B_box: B-box zinc 36.6 22 0.00047 18.3 1.1 15 72-86 13-27 (42)
68 PF10497 zf-4CXXC_R1: Zinc-fin 35.8 16 0.00034 23.6 0.5 14 30-43 69-82 (105)
69 PF03604 DNA_RNApol_7kD: DNA d 35.6 21 0.00046 17.9 0.9 12 76-87 19-30 (32)
70 PF08792 A2L_zn_ribbon: A2L zi 35.4 26 0.00057 17.6 1.2 11 73-83 20-30 (33)
71 smart00508 PostSET Cysteine-ri 34.9 19 0.00041 17.3 0.6 8 11-18 4-11 (26)
72 KOG2463 Predicted RNA-binding 33.9 17 0.00036 28.5 0.5 16 69-84 252-267 (376)
73 COG2888 Predicted Zn-ribbon RN 33.5 47 0.001 19.3 2.2 19 69-87 22-40 (61)
74 PF09862 DUF2089: Protein of u 33.5 49 0.0011 21.7 2.5 20 70-89 8-27 (113)
75 PHA00626 hypothetical protein 33.2 19 0.0004 20.7 0.5 8 76-83 2-9 (59)
76 TIGR01053 LSD1 zinc finger dom 30.8 44 0.00096 16.6 1.6 13 76-88 3-15 (31)
77 PF08600 Rsm1: Rsm1-like; Int 30.7 24 0.00052 22.0 0.7 20 32-51 20-39 (91)
78 PF01258 zf-dskA_traR: Prokary 30.5 29 0.00063 17.5 0.9 13 75-87 4-16 (36)
79 PF02943 FeThRed_B: Ferredoxin 30.5 17 0.00037 23.6 0.0 9 8-16 77-85 (108)
80 TIGR03831 YgiT_finger YgiT-typ 30.3 26 0.00055 18.2 0.7 15 72-86 30-44 (46)
81 smart00834 CxxC_CXXC_SSSS Puta 29.9 25 0.00055 17.9 0.7 10 75-84 27-36 (41)
82 PF02591 DUF164: Putative zinc 29.4 30 0.00064 19.3 0.9 11 72-82 44-54 (56)
83 COG1579 Zn-ribbon protein, pos 29.3 14 0.00031 27.4 -0.5 16 73-88 220-235 (239)
84 PRK00564 hypA hydrogenase nick 29.3 22 0.00048 23.3 0.4 12 77-88 91-102 (117)
85 PF04606 Ogr_Delta: Ogr/Delta- 27.6 33 0.00071 18.5 0.8 12 77-88 2-13 (47)
86 PF09855 DUF2082: Nucleic-acid 27.0 1.4E+02 0.003 17.5 3.7 26 64-89 26-51 (64)
87 PF14952 zf-tcix: Putative tre 26.6 31 0.00066 18.7 0.6 9 76-84 13-21 (44)
88 PRK12380 hydrogenase nickel in 26.6 25 0.00055 22.8 0.3 12 75-86 87-98 (113)
89 PF04423 Rad50_zn_hook: Rad50 26.6 32 0.0007 19.0 0.7 11 76-86 22-32 (54)
90 PF05207 zf-CSL: CSL zinc fing 26.6 98 0.0021 17.3 2.8 19 6-25 15-33 (55)
91 PRK11586 napB nitrate reductas 26.5 28 0.00061 23.9 0.6 15 71-85 117-131 (149)
92 PF06397 Desulfoferrod_N: Desu 26.5 56 0.0012 16.9 1.6 17 72-88 4-20 (36)
93 PRK15103 paraquat-inducible me 26.2 36 0.00078 27.4 1.2 17 73-89 29-45 (419)
94 COG1885 Uncharacterized protei 25.9 30 0.00066 22.4 0.6 13 75-87 50-62 (115)
95 COG0375 HybF Zn finger protein 25.8 80 0.0017 20.8 2.6 18 72-89 84-101 (115)
96 PF13824 zf-Mss51: Zinc-finger 25.7 32 0.00069 19.6 0.6 16 73-88 13-28 (55)
97 PHA02450 hypothetical protein 25.5 25 0.00055 19.3 0.1 16 7-23 12-27 (53)
98 PF06054 CoiA: Competence prot 25.2 43 0.00092 26.5 1.4 18 72-89 28-45 (375)
99 PRK03954 ribonuclease P protei 25.1 11 0.00024 25.0 -1.6 18 69-86 59-76 (121)
100 PF11781 RRN7: RNA polymerase 25.1 64 0.0014 16.5 1.6 11 76-86 10-20 (36)
101 smart00067 GHA Glycoprotein ho 24.7 27 0.00059 21.5 0.2 10 30-39 75-84 (87)
102 COG4306 Uncharacterized protei 24.7 21 0.00044 24.1 -0.4 16 73-88 67-82 (160)
103 PF14446 Prok-RING_1: Prokaryo 24.4 48 0.001 18.8 1.2 13 73-85 20-32 (54)
104 PF10892 DUF2688: Protein of u 24.4 19 0.00042 20.6 -0.5 14 75-88 11-24 (60)
105 smart00673 CARP Domain in CAPs 24.0 1.1E+02 0.0023 15.2 2.4 26 14-40 1-26 (38)
106 COG3058 FdhE Uncharacterized p 24.0 33 0.00071 26.3 0.5 13 72-84 183-195 (308)
107 PRK05550 bifunctional methioni 23.5 2.3E+02 0.0049 21.7 5.0 31 73-103 81-116 (283)
108 PTZ00157 60S ribosomal protein 23.4 39 0.00085 21.0 0.7 16 72-87 7-22 (84)
109 TIGR00373 conserved hypothetic 23.4 43 0.00093 23.1 1.0 13 75-87 129-141 (158)
110 PF09538 FYDLN_acid: Protein o 23.1 29 0.00063 22.5 0.1 17 73-89 8-24 (108)
111 PF00471 Ribosomal_L33: Riboso 23.1 1.1E+02 0.0024 16.7 2.4 19 69-87 27-45 (48)
112 TIGR01206 lysW lysine biosynth 22.9 50 0.0011 18.7 1.0 12 76-87 4-15 (54)
113 PF12674 Zn_ribbon_2: Putative 22.8 36 0.00079 20.8 0.5 14 75-88 1-14 (81)
114 COG2174 RPL34A Ribosomal prote 22.7 43 0.00093 21.1 0.8 23 70-92 30-52 (93)
115 PF09723 Zn-ribbon_8: Zinc rib 22.3 47 0.001 17.5 0.8 11 72-82 24-34 (42)
116 TIGR02419 C4_traR_proteo phage 22.3 33 0.00072 19.9 0.2 15 73-87 30-44 (63)
117 PF12172 DUF35_N: Rubredoxin-l 22.1 1.1E+02 0.0023 15.3 2.2 13 73-85 10-22 (37)
118 KOG3362 Predicted BBOX Zn-fing 22.1 29 0.00062 23.9 -0.1 12 71-82 115-126 (156)
119 PF01907 Ribosomal_L37e: Ribos 22.1 88 0.0019 17.8 1.9 17 72-88 13-29 (55)
120 COG3043 NapB Nitrate reductase 22.0 37 0.0008 23.4 0.4 13 72-84 124-136 (155)
121 PRK05767 rpl44e 50S ribosomal 22.0 42 0.00092 21.2 0.7 16 72-87 6-21 (92)
122 PF06052 3-HAO: 3-hydroxyanthr 21.8 1.2E+02 0.0025 21.1 2.8 20 68-87 113-132 (151)
123 smart00105 ArfGap Putative GTP 21.6 66 0.0014 20.7 1.6 7 76-82 5-11 (112)
124 PRK13130 H/ACA RNA-protein com 21.6 46 0.00099 19.0 0.7 14 74-87 17-30 (56)
125 TIGR00155 pqiA_fam integral me 21.6 48 0.001 26.5 1.1 16 74-89 33-48 (403)
126 TIGR03830 CxxCG_CxxCG_HTH puta 21.2 84 0.0018 20.1 2.0 16 72-87 29-44 (127)
127 PF14255 Cys_rich_CPXG: Cystei 21.1 55 0.0012 18.3 1.0 13 76-88 2-14 (52)
128 PF06750 DiS_P_DiS: Bacterial 20.8 37 0.00081 21.2 0.3 16 72-87 31-46 (92)
129 PF03226 Yippee-Mis18: Yippee 20.3 46 0.001 20.6 0.6 20 70-89 53-72 (96)
130 PRK00595 rpmG 50S ribosomal pr 20.2 1.1E+02 0.0025 17.1 2.2 18 70-87 33-50 (53)
131 PF14690 zf-ISL3: zinc-finger 20.2 84 0.0018 16.4 1.6 9 72-80 39-47 (47)
132 PF06220 zf-U1: U1 zinc finger 20.2 40 0.00087 17.5 0.3 14 73-86 2-15 (38)
133 PF01601 Corona_S2: Coronaviru 20.1 34 0.00075 28.8 0.0 24 69-93 365-388 (610)
134 cd06008 NF-X1-zinc-finger Pres 20.1 60 0.0013 17.7 1.0 15 7-21 31-45 (49)
135 PF13453 zf-TFIIB: Transcripti 20.0 49 0.0011 17.2 0.6 9 77-85 2-10 (41)
No 1
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=99.98 E-value=2.4e-32 Score=184.78 Aligned_cols=115 Identities=26% Similarity=0.457 Sum_probs=95.0
Q ss_pred EEEeeeCCCeEEEEEeCCCCeeeecCCchhccCCc-ee---EEEcCCCeEEccCCcccceeeeeCCceEeEEeCCCCCce
Q 037013 8 HKGGCRCRKLRWRVRAPRSVEAWKCNCSDCSMRGN-VH---FTVAPENFELLGNSEEFLTTHTFGTGTAKHVFCKVCGIT 83 (128)
Q Consensus 8 ~~G~C~CGav~~~~~~~~~~~~~~ChC~~Crk~~g-~~---~~~~~~~~~i~~g~~~~l~~y~~s~~~~~r~FC~~CGs~ 83 (128)
+.|+||||||+|++++++.. +.+|||++|||++| .+ ..++.+.|+++.| +..|.+++..+.|.||++||++
T Consensus 4 ~~G~C~CGaVrf~v~~~~~~-~~~ChCs~Crk~~G~~~~~~~~~~~~~~~~~~g----~~~~~~~s~~~~r~FC~~CGs~ 78 (133)
T COG3791 4 IEGGCLCGAVRFEVEGDPGH-VSACHCSDCRKASGAAFAAYAVVPRDALRGTRG----LPTYYFSSGSAGRGFCPTCGSP 78 (133)
T ss_pred cccceeeceEEEEEecCCCC-ceeeCchHhhhhhCCceeeeeecccceeeecCC----CceEEeecCCCCCeecccCCCc
Confidence 44999999999999999986 67999999999965 33 4556777877755 3444447788999999999999
Q ss_pred EEeccCCCCCeEEEEecccCCCC-C-CceEEEEecCCCcccccccc
Q 037013 84 SFYVPRGTPNGVAVTFRGVDPGT-L-SHVEIKHYDGHNWESSLDQF 127 (128)
Q Consensus 84 l~~~~~~~~~~~~v~~g~ld~~~-~-~~~~i~~~~~~~w~~~~~~~ 127 (128)
||+...+....+.|++++||+++ + |++|+|+.++++|++..+++
T Consensus 79 l~~~~~~~~~~~~v~~~~ld~p~~~~p~~~~~~~~~~~w~~~~~~~ 124 (133)
T COG3791 79 LFWRGPDEDPFVGVNAGALDDPEFLPPQVQIFVGSKLPWLDIADDL 124 (133)
T ss_pred eEEecCCCCceEEEEEeeecCcccCCCceeeeeeccCCcccccCCC
Confidence 99987654468999999999765 3 68999999999999988765
No 2
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=99.96 E-value=2.7e-29 Score=176.50 Aligned_cols=112 Identities=17% Similarity=0.234 Sum_probs=95.1
Q ss_pred eeEEEe---eeCC--CeEEEEEeCCCCeeeecCCchhccCCc----eeEEEcCCCeEEccCCcccceeeeeCCceEeEEe
Q 037013 6 VLHKGG---CRCR--KLRWRVRAPRSVEAWKCNCSDCSMRGN----VHFTVAPENFELLGNSEEFLTTHTFGTGTAKHVF 76 (128)
Q Consensus 6 ~~~~G~---C~CG--av~~~~~~~~~~~~~~ChC~~Crk~~g----~~~~~~~~~~~i~~g~~~~l~~y~~s~~~~~r~F 76 (128)
..++|+ |+|| +|+|+++++|.. +.+|||++|||++| .++.+|.++|+|++|+ +.++.|. +++.+.|.|
T Consensus 15 ~~~~GgtasClCGsvaV~y~v~~~p~~-v~~CHCs~CRK~TGsafs~~~~v~~~~~~i~~G~-~~l~~Y~-ss~~~~R~F 91 (182)
T TIGR02820 15 TSFAGGTLKCLCTSNKVTVKIKGQSAH-NHACGCSKCWKPEGAIFSVVAVVPRDNVTVTANG-DKLKVVD-ASATIQRHA 91 (182)
T ss_pred CCCCCCCcEEccCCCEEEEEEecCCCc-eeeeChHHhhccccCcceEEEEEEhhheEEecCC-cceEEEe-CCCCEEeec
Confidence 458899 9999 699999999875 78999999999976 3678999999998884 7788897 788899999
Q ss_pred CCCCCceEEeccCC-CC---CeEEEEecccCCCCC--CceEEEEecCCCc
