Query 040416
Match_columns 47
No_of_seqs 124 out of 236
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 08:12:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040416.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040416hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01780 Ribosomal_L37ae: Ribo 99.9 1.1E-25 2.4E-30 135.0 4.6 45 2-46 46-90 (90)
2 TIGR00280 L37a ribosomal prote 99.9 2.6E-25 5.6E-30 133.7 5.3 46 2-47 46-91 (91)
3 PTZ00255 60S ribosomal protein 99.9 3.4E-24 7.3E-29 128.5 4.8 44 2-45 47-90 (90)
4 PRK03976 rpl37ae 50S ribosomal 99.9 9E-24 1.9E-28 126.7 4.7 43 2-44 47-89 (90)
5 KOG0402 60S ribosomal protein 99.9 6.9E-23 1.5E-27 123.6 3.7 47 1-47 46-92 (92)
6 COG1997 RPL43A Ribosomal prote 99.8 3.3E-21 7.1E-26 115.9 3.7 45 1-45 45-89 (89)
7 cd00729 rubredoxin_SM Rubredox 88.5 0.38 8.3E-06 23.8 1.6 15 9-23 2-16 (34)
8 COG1592 Rubrerythrin [Energy p 86.5 0.34 7.5E-06 31.6 1.0 13 9-21 134-146 (166)
9 PF00096 zf-C2H2: Zinc finger, 85.9 0.69 1.5E-05 19.9 1.6 11 10-20 1-11 (23)
10 PF13894 zf-C2H2_4: C2H2-type 84.6 0.74 1.6E-05 19.2 1.3 11 10-20 1-11 (24)
11 cd00350 rubredoxin_like Rubred 84.4 0.58 1.3E-05 22.7 1.0 14 9-22 1-14 (33)
12 COG1998 RPS31 Ribosomal protei 82.9 0.64 1.4E-05 25.7 0.9 10 10-19 38-47 (51)
13 PF12874 zf-met: Zinc-finger o 78.0 1.8 3.9E-05 18.9 1.4 12 10-21 1-12 (25)
14 PF01807 zf-CHC2: CHC2 zinc fi 77.6 1.7 3.8E-05 25.1 1.6 35 8-44 53-88 (97)
15 PF13465 zf-H2C2_2: Zinc-finge 75.2 2.3 5E-05 19.4 1.4 11 10-20 15-25 (26)
16 PF14311 DUF4379: Domain of un 73.3 2.2 4.8E-05 22.3 1.2 12 9-20 28-39 (55)
17 smart00400 ZnF_CHCC zinc finge 68.7 2.2 4.8E-05 22.2 0.6 17 7-25 21-37 (55)
18 PF13912 zf-C2H2_6: C2H2-type 68.3 4 8.7E-05 18.0 1.3 11 10-20 2-12 (27)
19 PF01927 Mut7-C: Mut7-C RNAse 68.3 3.6 7.8E-05 25.3 1.5 15 9-23 124-138 (147)
20 PF02977 CarbpepA_inh: Carboxy 67.9 0.73 1.6E-05 25.0 -1.4 22 7-28 19-41 (46)
21 PF08209 Sgf11: Sgf11 (transcr 67.0 3.7 8.1E-05 20.5 1.2 17 10-26 5-21 (33)
22 PHA00626 hypothetical protein 67.0 3 6.5E-05 23.7 0.9 18 8-25 22-39 (59)
23 PF08273 Prim_Zn_Ribbon: Zinc- 67.0 3.3 7.1E-05 21.4 1.0 17 4-21 21-37 (40)
24 PRK00432 30S ribosomal protein 66.9 3.2 7E-05 22.1 1.0 12 8-19 36-47 (50)
25 PF08790 zf-LYAR: LYAR-type C2 66.0 7.1 0.00015 19.0 2.0 18 11-28 2-19 (28)
26 COG3677 Transposase and inacti 65.7 2.6 5.6E-05 26.1 0.5 13 9-21 53-65 (129)
27 PF05191 ADK_lid: Adenylate ki 65.3 5.4 0.00012 19.9 1.6 11 10-20 2-12 (36)
28 PF08646 Rep_fac-A_C: Replicat 65.0 3.7 8.1E-05 24.7 1.1 18 7-24 35-52 (146)
29 PF12760 Zn_Tnp_IS1595: Transp 64.6 3.5 7.7E-05 21.0 0.8 12 7-18 35-46 (46)
30 PF09986 DUF2225: Uncharacteri 63.5 3.8 8.3E-05 26.8 1.0 18 8-25 47-64 (214)
31 PRK03824 hypA hydrogenase nick 62.8 6.2 0.00013 24.4 1.8 15 8-22 69-83 (135)
32 PF01599 Ribosomal_S27: Riboso 62.5 4.5 9.7E-05 21.7 1.0 9 10-18 39-47 (47)
33 TIGR03831 YgiT_finger YgiT-typ 62.2 3.9 8.5E-05 19.8 0.7 15 6-20 29-43 (46)
34 PF01586 Basic: Myogenic Basic 62.2 2.7 5.9E-05 25.1 0.1 11 9-19 72-82 (86)
35 PF05899 Cupin_3: Protein of u 62.1 6.9 0.00015 21.4 1.8 18 3-20 5-22 (74)
36 PF00641 zf-RanBP: Zn-finger i 61.1 4.4 9.6E-05 18.8 0.7 11 8-18 3-13 (30)
37 PF04981 NMD3: NMD3 family ; 60.5 11 0.00023 24.8 2.7 20 8-27 34-53 (236)
38 PF06397 Desulfoferrod_N: Desu 60.3 6.9 0.00015 19.9 1.4 12 8-19 5-16 (36)
39 COG3357 Predicted transcriptio 58.1 3.6 7.8E-05 25.3 0.1 11 11-21 60-70 (97)
40 PF13913 zf-C2HC_2: zinc-finge 57.7 5.7 0.00012 18.2 0.8 11 11-21 4-14 (25)
41 smart00547 ZnF_RBZ Zinc finger 57.6 3.6 7.8E-05 18.3 0.1 11 8-18 1-11 (26)
42 COG1773 Rubredoxin [Energy pro 55.2 8.3 0.00018 21.4 1.3 11 9-19 3-13 (55)
43 PF09855 DUF2082: Nucleic-acid 54.6 4.7 0.0001 22.6 0.2 9 10-18 1-9 (64)
44 COG5034 TNG2 Chromatin remodel 54.1 3.4 7.3E-05 29.3 -0.5 11 8-18 260-270 (271)
45 PF14443 DBC1: DBC1 53.9 15 0.00032 23.3 2.4 28 18-45 20-54 (126)
46 PF13717 zinc_ribbon_4: zinc-r 51.7 8.6 0.00019 19.0 0.9 10 10-19 26-35 (36)
47 cd00974 DSRD Desulforedoxin (D 51.3 15 0.00032 17.6 1.7 13 8-20 3-15 (34)
48 PF07282 OrfB_Zn_ribbon: Putat 51.0 11 0.00025 19.9 1.4 15 5-19 42-56 (69)
49 cd04476 RPA1_DBD_C RPA1_DBD_C: 50.0 7.1 0.00015 23.9 0.5 12 8-19 50-61 (166)
50 TIGR00319 desulf_FeS4 desulfof 49.7 16 0.00035 17.3 1.7 13 8-20 6-18 (34)
51 PF02892 zf-BED: BED zinc fing 49.6 11 0.00024 18.4 1.1 16 7-22 14-29 (45)
52 smart00355 ZnF_C2H2 zinc finge 49.6 5.1 0.00011 16.4 -0.1 11 11-21 2-12 (26)
53 smart00834 CxxC_CXXC_SSSS Puta 49.3 11 0.00023 18.0 1.0 11 10-20 6-16 (41)
54 TIGR03655 anti_R_Lar restricti 49.2 13 0.00029 19.3 1.5 15 5-19 22-36 (53)
55 PF09723 Zn-ribbon_8: Zinc rib 49.0 13 0.00028 18.7 1.3 10 10-19 6-15 (42)
56 PF03107 C1_2: C1 domain; Int 48.3 6.3 0.00014 18.6 0.1 16 10-25 1-17 (30)
57 PHA02768 hypothetical protein; 47.1 7.6 0.00016 21.4 0.3 13 10-22 6-18 (55)
58 cd00730 rubredoxin Rubredoxin; 47.0 10 0.00022 20.3 0.8 12 9-20 1-12 (50)
59 COG0675 Transposase and inacti 46.6 14 0.0003 23.4 1.5 13 7-19 320-332 (364)
60 PRK12366 replication factor A; 46.4 8.5 0.00019 29.1 0.6 12 7-18 546-557 (637)
61 smart00778 Prim_Zn_Ribbon Zinc 45.8 8.5 0.00018 19.5 0.4 14 4-17 20-33 (37)
62 PF07295 DUF1451: Protein of u 45.7 14 0.00031 23.4 1.5 16 5-20 108-123 (146)
63 PF08792 A2L_zn_ribbon: A2L zi 44.9 11 0.00025 18.5 0.7 9 9-17 3-11 (33)
64 PF12171 zf-C2H2_jaz: Zinc-fin 44.7 11 0.00023 16.9 0.6 12 10-21 2-13 (27)
65 PF13397 DUF4109: Domain of un 44.1 11 0.00023 23.3 0.7 10 9-18 50-59 (105)
66 PF00301 Rubredoxin: Rubredoxi 44.1 19 0.00041 19.0 1.5 12 10-21 2-13 (47)
67 PF06353 DUF1062: Protein of u 43.5 12 0.00027 23.7 0.9 12 9-20 13-24 (142)
68 KOG4167 Predicted DNA-binding 43.5 3.5 7.5E-05 33.2 -1.9 14 6-19 789-802 (907)
69 COG1545 Predicted nucleic-acid 42.9 14 0.00031 22.8 1.1 9 11-19 31-39 (140)
70 PF08821 CGGC: CGGC domain; I 42.7 41 0.0009 20.1 3.1 12 5-16 39-50 (107)
71 smart00440 ZnF_C2C2 C2C2 Zinc 42.6 20 0.00044 17.9 1.5 13 7-19 26-38 (40)
72 TIGR02605 CxxC_CxxC_SSSS putat 42.3 18 0.00039 18.3 1.3 12 10-21 6-17 (52)
73 PF04071 zf-like: Cysteine-ric 42.0 12 0.00025 22.3 0.6 9 9-17 51-59 (86)
74 COG5533 UBP5 Ubiquitin C-termi 40.2 9.9 0.00021 28.3 0.1 10 9-18 284-293 (415)
75 COG2956 Predicted N-acetylgluc 40.1 13 0.00028 27.6 0.7 9 9-17 368-376 (389)
76 PF00645 zf-PARP: Poly(ADP-rib 40.1 18 0.00039 19.8 1.1 17 11-27 9-25 (82)
77 smart00614 ZnF_BED BED zinc fi 40.0 39 0.00084 17.1 2.4 14 11-24 20-33 (50)
78 PF14353 CpXC: CpXC protein 39.8 16 0.00036 21.5 1.0 12 9-20 38-49 (128)
79 COG2401 ABC-type ATPase fused 39.6 15 0.00033 28.4 1.0 15 5-19 126-140 (593)
80 PRK00464 nrdR transcriptional 39.4 13 0.00029 23.7 0.6 12 10-21 29-40 (154)
81 COG3755 Uncharacterized protei 39.2 31 0.00067 21.8 2.2 28 19-46 95-122 (127)
82 TIGR01391 dnaG DNA primase, ca 38.7 15 0.00033 26.1 0.8 35 7-43 53-88 (415)
83 COG2158 Uncharacterized protei 38.6 14 0.0003 23.2 0.6 24 9-39 62-85 (112)
84 PF13240 zinc_ribbon_2: zinc-r 38.5 11 0.00023 17.1 0.1 12 11-22 1-12 (23)
85 smart00451 ZnF_U1 U1-like zinc 38.4 12 0.00025 17.2 0.1 13 8-20 2-14 (35)
86 PF10571 UPF0547: Uncharacteri 38.2 12 0.00026 17.5 0.2 9 11-19 16-24 (26)
87 PF01096 TFIIS_C: Transcriptio 38.1 32 0.0007 17.0 1.8 13 7-19 26-38 (39)
88 COG3478 Predicted nucleic-acid 38.0 13 0.00028 21.6 0.3 11 9-19 4-14 (68)
89 PF09538 FYDLN_acid: Protein o 37.2 12 0.00025 22.7 0.1 9 11-19 11-19 (108)
90 PF11672 DUF3268: Protein of u 36.8 29 0.00062 21.1 1.7 35 9-44 31-65 (102)
91 COG4740 Predicted metalloprote 36.4 9 0.00019 25.6 -0.5 25 19-43 38-64 (176)
92 TIGR00617 rpa1 replication fac 36.3 13 0.00029 28.0 0.2 14 7-20 491-504 (608)
93 TIGR02098 MJ0042_CXXC MJ0042 f 36.1 23 0.00049 16.9 1.0 9 11-19 27-35 (38)
94 COG1379 PHP family phosphoeste 36.1 12 0.00026 27.8 0.0 14 9-22 265-278 (403)
95 PF15135 UPF0515: Uncharacteri 36.1 19 0.0004 25.7 1.0 19 5-23 151-169 (278)
96 COG1852 Uncharacterized conser 36.0 16 0.00034 25.1 0.5 13 9-21 111-123 (209)
97 PF12523 DUF3725: Protein of u 35.8 19 0.00042 21.1 0.8 12 8-19 58-69 (74)
98 PF09943 DUF2175: Uncharacteri 35.7 20 0.00043 22.0 0.9 15 9-23 2-16 (101)