Q 037013 77 CKVCGITSFYVPRG-TP---NGVAVTFRGVDPGTL--SHVEIKHYDGHNW 120 (128)
Q Consensus 77 C~~CGs~l~~~~~~-~~---~~~~v~~g~ld~~~~--~~~~i~~~~~~~w 120 (128)
|++||++||+.... .+ +.+.|++|+||++.+ |.+|||+.++++-
T Consensus 92 C~~CGS~L~~~~~~~~~~~~g~v~I~aGtLDd~~~~~P~~hIft~s~~~~ 141 (182)
T TIGR02820 92 CKGCGTHMYGRIENKDHPFYGLDFIHTELSAEDGWSAPGFAAFVSSIIET 141 (182)
T ss_pred CCCCCCcccccccccCCCccceeEEEEeecCCCCcCCCeEEEEEeecccc
Confidence 99999999988642 22 455999999998665 6899999999753
No 3
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=99.96 E-value=6.4e-29 Score=176.02 Aligned_cols=113 Identities=19% Similarity=0.244 Sum_probs=97.9
Q ss_pred CceeEEEe---eeCCC--eEEEEEeCCCCeeeecCCchhccCCc----eeEEEcCCCeEEccCCcccceeeeeCCceEeE
Q 037013 4 DSVLHKGG---CRCRK--LRWRVRAPRSVEAWKCNCSDCSMRGN----VHFTVAPENFELLGNSEEFLTTHTFGTGTAKH 74 (128)
Q Consensus 4 ~~~~~~G~---C~CGa--v~~~~~~~~~~~~~~ChC~~Crk~~g----~~~~~~~~~~~i~~g~~~~l~~y~~s~~~~~r 74 (128)
.+..++|+ |+||+ |+|+++++|.. +..|||++|||.+| .++.+|.++|+|++|+ +.++.|. +++.++|
T Consensus 17 ~~~~f~Gg~l~ClCG~~aVry~v~g~p~~-~~~CHCs~CrK~sGs~fs~~a~vp~d~~~it~g~-~~l~~y~-ss~~i~R 93 (191)
T PRK05417 17 GAEGFAGGTLVCKCTSNPVEVRVKAQTAH-NHACGCTKCWKPEGALFSVVAVVPRDNVTVTANG-DKLKVVD-ESATIQR 93 (191)
T ss_pred CcCccCCCCcEEeCCCcEEEEEEecCCCc-eeeeChhhhhccccCcceEEEEEEhhheEEEeCC-cceEEEe-CCCCeEe
Confidence 34568999 99996 99999999876 78999999999976 3678999999998774 6788887 7888999
Q ss_pred EeCCCCCceEEeccC----CCCCeEEEEecccCCCCC--CceEEEEecCCC
Q 037013 75 VFCKVCGITSFYVPR----GTPNGVAVTFRGVDPGTL--SHVEIKHYDGHN 119 (128)
Q Consensus 75 ~FC~~CGs~l~~~~~----~~~~~~~v~~g~ld~~~~--~~~~i~~~~~~~ 119 (128)
+||++||++||.+.+ ..++.+.|++|+||++.+ |..|+|+.++.+
T Consensus 94 ~FC~~CGS~L~~~~e~~~~~~pgl~fV~~gllDd~~~~~P~~~ifvsS~~e 144 (191)
T PRK05417 94 HACKECGVHMYGRIENKDHPFYGLDFVHTELSQEQGWSAPGFAAFVSSIIE 144 (191)
T ss_pred eeCCCCCCccccccccccCCCCCeEEEehhhcCCCCCCCceEEeeeeeccc
Confidence 999999999999866 456899999999998763 689999999864
No 4
>KOG4192 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.91 E-value=4.2e-24 Score=138.71 Aligned_cols=124 Identities=42% Similarity=0.867 Sum_probs=113.5
Q ss_pred CCCCceeEEEeeeCCCeEEEEEeCCCCeeeecCCchhccCCceeEEEcCCCeEEccCCcccceeeeeCCceEeEEeCCCC
Q 037013 1 MDQDSVLHKGGCRCRKLRWRVRAPRSVEAWKCNCSDCSMRGNVHFTVAPENFELLGNSEEFLTTHTFGTGTAKHVFCKVC 80 (128)
Q Consensus 1 m~~~~~~~~G~C~CGav~~~~~~~~~~~~~~ChC~~Crk~~g~~~~~~~~~~~i~~g~~~~l~~y~~s~~~~~r~FC~~C 80 (128)
|.+.+...+|+||||||+|++.+|....+..|+|++|++.....+.+|...|.+..| .+.+.+|.++...+++.||+.|
T Consensus 1 ~~~~lV~H~GgCHCGaVkw~v~ap~~l~~~~Cncrics~k~~~hfivpas~f~ll~g-~efitty~~gth~aqhtfck~c 79 (134)
T KOG4192|consen 1 EYMGLVQHTGGCHCGAVKWSVWAPADLDGCDCNCRICSKKQNRHFIVPASRFVLLVG-AEFITTYTFGTHQAQHTFCKRC 79 (134)
T ss_pred CcccceeecCCcccceEEEEEecccceEEeeccchhhhhccceEEEEeccceEEEeC-cceEEEEEeccchhheeeeccc
Confidence 556778899999999999999999887788899999999998999999999999989 5889999999999999999999
Q ss_pred CceEEeccCCCCCeEEEEecccCCCCCCceEEEEecCCCcccccc
Q 037013 81 GITSFYVPRGTPNGVAVTFRGVDPGTLSHVEIKHYDGHNWESSLD 125 (128)
Q Consensus 81 Gs~l~~~~~~~~~~~~v~~g~ld~~~~~~~~i~~~~~~~w~~~~~ 125 (128)
|..-|+.++.+|..+.|..-+||+..+..+.+-..++.+|....+
T Consensus 80 GV~sf~~~rs~p~~~~i~phCld~gTlr~v~~~~fnGqdwe~~~e 124 (134)
T KOG4192|consen 80 GVQSFYSPRSNPYGKGIAPHCLDEGTLRSVVWEEFNGQDWEATME 124 (134)
T ss_pred cceeccccccCCCceeecceeecCCceeEEEEEEecCcchhHhhh
Confidence 999999998889999999999999999989899999999976543
No 5
>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=99.91 E-value=1.1e-24 Score=137.64 Aligned_cols=86 Identities=24% Similarity=0.444 Sum_probs=67.7
Q ss_pred eecCCchhccCCc----eeEEEcCCCeEEccCCcccceeeeeCCceEeEEeCCCCCceEEeccCCCCCeEEEEecccCCC
Q 037013 30 WKCNCSDCSMRGN----VHFTVAPENFELLGNSEEFLTTHTFGTGTAKHVFCKVCGITSFYVPRGTPNGVAVTFRGVDPG 105 (128)
Q Consensus 30 ~~ChC~~Crk~~g----~~~~~~~~~~~i~~g~~~~l~~y~~s~~~~~r~FC~~CGs~l~~~~~~~~~~~~v~~g~ld~~ 105 (128)
+.|||++|||.+| .++.+|+++|+|++|+ +.++.|+.+++.++|+||++||++|++.....++.+.|++|+||+.
T Consensus 1 ~~ChC~~Cr~~~g~~~~~~~~~~~~~~~~~~g~-~~l~~y~~s~~~~~r~FC~~CGs~l~~~~~~~~~~~~V~~g~ld~~ 79 (92)
T PF04828_consen 1 YVCHCSDCRKWSGSPFSAWAIVPKDDFRWTSGS-ENLKEYQFSGKGVERYFCPTCGSPLFSEDERDPDLVGVNAGTLDDP 79 (92)
T ss_dssp EEE-STTCHHHTT-SSEEEEEEEGGGEEEEE-G-GGEEEC--TTSSCEEEEETTT--EEEEEESSTTTEEEEEGGGBTT-
T ss_pred CEeeChHHhcccCCceeeEEEEcccceEEeecc-ccceEEEeCCCcCcCcccCCCCCeeecccCCCCCEEEEEeEeeCCC
Confidence 4799999999998 5788999999999884 6899998788999999999999999987666789999999999986
Q ss_pred C-C-CceEEEEec
Q 037013 106 T-L-SHVEIKHYD 116 (128)
Q Consensus 106 ~-~-~~~~i~~~~ 116 (128)
+ + |.+|||+++
T Consensus 80 ~~~~p~~hi~~~~ 92 (92)
T PF04828_consen 80 DEFKPKAHIFTSE 92 (92)
T ss_dssp -S--EEEEESG--
T ss_pred CCCCCEEEEEEeC
Confidence 5 4 689999864
No 6
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=92.29 E-value=0.036 Score=26.02 Aligned_cols=11 Identities=36% Similarity=0.869 Sum_probs=8.9
Q ss_pred EEeCCCCCceE
Q 037013 74 HVFCKVCGITS 84 (128)
Q Consensus 74 r~FC~~CGs~l 84 (128)
-.||++||++|
T Consensus 13 ~~fC~~CG~~l 23 (23)
T PF13240_consen 13 AKFCPNCGTPL 23 (23)
T ss_pred CcchhhhCCcC
Confidence 46899999875
No 7
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=91.71 E-value=0.048 Score=26.26 Aligned_cols=13 Identities=31% Similarity=0.751 Sum_probs=10.0
Q ss_pred EeEEeCCCCCceE
Q 037013 72 AKHVFCKVCGITS 84 (128)
Q Consensus 72 ~~r~FC~~CGs~l 84 (128)
....||++||++|
T Consensus 14 ~~~~fC~~CG~~L 26 (26)
T PF13248_consen 14 PDAKFCPNCGAKL 26 (26)
T ss_pred cccccChhhCCCC
Confidence 3457999999875
No 8
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=90.64 E-value=0.1 Score=26.90 Aligned_cols=14 Identities=29% Similarity=0.382 Sum_probs=6.8
Q ss_pred EeCCCCCceEEecc
Q 037013 75 VFCKVCGITSFYVP 88 (128)
Q Consensus 75 ~FC~~CGs~l~~~~ 88 (128)
.||+.||.+|-...
T Consensus 1 kfC~~CG~~l~~~i 14 (34)
T PF14803_consen 1 KFCPQCGGPLERRI 14 (34)
T ss_dssp -B-TTT--B-EEE-
T ss_pred CccccccChhhhhc
Confidence 39999999987654
No 9
>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=88.70 E-value=0.33 Score=24.36 Aligned_cols=16 Identities=38% Similarity=0.804 Sum_probs=9.3
Q ss_pred EEeCCCCCceEEeccC
Q 037013 74 HVFCKVCGITSFYVPR 89 (128)
Q Consensus 74 r~FC~~CGs~l~~~~~ 89 (128)
..||+.||+++.....
T Consensus 3 ~rfC~~CG~~t~~~~~ 18 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPG 18 (32)
T ss_dssp TSB-TTT--BEEE-SS
T ss_pred CcccCcCCccccCCCC
Confidence 4699999999987554
No 10
>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=87.83 E-value=0.28 Score=25.34 Aligned_cols=15 Identities=27% Similarity=0.565 Sum_probs=11.8
Q ss_pred EeCCCCCceEEeccC
Q 037013 75 VFCKVCGITSFYVPR 89 (128)
Q Consensus 75 ~FC~~CGs~l~~~~~ 89 (128)
.||++||.-|+-...
T Consensus 2 ~FCp~C~nlL~p~~~ 16 (35)
T PF02150_consen 2 RFCPECGNLLYPKED 16 (35)
T ss_dssp -BETTTTSBEEEEEE
T ss_pred eeCCCCCccceEcCC
Confidence 599999999987644
No 11
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=86.09 E-value=0.65 Score=25.60 Aligned_cols=11 Identities=27% Similarity=0.933 Sum_probs=6.6
Q ss_pred EEeCCCCCceE
Q 037013 74 HVFCKVCGITS 84 (128)
Q Consensus 74 r~FC~~CGs~l 84 (128)
++.|+.||-+.
T Consensus 20 ~~vC~~Cg~~~ 30 (52)
T smart00661 20 RFVCRKCGYEE 30 (52)
T ss_pred EEECCcCCCeE
Confidence 56677776543
No 12
>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=81.37 E-value=1.2 Score=21.74 Aligned_cols=14 Identities=29% Similarity=0.508 Sum_probs=7.7
Q ss_pred eCCCCCceEEeccC
Q 037013 76 FCKVCGITSFYVPR 89 (128)
Q Consensus 76 FC~~CGs~l~~~~~ 89 (128)
+|+.||+.|....+
T Consensus 1 ~CP~C~s~l~~~~~ 14 (28)
T PF03119_consen 1 TCPVCGSKLVREEG 14 (28)
T ss_dssp B-TTT--BEEE-CC
T ss_pred CcCCCCCEeEcCCC
Confidence 59999999985443
No 13
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=81.00 E-value=1.7 Score=24.32 Aligned_cols=16 Identities=38% Similarity=0.789 Sum_probs=11.3
Q ss_pred eEEeCCCCCceEEecc
Q 037013 73 KHVFCKVCGITSFYVP 88 (128)
Q Consensus 73 ~r~FC~~CGs~l~~~~ 88 (128)
.+.||++||-.+|...
T Consensus 18 k~~~CPrCG~gvfmA~ 33 (51)
T COG1998 18 KNRFCPRCGPGVFMAD 33 (51)
T ss_pred ccccCCCCCCcchhhh
Confidence 4468999997666544
No 14
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=80.75 E-value=1.5 Score=24.46 Aligned_cols=22 Identities=27% Similarity=0.504 Sum_probs=13.3
Q ss_pred ceeeeeCCceE--eEEeCCCCCce
Q 037013 62 LTTHTFGTGTA--KHVFCKVCGIT 83 (128)
Q Consensus 62 l~~y~~s~~~~--~r~FC~~CGs~ 83 (128)
+..|.-.+..+ .+.||++||+.
T Consensus 6 ~~~y~v~~~~v~~~~~fCP~Cg~~ 29 (50)
T PRK00432 6 REYYEVDGGKVKRKNKFCPRCGSG 29 (50)
T ss_pred eeeEEECCCEEEEccCcCcCCCcc
Confidence 44454333333 34699999996
No 15
>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=80.67 E-value=0.48 Score=28.70 Aligned_cols=16 Identities=25% Similarity=0.688 Sum_probs=6.5
Q ss_pred ceEeEEeCCCCCceEE
Q 037013 70 GTAKHVFCKVCGITSF 85 (128)
Q Consensus 70 ~~~~r~FC~~CGs~l~ 85 (128)
+...+.||+.||-...
T Consensus 20 ~~~~k~FCp~CGn~TL 35 (73)
T PF08772_consen 20 KDMTKQFCPKCGNATL 35 (73)
T ss_dssp S-SS--S-SSS--S--
T ss_pred CCCCceeCcccCCCcc
Confidence 4577899999998643
No 16
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=76.33 E-value=1.2 Score=29.99 Aligned_cols=19 Identities=21% Similarity=0.392 Sum_probs=14.5
Q ss_pred CceEeEEeCCCCCceEEec
Q 037013 69 TGTAKHVFCKVCGITSFYV 87 (128)
Q Consensus 69 ~~~~~r~FC~~CGs~l~~~ 87 (128)
+....-.-|+.||+|||-.
T Consensus 23 GAkML~~hCp~Cg~PLF~K 41 (131)
T COG1645 23 GAKMLAKHCPKCGTPLFRK 41 (131)
T ss_pred hhHHHHhhCcccCCcceee
Confidence 4445556799999999983
No 17
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=75.38 E-value=5.1 Score=27.13 Aligned_cols=29 Identities=17% Similarity=0.203 Sum_probs=21.5
Q ss_pred EeCCCCCceEEeccCCCC----CeEEEEecccC
Q 037013 75 VFCKVCGITSFYVPRGTP----NGVAVTFRGVD 103 (128)
Q Consensus 75 ~FC~~CGs~l~~~~~~~~----~~~~v~~g~ld 103 (128)
.-|++||+||-+...+.| ..+-||..+|+
T Consensus 90 v~C~~Cg~HLGHVF~DGP~ptg~RyCINs~sL~ 122 (134)
T TIGR00357 90 VRCRNCDAHLGHVFDDGPEPTGLRYCINSAALK 122 (134)
T ss_pred EEecCCCCccCcccCCCCCCCCceEeecceeEe
Confidence 789999999988766543 35677766665
No 18
>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=74.34 E-value=1.9 Score=23.07 Aligned_cols=13 Identities=23% Similarity=0.557 Sum_probs=11.0
Q ss_pred EEeCCCCCceEEe
Q 037013 74 HVFCKVCGITSFY 86 (128)
Q Consensus 74 r~FC~~CGs~l~~ 86 (128)
-..|+.||+||+-
T Consensus 17 ~~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 17 DEHCPDCGTPLMR 29 (41)
T ss_pred cCccCCCCCeeEE
Confidence 3569999999997
No 19
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=72.72 E-value=5.8 Score=27.13 Aligned_cols=42 Identities=12% Similarity=0.040 Sum_probs=26.2
Q ss_pred ceeeeeCCceEeE--EeCCCCCceEEeccCCCC----CeEEEEecccC
Q 037013 62 LTTHTFGTGTAKH--VFCKVCGITSFYVPRGTP----NGVAVTFRGVD 103 (128)
Q Consensus 62 l~~y~~s~~~~~r--~FC~~CGs~l~~~~~~~~----~~~~v~~g~ld 103 (128)
+....+.+....| .-|++||+||-+...+.| ..+-||...|+
T Consensus 78 V~~~~D~s~gm~RtEv~C~~Cg~HLGHVF~DGP~ptg~RyCINs~sL~ 125 (142)
T PRK00222 78 IRELRDTSHGMVRTEVRCANCDSHLGHVFPDGPKPTGLRYCINSASLK 125 (142)
T ss_pred eEEeeccCCCceEEEEEeCCCCCccCcccCCCCCCCCCEeeeceeeEE
Confidence 4444433333433 789999999988765432 35667766665
No 20
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=71.45 E-value=1.1 Score=27.29 Aligned_cols=17 Identities=29% Similarity=0.575 Sum_probs=9.4
Q ss_pred CceEeEEeCCCCCceEE
Q 037013 69 TGTAKHVFCKVCGITSF 85 (128)
Q Consensus 69 ~~~~~r~FC~~CGs~l~ 85 (128)
++...|.||+.||+.+.
T Consensus 41 ~~~~kr~~Ck~C~~~li 57 (85)
T PF04032_consen 41 PPEIKRTICKKCGSLLI 57 (85)
T ss_dssp STTCCCTB-TTT--B--
T ss_pred ChHHhcccccCCCCEEe
Confidence 34478899999999874
No 21
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=67.35 E-value=5.8 Score=21.35 Aligned_cols=16 Identities=31% Similarity=0.700 Sum_probs=12.9
Q ss_pred EEeCCCCCceEEeccC
Q 037013 74 HVFCKVCGITSFYVPR 89 (128)
Q Consensus 74 r~FC~~CGs~l~~~~~ 89 (128)
-..|+.||+++.....
T Consensus 21 ~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 21 GVRCPYCGYRILFKER 36 (46)
T ss_pred ceECCCCCCeEEEccC
Confidence 4679999999987554
No 22
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=67.18 E-value=8.8 Score=20.75 Aligned_cols=16 Identities=38% Similarity=0.812 Sum_probs=13.0
Q ss_pred EeCCCCCceEEeccCC
Q 037013 75 VFCKVCGITSFYVPRG 90 (128)
Q Consensus 75 ~FC~~CGs~l~~~~~~ 90 (128)
..|++||..+.+..+.
T Consensus 20 irC~~CG~rIlyK~R~ 35 (44)
T smart00659 20 VRCRECGYRILYKKRT 35 (44)
T ss_pred eECCCCCceEEEEeCC
Confidence 5699999999987653
No 23
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=65.75 E-value=6.1 Score=25.85 Aligned_cols=11 Identities=36% Similarity=0.941 Sum_probs=5.5
Q ss_pred eCCCCCceEEe
Q 037013 76 FCKVCGITSFY 86 (128)
Q Consensus 76 FC~~CGs~l~~ 86 (128)
||+.||+.|+.
T Consensus 4 FCp~Cgsll~p 14 (113)
T COG1594 4 FCPKCGSLLYP 14 (113)
T ss_pred ccCCccCeeEE
Confidence 45555555444
No 24
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=64.30 E-value=13 Score=24.67 Aligned_cols=31 Identities=19% Similarity=0.201 Sum_probs=21.3
Q ss_pred eEEeCCCCCceEEeccCCC-C----CeEEEEecccC
Q 037013 73 KHVFCKVCGITSFYVPRGT-P----NGVAVTFRGVD 103 (128)
Q Consensus 73 ~r~FC~~CGs~l~~~~~~~-~----~~~~v~~g~ld 103 (128)
.-.-|++||+||-+...+. | ..+-||..+|+
T Consensus 78 tEv~C~~C~~HLGHVF~d~gp~ptg~RyCINS~sL~ 113 (119)
T PRK05508 78 TEIVCANCGGHLGHVFEGEGFTPKNTRHCVNSISLK 113 (119)
T ss_pred EEEEeCCCCCccCcccCCCCCCCCCCEEeecceeEE
Confidence 3378999999998876522 1 35677766654
No 25
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=64.21 E-value=3.5 Score=32.07 Aligned_cols=15 Identities=27% Similarity=0.711 Sum_probs=13.3
Q ss_pred EEeCCCCCceEEecc
Q 037013 74 HVFCKVCGITSFYVP 88 (128)
Q Consensus 74 r~FC~~CGs~l~~~~ 88 (128)
|+||+.||++|.-..
T Consensus 25 ~ffCPaC~~~l~lK~ 39 (342)
T COG4469 25 RFFCPACGSQLILKQ 39 (342)
T ss_pred ccccCCCCCeeeeec
Confidence 799999999998764
No 26
>PF12773 DZR: Double zinc ribbon
Probab=63.72 E-value=2.2 Score=23.28 Aligned_cols=13 Identities=31% Similarity=0.657 Sum_probs=11.3
Q ss_pred eEEeCCCCCceEE
Q 037013 73 KHVFCKVCGITSF 85 (128)
Q Consensus 73 ~r~FC~~CGs~l~ 85 (128)
...||+.||+.|.
T Consensus 11 ~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 11 DAKFCPHCGTPLP 23 (50)
T ss_pred cccCChhhcCChh
Confidence 3579999999998
No 27
>PRK00420 hypothetical protein; Validated
Probab=63.17 E-value=3.5 Score=27.03 Aligned_cols=14 Identities=36% Similarity=0.887 Sum_probs=11.7
Q ss_pred EEeCCCCCceEEec
Q 037013 74 HVFCKVCGITSFYV 87 (128)
Q Consensus 74 r~FC~~CGs~l~~~ 87 (128)
-.-|+.||+++|..
T Consensus 23 ~~~CP~Cg~pLf~l 36 (112)
T PRK00420 23 SKHCPVCGLPLFEL 36 (112)
T ss_pred cCCCCCCCCcceec
Confidence 35699999999974
No 28
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=62.16 E-value=5.8 Score=25.41 Aligned_cols=15 Identities=27% Similarity=0.660 Sum_probs=12.4
Q ss_pred EeCCCCCceEEeccC
Q 037013 75 VFCKVCGITSFYVPR 89 (128)
Q Consensus 75 ~FC~~CGs~l~~~~~ 89 (128)
.||+.||..|.....
T Consensus 2 ~FCP~Cgn~Live~g 16 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESG 16 (105)
T ss_pred cccCCCCCEEEEecC
Confidence 599999999987654
No 29
>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=61.41 E-value=7.1 Score=19.61 Aligned_cols=12 Identities=25% Similarity=0.766 Sum_probs=7.6
Q ss_pred EeCCCCCceEEe
Q 037013 75 VFCKVCGITSFY 86 (128)
Q Consensus 75 ~FC~~CGs~l~~ 86 (128)
+.|+.||..+..
T Consensus 2 hlcpkcgvgvl~ 13 (36)
T PF09151_consen 2 HLCPKCGVGVLE 13 (36)
T ss_dssp -B-TTTSSSBEE
T ss_pred ccCCccCceEEE
Confidence 579999987654
No 30
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=61.09 E-value=5.4 Score=22.06 Aligned_cols=16 Identities=25% Similarity=0.380 Sum_probs=13.1
Q ss_pred EEeCCCCCceEEeccC
Q 037013 74 HVFCKVCGITSFYVPR 89 (128)
Q Consensus 74 r~FC~~CGs~l~~~~~ 89 (128)
..+|+.||..+.....
T Consensus 5 ~l~C~~CG~~m~~~~~ 20 (58)
T PF13408_consen 5 LLRCGHCGSKMTRRKR 20 (58)
T ss_pred cEEcccCCcEeEEEEC
Confidence 4789999999988654
No 31
>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=60.74 E-value=9.4 Score=19.46 Aligned_cols=13 Identities=31% Similarity=0.641 Sum_probs=10.6
Q ss_pred EEeCCCCCceEEe
Q 037013 74 HVFCKVCGITSFY 86 (128)
Q Consensus 74 r~FC~~CGs~l~~ 86 (128)
...|++||..++.
T Consensus 25 ~v~C~~C~~~~~~ 37 (38)
T TIGR02098 25 KVRCGKCGHVWYA 37 (38)
T ss_pred EEECCCCCCEEEe
Confidence 5679999998764
No 32
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=58.49 E-value=3.9 Score=25.96 Aligned_cols=12 Identities=33% Similarity=0.634 Sum_probs=9.7
Q ss_pred eCCCCCceEEec
Q 037013 76 FCKVCGITSFYV 87 (128)
Q Consensus 76 FC~~CGs~l~~~ 87 (128)
||++||..|...
T Consensus 2 fC~~Cg~~l~~~ 13 (104)
T TIGR01384 2 FCPKCGSLMTPK 13 (104)
T ss_pred CCcccCcccccC
Confidence 899999988653
No 33
>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=58.29 E-value=8.8 Score=20.33 Aligned_cols=9 Identities=33% Similarity=1.021 Sum_probs=4.1
Q ss_pred eCCCCCceE
Q 037013 76 FCKVCGITS 84 (128)
Q Consensus 76 FC~~CGs~l 84 (128)
.|+.||.-|
T Consensus 21 vC~~CG~Vl 29 (43)
T PF08271_consen 21 VCPNCGLVL 29 (43)
T ss_dssp EETTT-BBE
T ss_pred ECCCCCCEe
Confidence 455555544
No 34
>PRK12496 hypothetical protein; Provisional
Probab=57.44 E-value=4.2 Score=28.36 Aligned_cols=16 Identities=19% Similarity=0.397 Sum_probs=12.2
Q ss_pred eEEeCCCCCceEEecc
Q 037013 73 KHVFCKVCGITSFYVP 88 (128)
Q Consensus 73 ~r~FC~~CGs~l~~~~ 88 (128)
.+.||+.||++|.-..