99 TIGR03830 CxxCG_CxxCG_HTH puta 35.7 29 0.00062 19.8 1.6 16 6-21 28-43 (127)
100 PF09845 DUF2072: Zn-ribbon co 35.6 15 0.00032 23.5 0.3 13 11-23 3-15 (131)
101 smart00661 RPOL9 RNA polymeras 35.5 35 0.00076 16.9 1.7 16 9-24 20-35 (52)
102 COG1571 Predicted DNA-binding 35.5 13 0.00029 27.5 0.2 14 10-23 368-381 (421)
103 TIGR01384 TFS_arch transcripti 34.7 33 0.00071 19.5 1.7 14 9-22 90-103 (104)
104 PF13719 zinc_ribbon_5: zinc-r 34.2 25 0.00055 17.2 1.0 11 9-19 25-35 (37)
105 PF11781 RRN7: RNA polymerase 33.7 20 0.00042 17.9 0.6 14 5-18 21-34 (36)
106 COG3450 Predicted enzyme of th 33.4 27 0.00057 21.6 1.2 11 5-15 45-55 (116)
107 PRK05667 dnaG DNA primase; Val 33.0 23 0.0005 26.6 1.1 35 6-42 54-89 (580)
108 PF04959 ARS2: Arsenite-resist 32.3 26 0.00056 23.6 1.1 29 5-33 73-101 (214)
109 PHA00616 hypothetical protein 31.6 9.2 0.0002 20.2 -0.9 11 10-20 2-12 (44)
110 PF13408 Zn_ribbon_recom: Reco 31.3 28 0.0006 17.3 0.9 14 8-21 4-17 (58)
111 PF01363 FYVE: FYVE zinc finge 31.0 29 0.00062 18.2 1.0 12 11-22 27-38 (69)
112 PF07754 DUF1610: Domain of un 30.6 21 0.00046 16.7 0.4 12 12-23 1-12 (24)
113 PRK03681 hypA hydrogenase nick 30.6 34 0.00073 20.5 1.3 17 8-24 69-85 (114)
114 PRK12380 hydrogenase nickel in 30.5 35 0.00075 20.4 1.4 19 8-26 69-87 (113)
115 smart00520 BASIC Basic domain 30.2 7.9 0.00017 23.5 -1.5 10 9-18 72-81 (91)
116 PF10955 DUF2757: Protein of u 30.1 39 0.00084 19.7 1.5 12 9-20 4-15 (76)
117 PRK11032 hypothetical protein; 29.7 43 0.00094 21.7 1.8 16 5-20 120-135 (160)
118 PF13730 HTH_36: Helix-turn-he 29.4 55 0.0012 16.2 1.9 12 32-43 40-51 (55)
119 PRK00398 rpoP DNA-directed RNA 29.4 42 0.00091 16.8 1.4 11 10-20 4-14 (46)
120 PRK14890 putative Zn-ribbon RN 29.4 16 0.00034 20.6 -0.3 10 9-18 36-45 (59)
121 PRK12577 succinate dehydrogena 29.1 19 0.00042 24.9 0.1 12 7-18 206-217 (329)
122 PF13248 zf-ribbon_3: zinc-rib 28.9 20 0.00043 16.3 0.1 12 11-22 4-15 (26)
123 smart00659 RPOLCX RNA polymera 28.6 43 0.00094 17.2 1.4 11 10-20 3-13 (44)
124 PF10263 SprT-like: SprT-like 28.5 40 0.00087 20.0 1.4 13 7-19 121-133 (157)
125 KOG3816 Cell differentiation r 28.4 15 0.00032 28.0 -0.6 22 8-29 436-459 (526)
126 COG0052 RpsB Ribosomal protein 28.2 35 0.00076 23.9 1.3 34 12-45 84-118 (252)
127 PF09365 DUF2461: Conserved hy 28.1 56 0.0012 21.4 2.2 25 15-39 105-129 (212)
128 PF12756 zf-C2H2_2: C2H2 type 28.1 44 0.00096 17.7 1.4 11 10-20 51-61 (100)
129 COG1110 Reverse gyrase [DNA re 28.0 23 0.0005 29.6 0.4 35 9-45 694-733 (1187)
130 COG1779 C4-type Zn-finger prot 27.8 52 0.0011 22.4 2.0 18 3-20 37-54 (201)
131 PHA00689 hypothetical protein 27.4 22 0.00047 20.1 0.1 17 11-27 19-40 (62)
132 PF14952 zf-tcix: Putative tre 27.2 25 0.00053 18.9 0.3 11 7-17 9-19 (44)
133 COG3364 Zn-ribbon containing p 27.1 25 0.00055 22.1 0.4 12 11-22 4-15 (112)
134 KOG2462 C2H2-type Zn-finger pr 26.1 12 0.00027 26.5 -1.3 14 10-23 244-257 (279)
135 PHA02942 putative transposase; 25.6 44 0.00095 23.8 1.4 14 6-19 339-352 (383)
136 KOG1873 Ubiquitin-specific pro 25.6 41 0.00089 27.4 1.3 20 8-27 92-111 (877)
137 PF10825 DUF2752: Protein of u 25.6 13 0.00029 19.5 -0.9 13 5-18 6-18 (52)
138 TIGR02300 FYDLN_acid conserved 25.5 28 0.00062 22.2 0.4 11 10-20 10-20 (129)
139 PHA02611 51 baseplate hub asse 25.3 35 0.00076 23.8 0.8 9 10-18 83-91 (249)
140 PRK13552 frdB fumarate reducta 25.3 23 0.0005 23.6 -0.0 12 7-18 203-214 (239)
141 cd07153 Fur_like Ferric uptake 25.2 44 0.00095 18.8 1.1 11 10-20 74-84 (116)
142 PRK04351 hypothetical protein; 24.7 49 0.0011 20.9 1.4 11 9-19 112-122 (149)
143 smart00064 FYVE Protein presen 24.6 30 0.00066 18.1 0.4 14 11-24 28-41 (68)
144 PRK05950 sdhB succinate dehydr 24.5 27 0.00059 22.7 0.2 32 7-44 195-226 (232)
145 PF01155 HypA: Hydrogenase exp 24.5 68 0.0015 19.0 1.9 18 8-25 69-86 (113)
146 PF01831 Peptidase_C16: Peptid 24.4 16 0.00036 25.5 -0.9 14 5-18 108-121 (249)
147 PRK09710 lar restriction allev 24.4 90 0.002 17.7 2.3 20 7-29 25-44 (64)
148 TIGR02453 conserved hypothetic 24.3 69 0.0015 21.2 2.1 24 16-39 107-130 (217)
149 COG0777 AccD Acetyl-CoA carbox 24.2 38 0.00083 24.3 0.9 13 7-19 25-38 (294)
150 PRK08640 sdhB succinate dehydr 24.1 31 0.00068 23.1 0.4 32 6-43 205-236 (249)
151 PF12322 T4_baseplate: T4 bact 24.0 48 0.001 21.9 1.3 11 9-19 78-88 (205)
152 KOG1973 Chromatin remodeling p 23.9 20 0.00044 24.3 -0.5 12 7-18 257-268 (274)
153 PF13453 zf-TFIIB: Transcripti 23.8 70 0.0015 15.6 1.6 13 6-18 16-28 (41)
154 TIGR02760 TraI_TIGR conjugativ 23.6 37 0.0008 29.2 0.8 35 6-42 1602-1637(1960)
155 KOG3960 Myogenic helix-loop-he 23.2 18 0.0004 25.8 -0.9 33 9-46 103-135 (284)
156 TIGR03037 anthran_nbaC 3-hydro 22.9 1.3E+02 0.0027 19.6 3.0 34 9-43 114-147 (159)
157 PF01475 FUR: Ferric uptake re 22.1 52 0.0011 18.8 1.1 12 9-20 80-91 (120)
158 cd00065 FYVE FYVE domain; Zinc 21.9 37 0.00081 17.0 0.4 17 11-27 20-36 (57)
159 PRK12575 succinate dehydrogena 21.3 33 0.00071 23.0 0.1 31 7-43 198-228 (235)
160 COG1656 Uncharacterized conser 21.2 48 0.001 21.9 0.9 36 3-43 124-159 (165)
161 TIGR00100 hypA hydrogenase nic 21.1 68 0.0015 19.1 1.4 18 8-25 69-86 (115)
162 PF04475 DUF555: Protein of un 21.1 34 0.00074 21.2 0.1 16 4-19 42-57 (102)
163 PF01428 zf-AN1: AN1-like Zinc 21.0 63 0.0014 16.0 1.1 11 11-21 15-25 (43)
164 PF08134 cIII: cIII protein fa 20.4 1.3E+02 0.0029 16.0 2.3 28 18-45 5-37 (44)
165 COG1594 RPB9 DNA-directed RNA 20.4 71 0.0015 19.2 1.4 11 9-19 100-110 (113)
166 smart00731 SprT SprT homologue 20.1 54 0.0012 19.9 0.8 13 7-19 110-122 (146)
167 PF03367 zf-ZPR1: ZPR1 zinc-fi 20.0 71 0.0015 20.3 1.4 19 9-27 30-52 (161)
No 1
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=99.92 E-value=1.1e-25 Score=134.98 Aligned_cols=45 Identities=51% Similarity=0.738 Sum_probs=42.1
Q ss_pred ceeeEEEEEeeCCCCeeEEcccccccccHHHHHHHHHHHHHhhhh
Q 040416 2 AVRKAVGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLREQTE 46 (47)
Q Consensus 2 ~~R~avGIW~C~~C~~~~AGGAy~~~T~~a~tvk~~irrl~e~~e 46 (47)
|+|+++|||+|++|+++||||||+|+||++.+|+++|+||+|++|
T Consensus 46 vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~~~i~rl~e~~e 90 (90)
T PF01780_consen 46 VKRVATGIWKCKKCGKKFAGGAYTPSTPAAKTVKRAIRRLRELKE 90 (90)
T ss_dssp EEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHHHHHHHHHHHH
T ss_pred eEEeeeEEeecCCCCCEEeCCCccccchHHHHHHHHHHHHHHhcC
Confidence 799999999999999999999999999999999999999999987
No 2
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=99.92 E-value=2.6e-25 Score=133.66 Aligned_cols=46 Identities=41% Similarity=0.637 Sum_probs=44.7
Q ss_pred ceeeEEEEEeeCCCCeeEEcccccccccHHHHHHHHHHHHHhhhhC
Q 040416 2 AVRKAVGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLREQTES 47 (47)
Q Consensus 2 ~~R~avGIW~C~~C~~~~AGGAy~~~T~~a~tvk~~irrl~e~~e~ 47 (47)
|+|.++|||+|++||++||||||+|+||++.++.++|+||+|++|+
T Consensus 46 vkR~a~GIW~C~~C~~~~AGGAy~p~T~~~~t~~~~irrl~e~~~~ 91 (91)
T TIGR00280 46 VKRGSTGIWTCRKCGAKFAGGAYTPVTPAGKTVRKTIRRIVEMKEA 91 (91)
T ss_pred eEEEeeEEEEcCCCCCEEeCCccccccchhHHHHHHHHHHHHhhcC
Confidence 7999999999999999999999999999999999999999999874
No 3
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=99.90 E-value=3.4e-24 Score=128.55 Aligned_cols=44 Identities=55% Similarity=0.841 Sum_probs=42.7
Q ss_pred ceeeEEEEEeeCCCCeeEEcccccccccHHHHHHHHHHHHHhhh
Q 040416 2 AVRKAVGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLREQT 45 (47)
Q Consensus 2 ~~R~avGIW~C~~C~~~~AGGAy~~~T~~a~tvk~~irrl~e~~ 45 (47)
|+|.++|||+|++|+++||||||+|+||+++++.++|+||+|++
T Consensus 47 vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~~~irr~~e~~ 90 (90)
T PTZ00255 47 VKRQAVGIWRCKGCKKTVAGGAWTLSTPAASTVRSTIRRLRKLK 90 (90)
T ss_pred eeeeeeEEEEcCCCCCEEeCCccccccchhHHHHHHHHHHHhcC
Confidence 79999999999999999999999999999999999999999974
No 4
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=99.89 E-value=9e-24 Score=126.70 Aligned_cols=43 Identities=37% Similarity=0.596 Sum_probs=41.9
Q ss_pred ceeeEEEEEeeCCCCeeEEcccccccccHHHHHHHHHHHHHhh
Q 040416 2 AVRKAVGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLREQ 44 (47)
Q Consensus 2 ~~R~avGIW~C~~C~~~~AGGAy~~~T~~a~tvk~~irrl~e~ 44 (47)
|+|.++|||+|++|+++||||||+|+||++.++.++|+||+|.
T Consensus 47 vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~~~irr~~~~ 89 (90)
T PRK03976 47 VKRVGTGIWECRKCGAKFAGGAYTPETPAGKTVTRAIRRAVEE 89 (90)
T ss_pred eEEEEEEEEEcCCCCCEEeCCccccccchhhhHHHHHHHHhhc
Confidence 7999999999999999999999999999999999999999985
No 5
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=99.87 E-value=6.9e-23 Score=123.59 Aligned_cols=47 Identities=57% Similarity=0.856 Sum_probs=45.2
Q ss_pred CceeeEEEEEeeCCCCeeEEcccccccccHHHHHHHHHHHHHhhhhC
Q 040416 1 YAVRKAVGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLREQTES 47 (47)
Q Consensus 1 ~~~R~avGIW~C~~C~~~~AGGAy~~~T~~a~tvk~~irrl~e~~e~ 47 (47)
+|+|.|+|||.|++|+++||||||+++|++|.+++++||||||++|+
T Consensus 46 ~vKR~AvGiW~C~~C~kv~agga~~~~t~aa~t~rs~irrlre~~e~ 92 (92)
T KOG0402|consen 46 TVKRKAVGIWKCGSCKKVVAGGAYTVTTAAAATVRSTIRRLRELVEQ 92 (92)
T ss_pred hhhhhceeEEecCCccceeccceEEeccchhHHHHHHHHHHHHHhcC
Confidence 47999999999999999999999999999999999999999999885
No 6
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=99.83 E-value=3.3e-21 Score=115.90 Aligned_cols=45 Identities=38% Similarity=0.532 Sum_probs=43.0
Q ss_pred CceeeEEEEEeeCCCCeeEEcccccccccHHHHHHHHHHHHHhhh
Q 040416 1 YAVRKAVGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLREQT 45 (47)
Q Consensus 1 ~~~R~avGIW~C~~C~~~~AGGAy~~~T~~a~tvk~~irrl~e~~ 45 (47)
.|+|.++|||.|++||++||||||+|.|+++++++++|+|+.|.+
T Consensus 45 ~VkR~a~GIW~C~kCg~~fAGgay~P~t~~~k~~~~~i~r~~e~k 89 (89)
T COG1997 45 TVKRIATGIWKCRKCGAKFAGGAYTPVTPAGKAVKRTIRREVEMK 89 (89)
T ss_pred ceeeeccCeEEcCCCCCeeccccccccchHHHHHHHHHHHHhccC
Confidence 489999999999999999999999999999999999999999864
No 7
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=88.50 E-value=0.38 Score=23.76 Aligned_cols=15 Identities=20% Similarity=0.665 Sum_probs=13.0
Q ss_pred EEeeCCCCeeEEccc
Q 040416 9 IWGCKDSSKVKAGGA 23 (47)
Q Consensus 9 IW~C~~C~~~~AGGA 23 (47)
+|.|..||+++-|..
T Consensus 2 ~~~C~~CG~i~~g~~ 16 (34)
T cd00729 2 VWVCPVCGYIHEGEE 16 (34)
T ss_pred eEECCCCCCEeECCc
Confidence 699999999998753
No 8
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=86.51 E-value=0.34 Score=31.63 Aligned_cols=13 Identities=23% Similarity=0.708 Sum_probs=12.6
Q ss_pred EEeeCCCCeeEEc
Q 040416 9 IWGCKDSSKVKAG 21 (47)
Q Consensus 9 IW~C~~C~~~~AG 21 (47)
+|.|+.||+++.|
T Consensus 134 ~~vC~vCGy~~~g 146 (166)
T COG1592 134 VWVCPVCGYTHEG 146 (166)
T ss_pred EEEcCCCCCcccC
Confidence 8999999999998
No 9
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=85.94 E-value=0.69 Score=19.88 Aligned_cols=11 Identities=18% Similarity=0.323 Sum_probs=9.6
Q ss_pred EeeCCCCeeEE
Q 040416 10 WGCKDSSKVKA 20 (47)
Q Consensus 10 W~C~~C~~~~A 20 (47)
+.|..|++.|.
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 68999999985
No 10
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=84.63 E-value=0.74 Score=19.16 Aligned_cols=11 Identities=18% Similarity=0.259 Sum_probs=7.7
Q ss_pred EeeCCCCeeEE
Q 040416 10 WGCKDSSKVKA 20 (47)
Q Consensus 10 W~C~~C~~~~A 20 (47)
|.|..|+++|.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 78999999875
No 11
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=84.42 E-value=0.58 Score=22.69 Aligned_cols=14 Identities=14% Similarity=0.278 Sum_probs=11.8
Q ss_pred EEeeCCCCeeEEcc
Q 040416 9 IWGCKDSSKVKAGG 22 (47)
Q Consensus 9 IW~C~~C~~~~AGG 22 (47)
+|.|+.||++.-+.
T Consensus 1 ~~~C~~CGy~y~~~ 14 (33)
T cd00350 1 KYVCPVCGYIYDGE 14 (33)
T ss_pred CEECCCCCCEECCC
Confidence 59999999988764
No 12
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=82.95 E-value=0.64 Score=25.73 Aligned_cols=10 Identities=20% Similarity=0.840 Sum_probs=8.8
Q ss_pred EeeCCCCeeE
Q 040416 10 WGCKDSSKVK 19 (47)
Q Consensus 10 W~C~~C~~~~ 19 (47)
|.|.+||+|-
T Consensus 38 ~~CGkCgyTe 47 (51)
T COG1998 38 WACGKCGYTE 47 (51)
T ss_pred eEeccccceE
Confidence 9999999873
No 13
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=78.03 E-value=1.8 Score=18.86 Aligned_cols=12 Identities=17% Similarity=0.257 Sum_probs=10.4
Q ss_pred EeeCCCCeeEEc
Q 040416 10 WGCKDSSKVKAG 21 (47)
Q Consensus 10 W~C~~C~~~~AG 21 (47)
|.|.-|+++|..
T Consensus 1 ~~C~~C~~~f~s 12 (25)
T PF12874_consen 1 FYCDICNKSFSS 12 (25)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCCcCC
Confidence 889999999864
No 14
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=77.55 E-value=1.7 Score=25.14 Aligned_cols=35 Identities=14% Similarity=0.259 Sum_probs=20.8
Q ss_pred EEEeeCCCCeeEEccccccc-ccHHHHHHHHHHHHHhh
Q 040416 8 GIWGCKDSSKVKAGGAYTLN-IGSAVTARVTIRRLREQ 44 (47)
Q Consensus 8 GIW~C~~C~~~~AGGAy~~~-T~~a~tvk~~irrl~e~ 44 (47)
++|+|-.||+ .|.+..+- .--..+++.|++.|.+.
T Consensus 53 ~~~~Cf~Cg~--~Gd~i~~v~~~~~~~f~eAv~~l~~~ 88 (97)
T PF01807_consen 53 NRFKCFGCGK--GGDVIDFVMKYEGCSFKEAVKWLAEE 88 (97)
T ss_dssp TEEEETTT----EE-HHHHHHHHHT--HHHHHHHHHHH
T ss_pred CeEEECCCCC--CCcHHhHHHHHhCCCHHHHHHHHHHH
Confidence 7899999995 46666553 23345677788877664
No 15
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=75.19 E-value=2.3 Score=19.40 Aligned_cols=11 Identities=18% Similarity=0.353 Sum_probs=9.7
Q ss_pred EeeCCCCeeEE
Q 040416 10 WGCKDSSKVKA 20 (47)
Q Consensus 10 W~C~~C~~~~A 20 (47)
..|..|++.|+
T Consensus 15 ~~C~~C~k~F~ 25 (26)
T PF13465_consen 15 YKCPYCGKSFS 25 (26)
T ss_dssp EEESSSSEEES
T ss_pred CCCCCCcCeeC
Confidence 68999999985
No 16
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=73.28 E-value=2.2 Score=22.28 Aligned_cols=12 Identities=17% Similarity=0.501 Sum_probs=9.9
Q ss_pred EEeeCCCCeeEE
Q 040416 9 IWGCKDSSKVKA 20 (47)
Q Consensus 9 IW~C~~C~~~~A 20 (47)
-|.|..||..+-
T Consensus 28 ~W~C~~Cgh~w~ 39 (55)
T PF14311_consen 28 WWKCPKCGHEWK 39 (55)
T ss_pred EEECCCCCCeeE
Confidence 499999988764
No 17
>smart00400 ZnF_CHCC zinc finger.
Probab=68.71 E-value=2.2 Score=22.21 Aligned_cols=17 Identities=12% Similarity=0.341 Sum_probs=11.8
Q ss_pred EEEEeeCCCCeeEEccccc
Q 040416 7 VGIWGCKDSSKVKAGGAYT 25 (47)
Q Consensus 7 vGIW~C~~C~~~~AGGAy~ 25 (47)
-++|+|-.|++ .|++-.
T Consensus 21 kn~~~Cf~cg~--gGd~i~ 37 (55)
T smart00400 21 KQFFHCFGCGA--GGNVIS 37 (55)
T ss_pred CCEEEEeCCCC--CCCHHH
Confidence 47899999984 444433
No 18
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=68.30 E-value=4 Score=17.99 Aligned_cols=11 Identities=18% Similarity=0.576 Sum_probs=9.4
Q ss_pred EeeCCCCeeEE
Q 040416 10 WGCKDSSKVKA 20 (47)
Q Consensus 10 W~C~~C~~~~A 20 (47)
-.|..|+++|.
T Consensus 2 ~~C~~C~~~F~ 12 (27)
T PF13912_consen 2 FECDECGKTFS 12 (27)
T ss_dssp EEETTTTEEES
T ss_pred CCCCccCCccC
Confidence 57999999985
No 19
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=68.30 E-value=3.6 Score=25.29 Aligned_cols=15 Identities=27% Similarity=0.738 Sum_probs=13.2
Q ss_pred EEeeCCCCeeEEccc
Q 040416 9 IWGCKDSSKVKAGGA 23 (47)
Q Consensus 9 IW~C~~C~~~~AGGA 23 (47)
.|.|.+||+.+=.|.
T Consensus 124 f~~C~~C~kiyW~Gs 138 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGS 138 (147)
T ss_pred EEECCCCCCEecccc
Confidence 799999999987764
No 20
>PF02977 CarbpepA_inh: Carboxypeptidase A inhibitor; InterPro: IPR004231 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This family is represented by the well-characterised metallocarboxypeptidase A inhibitor (MCPI) from potatoes, which belongs to the MEROPS inhibitor family I37, clan IE. It inhibits metallopeptidases belonging to MEROPS peptidase family M14, carboxypeptidase A. In Russet Burbank potatoes, it is a mixture of approximately equal amounts of two polypeptide chains containing 38 or 39 amino acid residues. The chains differ in their amino terminal sequence only [] and are resistant to fragmentation by proteases []. The structure of the complex between bovine carboxypeptidase A and the 39-amino-acid carboxypeptidase A inhibitor from potatoes has been determined at 2.5-A resolution []. The potato inhibitor is synthesised as a precursor, having a 29 residue N-terminal signal peptide, a 27 residue pro-peptide, the 39 residue mature inhibitor region and a 7 residue C-terminal extension. The 7 residue C-terminal extension is involved in inhibitor inactivation and may be required for targeting to the vacuole where the mature active inhibitor accumulates []. The N-terminal region and the mature inhibitor are weakly related to other solananaceous proteins found in this entry, from potato, tomato and henbane, which have been incorrectly described as metallocarboxipeptidase inhibitors [].; GO: 0008191 metalloendopeptidase inhibitor activity; PDB: 4CPA_I 1H20_A 2HLG_A.
Probab=67.92 E-value=0.73 Score=25.01 Aligned_cols=22 Identities=27% Similarity=0.279 Sum_probs=16.0
Q ss_pred EEEEeeCCC-CeeEEcccccccc
Q 040416 7 VGIWGCKDS-SKVKAGGAYTLNI 28 (47)
Q Consensus 7 vGIW~C~~C-~~~~AGGAy~~~T 28 (47)
.|||-|.-| +.+..+|-|+.++
T Consensus 19 ~g~tlC~~C~k~~~t~~g~~~~~ 41 (46)
T PF02977_consen 19 SGITLCQWCWKLKKTCGGYVGSA 41 (46)
T ss_dssp TTSSSS-EE-CCCEBCC--EEEE
T ss_pred cceeehHHHHhcccCCCCcccce
Confidence 589999999 8888888887765
No 21
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=67.04 E-value=3.7 Score=20.48 Aligned_cols=17 Identities=12% Similarity=0.305 Sum_probs=13.6
Q ss_pred EeeCCCCeeEEcccccc
Q 040416 10 WGCKDSSKVKAGGAYTL 26 (47)
Q Consensus 10 W~C~~C~~~~AGGAy~~ 26 (47)
-.|..|++.++.+-|.|
T Consensus 5 ~~C~nC~R~v~a~RfA~ 21 (33)
T PF08209_consen 5 VECPNCGRPVAASRFAP 21 (33)
T ss_dssp EE-TTTSSEEEGGGHHH
T ss_pred EECCCCcCCcchhhhHH
Confidence 47999999999987765
No 22
>PHA00626 hypothetical protein
Probab=67.01 E-value=3 Score=23.66 Aligned_cols=18 Identities=17% Similarity=0.255 Sum_probs=15.2
Q ss_pred EEEeeCCCCeeEEccccc
Q 040416 8 GIWGCKDSSKVKAGGAYT 25 (47)
Q Consensus 8 GIW~C~~C~~~~AGGAy~ 25 (47)
.-..|+.||+.|.-.|+-
T Consensus 22 nrYkCkdCGY~ft~~~~~ 39 (59)
T PHA00626 22 DDYVCCDCGYNDSKDAFG 39 (59)
T ss_pred cceEcCCCCCeechhhhh
Confidence 568999999999887764
No 23
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=66.99 E-value=3.3 Score=21.39 Aligned_cols=17 Identities=29% Similarity=0.812 Sum_probs=8.4
Q ss_pred eeEEEEEeeCCCCeeEEc
Q 040416 4 RKAVGIWGCKDSSKVKAG 21 (47)
Q Consensus 4 R~avGIW~C~~C~~~~AG 21 (47)
+...|-|.|..|+. .+|
T Consensus 21 ~~~~G~~~C~~C~~-~~G 37 (40)
T PF08273_consen 21 KDGRGTWICRQCGG-DAG 37 (40)
T ss_dssp ----S-EEETTTTB-E--
T ss_pred cccCCCEECCCCCC-cCC
Confidence 34568999999955 444
No 24
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=66.94 E-value=3.2 Score=22.07 Aligned_cols=12 Identities=17% Similarity=0.584 Sum_probs=10.1
Q ss_pred EEEeeCCCCeeE
Q 040416 8 GIWGCKDSSKVK 19 (47)
Q Consensus 8 GIW~C~~C~~~~ 19 (47)
+-|.|.+||.+.