T Consensus 142 ~~~~C~~CG~~~~r~~ 157 (164)
T PRK12496 142 PDDVCEICGSPVKRKM 157 (164)
T ss_pred CCCcCCCCCChhhhcc
Confidence 4578999999986543
No 35
>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=57.38 E-value=8.7 Score=19.84 Aligned_cols=13 Identities=23% Similarity=0.736 Sum_probs=9.5
Q ss_pred EEeCCCCCceEEec
Q 037013 74 HVFCKVCGITSFYV 87 (128)
Q Consensus 74 r~FC~~CGs~l~~~ 87 (128)
|..|+.||. +|+.
T Consensus 1 Rr~C~~Cg~-~Yh~ 13 (36)
T PF05191_consen 1 RRICPKCGR-IYHI 13 (36)
T ss_dssp EEEETTTTE-EEET
T ss_pred CcCcCCCCC-cccc
Confidence 567899987 5554
No 36
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=56.55 E-value=9.9 Score=22.40 Aligned_cols=21 Identities=19% Similarity=0.082 Sum_probs=13.3
Q ss_pred eCCCCCceEEeccCCCCCeEEEE
Q 037013 76 FCKVCGITSFYVPRGTPNGVAVT 98 (128)
Q Consensus 76 FC~~CGs~l~~~~~~~~~~~~v~ 98 (128)
.|+.||+.-+ .+.+.+.+.|-
T Consensus 19 ~Cp~Cgs~~~--S~~w~G~v~i~ 39 (64)
T PRK06393 19 TCPVHGDEKT--TTEWFGFLIIT 39 (64)
T ss_pred cCCCCCCCcC--CcCcceEEEEE
Confidence 7999999733 23345555554
No 37
>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=56.40 E-value=6.7 Score=18.50 Aligned_cols=10 Identities=40% Similarity=0.757 Sum_probs=8.0
Q ss_pred EeEEeCCCCC
Q 037013 72 AKHVFCKVCG 81 (128)
Q Consensus 72 ~~r~FC~~CG 81 (128)
..++-|++||
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 5567899998
No 38
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=55.86 E-value=17 Score=20.19 Aligned_cols=17 Identities=24% Similarity=0.479 Sum_probs=13.2
Q ss_pred EEeCCCCCceEEeccCC
Q 037013 74 HVFCKVCGITSFYVPRG 90 (128)
Q Consensus 74 r~FC~~CGs~l~~~~~~ 90 (128)
..-|+.||..++.....
T Consensus 24 ~irCp~Cg~rIl~K~R~ 40 (49)
T COG1996 24 GIRCPYCGSRILVKERP 40 (49)
T ss_pred ceeCCCCCcEEEEeccC
Confidence 35699999999887653
No 39
>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=54.90 E-value=15 Score=19.14 Aligned_cols=15 Identities=20% Similarity=0.281 Sum_probs=11.3
Q ss_pred eCCCCCceEEeccCC
Q 037013 76 FCKVCGITSFYVPRG 90 (128)
Q Consensus 76 FC~~CGs~l~~~~~~ 90 (128)
.|+.||..|..+...
T Consensus 3 ~CP~Cg~~lv~r~~k 17 (39)
T PF01396_consen 3 KCPKCGGPLVLRRGK 17 (39)
T ss_pred CCCCCCceeEEEECC
Confidence 499999888776543
No 40
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=54.77 E-value=5.1 Score=30.46 Aligned_cols=17 Identities=29% Similarity=0.735 Sum_probs=13.2
Q ss_pred EeEEeCCCCCceEEecc
Q 037013 72 AKHVFCKVCGITSFYVP 88 (128)
Q Consensus 72 ~~r~FC~~CGs~l~~~~ 88 (128)
..+.||+.||++++...
T Consensus 109 ~~~RFCg~CG~~~~~~~ 125 (279)
T COG2816 109 RSHRFCGRCGTKTYPRE 125 (279)
T ss_pred hhCcCCCCCCCcCcccc
Confidence 35679999999988753
No 41
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=54.62 E-value=30 Score=23.07 Aligned_cols=33 Identities=18% Similarity=0.203 Sum_probs=21.6
Q ss_pred eEeEEeCCCCCceEEeccCCCC-----CeEEEEecccC
Q 037013 71 TAKHVFCKVCGITSFYVPRGTP-----NGVAVTFRGVD 103 (128)
Q Consensus 71 ~~~r~FC~~CGs~l~~~~~~~~-----~~~~v~~g~ld 103 (128)
...-..|++||+||-+...+.| ..+-||..+|+
T Consensus 83 ~R~Ev~C~~Cg~HLGHVF~DGp~~~tg~RyCINS~sL~ 120 (124)
T PF01641_consen 83 VRTEVRCARCGSHLGHVFDDGPPPPTGLRYCINSASLK 120 (124)
T ss_dssp EEEEEEETTTCCEEEEEESTSSTTCTSCEEEE-GGGEE
T ss_pred eEEEEEecCCCCccccEeCCCCCCCCCcEEEeeeeeEE
Confidence 3444689999999988765422 45677766553
No 42
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=52.00 E-value=23 Score=24.06 Aligned_cols=42 Identities=14% Similarity=0.062 Sum_probs=26.6
Q ss_pred ceeeeeCCceEeE--EeCCCCCceEEeccCCCC-----CeEEEEecccC
Q 037013 62 LTTHTFGTGTAKH--VFCKVCGITSFYVPRGTP-----NGVAVTFRGVD 103 (128)
Q Consensus 62 l~~y~~s~~~~~r--~FC~~CGs~l~~~~~~~~-----~~~~v~~g~ld 103 (128)
+....+.+....| ..|++|++||-+..++.| -.+-||-..|.
T Consensus 77 I~~~~D~S~gM~RtEVrc~~c~sHLGHVF~DGP~~tgglRYCINSasL~ 125 (140)
T COG0229 77 ITYKEDRSHGMVRTEVRCANCDSHLGHVFPDGPPPTGGLRYCINSASLR 125 (140)
T ss_pred ceEeeccCCCcEEEEEEecCCCCccccccCCCCCCCCCeeEeecchhee
Confidence 4444444444444 589999999998876543 24566655554
No 43
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=51.63 E-value=7.9 Score=23.62 Aligned_cols=17 Identities=24% Similarity=0.600 Sum_probs=13.8
Q ss_pred eEEeCCCCCceEEeccC
Q 037013 73 KHVFCKVCGITSFYVPR 89 (128)
Q Consensus 73 ~r~FC~~CGs~l~~~~~ 89 (128)
-+++|+.||+.|.....
T Consensus 3 i~Y~CRHCg~~IG~i~~ 19 (76)
T PF10955_consen 3 IHYYCRHCGTKIGTIDA 19 (76)
T ss_pred eEEEecCCCCEEEEeec
Confidence 47899999999977653
No 44
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=50.78 E-value=12 Score=18.75 Aligned_cols=13 Identities=15% Similarity=0.590 Sum_probs=10.6
Q ss_pred eEEeCCCCCceEE
Q 037013 73 KHVFCKVCGITSF 85 (128)
Q Consensus 73 ~r~FC~~CGs~l~ 85 (128)
++++|..|+.+|=
T Consensus 15 T~~~C~~C~v~lC 27 (32)
T PF13842_consen 15 TRYMCSKCDVPLC 27 (32)
T ss_pred eEEEccCCCCccc
Confidence 7899999987663
No 45
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=49.90 E-value=7.9 Score=27.46 Aligned_cols=15 Identities=27% Similarity=0.569 Sum_probs=12.0
Q ss_pred eEEeCCCCCceEEec
Q 037013 73 KHVFCKVCGITSFYV 87 (128)
Q Consensus 73 ~r~FC~~CGs~l~~~ 87 (128)
...||+.||+++--.
T Consensus 152 ~~~~Cp~CG~~~~~~ 166 (177)
T COG1439 152 PKDFCPICGSPLKRK 166 (177)
T ss_pred CCCcCCCCCCceEEe
Confidence 468999999997544
No 46
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=49.73 E-value=14 Score=21.46 Aligned_cols=16 Identities=19% Similarity=0.330 Sum_probs=12.4
Q ss_pred EeEEeCCCCCceEEec
Q 037013 72 AKHVFCKVCGITSFYV 87 (128)
Q Consensus 72 ~~r~FC~~CGs~l~~~ 87 (128)
-..++|++||..|...
T Consensus 50 d~~H~Cp~C~~~lg~~ 65 (67)
T smart00714 50 DVNHYCPNCGAFLGTY 65 (67)
T ss_pred CccEECCCCCCEeEEe
Confidence 4568999999988643
No 47
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=49.41 E-value=14 Score=21.59 Aligned_cols=20 Identities=25% Similarity=0.340 Sum_probs=12.7
Q ss_pred eCCCCCceEEeccCCCCCeEEE
Q 037013 76 FCKVCGITSFYVPRGTPNGVAV 97 (128)
Q Consensus 76 FC~~CGs~l~~~~~~~~~~~~v 97 (128)
.|++||+.-+.. ++.+.+.|
T Consensus 17 ~CP~Cgs~~~T~--~W~G~viI 36 (61)
T PRK08351 17 RCPVCGSRDLSD--EWFDLVII 36 (61)
T ss_pred cCCCCcCCcccc--ccccEEEE
Confidence 599999977543 34454443
No 48
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=47.62 E-value=6.8 Score=29.24 Aligned_cols=15 Identities=33% Similarity=0.685 Sum_probs=12.1
Q ss_pred eEEeCCCCCceEEec
Q 037013 73 KHVFCKVCGITSFYV 87 (128)
Q Consensus 73 ~r~FC~~CGs~l~~~ 87 (128)
.+.||+.||+++...
T Consensus 98 ~~~fC~~CG~~~~~~ 112 (256)
T PRK00241 98 SHRFCGYCGHPMHPS 112 (256)
T ss_pred cCccccccCCCCeec
Confidence 467999999998654
No 49
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=47.60 E-value=16 Score=23.91 Aligned_cols=17 Identities=18% Similarity=0.446 Sum_probs=13.2
Q ss_pred EeEEeCCCCCceEEecc
Q 037013 72 AKHVFCKVCGITSFYVP 88 (128)
Q Consensus 72 ~~r~FC~~CGs~l~~~~ 88 (128)
..-++|+.||+.+=...
T Consensus 72 irEyyCP~Cgt~levE~ 88 (112)
T PF08882_consen 72 IREYYCPGCGTQLEVEA 88 (112)
T ss_pred EEEEECCCCcceeEEcc
Confidence 44589999999886654
No 50
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=46.95 E-value=17 Score=21.02 Aligned_cols=16 Identities=31% Similarity=0.677 Sum_probs=12.5
Q ss_pred EeEEeCCCCCceEEec
Q 037013 72 AKHVFCKVCGITSFYV 87 (128)
Q Consensus 72 ~~r~FC~~CGs~l~~~ 87 (128)
..++.|++||..+.++
T Consensus 23 ~~~F~CPnCG~~~I~R 38 (59)
T PRK14890 23 AVKFLCPNCGEVIIYR 38 (59)
T ss_pred cCEeeCCCCCCeeEee
Confidence 5678999999985554
No 51
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=46.77 E-value=23 Score=29.40 Aligned_cols=29 Identities=10% Similarity=-0.074 Sum_probs=21.9
Q ss_pred EeCCCCCceEEeccCCCC-----CeEEEEecccC
Q 037013 75 VFCKVCGITSFYVPRGTP-----NGVAVTFRGVD 103 (128)
Q Consensus 75 ~FC~~CGs~l~~~~~~~~-----~~~~v~~g~ld 103 (128)
..|++||+||-+..++.| ..+-||..+|+
T Consensus 468 v~c~~c~~HLGHvf~dgp~~~~g~RyCiNs~~l~ 501 (521)
T PRK14018 468 VRSRAADSHLGHVFPDGPRDKGGLRYCINGASLK 501 (521)
T ss_pred EEECCCCCcCCcccCCCCCCCCCCEeeeceeEEE
Confidence 789999999988876544 25777777665
No 52
>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=46.30 E-value=17 Score=20.00 Aligned_cols=17 Identities=24% Similarity=0.471 Sum_probs=11.0
Q ss_pred eEEeCC--CCCceEEeccC
Q 037013 73 KHVFCK--VCGITSFYVPR 89 (128)
Q Consensus 73 ~r~FC~--~CGs~l~~~~~ 89 (128)
.|..|+ +||.-+|....
T Consensus 17 ~rk~CP~~~CG~GvFMA~H 35 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEH 35 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-
T ss_pred hhhcCCCcccCCceEeeec
Confidence 357899 89988776543
No 53
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=45.32 E-value=16 Score=24.49 Aligned_cols=19 Identities=26% Similarity=0.576 Sum_probs=15.6
Q ss_pred ceEeEEeCCCCCceEEecc
Q 037013 70 GTAKHVFCKVCGITSFYVP 88 (128)
Q Consensus 70 ~~~~r~FC~~CGs~l~~~~ 88 (128)
....++||..||++|-...
T Consensus 24 ~~~~~~tC~~Cg~~L~lh~ 42 (128)
T PF11682_consen 24 APYDHWTCHSCGCPLILHP 42 (128)
T ss_pred CCCCeEEEecCCceEEEec
Confidence 3567899999999997764
No 54
>PRK12495 hypothetical protein; Provisional
Probab=44.63 E-value=7.5 Score=28.54 Aligned_cols=19 Identities=26% Similarity=0.499 Sum_probs=15.0
Q ss_pred CceEeEEeCCCCCceEEec
Q 037013 69 TGTAKHVFCKVCGITSFYV 87 (128)
Q Consensus 69 ~~~~~r~FC~~CGs~l~~~ 87 (128)
+......+|..||.+||..