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 579999999875
No 25
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=65.97 E-value=7.1 Score=19.05 Aligned_cols=18 Identities=33% Similarity=0.514 Sum_probs=14.3
Q ss_pred eeCCCCeeEEcccccccc
Q 040416 11 GCKDSSKVKAGGAYTLNI 28 (47)
Q Consensus 11 ~C~~C~~~~AGGAy~~~T 28 (47)
.|=.|++.|.|..|.-.|
T Consensus 2 sCiDC~~~F~~~~y~~Ht 19 (28)
T PF08790_consen 2 SCIDCSKDFDGDSYKSHT 19 (28)
T ss_dssp EETTTTEEEEGGGTTT--
T ss_pred eeecCCCCcCcCCcCCCC
Confidence 588999999999997655
No 26
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=65.70 E-value=2.6 Score=26.06 Aligned_cols=13 Identities=15% Similarity=0.268 Sum_probs=11.0
Q ss_pred EEeeCCCCeeEEc
Q 040416 9 IWGCKDSSKVKAG 21 (47)
Q Consensus 9 IW~C~~C~~~~AG 21 (47)
=|.|++|+++|.=
T Consensus 53 RyrC~~C~~tf~~ 65 (129)
T COG3677 53 RYKCKSCGSTFTV 65 (129)
T ss_pred ccccCCcCcceee
Confidence 3899999999963
No 27
>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=65.32 E-value=5.4 Score=19.93 Aligned_cols=11 Identities=9% Similarity=0.265 Sum_probs=9.0
Q ss_pred EeeCCCCeeEE
Q 040416 10 WGCKDSSKVKA 20 (47)
Q Consensus 10 W~C~~C~~~~A 20 (47)
|.|.+||+++-
T Consensus 2 r~C~~Cg~~Yh 12 (36)
T PF05191_consen 2 RICPKCGRIYH 12 (36)
T ss_dssp EEETTTTEEEE
T ss_pred cCcCCCCCccc
Confidence 78999998763
No 28
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=65.01 E-value=3.7 Score=24.68 Aligned_cols=18 Identities=22% Similarity=0.499 Sum_probs=12.8
Q ss_pred EEEEeeCCCCeeEEcccc
Q 040416 7 VGIWGCKDSSKVKAGGAY 24 (47)
Q Consensus 7 vGIW~C~~C~~~~AGGAy 24 (47)
.|-|.|.+|++.+.---|
T Consensus 35 ~~~y~C~~C~~~~~~~~~ 52 (146)
T PF08646_consen 35 DGSYRCEKCNKTVENPKY 52 (146)
T ss_dssp TTEEEETTTTEEESS-EE
T ss_pred CcEEECCCCCCcCCCeeE
Confidence 478999999988754433
No 29
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=64.62 E-value=3.5 Score=20.96 Aligned_cols=12 Identities=33% Similarity=0.592 Sum_probs=9.6
Q ss_pred EEEEeeCCCCee
Q 040416 7 VGIWGCKDSSKV 18 (47)
Q Consensus 7 vGIW~C~~C~~~ 18 (47)
.+.|+|++|++.
T Consensus 35 ~~~~~C~~C~~q 46 (46)
T PF12760_consen 35 RGRYRCKACRKQ 46 (46)
T ss_pred CCeEECCCCCCc
Confidence 378999999863
No 30
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=63.46 E-value=3.8 Score=26.84 Aligned_cols=18 Identities=11% Similarity=0.434 Sum_probs=15.3
Q ss_pred EEEeeCCCCeeEEccccc
Q 040416 8 GIWGCKDSSKVKAGGAYT 25 (47)
Q Consensus 8 GIW~C~~C~~~~AGGAy~ 25 (47)
-||.|+.||+.+.-.-+.
T Consensus 47 ~V~vCP~CgyA~~~~~F~ 64 (214)
T PF09986_consen 47 EVWVCPHCGYAAFEEDFE 64 (214)
T ss_pred eEEECCCCCCcccccccc
Confidence 589999999998877665
No 31
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=62.79 E-value=6.2 Score=24.35 Aligned_cols=15 Identities=7% Similarity=0.218 Sum_probs=12.8
Q ss_pred EEEeeCCCCeeEEcc
Q 040416 8 GIWGCKDSSKVKAGG 22 (47)
Q Consensus 8 GIW~C~~C~~~~AGG 22 (47)
..|.|..||+.|.-.
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 679999999998764
No 32
>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=62.50 E-value=4.5 Score=21.74 Aligned_cols=9 Identities=11% Similarity=0.169 Sum_probs=7.0
Q ss_pred EeeCCCCee
Q 040416 10 WGCKDSSKV 18 (47)
Q Consensus 10 W~C~~C~~~ 18 (47)
|.|.+|+.|
T Consensus 39 ~~CGKCg~T 47 (47)
T PF01599_consen 39 HYCGKCGYT 47 (47)
T ss_dssp EEETTTSS-
T ss_pred ccCCCcccC
Confidence 889999875
No 33
>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=62.22 E-value=3.9 Score=19.78 Aligned_cols=15 Identities=13% Similarity=0.113 Sum_probs=11.7
Q ss_pred EEEEEeeCCCCeeEE
Q 040416 6 AVGIWGCKDSSKVKA 20 (47)
Q Consensus 6 avGIW~C~~C~~~~A 20 (47)
.+--|.|..||..+-
T Consensus 29 ~vp~~~C~~CGE~~~ 43 (46)
T TIGR03831 29 NVPALVCPQCGEEYL 43 (46)
T ss_pred CCCccccccCCCEee
Confidence 345699999998764
No 34
>PF01586 Basic: Myogenic Basic domain; InterPro: IPR002546 This basic domain is found in the MyoD family of muscle specific proteins that control muscle development. The bHLH region of the MyoD family includes the basic domain and the Helix-loop-helix (HLH) motif. The bHLH region mediates specific DNA binding []. With 12 residues of the basic domain involved in DNA binding []. The basic domain forms an extended alpha helix in the structure.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007517 muscle organ development, 0005634 nucleus; PDB: 1MDY_C.
Probab=62.17 E-value=2.7 Score=25.05 Aligned_cols=11 Identities=27% Similarity=1.005 Sum_probs=0.9
Q ss_pred EEeeCCCCeeE
Q 040416 9 IWGCKDSSKVK 19 (47)
Q Consensus 9 IW~C~~C~~~~ 19 (47)
+|-||.|+++-
T Consensus 72 ~WACKaCKRKt 82 (86)
T PF01586_consen 72 LWACKACKRKT 82 (86)
T ss_dssp -------S---
T ss_pred HHHhHhhhccC
Confidence 69999999873
No 35
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=62.14 E-value=6.9 Score=21.44 Aligned_cols=18 Identities=17% Similarity=0.350 Sum_probs=13.5
Q ss_pred eeeEEEEEeeCCCCeeEE
Q 040416 3 VRKAVGIWGCKDSSKVKA 20 (47)
Q Consensus 3 ~R~avGIW~C~~C~~~~A 20 (47)
.+...|||+|.+....+.
T Consensus 5 g~~~~g~w~~~pg~~~~~ 22 (74)
T PF05899_consen 5 GVFSAGVWECTPGKFPWP 22 (74)
T ss_dssp TSEEEEEEEEECEEEEEE
T ss_pred CCEEEEEEEECCceeEee
Confidence 356899999998765544
No 36
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=61.05 E-value=4.4 Score=18.83 Aligned_cols=11 Identities=27% Similarity=0.824 Sum_probs=9.2
Q ss_pred EEEeeCCCCee
Q 040416 8 GIWGCKDSSKV 18 (47)
Q Consensus 8 GIW~C~~C~~~ 18 (47)
|-|.|..|...
T Consensus 3 g~W~C~~C~~~ 13 (30)
T PF00641_consen 3 GDWKCPSCTFM 13 (30)
T ss_dssp SSEEETTTTEE
T ss_pred cCccCCCCcCC
Confidence 56999999865
No 37
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=60.49 E-value=11 Score=24.85 Aligned_cols=20 Identities=15% Similarity=0.360 Sum_probs=17.7
Q ss_pred EEEeeCCCCeeEEccccccc
Q 040416 8 GIWGCKDSSKVKAGGAYTLN 27 (47)
Q Consensus 8 GIW~C~~C~~~~AGGAy~~~ 27 (47)
-|=.|+.||.-+-+|.|...
T Consensus 34 ~v~~C~~Cg~~~~~~~W~~~ 53 (236)
T PF04981_consen 34 EVTICPKCGRYRIGGRWVDP 53 (236)
T ss_pred CceECCCCCCEECCCEeeec
Confidence 35579999999999999987
No 38
>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=60.26 E-value=6.9 Score=19.92 Aligned_cols=12 Identities=8% Similarity=0.529 Sum_probs=7.7
Q ss_pred EEEeeCCCCeeE
Q 040416 8 GIWGCKDSSKVK 19 (47)
Q Consensus 8 GIW~C~~C~~~~ 19 (47)
-|++|..||..+
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 489999999887
No 39
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=58.07 E-value=3.6 Score=25.31 Aligned_cols=11 Identities=18% Similarity=0.175 Sum_probs=9.1
Q ss_pred eeCCCCeeEEc
Q 040416 11 GCKDSSKVKAG 21 (47)
Q Consensus 11 ~C~~C~~~~AG 21 (47)
.|++||+.|-.
T Consensus 60 ~CkkCGfef~~ 70 (97)
T COG3357 60 RCKKCGFEFRD 70 (97)
T ss_pred hhcccCccccc
Confidence 59999998854
No 40
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=57.70 E-value=5.7 Score=18.20 Aligned_cols=11 Identities=9% Similarity=0.057 Sum_probs=9.1
Q ss_pred eeCCCCeeEEc
Q 040416 11 GCKDSSKVKAG 21 (47)
Q Consensus 11 ~C~~C~~~~AG 21 (47)
.|..||.+|.=
T Consensus 4 ~C~~CgR~F~~ 14 (25)
T PF13913_consen 4 PCPICGRKFNP 14 (25)
T ss_pred cCCCCCCEECH
Confidence 59999999953
No 41
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=57.64 E-value=3.6 Score=18.34 Aligned_cols=11 Identities=27% Similarity=0.815 Sum_probs=8.3
Q ss_pred EEEeeCCCCee
Q 040416 8 GIWGCKDSSKV 18 (47)
Q Consensus 8 GIW~C~~C~~~ 18 (47)
|-|.|..|+..
T Consensus 1 g~W~C~~C~~~ 11 (26)
T smart00547 1 GDWECPACTFL 11 (26)
T ss_pred CcccCCCCCCc
Confidence 46999999753
No 42
>COG1773 Rubredoxin [Energy production and conversion]
Probab=55.23 E-value=8.3 Score=21.36 Aligned_cols=11 Identities=27% Similarity=0.582 Sum_probs=9.1
Q ss_pred EEeeCCCCeeE
Q 040416 9 IWGCKDSSKVK 19 (47)
Q Consensus 9 IW~C~~C~~~~ 19 (47)
-|+|+-||+.+
T Consensus 3 ~~~C~~CG~vY 13 (55)
T COG1773 3 RWRCSVCGYVY 13 (55)
T ss_pred ceEecCCceEe
Confidence 38999999875
No 43
>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=54.56 E-value=4.7 Score=22.64 Aligned_cols=9 Identities=11% Similarity=0.512 Sum_probs=6.8
Q ss_pred EeeCCCCee
Q 040416 10 WGCKDSSKV 18 (47)
Q Consensus 10 W~C~~C~~~ 18 (47)
|.|.|||.+
T Consensus 1 y~C~KCg~~ 9 (64)
T PF09855_consen 1 YKCPKCGNE 9 (64)
T ss_pred CCCCCCCCc
Confidence 678888864
No 44
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=54.12 E-value=3.4 Score=29.28 Aligned_cols=11 Identities=36% Similarity=0.963 Sum_probs=9.5
Q ss_pred EEEeeCCCCee
Q 040416 8 GIWGCKDSSKV 18 (47)
Q Consensus 8 GIW~C~~C~~~ 18 (47)
|+|.|+.|.+.
T Consensus 260 G~WYC~eCk~~ 270 (271)
T COG5034 260 GKWYCPECKKA 270 (271)
T ss_pred CcEeCHHhHhc
Confidence 89999999763
No 45
>PF14443 DBC1: DBC1
Probab=53.94 E-value=15 Score=23.34 Aligned_cols=28 Identities=25% Similarity=0.419 Sum_probs=21.2
Q ss_pred eEEccccccc-------ccHHHHHHHHHHHHHhhh
Q 040416 18 VKAGGAYTLN-------IGSAVTARVTIRRLREQT 45 (47)
Q Consensus 18 ~~AGGAy~~~-------T~~a~tvk~~irrl~e~~ 45 (47)
.-.||.|+|+ .-...-++-|||-.|++.