T Consensus 37 gatmsa~hC~~CG~PIpa~ 55 (226)
T PRK12495 37 GATMTNAHCDECGDPIFRH 55 (226)
T ss_pred hcccchhhcccccCcccCC
Confidence 4556778999999999943
No 55
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=44.33 E-value=9.2 Score=29.68 Aligned_cols=17 Identities=29% Similarity=0.440 Sum_probs=13.9
Q ss_pred eEEeCCCCCceEEeccC
Q 037013 73 KHVFCKVCGITSFYVPR 89 (128)
Q Consensus 73 ~r~FC~~CGs~l~~~~~ 89 (128)
+..||+.||++++.+..
T Consensus 149 kykFCp~CG~~tkp~e~ 165 (345)
T KOG3084|consen 149 KYKFCPGCGSPTKPEEA 165 (345)
T ss_pred HhccCcccCCCcccccC
Confidence 45799999999987643
No 56
>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=43.15 E-value=19 Score=21.64 Aligned_cols=17 Identities=29% Similarity=0.505 Sum_probs=10.0
Q ss_pred ceEeEEeCCCCCceEEe
Q 037013 70 GTAKHVFCKVCGITSFY 86 (128)
Q Consensus 70 ~~~~r~FC~~CGs~l~~ 86 (128)
.-....+|++||.+|--
T Consensus 26 ~~~~~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 26 DYKKEAFCPDCGQPLEV 42 (70)
T ss_dssp EEEEEEE-TTT-SB-EE
T ss_pred cceecccCCCcccHHHH
Confidence 34566899999988753
No 57
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.59 E-value=12 Score=22.09 Aligned_cols=13 Identities=31% Similarity=0.680 Sum_probs=10.7
Q ss_pred EeCCCCCceEEec
Q 037013 75 VFCKVCGITSFYV 87 (128)
Q Consensus 75 ~FC~~CGs~l~~~ 87 (128)
.=|++||.++-..
T Consensus 8 v~CP~Cgkpv~w~ 20 (65)
T COG3024 8 VPCPTCGKPVVWG 20 (65)
T ss_pred ccCCCCCCccccc
Confidence 3499999999874
No 58
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=42.39 E-value=18 Score=18.69 Aligned_cols=19 Identities=16% Similarity=0.333 Sum_probs=13.7
Q ss_pred ceeeeeCCceEeEEeCCCC
Q 037013 62 LTTHTFGTGTAKHVFCKVC 80 (128)
Q Consensus 62 l~~y~~s~~~~~r~FC~~C 80 (128)
+..+..+....+|+.|..|
T Consensus 17 v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 17 VKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred ceeCCCCCCCCEeEecCcC
Confidence 4444445667899999998
No 59
>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=41.95 E-value=24 Score=18.76 Aligned_cols=12 Identities=25% Similarity=0.254 Sum_probs=9.8
Q ss_pred EeCCCCCceEEe
Q 037013 75 VFCKVCGITSFY 86 (128)
Q Consensus 75 ~FC~~CGs~l~~ 86 (128)
..|+.||..|..
T Consensus 3 ~~C~~Cg~~l~~ 14 (47)
T PF13005_consen 3 RACPDCGGELKE 14 (47)
T ss_pred CcCCCCCceeeE
Confidence 369999999874
No 60
>PF11062 DUF2863: Protein of unknown function (DUF2863); InterPro: IPR021292 This bacterial family of proteins have no known function.
Probab=41.43 E-value=11 Score=29.97 Aligned_cols=16 Identities=31% Similarity=0.739 Sum_probs=12.9
Q ss_pred EEeCCCCCceEEeccC
Q 037013 74 HVFCKVCGITSFYVPR 89 (128)
Q Consensus 74 r~FC~~CGs~l~~~~~ 89 (128)
--||-.||.|+|-...
T Consensus 364 ~E~CdDCGaPlypd~~ 379 (398)
T PF11062_consen 364 PEFCDDCGAPLYPDPE 379 (398)
T ss_pred chhcccCCCCCCCCCC
Confidence 3599999999997543
No 61
>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=40.92 E-value=26 Score=20.68 Aligned_cols=15 Identities=20% Similarity=0.301 Sum_probs=12.2
Q ss_pred EeEEeCCCCCceEEe
Q 037013 72 AKHVFCKVCGITSFY 86 (128)
Q Consensus 72 ~~r~FC~~CGs~l~~ 86 (128)
-..++|++||..|..
T Consensus 56 d~~H~Cp~C~~~lg~ 70 (73)
T PF10601_consen 56 DVYHYCPNCGAFLGT 70 (73)
T ss_pred CceEECCCCCCEeEE
Confidence 456889999998865
No 62
>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=40.03 E-value=13 Score=17.69 Aligned_cols=9 Identities=44% Similarity=1.139 Sum_probs=6.8
Q ss_pred EEeCCCCCc
Q 037013 74 HVFCKVCGI 82 (128)
Q Consensus 74 r~FC~~CGs 82 (128)
-.+|+.||-
T Consensus 14 ~~~Cp~CG~ 22 (26)
T PF10571_consen 14 AKFCPHCGY 22 (26)
T ss_pred cCcCCCCCC
Confidence 357999985
No 63
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=37.48 E-value=5.1 Score=25.95 Aligned_cols=18 Identities=22% Similarity=0.333 Sum_probs=14.7
Q ss_pred CceEeEEeCCCCCceEEe
Q 037013 69 TGTAKHVFCKVCGITSFY 86 (128)
Q Consensus 69 ~~~~~r~FC~~CGs~l~~ 86 (128)
.....|.||+.|.++|.-
T Consensus 51 p~~iKR~~CkkC~t~Lvp 68 (105)
T COG2023 51 PREIKRTICKKCYTPLVP 68 (105)
T ss_pred CHHHHHHhccccCccccc
Confidence 456789999999998764
No 64
>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=37.28 E-value=15 Score=21.26 Aligned_cols=12 Identities=33% Similarity=0.553 Sum_probs=9.4
Q ss_pred EeCCCCCceEEe
Q 037013 75 VFCKVCGITSFY 86 (128)
Q Consensus 75 ~FC~~CGs~l~~ 86 (128)
.-|..||.++-.
T Consensus 4 kHC~~CG~~Ip~ 15 (59)
T PF09889_consen 4 KHCPVCGKPIPP 15 (59)
T ss_pred CcCCcCCCcCCc
Confidence 459999998853
No 65
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=37.04 E-value=29 Score=20.36 Aligned_cols=21 Identities=24% Similarity=0.365 Sum_probs=13.3
Q ss_pred EeCCCCCceEEeccCCCCCeEEE
Q 037013 75 VFCKVCGITSFYVPRGTPNGVAV 97 (128)
Q Consensus 75 ~FC~~CGs~l~~~~~~~~~~~~v 97 (128)
--|+.||+.=+.. .+.+.+.|
T Consensus 19 e~CP~Cgs~~~te--~W~G~~iI 39 (64)
T COG2093 19 EICPVCGSTDLTE--EWFGLLII 39 (64)
T ss_pred ccCCCCCCcccch--hhccEEEE
Confidence 3599999986543 34455444
No 66
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=36.83 E-value=7.7 Score=25.47 Aligned_cols=16 Identities=25% Similarity=0.341 Sum_probs=12.4
Q ss_pred eEEeCCCCCceEEecc
Q 037013 73 KHVFCKVCGITSFYVP 88 (128)
Q Consensus 73 ~r~FC~~CGs~l~~~~ 88 (128)
.-.||+.||+-|....
T Consensus 6 ~~~FC~~CG~ll~~~~ 21 (116)
T KOG2907|consen 6 DLDFCSDCGSLLEEPS 21 (116)
T ss_pred Ccchhhhhhhhccccc
Confidence 3479999999887643
No 67
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=36.62 E-value=22 Score=18.32 Aligned_cols=15 Identities=20% Similarity=0.470 Sum_probs=11.5
Q ss_pred EeEEeCCCCCceEEe
Q 037013 72 AKHVFCKVCGITSFY 86 (128)
Q Consensus 72 ~~r~FC~~CGs~l~~ 86 (128)
....||.+|+.+|=.
T Consensus 13 ~~~~~C~~C~~~~C~ 27 (42)
T PF00643_consen 13 PLSLFCEDCNEPLCS 27 (42)
T ss_dssp BEEEEETTTTEEEEH
T ss_pred ceEEEecCCCCccCc
Confidence 356899999987753
No 68
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=35.80 E-value=16 Score=23.55 Aligned_cols=14 Identities=36% Similarity=0.655 Sum_probs=11.9
Q ss_pred eecCCchhccCCce
Q 037013 30 WKCNCSDCSMRGNV 43 (128)
Q Consensus 30 ~~ChC~~Crk~~g~ 43 (128)
.+|+|+.|||..|.
T Consensus 69 giCnCs~Crrk~g~ 82 (105)
T PF10497_consen 69 GICNCSFCRRKRGW 82 (105)
T ss_pred CeeCCHhhhccCCC
Confidence 57999999999764
No 69
>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=35.60 E-value=21 Score=17.92 Aligned_cols=12 Identities=33% Similarity=0.772 Sum_probs=8.6
Q ss_pred eCCCCCceEEec
Q 037013 76 FCKVCGITSFYV 87 (128)
Q Consensus 76 FC~~CGs~l~~~ 87 (128)
-|+.||..+.+.
T Consensus 19 rC~~CG~RIlyK 30 (32)
T PF03604_consen 19 RCPECGHRILYK 30 (32)
T ss_dssp SBSSSS-SEEBE
T ss_pred ECCcCCCeEEEe
Confidence 599999887664
No 70
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=35.43 E-value=26 Score=17.65 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=8.9
Q ss_pred eEEeCCCCCce
Q 037013 73 KHVFCKVCGIT 83 (128)
Q Consensus 73 ~r~FC~~CGs~ 83 (128)
...||..||..
T Consensus 20 ~~~~C~~Cg~~ 30 (33)
T PF08792_consen 20 DYEVCIFCGSS 30 (33)
T ss_pred CeEEcccCCcE
Confidence 45899999975
No 71
>smart00508 PostSET Cysteine-rich motif following a subset of SET domains.
Probab=34.86 E-value=19 Score=17.28 Aligned_cols=8 Identities=25% Similarity=0.658 Sum_probs=5.7
Q ss_pred eeeCCCeE
Q 037013 11 GCRCRKLR 18 (128)
Q Consensus 11 ~C~CGav~ 18 (128)
.|+||+..
T Consensus 4 ~C~CGs~~ 11 (26)
T smart00508 4 PCLCGAPN 11 (26)
T ss_pred eeeCCCcc
Confidence 48888764
No 72
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=33.91 E-value=17 Score=28.48 Aligned_cols=16 Identities=31% Similarity=0.700 Sum_probs=12.5
Q ss_pred CceEeEEeCCCCCceE
Q 037013 69 TGTAKHVFCKVCGITS 84 (128)
Q Consensus 69 ~~~~~r~FC~~CGs~l 84 (128)
.....+.||+.||-..
T Consensus 252 t~~m~k~FCp~CG~~T 267 (376)
T KOG2463|consen 252 TSEMPKDFCPSCGHKT 267 (376)
T ss_pred cCccchhcccccCCCe
Confidence 3557789999999753
No 73
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=33.51 E-value=47 Score=19.30 Aligned_cols=19 Identities=32% Similarity=0.515 Sum_probs=13.0
Q ss_pred CceEeEEeCCCCCceEEec
Q 037013 69 TGTAKHVFCKVCGITSFYV 87 (128)
Q Consensus 69 ~~~~~r~FC~~CGs~l~~~ 87 (128)
......+-|++||-.+.++
T Consensus 22 ~e~~v~F~CPnCGe~~I~R 40 (61)
T COG2888 22 GETAVKFPCPNCGEVEIYR 40 (61)
T ss_pred CCceeEeeCCCCCceeeeh
Confidence 3445668899999655554
No 74
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=33.51 E-value=49 Score=21.74 Aligned_cols=20 Identities=15% Similarity=0.122 Sum_probs=16.3
Q ss_pred ceEeEEeCCCCCceEEeccC
Q 037013 70 GTAKHVFCKVCGITSFYVPR 89 (128)
Q Consensus 70 ~~~~r~FC~~CGs~l~~~~~ 89 (128)
-.+++..|++||+.+-....
T Consensus 8 l~vt~l~C~~C~t~i~G~F~ 27 (113)
T PF09862_consen 8 LVVTRLKCPSCGTEIEGEFE 27 (113)
T ss_pred eEEEEEEcCCCCCEEEeeec
Confidence 35788999999999977654
No 75
>PHA00626 hypothetical protein
Probab=33.16 E-value=19 Score=20.73 Aligned_cols=8 Identities=38% Similarity=0.899 Sum_probs=6.8
Q ss_pred eCCCCCce
Q 037013 76 FCKVCGIT 83 (128)
Q Consensus 76 FC~~CGs~ 83 (128)
.||+||+.
T Consensus 2 ~CP~CGS~ 9 (59)
T PHA00626 2 SCPKCGSG 9 (59)
T ss_pred CCCCCCCc
Confidence 69999995
No 76
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=30.76 E-value=44 Score=16.59 Aligned_cols=13 Identities=23% Similarity=0.524 Sum_probs=10.5
Q ss_pred eCCCCCceEEecc
Q 037013 76 FCKVCGITSFYVP 88 (128)
Q Consensus 76 FC~~CGs~l~~~~ 88 (128)
-|+.|++.|.+-.