T Consensus 20 ~aiGG~WspsLDG~DP~~dp~~LI~TAiR~~K~~t 54 (126)
T PF14443_consen 20 MAIGGPWSPSLDGGDPSSDPSVLIRTAIRTCKALT 54 (126)
T ss_pred EecCCcCCcccCCCCCCCCcHHHHHHHHHHHHHHh
Confidence 4469999987 225577888999988874
No 46
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=51.68 E-value=8.6 Score=18.97 Aligned_cols=10 Identities=20% Similarity=0.325 Sum_probs=7.2
Q ss_pred EeeCCCCeeE
Q 040416 10 WGCKDSSKVK 19 (47)
Q Consensus 10 W~C~~C~~~~ 19 (47)
=+|.+|+.+|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 3688888776
No 47
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=51.32 E-value=15 Score=17.58 Aligned_cols=13 Identities=8% Similarity=0.434 Sum_probs=11.1
Q ss_pred EEEeeCCCCeeEE
Q 040416 8 GIWGCKDSSKVKA 20 (47)
Q Consensus 8 GIW~C~~C~~~~A 20 (47)
.+++|..||..+.
T Consensus 3 ~~ykC~~CGniv~ 15 (34)
T cd00974 3 EVYKCEICGNIVE 15 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 4789999999885
No 48
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=50.99 E-value=11 Score=19.89 Aligned_cols=15 Identities=7% Similarity=0.270 Sum_probs=11.7
Q ss_pred eEEEEEeeCCCCeeE
Q 040416 5 KAVGIWGCKDSSKVK 19 (47)
Q Consensus 5 ~avGIW~C~~C~~~~ 19 (47)
...-+|.|..||..+
T Consensus 42 ~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 42 RSGRVFTCPNCGFEM 56 (69)
T ss_pred cccceEEcCCCCCEE
Confidence 345689999999874
No 49
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=50.00 E-value=7.1 Score=23.89 Aligned_cols=12 Identities=25% Similarity=0.661 Sum_probs=10.7
Q ss_pred EEEeeCCCCeeE
Q 040416 8 GIWGCKDSSKVK 19 (47)
Q Consensus 8 GIW~C~~C~~~~ 19 (47)
|.|.|.+|++.+
T Consensus 50 ~~~~C~~C~~~~ 61 (166)
T cd04476 50 GTYRCEKCNKSV 61 (166)
T ss_pred CcEECCCCCCcC
Confidence 789999999986
No 50
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=49.72 E-value=16 Score=17.35 Aligned_cols=13 Identities=8% Similarity=0.452 Sum_probs=11.4
Q ss_pred EEEeeCCCCeeEE
Q 040416 8 GIWGCKDSSKVKA 20 (47)
Q Consensus 8 GIW~C~~C~~~~A 20 (47)
.+++|..||..+.
T Consensus 6 ~~ykC~~Cgniv~ 18 (34)
T TIGR00319 6 QVYKCEVCGNIVE 18 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 5899999999885
No 51
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=49.58 E-value=11 Score=18.40 Aligned_cols=16 Identities=25% Similarity=0.071 Sum_probs=9.5
Q ss_pred EEEEeeCCCCeeEEcc
Q 040416 7 VGIWGCKDSSKVKAGG 22 (47)
Q Consensus 7 vGIW~C~~C~~~~AGG 22 (47)
.....|+.|++.+.++
T Consensus 14 ~~~a~C~~C~~~~~~~ 29 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYS 29 (45)
T ss_dssp SS-EEETTTTEE----
T ss_pred cCeEEeCCCCeEEeeC
Confidence 3567899999999997
No 52
>smart00355 ZnF_C2H2 zinc finger.
Probab=49.56 E-value=5.1 Score=16.37 Aligned_cols=11 Identities=27% Similarity=0.498 Sum_probs=8.5
Q ss_pred eeCCCCeeEEc
Q 040416 11 GCKDSSKVKAG 21 (47)
Q Consensus 11 ~C~~C~~~~AG 21 (47)
.|..|++.|..
T Consensus 2 ~C~~C~~~f~~ 12 (26)
T smart00355 2 RCPECGKVFKS 12 (26)
T ss_pred CCCCCcchhCC
Confidence 68889888754
No 53
>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=49.34 E-value=11 Score=17.99 Aligned_cols=11 Identities=18% Similarity=0.555 Sum_probs=8.8
Q ss_pred EeeCCCCeeEE
Q 040416 10 WGCKDSSKVKA 20 (47)
Q Consensus 10 W~C~~C~~~~A 20 (47)
..|.+||+.|-
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 47999999774
No 54
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=49.23 E-value=13 Score=19.31 Aligned_cols=15 Identities=7% Similarity=0.193 Sum_probs=11.6
Q ss_pred eEEEEEeeCCCCeeE
Q 040416 5 KAVGIWGCKDSSKVK 19 (47)
Q Consensus 5 ~avGIW~C~~C~~~~ 19 (47)
...|+|.|..|+...
T Consensus 22 ~~~~~~~C~~Cga~~ 36 (53)
T TIGR03655 22 DLSHYFECSTCGASG 36 (53)
T ss_pred CCEEEEECCCCCCCc
Confidence 356889999998763
No 55
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=48.99 E-value=13 Score=18.68 Aligned_cols=10 Identities=10% Similarity=0.481 Sum_probs=7.6
Q ss_pred EeeCCCCeeE
Q 040416 10 WGCKDSSKVK 19 (47)
Q Consensus 10 W~C~~C~~~~ 19 (47)
.+|.+||..|
T Consensus 6 y~C~~Cg~~f 15 (42)
T PF09723_consen 6 YRCEECGHEF 15 (42)
T ss_pred EEeCCCCCEE
Confidence 4788888766
No 56
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=48.27 E-value=6.3 Score=18.55 Aligned_cols=16 Identities=19% Similarity=0.289 Sum_probs=11.6
Q ss_pred EeeCCCCeeEEcc-ccc
Q 040416 10 WGCKDSSKVKAGG-AYT 25 (47)
Q Consensus 10 W~C~~C~~~~AGG-Ay~ 25 (47)
|.|.-|++++.|- .|.
T Consensus 1 ~~C~~C~~~~~~~~~Y~ 17 (30)
T PF03107_consen 1 FWCDVCRRKIDGFYFYH 17 (30)
T ss_pred CCCCCCCCCcCCCEeEE
Confidence 6778888887776 554
No 57
>PHA02768 hypothetical protein; Provisional
Probab=47.10 E-value=7.6 Score=21.40 Aligned_cols=13 Identities=8% Similarity=0.263 Sum_probs=10.1
Q ss_pred EeeCCCCeeEEcc
Q 040416 10 WGCKDSSKVKAGG 22 (47)
Q Consensus 10 W~C~~C~~~~AGG 22 (47)
..|..||+.|+-.
T Consensus 6 y~C~~CGK~Fs~~ 18 (55)
T PHA02768 6 YECPICGEIYIKR 18 (55)
T ss_pred cCcchhCCeeccH
Confidence 3799999988744
No 58
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=47.03 E-value=10 Score=20.25 Aligned_cols=12 Identities=8% Similarity=0.299 Sum_probs=9.9
Q ss_pred EEeeCCCCeeEE
Q 040416 9 IWGCKDSSKVKA 20 (47)
Q Consensus 9 IW~C~~C~~~~A 20 (47)
.|.|..||+..-
T Consensus 1 ~y~C~~CgyiYd 12 (50)
T cd00730 1 KYECRICGYIYD 12 (50)
T ss_pred CcCCCCCCeEEC
Confidence 489999998865
No 59
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=46.63 E-value=14 Score=23.44 Aligned_cols=13 Identities=15% Similarity=0.330 Sum_probs=11.0
Q ss_pred EEEEeeCCCCeeE
Q 040416 7 VGIWGCKDSSKVK 19 (47)
Q Consensus 7 vGIW~C~~C~~~~ 19 (47)
.+.|.|..||..+
T Consensus 320 ~r~~~C~~cg~~~ 332 (364)
T COG0675 320 GRLFKCPRCGFVH 332 (364)
T ss_pred ceeEECCCCCCee
Confidence 5789999999874
No 60
>PRK12366 replication factor A; Reviewed
Probab=46.37 E-value=8.5 Score=29.08 Aligned_cols=12 Identities=25% Similarity=0.387 Sum_probs=10.6
Q ss_pred EEEEeeCCCCee
Q 040416 7 VGIWGCKDSSKV 18 (47)
Q Consensus 7 vGIW~C~~C~~~ 18 (47)
-|.|.|.+|+++
T Consensus 546 ~g~~~C~~c~~~ 557 (637)
T PRK12366 546 DGEYICEFCGEV 557 (637)
T ss_pred CCcEECCCCCCC
Confidence 388999999987
No 61
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=45.79 E-value=8.5 Score=19.54 Aligned_cols=14 Identities=21% Similarity=0.608 Sum_probs=10.9
Q ss_pred eeEEEEEeeCCCCe
Q 040416 4 RKAVGIWGCKDSSK 17 (47)
Q Consensus 4 R~avGIW~C~~C~~ 17 (47)
+.+.|-|.|..|+.
T Consensus 20 ~~g~G~~~C~~Cg~ 33 (37)
T smart00778 20 KDGRGTWFCSVCGA 33 (37)
T ss_pred CCCCcCEEeCCCCC
Confidence 34568999999974
No 62
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=45.69 E-value=14 Score=23.38 Aligned_cols=16 Identities=13% Similarity=0.239 Sum_probs=13.7
Q ss_pred eEEEEEeeCCCCeeEE
Q 040416 5 KAVGIWGCKDSSKVKA 20 (47)
Q Consensus 5 ~avGIW~C~~C~~~~A 20 (47)
.+-|+-.|.+||..+.
T Consensus 108 ~g~G~l~C~~Cg~~~~ 123 (146)
T PF07295_consen 108 VGPGTLVCENCGHEVE 123 (146)
T ss_pred ecCceEecccCCCEEE
Confidence 5779999999999874
No 63
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=44.86 E-value=11 Score=18.49 Aligned_cols=9 Identities=11% Similarity=0.361 Sum_probs=6.6
Q ss_pred EEeeCCCCe
Q 040416 9 IWGCKDSSK 17 (47)
Q Consensus 9 IW~C~~C~~ 17 (47)
+|.|..|+.
T Consensus 3 ~~~C~~C~~ 11 (33)
T PF08792_consen 3 LKKCSKCGG 11 (33)
T ss_pred ceEcCCCCC
Confidence 678887864
No 64
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=44.66 E-value=11 Score=16.92 Aligned_cols=12 Identities=17% Similarity=0.340 Sum_probs=9.6
Q ss_pred EeeCCCCeeEEc
Q 040416 10 WGCKDSSKVKAG 21 (47)
Q Consensus 10 W~C~~C~~~~AG 21 (47)
+.|..|++.|..
T Consensus 2 ~~C~~C~k~f~~ 13 (27)
T PF12171_consen 2 FYCDACDKYFSS 13 (27)
T ss_dssp CBBTTTTBBBSS
T ss_pred CCcccCCCCcCC
Confidence 579999998754
No 65
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=44.14 E-value=11 Score=23.30 Aligned_cols=10 Identities=20% Similarity=0.667 Sum_probs=8.8
Q ss_pred EEeeCCCCee
Q 040416 9 IWGCKDSSKV 18 (47)
Q Consensus 9 IW~C~~C~~~ 18 (47)
.|.|+.||..
T Consensus 50 ~WeC~~cG~~ 59 (105)
T PF13397_consen 50 TWECPRCGLP 59 (105)
T ss_pred ceeCCCCCCc
Confidence 5999999975
No 66
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=44.08 E-value=19 Score=18.99 Aligned_cols=12 Identities=17% Similarity=0.249 Sum_probs=9.6
Q ss_pred EeeCCCCeeEEc
Q 040416 10 WGCKDSSKVKAG 21 (47)
Q Consensus 10 W~C~~C~~~~AG 21 (47)
|+|..|++..--
T Consensus 2 y~C~~CgyvYd~ 13 (47)
T PF00301_consen 2 YQCPVCGYVYDP 13 (47)
T ss_dssp EEETTTSBEEET
T ss_pred cCCCCCCEEEcC
Confidence 889999987653
No 67
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=43.55 E-value=12 Score=23.68 Aligned_cols=12 Identities=17% Similarity=0.418 Sum_probs=10.0
Q ss_pred EEeeCCCCeeEE
Q 040416 9 IWGCKDSSKVKA 20 (47)
Q Consensus 9 IW~C~~C~~~~A 20 (47)
|..|.+|+.|+-
T Consensus 13 IYrC~~C~~TwN 24 (142)
T PF06353_consen 13 IYRCEKCDYTWN 24 (142)
T ss_pred EEEcccCcCccc
Confidence 678999998864
No 68
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=43.47 E-value=3.5 Score=33.20 Aligned_cols=14 Identities=36% Similarity=0.800 Sum_probs=12.7
Q ss_pred EEEEEeeCCCCeeE
Q 040416 6 AVGIWGCKDSSKVK 19 (47)
Q Consensus 6 avGIW~C~~C~~~~ 19 (47)
+.||..|+.|+|.|
T Consensus 789 ~~giFpCreC~kvF 802 (907)
T KOG4167|consen 789 PTGIFPCRECGKVF 802 (907)
T ss_pred CCceeehHHHHHHH
Confidence 58999999999987
No 69
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=42.91 E-value=14 Score=22.83 Aligned_cols=9 Identities=33% Similarity=0.689 Sum_probs=7.4
Q ss_pred eeCCCCeeE
Q 040416 11 GCKDSSKVK 19 (47)
Q Consensus 11 ~C~~C~~~~ 19 (47)
+|++||..+
T Consensus 31 kC~~CG~v~ 39 (140)
T COG1545 31 KCKKCGRVY 39 (140)
T ss_pred EcCCCCeEE
Confidence 699999876
No 70
>PF08821 CGGC: CGGC domain; InterPro: IPR014925 Proteins in this entry are a quite highly conserved sequence of CGGC in its central region. The region has many conserved cysteines and histidines suggestive of a zinc binding function.
Probab=42.74 E-value=41 Score=20.15 Aligned_cols=12 Identities=25% Similarity=0.681 Sum_probs=10.0
Q ss_pred eEEEEEeeCCCC
Q 040416 5 KAVGIWGCKDSS 16 (47)
Q Consensus 5 ~avGIW~C~~C~ 16 (47)
+=+|++.|..|.
T Consensus 39 elvgf~~CgGCp 50 (107)
T PF08821_consen 39 ELVGFFTCGGCP 50 (107)
T ss_pred EEEEEeeCCCCC
Confidence 347999999998
No 71
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=42.58 E-value=20 Score=17.92 Aligned_cols=13 Identities=8% Similarity=0.161 Sum_probs=10.4
Q ss_pred EEEEeeCCCCeeE
Q 040416 7 VGIWGCKDSSKVK 19 (47)
Q Consensus 7 vGIW~C~~C~~~~ 19 (47)
+=++.|.+|++++
T Consensus 26 T~fy~C~~C~~~w 38 (40)
T smart00440 26 TVFYVCTKCGHRW 38 (40)
T ss_pred eEEEEeCCCCCEe
Confidence 4578899999876
No 72
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=42.33 E-value=18 Score=18.26 Aligned_cols=12 Identities=8% Similarity=0.194 Sum_probs=9.0
Q ss_pred EeeCCCCeeEEc
Q 040416 10 WGCKDSSKVKAG 21 (47)
Q Consensus 10 W~C~~C~~~~AG 21 (47)
.+|.+||..|--
T Consensus 6 y~C~~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCTACGHRFEV 17 (52)
T ss_pred EEeCCCCCEeEE
Confidence 478899987763
No 73
>PF04071 zf-like: Cysteine-rich small domain; InterPro: IPR007212 This is a probable metal-binding domain. It is found in a probable precorrin-3B C17-methyltransferase from Methanobacterium thermoautotrophicum, that catalyses the methylation of C-17 in precorrin-3B to form precorrin-4.
Probab=41.99 E-value=12 Score=22.28 Aligned_cols=9 Identities=33% Similarity=1.228 Sum_probs=8.1
Q ss_pred EEeeCCCCe
Q 040416 9 IWGCKDSSK 17 (47)
Q Consensus 9 IW~C~~C~~ 17 (47)
||.|..|..
T Consensus 51 vw~C~~C~~ 59 (86)
T PF04071_consen 51 VWDCSDCTL 59 (86)
T ss_pred eeECccCCC
Confidence 999999974
No 74
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=40.23 E-value=9.9 Score=28.26 Aligned_cols=10 Identities=20% Similarity=0.843 Sum_probs=8.7
Q ss_pred EEeeCCCCee
Q 040416 9 IWGCKDSSKV 18 (47)
Q Consensus 9 IW~C~~C~~~ 18 (47)
-|+|.+|+++
T Consensus 284 ~W~CpkC~~k 293 (415)
T COG5533 284 AWRCPKCGRK 293 (415)
T ss_pred cccCchhccc
Confidence 4999999975
No 75
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=40.12 E-value=13 Score=27.59 Aligned_cols=9 Identities=22% Similarity=0.851 Sum_probs=7.8
Q ss_pred EEeeCCCCe
Q 040416 9 IWGCKDSSK 17 (47)
Q Consensus 9 IW~C~~C~~ 17 (47)
-|+|++|++
T Consensus 368 ~W~CPsC~~ 376 (389)
T COG2956 368 YWHCPSCRA 376 (389)
T ss_pred eeeCCCccc
Confidence 599999985
No 76
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=40.09 E-value=18 Score=19.80 Aligned_cols=17 Identities=29% Similarity=0.475 Sum_probs=12.6
Q ss_pred eeCCCCeeEEccccccc
Q 040416 11 GCKDSSKVKAGGAYTLN 27 (47)
Q Consensus 11 ~C~~C~~~~AGGAy~~~ 27 (47)
.|+.|+++++=|..-+.
T Consensus 9 ~Ck~C~~~I~kg~lRiG 25 (82)
T PF00645_consen 9 KCKGCKKKIAKGELRIG 25 (82)
T ss_dssp BETTTSCBE-TTSEEEE
T ss_pred cCcccCCcCCCCCEEEE
Confidence 69999999987765543
No 77
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=40.01 E-value=39 Score=17.13 Aligned_cols=14 Identities=21% Similarity=0.245 Sum_probs=11.4
Q ss_pred eeCCCCeeEEcccc
Q 040416 11 GCKDSSKVKAGGAY 24 (47)
Q Consensus 11 ~C~~C~~~~AGGAy 24 (47)
.|+.|++.+.....
T Consensus 20 ~C~~C~~~l~~~~~ 33 (50)
T smart00614 20 KCKYCGKKLSRSSK 33 (50)
T ss_pred EecCCCCEeeeCCC
Confidence 69999999986544
No 78
>PF14353 CpXC: CpXC protein
Probab=39.77 E-value=16 Score=21.50 Aligned_cols=12 Identities=8% Similarity=0.213 Sum_probs=9.8
Q ss_pred EEeeCCCCeeEE
Q 040416 9 IWGCKDSSKVKA 20 (47)
Q Consensus 9 IW~C~~C~~~~A 20 (47)
...|.+||+++.
T Consensus 38 ~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 38 SFTCPSCGHKFR 49 (128)
T ss_pred EEECCCCCCcee
Confidence 478999998875
No 79
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=39.56 E-value=15 Score=28.44 Aligned_cols=15 Identities=20% Similarity=0.789 Sum_probs=12.0
Q ss_pred eEEEEEeeCCCCeeE
Q 040416 5 KAVGIWGCKDSSKVK 19 (47)
Q Consensus 5 ~avGIW~C~~C~~~~ 19 (47)
.-|.||.|.+||..+
T Consensus 126 ~~va~w~c~~cg~~i 140 (593)
T COG2401 126 EKVALWRCEKCGTII 140 (593)
T ss_pred ceEEEEecchhchhh
Confidence 457899999998654
No 80
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=39.43 E-value=13 Score=23.72 Aligned_cols=12 Identities=17% Similarity=0.130 Sum_probs=10.2
Q ss_pred EeeCCCCeeEEc
Q 040416 10 WGCKDSSKVKAG 21 (47)
Q Consensus 10 W~C~~C~~~~AG 21 (47)
-+|..||++|.+
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 689999999864
No 81
>COG3755 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.18 E-value=31 Score=21.84 Aligned_cols=28 Identities=21% Similarity=0.107 Sum_probs=25.4
Q ss_pred EEcccccccccHHHHHHHHHHHHHhhhh
Q 040416 19 KAGGAYTLNIGSAVTARVTIRRLREQTE 46 (47)
Q Consensus 19 ~AGGAy~~~T~~a~tvk~~irrl~e~~e 46 (47)
-.||.+.|........+.+-+|+.||++
T Consensus 95 ~~ggs~~~~~~~~C~~d~T~~R~~eL~~ 122 (127)
T COG3755 95 LDGGSIAPMEVLSCLLDLTNQRTAELEE 122 (127)
T ss_pred ccCCCcchHHHHHHHHHHHHHHHHHHHH
Confidence 4699999999999999999999999975
No 82
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=38.72 E-value=15 Score=26.10 Aligned_cols=35 Identities=11% Similarity=0.243 Sum_probs=19.5
Q ss_pred EEEEeeCCCCeeEEcccccccccH-HHHHHHHHHHHHh
Q 040416 7 VGIWGCKDSSKVKAGGAYTLNIGS-AVTARVTIRRLRE 43 (47)
Q Consensus 7 vGIW~C~~C~~~~AGGAy~~~T~~-a~tvk~~irrl~e 43 (47)
-|+|+|-+||. .|.+..+-.-. +.++..|++.|.+
T Consensus 53 k~~~~Cf~Cg~--~Gd~i~fv~~~~~~sf~eA~~~La~ 88 (415)
T TIGR01391 53 KQFYHCFGCGA--GGDAIKFLMEIEGISFVEAVEELAK 88 (415)
T ss_pred CCcEEECCCCC--CCCHHHHHHHHhCCCHHHHHHHHHH
Confidence 47999999997 45554432211 1234455555533
No 83
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=38.61 E-value=14 Score=23.24 Aligned_cols=24 Identities=17% Similarity=0.407 Sum_probs=16.2
Q ss_pred EEeeCCCCeeEEcccccccccHHHHHHHHHH
Q 040416 9 IWGCKDSSKVKAGGAYTLNIGSAVTARVTIR 39 (47)
Q Consensus 9 IW~C~~C~~~~AGGAy~~~T~~a~tvk~~ir 39 (47)
+|.|..|- |..+-..+..+.+.|.
T Consensus 62 VwSC~dC~-------~iH~ke~~~~ilr~ll 85 (112)
T COG2158 62 VWSCSDCH-------WIHRKEGAEEILRELL 85 (112)
T ss_pred Eeeccccc-------eecccchHHHHHHHHH
Confidence 99999995 5555556665554443
No 84
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=38.52 E-value=11 Score=17.12 Aligned_cols=12 Identities=8% Similarity=0.152 Sum_probs=8.2
Q ss_pred eeCCCCeeEEcc
Q 040416 11 GCKDSSKVKAGG 22 (47)
Q Consensus 11 ~C~~C~~~~AGG 22 (47)
.|.+||+.+.-+
T Consensus 1 ~Cp~CG~~~~~~ 12 (23)
T PF13240_consen 1 YCPNCGAEIEDD 12 (23)
T ss_pred CCcccCCCCCCc
Confidence 478888776544
No 85
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=38.37 E-value=12 Score=17.18 Aligned_cols=13 Identities=23% Similarity=0.232 Sum_probs=10.9
Q ss_pred EEEeeCCCCeeEE
Q 040416 8 GIWGCKDSSKVKA 20 (47)
Q Consensus 8 GIW~C~~C~~~~A 20 (47)
|-+.|.-|++.|.
T Consensus 2 ~~~~C~~C~~~~~ 14 (35)
T smart00451 2 GGFYCKLCNVTFT 14 (35)
T ss_pred cCeEccccCCccC
Confidence 4578999999887
No 86
>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=38.19 E-value=12 Score=17.53 Aligned_cols=9 Identities=11% Similarity=-0.060 Sum_probs=6.6
Q ss_pred eeCCCCeeE
Q 040416 11 GCKDSSKVK 19 (47)
Q Consensus 11 ~C~~C~~~~ 19 (47)
.|..||+.|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 577788766
No 87
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=38.13 E-value=32 Score=17.04 Aligned_cols=13 Identities=8% Similarity=0.102 Sum_probs=10.1
Q ss_pred EEEEeeCCCCeeE
Q 040416 7 VGIWGCKDSSKVK 19 (47)
Q Consensus 7 vGIW~C~~C~~~~ 19 (47)
+=+..|.+|+++|
T Consensus 26 T~fy~C~~C~~~w 38 (39)
T PF01096_consen 26 TLFYVCCNCGHRW 38 (39)
T ss_dssp EEEEEESSSTEEE
T ss_pred eEEEEeCCCCCee
Confidence 4567899999876
No 88
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=37.96 E-value=13 Score=21.61 Aligned_cols=11 Identities=9% Similarity=0.462 Sum_probs=7.8
Q ss_pred EEeeCCCCeeE
Q 040416 9 IWGCKDSSKVK 19 (47)
Q Consensus 9 IW~C~~C~~~~ 19 (47)
-|+|.+||.+-
T Consensus 4 ~~kCpKCgn~~ 14 (68)
T COG3478 4 AFKCPKCGNTN 14 (68)
T ss_pred cccCCCcCCcc
Confidence 47788888653
No 89
>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=37.24 E-value=12 Score=22.74 Aligned_cols=9 Identities=11% Similarity=0.202 Sum_probs=6.6
Q ss_pred eeCCCCeeE
Q 040416 11 GCKDSSKVK 19 (47)
Q Consensus 11 ~C~~C~~~~ 19 (47)
.|.+||++|
T Consensus 11 ~Cp~CG~kF 19 (108)
T PF09538_consen 11 TCPSCGAKF 19 (108)
T ss_pred cCCCCcchh
Confidence 477777776
No 90
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=36.79 E-value=29 Score=21.08 Aligned_cols=35 Identities=17% Similarity=0.263 Sum_probs=21.1
Q ss_pred EEeeCCCCeeEEcccccccccHHHHHHHHHHHHHhh
Q 040416 9 IWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLREQ 44 (47)
Q Consensus 9 IW~C~~C~~~~AGGAy~~~T~~a~tvk~~irrl~e~ 44 (47)
+|.|..|+-=|--=. .-+.|.+..+...+|++|..