T Consensus 3 ~C~~C~t~L~yP~ 15 (31)
T TIGR01053 3 VCGGCRTLLMYPR 15 (31)
T ss_pred CcCCCCcEeecCC
Confidence 4999999998744
No 77
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=30.69 E-value=24 Score=22.02 Aligned_cols=20 Identities=25% Similarity=0.363 Sum_probs=16.6
Q ss_pred cCCchhccCCceeEEEcCCC
Q 037013 32 CNCSDCSMRGNVHFTVAPEN 51 (128)
Q Consensus 32 ChC~~Crk~~g~~~~~~~~~ 51 (128)
=+|+.|.|.-|+|++-+.+.
T Consensus 20 ~~C~~C~Rr~GLW~f~~~~s 39 (91)
T PF08600_consen 20 LSCSYCFRRLGLWMFKSKES 39 (91)
T ss_pred EEccccCcEeeeeecccCcc
Confidence 37999999999998877653
No 78
>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=30.50 E-value=29 Score=17.52 Aligned_cols=13 Identities=23% Similarity=0.330 Sum_probs=9.5
Q ss_pred EeCCCCCceEEec
Q 037013 75 VFCKVCGITSFYV 87 (128)
Q Consensus 75 ~FC~~CGs~l~~~ 87 (128)
.+|..||-+|...
T Consensus 4 g~C~~CGe~I~~~ 16 (36)
T PF01258_consen 4 GICEDCGEPIPEE 16 (36)
T ss_dssp SB-TTTSSBEEHH
T ss_pred CCccccCChHHHH
Confidence 4599999998754
No 79
>PF02943 FeThRed_B: Ferredoxin thioredoxin reductase catalytic beta chain; InterPro: IPR004209 Ferredoxin thioredoxin reductase is a [4FE-4S] protein present in organisms performing oxygenic photosynthesis, and plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthetis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit alpha and subunit beta. Subunit alpha is the variable subunit, and beta is the catalytic chain []. The structure of the beta subunit has been determined and found to fold around the FeS cluster [].; GO: 0008937 ferredoxin-NAD(P) reductase activity, 0055114 oxidation-reduction process; PDB: 2PUK_E 2PVD_A 2PVG_A 2PUO_A 2PU9_A 1DJ7_A 2PVO_A.
Probab=30.47 E-value=17 Score=23.65 Aligned_cols=9 Identities=33% Similarity=0.888 Sum_probs=2.8
Q ss_pred EEEeeeCCC
Q 037013 8 HKGGCRCRK 16 (128)
Q Consensus 8 ~~G~C~CGa 16 (128)
..|+||||-
T Consensus 77 ~~G~ChC~L 85 (108)
T PF02943_consen 77 EYGHCHCGL 85 (108)
T ss_dssp -----TTSS
T ss_pred ccccceEee
Confidence 457888874
No 80
>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=30.35 E-value=26 Score=18.22 Aligned_cols=15 Identities=20% Similarity=0.503 Sum_probs=11.6
Q ss_pred EeEEeCCCCCceEEe
Q 037013 72 AKHVFCKVCGITSFY 86 (128)
Q Consensus 72 ~~r~FC~~CGs~l~~ 86 (128)
+.-++|+.||-.++.
T Consensus 30 vp~~~C~~CGE~~~~ 44 (46)
T TIGR03831 30 VPALVCPQCGEEYLD 44 (46)
T ss_pred CCccccccCCCEeeC
Confidence 345789999998874
No 81
>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=29.92 E-value=25 Score=17.86 Aligned_cols=10 Identities=30% Similarity=0.650 Sum_probs=7.6
Q ss_pred EeCCCCCceE
Q 037013 75 VFCKVCGITS 84 (128)
Q Consensus 75 ~FC~~CGs~l 84 (128)
.-|+.||..+
T Consensus 27 ~~CP~Cg~~~ 36 (41)
T smart00834 27 ATCPECGGDV 36 (41)
T ss_pred CCCCCCCCcc
Confidence 4599999854
No 82
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=29.38 E-value=30 Score=19.32 Aligned_cols=11 Identities=45% Similarity=1.014 Sum_probs=8.5
Q ss_pred EeEEeCCCCCc
Q 037013 72 AKHVFCKVCGI 82 (128)
Q Consensus 72 ~~r~FC~~CGs 82 (128)
..-.||++||-
T Consensus 44 ~~i~~Cp~CgR 54 (56)
T PF02591_consen 44 DEIVFCPNCGR 54 (56)
T ss_pred CCeEECcCCCc
Confidence 34578999995
No 83
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=29.30 E-value=14 Score=27.42 Aligned_cols=16 Identities=38% Similarity=0.868 Sum_probs=12.7
Q ss_pred eEEeCCCCCceEEecc
Q 037013 73 KHVFCKVCGITSFYVP 88 (128)
Q Consensus 73 ~r~FC~~CGs~l~~~~ 88 (128)
.-.|||.||.-||+..
T Consensus 220 ~iv~CP~CgRILy~~e 235 (239)
T COG1579 220 EIVFCPYCGRILYYDE 235 (239)
T ss_pred CCccCCccchHHHhhh
Confidence 3478999999888754
No 84
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.29 E-value=22 Score=23.27 Aligned_cols=12 Identities=17% Similarity=0.636 Sum_probs=9.0
Q ss_pred CCCCCceEEecc
Q 037013 77 CKVCGITSFYVP 88 (128)
Q Consensus 77 C~~CGs~l~~~~ 88 (128)
||.||++-....
T Consensus 91 CP~Cgs~~~~i~ 102 (117)
T PRK00564 91 CEKCHSKNVIIT 102 (117)
T ss_pred CcCCCCCceEEe
Confidence 999999755433
No 85
>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=27.57 E-value=33 Score=18.54 Aligned_cols=12 Identities=25% Similarity=0.573 Sum_probs=9.5
Q ss_pred CCCCCceEEecc
Q 037013 77 CKVCGITSFYVP 88 (128)
Q Consensus 77 C~~CGs~l~~~~ 88 (128)
|+.||+..-.+.
T Consensus 2 CP~Cg~~a~ir~ 13 (47)
T PF04606_consen 2 CPHCGSKARIRT 13 (47)
T ss_pred cCCCCCeeEEEE
Confidence 999999876553
No 86
>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=27.02 E-value=1.4e+02 Score=17.46 Aligned_cols=26 Identities=27% Similarity=0.534 Sum_probs=17.5
Q ss_pred eeeeCCceEeEEeCCCCCceEEeccC
Q 037013 64 THTFGTGTAKHVFCKVCGITSFYVPR 89 (128)
Q Consensus 64 ~y~~s~~~~~r~FC~~CGs~l~~~~~ 89 (128)
.+.-..+...-.-|++||=.=++...
T Consensus 26 iFdvq~~~f~~v~C~~CGYTE~Y~~~ 51 (64)
T PF09855_consen 26 IFDVQNKKFTTVSCTNCGYTEFYKAK 51 (64)
T ss_pred EEEecCcEEEEEECCCCCCEEEEeec
Confidence 34444555666789999988666543
No 87
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=26.64 E-value=31 Score=18.74 Aligned_cols=9 Identities=33% Similarity=0.829 Sum_probs=7.0
Q ss_pred eCCCCCceE
Q 037013 76 FCKVCGITS 84 (128)
Q Consensus 76 FC~~CGs~l 84 (128)
-|+.||+-=
T Consensus 13 kCp~CGt~N 21 (44)
T PF14952_consen 13 KCPKCGTYN 21 (44)
T ss_pred cCCcCcCcc
Confidence 499999854
No 88
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=26.64 E-value=25 Score=22.82 Aligned_cols=12 Identities=17% Similarity=0.332 Sum_probs=8.7
Q ss_pred EeCCCCCceEEe
Q 037013 75 VFCKVCGITSFY 86 (128)
Q Consensus 75 ~FC~~CGs~l~~ 86 (128)
..||.||++-..
T Consensus 87 ~~CP~Cgs~~~~ 98 (113)
T PRK12380 87 AQCPHCHGERLR 98 (113)
T ss_pred ccCcCCCCCCcE
Confidence 459999987443
No 89
>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=26.62 E-value=32 Score=19.01 Aligned_cols=11 Identities=27% Similarity=0.558 Sum_probs=5.7
Q ss_pred eCCCCCceEEe
Q 037013 76 FCKVCGITSFY 86 (128)
Q Consensus 76 FC~~CGs~l~~ 86 (128)
-||-||.++-.
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 69999998853
No 90
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=26.59 E-value=98 Score=17.34 Aligned_cols=19 Identities=16% Similarity=0.347 Sum_probs=15.4
Q ss_pred eeEEEeeeCCCeEEEEEeCC
Q 037013 6 VLHKGGCRCRKLRWRVRAPR 25 (128)
Q Consensus 6 ~~~~G~C~CGav~~~~~~~~ 25 (128)
..+.=.|.||.. |.++.+.
T Consensus 15 ~~~~y~CRCG~~-f~i~e~~ 33 (55)
T PF05207_consen 15 GVYSYPCRCGGE-FEISEED 33 (55)
T ss_dssp TEEEEEETTSSE-EEEEHHH
T ss_pred CEEEEcCCCCCE-EEEcchh
Confidence 458888999999 9998654
No 91
>PRK11586 napB nitrate reductase cytochrome C550 subunit; Provisional
Probab=26.54 E-value=28 Score=23.93 Aligned_cols=15 Identities=20% Similarity=0.649 Sum_probs=11.5
Q ss_pred eEeEEeCCCCCceEE
Q 037013 71 TAKHVFCKVCGITSF 85 (128)
Q Consensus 71 ~~~r~FC~~CGs~l~ 85 (128)
.-.|+||..|..+=.
T Consensus 117 sprRYfCtQCHVPQa 131 (149)
T PRK11586 117 APRRYFCLQCHVPQA 131 (149)
T ss_pred CccceeeccccCccc
Confidence 357999999977643
No 92
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=26.49 E-value=56 Score=16.89 Aligned_cols=17 Identities=24% Similarity=0.372 Sum_probs=9.4
Q ss_pred EeEEeCCCCCceEEecc
Q 037013 72 AKHVFCKVCGITSFYVP 88 (128)
Q Consensus 72 ~~r~FC~~CGs~l~~~~ 88 (128)
.+.+.|..||.-+--..
T Consensus 4 ~~~YkC~~CGniVev~~ 20 (36)
T PF06397_consen 4 GEFYKCEHCGNIVEVVH 20 (36)
T ss_dssp TEEEE-TTT--EEEEEE
T ss_pred ccEEEccCCCCEEEEEE
Confidence 45678999999775443
No 93
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=26.20 E-value=36 Score=27.37 Aligned_cols=17 Identities=24% Similarity=0.317 Sum_probs=13.2
Q ss_pred eEEeCCCCCceEEeccC
Q 037013 73 KHVFCKVCGITSFYVPR 89 (128)
Q Consensus 73 ~r~FC~~CGs~l~~~~~ 89 (128)
++..|++||+.|+....
T Consensus 29 ~~a~CpRCg~~L~~~~~ 45 (419)
T PRK15103 29 QKAACPRCGTTLTVRWD 45 (419)
T ss_pred CeeECCCCCCCCcCCCC
Confidence 35779999999976543
No 94
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.88 E-value=30 Score=22.44 Aligned_cols=13 Identities=23% Similarity=0.345 Sum_probs=9.9
Q ss_pred EeCCCCCceEEec
Q 037013 75 VFCKVCGITSFYV 87 (128)
Q Consensus 75 ~FC~~CGs~l~~~ 87 (128)
.-|+.||.++-..
T Consensus 50 t~CP~Cg~~~e~~ 62 (115)
T COG1885 50 TSCPKCGEPFESA 62 (115)
T ss_pred ccCCCCCCcccee
Confidence 4599999987443
No 95
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=25.84 E-value=80 Score=20.80 Aligned_cols=18 Identities=17% Similarity=0.362 Sum_probs=12.5
Q ss_pred EeEEeCCCCCceEEeccC
Q 037013 72 AKHVFCKVCGITSFYVPR 89 (128)
Q Consensus 72 ~~r~FC~~CGs~l~~~~~ 89 (128)
...+.||.||+.-+-...
T Consensus 84 ~~~~~CP~C~s~~~~i~~ 101 (115)
T COG0375 84 ELDYRCPKCGSINLRIIG 101 (115)
T ss_pred hheeECCCCCCCceEEec
Confidence 344559999998766543
No 96
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=25.71 E-value=32 Score=19.64 Aligned_cols=16 Identities=25% Similarity=0.528 Sum_probs=12.3
Q ss_pred eEEeCCCCCceEEecc
Q 037013 73 KHVFCKVCGITSFYVP 88 (128)
Q Consensus 73 ~r~FC~~CGs~l~~~~ 88 (128)
..+-|+.||.+.+...