T Consensus 31 ~y~C~~C~AyVG~H~-~t~~PlGtLAd~~lR~~R~~ 65 (102)
T PF11672_consen 31 LYVCTPCDAYVGCHP-GTDIPLGTLADAELRRARKA 65 (102)
T ss_pred eEECCCCCceeeeeC-CCCCcCcccCCHHHHHHHHH
Confidence 499999875442211 11456777777677766643
No 91
>COG4740 Predicted metalloprotease [General function prediction only]
Probab=36.44 E-value=9 Score=25.61 Aligned_cols=25 Identities=28% Similarity=0.531 Sum_probs=18.4
Q ss_pred EEcccccccccHHHH--HHHHHHHHHh
Q 040416 19 KAGGAYTLNIGSAVT--ARVTIRRLRE 43 (47)
Q Consensus 19 ~AGGAy~~~T~~a~t--vk~~irrl~e 43 (47)
-+||+|++.+..+.+ |+.-|.++-|
T Consensus 38 ~~GG~WSyr~~~~~svAvkd~it~~de 64 (176)
T COG4740 38 QHGGAWSYRDGDVSSVAVKDVITKLDE 64 (176)
T ss_pred ccCCcceeccCCceeeeehhhhhhccc
Confidence 479999999887765 5555776654
No 92
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=36.26 E-value=13 Score=27.99 Aligned_cols=14 Identities=29% Similarity=0.489 Sum_probs=11.6
Q ss_pred EEEEeeCCCCeeEE
Q 040416 7 VGIWGCKDSSKVKA 20 (47)
Q Consensus 7 vGIW~C~~C~~~~A 20 (47)
-|.|.|.+|++.+.
T Consensus 491 ~g~~~CekC~~~~~ 504 (608)
T TIGR00617 491 DGTYRCEKCNKNFA 504 (608)
T ss_pred CCCEECCCCCCCCC
Confidence 48899999998764
No 93
>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=36.13 E-value=23 Score=16.87 Aligned_cols=9 Identities=22% Similarity=0.405 Sum_probs=6.8
Q ss_pred eeCCCCeeE
Q 040416 11 GCKDSSKVK 19 (47)
Q Consensus 11 ~C~~C~~~~ 19 (47)
.|.+|+..|
T Consensus 27 ~C~~C~~~~ 35 (38)
T TIGR02098 27 RCGKCGHVW 35 (38)
T ss_pred ECCCCCCEE
Confidence 588888776
No 94
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=36.13 E-value=12 Score=27.79 Aligned_cols=14 Identities=21% Similarity=0.546 Sum_probs=11.3
Q ss_pred EEeeCCCCeeEEcc
Q 040416 9 IWGCKDSSKVKAGG 22 (47)
Q Consensus 9 IW~C~~C~~~~AGG 22 (47)
=|.|.+||.++-=|
T Consensus 265 ~wrCpkCGg~ikKG 278 (403)
T COG1379 265 RWRCPKCGGKIKKG 278 (403)
T ss_pred cccCcccccchhhh
Confidence 49999999887654
No 95
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=36.08 E-value=19 Score=25.70 Aligned_cols=19 Identities=16% Similarity=0.172 Sum_probs=16.1
Q ss_pred eEEEEEeeCCCCeeEEccc
Q 040416 5 KAVGIWGCKDSSKVKAGGA 23 (47)
Q Consensus 5 ~avGIW~C~~C~~~~AGGA 23 (47)
.+.|-.+|.+|+.+|.|=+
T Consensus 151 wG~aef~C~~C~h~F~G~~ 169 (278)
T PF15135_consen 151 WGIAEFHCPKCRHNFRGFA 169 (278)
T ss_pred cceeeeecccccccchhhh
Confidence 5788899999999998743
No 96
>COG1852 Uncharacterized conserved protein [Function unknown]
Probab=35.97 E-value=16 Score=25.13 Aligned_cols=13 Identities=31% Similarity=0.560 Sum_probs=10.5
Q ss_pred EEeeCCCCeeEEc
Q 040416 9 IWGCKDSSKVKAG 21 (47)
Q Consensus 9 IW~C~~C~~~~AG 21 (47)
+|.|++||+-+-|
T Consensus 111 G~~Ck~CgkCvi~ 123 (209)
T COG1852 111 GYECKKCGKCVIG 123 (209)
T ss_pred cceecccCCeehH
Confidence 6999999987644
No 97
>PF12523 DUF3725: Protein of unknown function (DUF3725); InterPro: IPR022199 This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with PF01577 from PFAM. There is a conserved FLE sequence motif.
Probab=35.78 E-value=19 Score=21.14 Aligned_cols=12 Identities=17% Similarity=0.819 Sum_probs=10.1
Q ss_pred EEEeeCCCCeeE
Q 040416 8 GIWGCKDSSKVK 19 (47)
Q Consensus 8 GIW~C~~C~~~~ 19 (47)
..|.|.+|+++-
T Consensus 58 Elw~Ch~C~~ts 69 (74)
T PF12523_consen 58 ELWECHSCDNTS 69 (74)
T ss_pred ceEEeecCCCch
Confidence 579999999864
No 98
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=35.74 E-value=20 Score=22.01 Aligned_cols=15 Identities=27% Similarity=0.441 Sum_probs=12.8
Q ss_pred EEeeCCCCeeEEccc
Q 040416 9 IWGCKDSSKVKAGGA 23 (47)
Q Consensus 9 IW~C~~C~~~~AGGA 23 (47)
.|+|--||+.+-.|-
T Consensus 2 kWkC~iCg~~I~~gq 16 (101)
T PF09943_consen 2 KWKCYICGKPIYEGQ 16 (101)
T ss_pred ceEEEecCCeeeecc
Confidence 499999999988773
No 99
>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=35.67 E-value=29 Score=19.84 Aligned_cols=16 Identities=19% Similarity=0.318 Sum_probs=12.3
Q ss_pred EEEEEeeCCCCeeEEc
Q 040416 6 AVGIWGCKDSSKVKAG 21 (47)
Q Consensus 6 avGIW~C~~C~~~~AG 21 (47)
.+-.|.|..||..+..
T Consensus 28 ~~~~~~C~~CGe~~~~ 43 (127)
T TIGR03830 28 GVPGWYCPACGEELLD 43 (127)
T ss_pred eeeeeECCCCCCEEEc
Confidence 4567999999987643
No 100
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=35.59 E-value=15 Score=23.50 Aligned_cols=13 Identities=23% Similarity=0.570 Sum_probs=10.9
Q ss_pred eeCCCCeeEEccc
Q 040416 11 GCKDSSKVKAGGA 23 (47)
Q Consensus 11 ~C~~C~~~~AGGA 23 (47)
+|-+||+.|.-|.
T Consensus 3 ~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 3 QCTKCGRVFEDGS 15 (131)
T ss_pred ccCcCCCCcCCCc
Confidence 5889999998776
No 101
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=35.48 E-value=35 Score=16.91 Aligned_cols=16 Identities=6% Similarity=0.065 Sum_probs=13.7
Q ss_pred EEeeCCCCeeEEcccc
Q 040416 9 IWGCKDSSKVKAGGAY 24 (47)
Q Consensus 9 IW~C~~C~~~~AGGAy 24 (47)
.|.|..|++.+--.+.
T Consensus 20 ~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 20 RFVCRKCGYEEPIEQK 35 (52)
T ss_pred EEECCcCCCeEECCCc
Confidence 7899999999877766
No 102
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=35.47 E-value=13 Score=27.54 Aligned_cols=14 Identities=14% Similarity=0.294 Sum_probs=11.1
Q ss_pred EeeCCCCeeEEccc
Q 040416 10 WGCKDSSKVKAGGA 23 (47)
Q Consensus 10 W~C~~C~~~~AGGA 23 (47)
|.|++||+++..-.
T Consensus 368 ~rC~kCg~~~~~~~ 381 (421)
T COG1571 368 FRCKKCGTRARETL 381 (421)
T ss_pred cccccccccCCccc
Confidence 89999999875433
No 103
>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=34.67 E-value=33 Score=19.54 Aligned_cols=14 Identities=14% Similarity=0.216 Sum_probs=8.8
Q ss_pred EEeeCCCCeeEEcc
Q 040416 9 IWGCKDSSKVKAGG 22 (47)
Q Consensus 9 IW~C~~C~~~~AGG 22 (47)
++.|-+|+++|-.+
T Consensus 90 fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 90 FYKCTKCGYVWREY 103 (104)
T ss_pred EEEeCCCCCeeEeC
Confidence 56677777766543
No 104
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=34.20 E-value=25 Score=17.20 Aligned_cols=11 Identities=18% Similarity=0.211 Sum_probs=8.1
Q ss_pred EEeeCCCCeeE
Q 040416 9 IWGCKDSSKVK 19 (47)
Q Consensus 9 IW~C~~C~~~~ 19 (47)
.=+|.+|+..|
T Consensus 25 ~vrC~~C~~~f 35 (37)
T PF13719_consen 25 KVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCcEe
Confidence 44788888776
No 105
>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=33.66 E-value=20 Score=17.85 Aligned_cols=14 Identities=14% Similarity=0.380 Sum_probs=11.0
Q ss_pred eEEEEEeeCCCCee
Q 040416 5 KAVGIWGCKDSSKV 18 (47)
Q Consensus 5 ~avGIW~C~~C~~~ 18 (47)
..-|-+.|..||.+
T Consensus 21 ~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 21 SDDGFYYCDRCGHQ 34 (36)
T ss_pred ccCCEEEhhhCceE
Confidence 45688999999865
No 106
>COG3450 Predicted enzyme of the cupin superfamily [General function prediction only]
Probab=33.44 E-value=27 Score=21.63 Aligned_cols=11 Identities=36% Similarity=1.017 Sum_probs=8.4
Q ss_pred eEEEEEeeCCC
Q 040416 5 KAVGIWGCKDS 15 (47)
Q Consensus 5 ~avGIW~C~~C 15 (47)
.-+|||.|..=
T Consensus 45 ~~~GiWe~TpG 55 (116)
T COG3450 45 VETGIWECTPG 55 (116)
T ss_pred eeEeEEEecCc
Confidence 46899999653
No 107
>PRK05667 dnaG DNA primase; Validated
Probab=33.00 E-value=23 Score=26.63 Aligned_cols=35 Identities=9% Similarity=0.193 Sum_probs=20.2
Q ss_pred EEEEEeeCCCCeeEEcccccccccH-HHHHHHHHHHHH
Q 040416 6 AVGIWGCKDSSKVKAGGAYTLNIGS-AVTARVTIRRLR 42 (47)
Q Consensus 6 avGIW~C~~C~~~~AGGAy~~~T~~-a~tvk~~irrl~ 42 (47)
.-++|+|-+||. .|.+..+-... +.++..+++.|-
T Consensus 54 ~k~~~~CF~Cg~--~Gd~i~fv~~~~~~sf~eAv~~La 89 (580)
T PRK05667 54 DKQFYHCFGCGA--GGDVIKFLMEYEGLSFVEAVEELA 89 (580)
T ss_pred CCCeEEECCCCC--CCCHHHHHHHHhCCCHHHHHHHHH
Confidence 358999999997 35554442221 223455555553
No 108
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=32.31 E-value=26 Score=23.59 Aligned_cols=29 Identities=14% Similarity=0.184 Sum_probs=18.5
Q ss_pred eEEEEEeeCCCCeeEEcccccccccHHHH
Q 040416 5 KAVGIWGCKDSSKVKAGGAYTLNIGSAVT 33 (47)
Q Consensus 5 ~avGIW~C~~C~~~~AGGAy~~~T~~a~t 33 (47)
.+-.=|.|+-|+|.|=|=-|.-..-.-++
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcC
Confidence 44566999999999988777655444433
No 109
>PHA00616 hypothetical protein
Probab=31.65 E-value=9.2 Score=20.23 Aligned_cols=11 Identities=9% Similarity=0.329 Sum_probs=8.3
Q ss_pred EeeCCCCeeEE
Q 040416 10 WGCKDSSKVKA 20 (47)
Q Consensus 10 W~C~~C~~~~A 20 (47)
.+|..||+.|.
T Consensus 2 YqC~~CG~~F~ 12 (44)
T PHA00616 2 YQCLRCGGIFR 12 (44)
T ss_pred CccchhhHHHh
Confidence 36888988774
No 110
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=31.27 E-value=28 Score=17.33 Aligned_cols=14 Identities=14% Similarity=0.373 Sum_probs=10.4
Q ss_pred EEEeeCCCCeeEEc
Q 040416 8 GIWGCKDSSKVKAG 21 (47)
Q Consensus 8 GIW~C~~C~~~~AG 21 (47)
|+=.|..||..+..
T Consensus 4 g~l~C~~CG~~m~~ 17 (58)
T PF13408_consen 4 GLLRCGHCGSKMTR 17 (58)
T ss_pred CcEEcccCCcEeEE
Confidence 55678888887765
No 111
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=30.97 E-value=29 Score=18.24 Aligned_cols=12 Identities=17% Similarity=0.589 Sum_probs=5.7
Q ss_pred eeCCCCeeEEcc
Q 040416 11 GCKDSSKVKAGG 22 (47)
Q Consensus 11 ~C~~C~~~~AGG 22 (47)
+|+.||..|=..