T Consensus 13 v~~~Cp~cGipthcS~ 28 (55)
T PF13824_consen 13 VNFECPDCGIPTHCSE 28 (55)
T ss_pred cCCcCCCCCCcCccCH
Confidence 3467999999988653
No 97
>PHA02450 hypothetical protein
Probab=25.46 E-value=25 Score=19.27 Aligned_cols=16 Identities=19% Similarity=0.573 Sum_probs=11.5
Q ss_pred eEEEeeeCCCeEEEEEe
Q 037013 7 LHKGGCRCRKLRWRVRA 23 (128)
Q Consensus 7 ~~~G~C~CGav~~~~~~ 23 (128)
-|-|-|-||++ |+..+
T Consensus 12 ryggdc~cg~i-yty~g 27 (53)
T PHA02450 12 RYGGDCTCGPI-YTYGG 27 (53)
T ss_pred eeCCcccccce-eeeCC
Confidence 47788999997 44444
No 98
>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=25.24 E-value=43 Score=26.46 Aligned_cols=18 Identities=22% Similarity=0.460 Sum_probs=14.9
Q ss_pred EeEEeCCCCCceEEeccC
Q 037013 72 AKHVFCKVCGITSFYVPR 89 (128)
Q Consensus 72 ~~r~FC~~CGs~l~~~~~ 89 (128)
...+||+.||.+|.....
T Consensus 28 ~~~~~CP~C~~~v~lk~G 45 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILKKG 45 (375)
T ss_pred CCcEECCCCCCeeEEEEc
Confidence 557999999999987643
No 99
>PRK03954 ribonuclease P protein component 4; Validated
Probab=25.13 E-value=11 Score=25.02 Aligned_cols=18 Identities=22% Similarity=0.301 Sum_probs=14.8
Q ss_pred CceEeEEeCCCCCceEEe
Q 037013 69 TGTAKHVFCKVCGITSFY 86 (128)
Q Consensus 69 ~~~~~r~FC~~CGs~l~~ 86 (128)
++...|.||..|.++|.-
T Consensus 59 p~~~KR~~CK~C~t~LiP 76 (121)
T PRK03954 59 PRKWKRRYCKRCHSFLVP 76 (121)
T ss_pred CHHHHHHHhhcCCCeeec
Confidence 456889999999999863
No 100
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=25.06 E-value=64 Score=16.50 Aligned_cols=11 Identities=55% Similarity=1.153 Sum_probs=8.6
Q ss_pred eCCCCCceEEe
Q 037013 76 FCKVCGITSFY 86 (128)
Q Consensus 76 FC~~CGs~l~~ 86 (128)
-|+.||+..|.
T Consensus 10 ~C~~C~~~~~~ 20 (36)
T PF11781_consen 10 PCPVCGSRWFY 20 (36)
T ss_pred cCCCCCCeEeE
Confidence 39999999444
No 101
>smart00067 GHA Glycoprotein hormone alpha chain homologues. Also called gonadotropins. Glycoprotein hormones consist of two glycosylated chains (alpha and beta) of similar topology.
Probab=24.66 E-value=27 Score=21.49 Aligned_cols=10 Identities=40% Similarity=1.115 Sum_probs=8.0
Q ss_pred eecCCchhcc
Q 037013 30 WKCNCSDCSM 39 (128)
Q Consensus 30 ~~ChC~~Crk 39 (128)
..|||+.|.-
T Consensus 75 T~ChCsTCyy 84 (87)
T smart00067 75 TECHCSTCYY 84 (87)
T ss_pred ccccccceeE
Confidence 4699999963
No 102
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.65 E-value=21 Score=24.09 Aligned_cols=16 Identities=25% Similarity=0.569 Sum_probs=12.3
Q ss_pred eEEeCCCCCceEEecc
Q 037013 73 KHVFCKVCGITSFYVP 88 (128)
Q Consensus 73 ~r~FC~~CGs~l~~~~ 88 (128)
--.||.+||++.-+..
T Consensus 67 ~psfchncgs~fpwte 82 (160)
T COG4306 67 PPSFCHNCGSRFPWTE 82 (160)
T ss_pred CcchhhcCCCCCCcHH
Confidence 3479999999876653
No 103
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=24.39 E-value=48 Score=18.81 Aligned_cols=13 Identities=31% Similarity=0.672 Sum_probs=9.9
Q ss_pred eEEeCCCCCceEE
Q 037013 73 KHVFCKVCGITSF 85 (128)
Q Consensus 73 ~r~FC~~CGs~l~ 85 (128)
....|+.||++-.
T Consensus 20 DiVvCp~CgapyH 32 (54)
T PF14446_consen 20 DIVVCPECGAPYH 32 (54)
T ss_pred CEEECCCCCCccc
Confidence 4567999999753
No 104
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=24.35 E-value=19 Score=20.61 Aligned_cols=14 Identities=21% Similarity=0.505 Sum_probs=10.9
Q ss_pred EeCCCCCceEEecc
Q 037013 75 VFCKVCGITSFYVP 88 (128)
Q Consensus 75 ~FC~~CGs~l~~~~ 88 (128)
.-|.+||.++-...
T Consensus 11 t~CrRCGk~i~tl~ 24 (60)
T PF10892_consen 11 TPCRRCGKSIRTLS 24 (60)
T ss_pred ehhhhhCccHHHHH
Confidence 45999999986554
No 105
>smart00673 CARP Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product.
Probab=24.00 E-value=1.1e+02 Score=15.22 Aligned_cols=26 Identities=19% Similarity=0.384 Sum_probs=16.6
Q ss_pred CCCeEEEEEeCCCCeeeecCCchhccC
Q 037013 14 CRKLRWRVRAPRSVEAWKCNCSDCSMR 40 (128)
Q Consensus 14 CGav~~~~~~~~~~~~~~ChC~~Crk~ 40 (128)
|-+..+.+.+.... +..-.|..|+-.
T Consensus 1 C~~~~i~v~g~~~~-v~id~~~~~~i~ 26 (38)
T smart00673 1 CESCTIQVSGKVNT-ISIDKCKKCSIY 26 (38)
T ss_pred CCcEEEEEeCccCE-EEEECCCCeEEE
Confidence 45666777766664 566677766654
No 106
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=23.98 E-value=33 Score=26.27 Aligned_cols=13 Identities=31% Similarity=0.889 Sum_probs=10.4
Q ss_pred EeEEeCCCCCceE
Q 037013 72 AKHVFCKVCGITS 84 (128)
Q Consensus 72 ~~r~FC~~CGs~l 84 (128)
-.|++|+.||+.-
T Consensus 183 e~~~~CPvCGS~P 195 (308)
T COG3058 183 ESRQYCPVCGSMP 195 (308)
T ss_pred cccccCCCcCCCC
Confidence 3578999999963
No 107
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=23.47 E-value=2.3e+02 Score=21.70 Aligned_cols=31 Identities=19% Similarity=0.231 Sum_probs=22.3
Q ss_pred eEEeCCCCCceEEeccC-CCC----CeEEEEecccC
Q 037013 73 KHVFCKVCGITSFYVPR-GTP----NGVAVTFRGVD 103 (128)
Q Consensus 73 ~r~FC~~CGs~l~~~~~-~~~----~~~~v~~g~ld 103 (128)
.-.-|++||+||-+... +.| ..+-||...|+
T Consensus 81 ~Ev~c~~c~~HLGHvF~ddgp~ptg~RyCiNs~sL~ 116 (283)
T PRK05550 81 TEIVCANCGAHLGHVFEGEGLTPKNTRHCVNSASLD 116 (283)
T ss_pred EEEEecCCCCccCcccCCCCCCCCCccccccccccc
Confidence 44679999999988765 222 35678877776
No 108
>PTZ00157 60S ribosomal protein L36a; Provisional
Probab=23.41 E-value=39 Score=21.00 Aligned_cols=16 Identities=25% Similarity=0.658 Sum_probs=12.9
Q ss_pred EeEEeCCCCCceEEec
Q 037013 72 AKHVFCKVCGITSFYV 87 (128)
Q Consensus 72 ~~r~FC~~CGs~l~~~ 87 (128)
..+.||+.|+.|.-+.
T Consensus 7 ~~~tyC~~C~kHt~Hk 22 (84)
T PTZ00157 7 NRKTYCKKCGKHTSHK 22 (84)
T ss_pred cccccCcCCCCCccEE
Confidence 4568999999987665
No 109
>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=23.38 E-value=43 Score=23.06 Aligned_cols=13 Identities=31% Similarity=0.679 Sum_probs=10.5
Q ss_pred EeCCCCCceEEec
Q 037013 75 VFCKVCGITSFYV 87 (128)
Q Consensus 75 ~FC~~CGs~l~~~ 87 (128)
+-|+.||..|-..
T Consensus 129 F~Cp~Cg~~L~~~ 141 (158)
T TIGR00373 129 FTCPRCGAMLDYL 141 (158)
T ss_pred CcCCCCCCEeeec
Confidence 5699999998664
No 110
>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=23.14 E-value=29 Score=22.54 Aligned_cols=17 Identities=18% Similarity=0.528 Sum_probs=11.7
Q ss_pred eEEeCCCCCceEEeccC
Q 037013 73 KHVFCKVCGITSFYVPR 89 (128)
Q Consensus 73 ~r~FC~~CGs~l~~~~~ 89 (128)
+...|++||+..|-.+.
T Consensus 8 tKR~Cp~CG~kFYDLnk 24 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNK 24 (108)
T ss_pred CcccCCCCcchhccCCC
Confidence 34568888887776554
No 111
>PF00471 Ribosomal_L33: Ribosomal protein L33; InterPro: IPR001705 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L33 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L33 has been shown to be on the surface of 50S subunit. L33 belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , ], groups: Eubacterial L33. Algal and plant chloroplast L33. Cyanelle L33. L33 is a small protein of 49 to 66 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3PIO_1 3PIP_1 3PYT_3 3MS1_3 3F1F_6 3F1H_6 3MRZ_3 3PYO_3 3D5B_6 3D5D_6 ....
Probab=23.14 E-value=1.1e+02 Score=16.74 Aligned_cols=19 Identities=11% Similarity=0.284 Sum_probs=14.3
Q ss_pred CceEeEEeCCCCCceEEec
Q 037013 69 TGTAKHVFCKVCGITSFYV 87 (128)
Q Consensus 69 ~~~~~r~FC~~CGs~l~~~ 87 (128)
.+-.-+-||+.|+.++.+.
T Consensus 27 ~rL~lkKycp~~~khtlhk 45 (48)
T PF00471_consen 27 ERLELKKYCPRCRKHTLHK 45 (48)
T ss_dssp SSSEEEEEETSSSSEEEEE
T ss_pred ceeeEeccCCCCCCEecEE
Confidence 3445678999999997653
No 112
>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=22.91 E-value=50 Score=18.68 Aligned_cols=12 Identities=25% Similarity=0.382 Sum_probs=9.4
Q ss_pred eCCCCCceEEec
Q 037013 76 FCKVCGITSFYV 87 (128)
Q Consensus 76 FC~~CGs~l~~~ 87 (128)
-|+.||..+-..
T Consensus 4 ~CP~CG~~iev~ 15 (54)
T TIGR01206 4 ECPDCGAEIELE 15 (54)
T ss_pred CCCCCCCEEecC
Confidence 599999988553
No 113
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=22.82 E-value=36 Score=20.83 Aligned_cols=14 Identities=29% Similarity=0.657 Sum_probs=11.4
Q ss_pred EeCCCCCceEEecc
Q 037013 75 VFCKVCGITSFYVP 88 (128)
Q Consensus 75 ~FC~~CGs~l~~~~ 88 (128)
.||..||-||....
T Consensus 1 k~CQSCGMPl~~~~ 14 (81)
T PF12674_consen 1 KFCQSCGMPLSKDE 14 (81)
T ss_pred CcCCcCcCccCCcc
Confidence 38999999997654
No 114
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=22.71 E-value=43 Score=21.15 Aligned_cols=23 Identities=30% Similarity=0.583 Sum_probs=16.8
Q ss_pred ceEeEEeCCCCCceEEeccCCCC
Q 037013 70 GTAKHVFCKVCGITSFYVPRGTP 92 (128)
Q Consensus 70 ~~~~r~FC~~CGs~l~~~~~~~~ 92 (128)
+.....-|+.||.+|-..+...|
T Consensus 30 K~~~~p~C~~cg~pL~Gi~r~RP 52 (93)
T COG2174 30 KKPTIPKCAICGRPLGGIPRGRP 52 (93)
T ss_pred ccCCCCcccccCCccCCccCCCc
Confidence 34455679999999988765543
No 115
>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=22.31 E-value=47 Score=17.46 Aligned_cols=11 Identities=36% Similarity=0.727 Sum_probs=8.2
Q ss_pred EeEEeCCCCCc
Q 037013 72 AKHVFCKVCGI 82 (128)
Q Consensus 72 ~~r~FC~~CGs 82 (128)
....-|+.||+
T Consensus 24 ~~~~~CP~Cg~ 34 (42)
T PF09723_consen 24 DDPVPCPECGS 34 (42)
T ss_pred CCCCcCCCCCC
Confidence 34466999998
No 116
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=22.26 E-value=33 Score=19.88 Aligned_cols=15 Identities=20% Similarity=0.211 Sum_probs=11.8
Q ss_pred eEEeCCCCCceEEec
Q 037013 73 KHVFCKVCGITSFYV 87 (128)
Q Consensus 73 ~r~FC~~CGs~l~~~ 87 (128)
...||..||.+|-..
T Consensus 30 s~g~C~~Cg~~Ip~~ 44 (63)
T TIGR02419 30 SLRECEDCGEPIPEA 44 (63)
T ss_pred CCCeeccCCCcChHH
Confidence 367999999998543
No 117
>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=22.14 E-value=1.1e+02 Score=15.31 Aligned_cols=13 Identities=31% Similarity=0.667 Sum_probs=5.9
Q ss_pred eEEeCCCCCceEE
Q 037013 73 KHVFCKVCGITSF 85 (128)
Q Consensus 73 ~r~FC~~CGs~l~ 85 (128)
.-..|..||...|
T Consensus 10 ~~~rC~~Cg~~~~ 22 (37)
T PF12172_consen 10 LGQRCRDCGRVQF 22 (37)
T ss_dssp EEEE-TTT--EEE
T ss_pred EEEEcCCCCCEec
Confidence 3455777777655
No 118
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=22.09 E-value=29 Score=23.90 Aligned_cols=12 Identities=42% Similarity=1.002 Sum_probs=9.7
Q ss_pred eEeEEeCCCCCc
Q 037013 71 TAKHVFCKVCGI 82 (128)
Q Consensus 71 ~~~r~FC~~CGs 82 (128)
.-.|.||..||-
T Consensus 115 KP~r~fCaVCG~ 126 (156)
T KOG3362|consen 115 KPLRKFCAVCGY 126 (156)
T ss_pred CCcchhhhhcCC
Confidence 356899999993
No 119
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=22.07 E-value=88 Score=17.82 Aligned_cols=17 Identities=29% Similarity=0.850 Sum_probs=12.9
Q ss_pred EeEEeCCCCCceEEecc
Q 037013 72 AKHVFCKVCGITSFYVP 88 (128)
Q Consensus 72 ~~r~FC~~CGs~l~~~~ 88 (128)
..+..|..||..-|+..
T Consensus 13 ktH~~CrRCG~~syH~q 29 (55)
T PF01907_consen 13 KTHTLCRRCGRRSYHIQ 29 (55)
T ss_dssp -SEEE-TTTSSEEEETT
T ss_pred ccEeeecccCCeeeecC
Confidence 47789999999999864
No 120
>COG3043 NapB Nitrate reductase cytochrome c-type subunit [Energy production and conversion]
Probab=22.03 E-value=37 Score=23.44 Aligned_cols=13 Identities=23% Similarity=0.792 Sum_probs=10.6
Q ss_pred EeEEeCCCCCceE
Q 037013 72 AKHVFCKVCGITS 84 (128)
Q Consensus 72 ~~r~FC~~CGs~l 84 (128)
-+|+||-.|..+=
T Consensus 124 PRRYFClQCHVPQ 136 (155)
T COG3043 124 PRRYFCLQCHVPQ 136 (155)
T ss_pred ccceeeeeccccc
Confidence 5799999997754
No 121
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=22.00 E-value=42 Score=21.21 Aligned_cols=16 Identities=13% Similarity=0.335 Sum_probs=12.8
Q ss_pred EeEEeCCCCCceEEec
Q 037013 72 AKHVFCKVCGITSFYV 87 (128)
Q Consensus 72 ~~r~FC~~CGs~l~~~ 87 (128)
..+.||+.|+.|.-+.
T Consensus 6 ~~~tyCp~CkkHt~Hk 21 (92)
T PRK05767 6 KIRTYCPYCKTHTEHE 21 (92)
T ss_pred cccccCcCCCCcccEE
Confidence 4578999999987664
No 122
>PF06052 3-HAO: 3-hydroxyanthranilic acid dioxygenase; InterPro: IPR010329 Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase (1.13.11.6 from EC). It is part of the kynurenine pathway for the degradation of tryptophan and the biosynthesis of nicotinic acid [].The prokaryotic homologue is involved in the 2-nitrobenzoate degradation pathway []. The enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.; GO: 0000334 3-hydroxyanthranilate 3,4-dioxygenase activity, 0005506 iron ion binding, 0008152 metabolic process, 0055114 oxidation-reduction process; PDB: 1ZVF_A 1YFX_A 1YFW_A 1YFY_A 1YFU_A 2QNK_A 3FE5_A.
Probab=21.78 E-value=1.2e+02 Score=21.07 Aligned_cols=20 Identities=15% Similarity=0.245 Sum_probs=14.7
Q ss_pred CCceEeEEeCCCCCceEEec
Q 037013 68 GTGTAKHVFCKVCGITSFYV 87 (128)
Q Consensus 68 s~~~~~r~FC~~CGs~l~~~ 87 (128)
.....-|+||.+|+..|+-.
T Consensus 113 ~~~D~l~WyC~~c~~~l~e~ 132 (151)
T PF06052_consen 113 GELDGLRWYCPNCNHILHEE 132 (151)
T ss_dssp TS-EEEEEESTTTSSEEEEE
T ss_pred CCcccEEEecCCCCCEEEEE
Confidence 34567789999999877653
No 123
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=21.61 E-value=66 Score=20.66 Aligned_cols=7 Identities=43% Similarity=0.918 Sum_probs=4.9
Q ss_pred eCCCCCc
Q 037013 76 FCKVCGI 82 (128)
Q Consensus 76 FC~~CGs 82 (128)
.|..||+
T Consensus 5 ~CaDC~~ 11 (112)
T smart00105 5 KCFDCGA 11 (112)
T ss_pred cccCCCC
Confidence 4777776
No 124
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=21.61 E-value=46 Score=19.01 Aligned_cols=14 Identities=29% Similarity=0.541 Sum_probs=9.4
Q ss_pred EEeCCCCCceEEec
Q 037013 74 HVFCKVCGITSFYV 87 (128)
Q Consensus 74 r~FC~~CGs~l~~~ 87 (128)
...|+.||+++...
T Consensus 17 k~~CP~CG~~t~~~ 30 (56)
T PRK13130 17 KEICPVCGGKTKNP 30 (56)
T ss_pred cccCcCCCCCCCCC
Confidence 35688888876553
No 125
>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=21.59 E-value=48 Score=26.50 Aligned_cols=16 Identities=25% Similarity=0.279 Sum_probs=12.6
Q ss_pred EEeCCCCCceEEeccC
Q 037013 74 HVFCKVCGITSFYVPR 89 (128)
Q Consensus 74 r~FC~~CGs~l~~~~~ 89 (128)
+..|++||+.|+....
T Consensus 33 ~a~CpRCg~~L~~~~~ 48 (403)
T TIGR00155 33 KAACPRCGTTLTVGWD 48 (403)
T ss_pred eeECCCCCCCCcCCCC
Confidence 5679999999976543
No 126
>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=21.17 E-value=84 Score=20.09 Aligned_cols=16 Identities=19% Similarity=0.463 Sum_probs=12.9
Q ss_pred EeEEeCCCCCceEEec
Q 037013 72 AKHVFCKVCGITSFYV 87 (128)
Q Consensus 72 ~~r~FC~~CGs~l~~~ 87 (128)
+..++|+.||..++..
T Consensus 29 ~~~~~C~~CGe~~~~~ 44 (127)
T TIGR03830 29 VPGWYCPACGEELLDP 44 (127)
T ss_pred eeeeECCCCCCEEEcH
Confidence 4557899999988865
No 127
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=21.07 E-value=55 Score=18.33 Aligned_cols=13 Identities=23% Similarity=0.398 Sum_probs=10.3
Q ss_pred eCCCCCceEEecc
Q 037013 76 FCKVCGITSFYVP 88 (128)
Q Consensus 76 FC~~CGs~l~~~~ 88 (128)
-|+.||.++-...
T Consensus 2 ~CPyCge~~~~~i 14 (52)
T PF14255_consen 2 QCPYCGEPIEILI 14 (52)
T ss_pred CCCCCCCeeEEEE
Confidence 4999999887654
No 128
>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=20.79 E-value=37 Score=21.22 Aligned_cols=16 Identities=19% Similarity=0.378 Sum_probs=12.8
Q ss_pred EeEEeCCCCCceEEec
Q 037013 72 AKHVFCKVCGITSFYV 87 (128)
Q Consensus 72 ~~r~FC~~CGs~l~~~ 87 (128)
..|.+|..|+.+|-..
T Consensus 31 ~~rS~C~~C~~~L~~~ 46 (92)
T PF06750_consen 31 FPRSHCPHCGHPLSWW 46 (92)
T ss_pred CCCCcCcCCCCcCccc
Confidence 3478899999998664
No 129
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=20.25 E-value=46 Score=20.58 Aligned_cols=20 Identities=20% Similarity=0.409 Sum_probs=16.0
Q ss_pred ceEeEEeCCCCCceEEeccC
Q 037013 70 GTAKHVFCKVCGITSFYVPR 89 (128)
Q Consensus 70 ~~~~r~FC~~CGs~l~~~~~ 89 (128)
......+|..|++.|.+...
T Consensus 53 ~~~~~l~C~~C~~~lGwkY~ 72 (96)
T PF03226_consen 53 HTVRDLFCSGCNTILGWKYE 72 (96)
T ss_pred EEEEEeEcccCChhHCcEEE
Confidence 55777899999999977643
No 130
>PRK00595 rpmG 50S ribosomal protein L33; Validated
Probab=20.23 E-value=1.1e+02 Score=17.06 Aligned_cols=18 Identities=6% Similarity=-0.158 Sum_probs=13.9
Q ss_pred ceEeEEeCCCCCceEEec
Q 037013 70 GTAKHVFCKVCGITSFYV 87 (128)
Q Consensus 70 ~~~~r~FC~~CGs~l~~~ 87 (128)
+-.-+-||+.|+.++.+.
T Consensus 33 rL~lkKycp~~~khtlhk 50 (53)
T PRK00595 33 KLELKKYDPVLRKHVLHK 50 (53)
T ss_pred ceEEECcCCCCCCEEeEE
Confidence 445678999999997653
No 131
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=20.19 E-value=84 Score=16.39 Aligned_cols=9 Identities=33% Similarity=0.836 Sum_probs=7.8
Q ss_pred EeEEeCCCC
Q 037013 72 AKHVFCKVC 80 (128)
Q Consensus 72 ~~r~FC~~C 80 (128)
..|++|++|
T Consensus 39 ~~R~~C~~C 47 (47)
T PF14690_consen 39 KRRYRCKNC 47 (47)
T ss_pred eEEEECcCC
Confidence 788999988
No 132
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=20.19 E-value=40 Score=17.47 Aligned_cols=14 Identities=14% Similarity=0.353 Sum_probs=5.9
Q ss_pred eEEeCCCCCceEEe
Q 037013 73 KHVFCKVCGITSFY 86 (128)
Q Consensus 73 ~r~FC~~CGs~l~~ 86 (128)
.|+||.-|...|..
T Consensus 2 ~ryyCdyC~~~~~~ 15 (38)
T PF06220_consen 2 PRYYCDYCKKYLTH 15 (38)
T ss_dssp -S-B-TTT--B-S-
T ss_pred cCeecccccceecC
Confidence 47899999988743
No 133
>PF01601 Corona_S2: Coronavirus S2 glycoprotein; InterPro: IPR002552 The type I glycoprotein S of Coronavirus, trimers of which constitute the typical viral spikes, is assembled into virions through noncovalent interactions with the M protein. The spike glycoprotein is translated as a large polypeptide that is subsequently cleaved to S1 IPR002551 from INTERPRO and S2 []. Both chimeric S proteins appeared to cause cell fusion when expressed individually, suggesting that they were biologically fully active []. The spike is a type I membrane glycoprotein that possesses a conserved transmembrane anchor and an unusual cysteine-rich (cys) domain that bridges the putative junction of the anchor and the cytoplasmic tail [].; GO: 0006944 cellular membrane fusion, 0046813 virion attachment, binding of host cell surface receptor, 0016021 integral to membrane, 0019031 viral envelope; PDB: 2BEQ_B 2FXP_A 1ZVB_A 1WNC_D 1ZV8_H 1ZV7_B 1WYY_B 1ZVA_A 2BEZ_F 1WDG_A ....
Probab=20.14 E-value=34 Score=28.83 Aligned_cols=24 Identities=29% Similarity=0.695 Sum_probs=0.0
Q ss_pred CceEeEEeCCCCCceEEeccCCCCC
Q 037013 69 TGTAKHVFCKVCGITSFYVPRGTPN 93 (128)
Q Consensus 69 ~~~~~r~FC~~CGs~l~~~~~~~~~ 93 (128)
+...+..||++ |+|||..+...|+
T Consensus 365 SQS~R~gFCGn-GtHv~Si~q~AP~ 388 (610)
T PF01601_consen 365 SQSSRYGFCGN-GTHVFSIPQAAPN 388 (610)
T ss_dssp -------------------------
T ss_pred ccccccceecC-CcEEEEecccCCc
Confidence 34577899997 9999998765553
No 134
>cd06008 NF-X1-zinc-finger Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms.
Probab=20.05 E-value=60 Score=17.67 Aligned_cols=15 Identities=40% Similarity=0.587 Sum_probs=10.4
Q ss_pred eEEEeeeCCCeEEEE
Q 037013 7 LHKGGCRCRKLRWRV 21 (128)
Q Consensus 7 ~~~G~C~CGav~~~~ 21 (128)
....+|.||+.+.++
T Consensus 31 ~~~~~C~CG~~~~~~ 45 (49)
T cd06008 31 TVKKKCRCGKTTKEV 45 (49)
T ss_pred ccCeEecCCCeeccc
Confidence 345689999886544
No 135
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=20.03 E-value=49 Score=17.17 Aligned_cols=9 Identities=33% Similarity=0.752 Sum_probs=7.0
Q ss_pred CCCCCceEE
Q 037013 77 CKVCGITSF 85 (128)
Q Consensus 77 C~~CGs~l~ 85 (128)
||.|++.|-
T Consensus 2 CP~C~~~l~ 10 (41)
T PF13453_consen 2 CPRCGTELE 10 (41)
T ss_pred cCCCCcccc
Confidence 899988654
Done!