T Consensus 27 hCr~CG~~vC~~ 38 (69)
T PF01363_consen 27 HCRNCGRVVCSS 38 (69)
T ss_dssp E-TTT--EEECC
T ss_pred ccCCCCCEECCc
Confidence 677777776543
No 112
>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=30.65 E-value=21 Score=16.73 Aligned_cols=12 Identities=17% Similarity=0.313 Sum_probs=9.1
Q ss_pred eCCCCeeEEccc
Q 040416 12 CKDSSKVKAGGA 23 (47)
Q Consensus 12 C~~C~~~~AGGA 23 (47)
|.+||..+|+.-
T Consensus 1 C~sC~~~i~~r~ 12 (24)
T PF07754_consen 1 CTSCGRPIAPRE 12 (24)
T ss_pred CccCCCcccCcc
Confidence 778888888653
No 113
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=30.55 E-value=34 Score=20.48 Aligned_cols=17 Identities=6% Similarity=-0.092 Sum_probs=12.4
Q ss_pred EEEeeCCCCeeEEcccc
Q 040416 8 GIWGCKDSSKVKAGGAY 24 (47)
Q Consensus 8 GIW~C~~C~~~~AGGAy 24 (47)
+...|+.|+..|.-..+
T Consensus 69 ~~~~C~~Cg~~~~~~~~ 85 (114)
T PRK03681 69 AECWCETCQQYVTLLTQ 85 (114)
T ss_pred cEEEcccCCCeeecCCc
Confidence 45789999988876433
No 114
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=30.49 E-value=35 Score=20.40 Aligned_cols=19 Identities=21% Similarity=-0.003 Sum_probs=13.9
Q ss_pred EEEeeCCCCeeEEcccccc
Q 040416 8 GIWGCKDSSKVKAGGAYTL 26 (47)
Q Consensus 8 GIW~C~~C~~~~AGGAy~~ 26 (47)
+...|+.||..|.-..+.+
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~ 87 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQHDA 87 (113)
T ss_pred cEEEcccCCCEEecCCcCc
Confidence 4578999998887655443
No 115
>smart00520 BASIC Basic domain in HLH proteins of MYOD family.
Probab=30.20 E-value=7.9 Score=23.54 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=8.5
Q ss_pred EEeeCCCCee
Q 040416 9 IWGCKDSSKV 18 (47)
Q Consensus 9 IW~C~~C~~~ 18 (47)
+|-||.|.++
T Consensus 72 ~WACk~CkrK 81 (91)
T smart00520 72 PWACKACKRK 81 (91)
T ss_pred HHHHHHhccc
Confidence 6999999875
No 116
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=30.06 E-value=39 Score=19.70 Aligned_cols=12 Identities=8% Similarity=0.274 Sum_probs=10.2
Q ss_pred EEeeCCCCeeEE
Q 040416 9 IWGCKDSSKVKA 20 (47)
Q Consensus 9 IW~C~~C~~~~A 20 (47)
-|.|+.||.++.
T Consensus 4 ~Y~CRHCg~~IG 15 (76)
T PF10955_consen 4 HYYCRHCGTKIG 15 (76)
T ss_pred EEEecCCCCEEE
Confidence 489999999875
No 117
>PRK11032 hypothetical protein; Provisional
Probab=29.75 E-value=43 Score=21.70 Aligned_cols=16 Identities=19% Similarity=0.260 Sum_probs=13.4
Q ss_pred eEEEEEeeCCCCeeEE
Q 040416 5 KAVGIWGCKDSSKVKA 20 (47)
Q Consensus 5 ~avGIW~C~~C~~~~A 20 (47)
++-|+=.|.+||....
T Consensus 120 vg~G~LvC~~Cg~~~~ 135 (160)
T PRK11032 120 VGLGNLVCEKCHHHLA 135 (160)
T ss_pred eecceEEecCCCCEEE
Confidence 5678999999999874
No 118
>PF13730 HTH_36: Helix-turn-helix domain
Probab=29.41 E-value=55 Score=16.17 Aligned_cols=12 Identities=33% Similarity=0.440 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHh
Q 040416 32 VTARVTIRRLRE 43 (47)
Q Consensus 32 ~tvk~~irrl~e 43 (47)
.||.++|..|.+
T Consensus 40 ~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 40 RTVQRAIKELEE 51 (55)
T ss_pred HHHHHHHHHHHH
Confidence 456666666665
No 119
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=29.40 E-value=42 Score=16.76 Aligned_cols=11 Identities=9% Similarity=0.407 Sum_probs=7.1
Q ss_pred EeeCCCCeeEE
Q 040416 10 WGCKDSSKVKA 20 (47)
Q Consensus 10 W~C~~C~~~~A 20 (47)
..|..||..+.
T Consensus 4 y~C~~CG~~~~ 14 (46)
T PRK00398 4 YKCARCGREVE 14 (46)
T ss_pred EECCCCCCEEE
Confidence 46777777663
No 120
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=29.35 E-value=16 Score=20.59 Aligned_cols=10 Identities=30% Similarity=0.730 Sum_probs=7.8
Q ss_pred EEeeCCCCee
Q 040416 9 IWGCKDSSKV 18 (47)
Q Consensus 9 IW~C~~C~~~ 18 (47)
||.|.+|.+.
T Consensus 36 I~RC~~CRk~ 45 (59)
T PRK14890 36 IYRCEKCRKQ 45 (59)
T ss_pred EeechhHHhc
Confidence 8888888764
No 121
>PRK12577 succinate dehydrogenase iron-sulfur subunit; Provisional
Probab=29.14 E-value=19 Score=24.90 Aligned_cols=12 Identities=33% Similarity=1.055 Sum_probs=9.5
Q ss_pred EEEEeeCCCCee
Q 040416 7 VGIWGCKDSSKV 18 (47)
Q Consensus 7 vGIW~C~~C~~~ 18 (47)
.|||.|-.|+.-
T Consensus 206 ~giw~C~~C~~C 217 (329)
T PRK12577 206 AGVWGCTRCYYC 217 (329)
T ss_pred CccccCcChhhh
Confidence 589999888754
No 122
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=28.95 E-value=20 Score=16.32 Aligned_cols=12 Identities=8% Similarity=0.063 Sum_probs=8.2
Q ss_pred eeCCCCeeEEcc
Q 040416 11 GCKDSSKVKAGG 22 (47)
Q Consensus 11 ~C~~C~~~~AGG 22 (47)
.|..||+.+..+
T Consensus 4 ~Cp~Cg~~~~~~ 15 (26)
T PF13248_consen 4 FCPNCGAEIDPD 15 (26)
T ss_pred CCcccCCcCCcc
Confidence 588888865443
No 123
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=28.57 E-value=43 Score=17.22 Aligned_cols=11 Identities=9% Similarity=0.450 Sum_probs=7.4
Q ss_pred EeeCCCCeeEE
Q 040416 10 WGCKDSSKVKA 20 (47)
Q Consensus 10 W~C~~C~~~~A 20 (47)
..|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 56777777654
No 124
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=28.54 E-value=40 Score=19.99 Aligned_cols=13 Identities=8% Similarity=0.286 Sum_probs=10.6
Q ss_pred EEEEeeCCCCeeE
Q 040416 7 VGIWGCKDSSKVK 19 (47)
Q Consensus 7 vGIW~C~~C~~~~ 19 (47)
.=.|.|..|+..+
T Consensus 121 ~~~~~C~~C~~~~ 133 (157)
T PF10263_consen 121 KYVYRCPSCGREY 133 (157)
T ss_pred ceEEEcCCCCCEe
Confidence 4579999999776
No 125
>KOG3816 consensus Cell differentiation regulator of the Headcase family [Signal transduction mechanisms]
Probab=28.44 E-value=15 Score=28.01 Aligned_cols=22 Identities=32% Similarity=0.675 Sum_probs=18.3
Q ss_pred EEEe--eCCCCeeEEccccccccc
Q 040416 8 GIWG--CKDSSKVKAGGAYTLNIG 29 (47)
Q Consensus 8 GIW~--C~~C~~~~AGGAy~~~T~ 29 (47)
|.|. |+.|++-|-|-.+.+-|-
T Consensus 436 g~~sI~C~~Ck~~wDGss~vLGTm 459 (526)
T KOG3816|consen 436 GDWSIICKNCKKDWDGSSFVLGTM 459 (526)
T ss_pred ccchHHHhhcCCCCCCcceeechh
Confidence 6788 999999999887776664
No 126
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=28.23 E-value=35 Score=23.88 Aligned_cols=34 Identities=21% Similarity=0.284 Sum_probs=25.6
Q ss_pred eCCCCeeEEcccccccccHH-HHHHHHHHHHHhhh
Q 040416 12 CKDSSKVKAGGAYTLNIGSA-VTARVTIRRLREQT 45 (47)
Q Consensus 12 C~~C~~~~AGGAy~~~T~~a-~tvk~~irrl~e~~ 45 (47)
+..||-.+--+-|.+-|=.. .|++..|+||+++.
T Consensus 84 A~r~g~~yV~~RwLgG~LTN~~ti~~si~rl~~lE 118 (252)
T COG0052 84 AERTGAYYVNGRWLGGMLTNFKTIRKSIKRLKELE 118 (252)
T ss_pred HHHhCCceecCcccCccccCchhHHHHHHHHHHHH
Confidence 45677777778888876543 68899999999664
No 127
>PF09365 DUF2461: Conserved hypothetical protein (DUF2461); InterPro: IPR012808 Members of this family are widely (though sparsely) distributed bacterial proteins, about 230 residues in length and in fungal proteins, which are around 400 residues in length. All members have a motif RxxRDxRFxxx[DN]KxxY. The function of this protein family is unknown.
Probab=28.12 E-value=56 Score=21.43 Aligned_cols=25 Identities=20% Similarity=0.220 Sum_probs=20.2
Q ss_pred CCeeEEcccccccccHHHHHHHHHH
Q 040416 15 SSKVKAGGAYTLNIGSAVTARVTIR 39 (47)
Q Consensus 15 C~~~~AGGAy~~~T~~a~tvk~~ir 39 (47)
-+-.++||-|.|+.+.-..+|..|.
T Consensus 105 ~~~~~g~G~~~p~~~~L~~iR~~I~ 129 (212)
T PF09365_consen 105 DGSFLGGGFYMPEKEQLKRIRQEID 129 (212)
T ss_pred CccEEEEEEeeCCHHHHHHHHHHHH
Confidence 3456789999999888888888775
No 128
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=28.12 E-value=44 Score=17.67 Aligned_cols=11 Identities=18% Similarity=0.335 Sum_probs=9.1
Q ss_pred EeeCCCCeeEE
Q 040416 10 WGCKDSSKVKA 20 (47)
Q Consensus 10 W~C~~C~~~~A 20 (47)
|.|.-|++.|.
T Consensus 51 ~~C~~C~~~f~ 61 (100)
T PF12756_consen 51 FRCPYCNKTFR 61 (100)
T ss_dssp EEBSSSS-EES
T ss_pred CCCCccCCCCc
Confidence 99999999975
No 129
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=28.01 E-value=23 Score=29.60 Aligned_cols=35 Identities=20% Similarity=0.229 Sum_probs=22.9
Q ss_pred EEeeCCCCeeEEcccccccccHH-----HHHHHHHHHHHhhh
Q 040416 9 IWGCKDSSKVKAGGAYTLNIGSA-----VTARVTIRRLREQT 45 (47)
Q Consensus 9 IW~C~~C~~~~AGGAy~~~T~~a-----~tvk~~irrl~e~~ 45 (47)
||.|..||+.|.+--. .-|-+ .-..+.|.-|||+.
T Consensus 694 IKrC~dcg~q~~~~~~--~cP~Cgs~~v~d~~~~ve~lRelA 733 (1187)
T COG1110 694 IKRCRDCGEQFVDSED--KCPRCGSRNVEDKTETVEALRELA 733 (1187)
T ss_pred HHHHhhcCceeccccc--cCCCCCCccccccHHHHHHHHHHH
Confidence 8999999999998732 22222 22455677777763
No 130
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=27.81 E-value=52 Score=22.39 Aligned_cols=18 Identities=6% Similarity=-0.010 Sum_probs=12.8
Q ss_pred eeeEEEEEeeCCCCeeEE
Q 040416 3 VRKAVGIWGCKDSSKVKA 20 (47)
Q Consensus 3 ~R~avGIW~C~~C~~~~A 20 (47)
+++-.--|.|++||+.++
T Consensus 37 G~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 37 GEVLISTGVCERCGYRST 54 (201)
T ss_pred ceEEEEEEEccccCCccc
Confidence 344455689999998765
No 131
>PHA00689 hypothetical protein
Probab=27.39 E-value=22 Score=20.07 Aligned_cols=17 Identities=35% Similarity=0.681 Sum_probs=12.6
Q ss_pred eeCCCCeeE-----Eccccccc
Q 040416 11 GCKDSSKVK-----AGGAYTLN 27 (47)
Q Consensus 11 ~C~~C~~~~-----AGGAy~~~ 27 (47)
.|+.|||+- .||-|.+-
T Consensus 19 tckrcgktglrweddggewvlm 40 (62)
T PHA00689 19 TCKRCGKTGLRWEDDGGEWVLM 40 (62)
T ss_pred ehhhccccCceeecCCCcEEEE
Confidence 599999873 57777753
No 132
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=27.23 E-value=25 Score=18.85 Aligned_cols=11 Identities=27% Similarity=0.543 Sum_probs=8.6
Q ss_pred EEEEeeCCCCe
Q 040416 7 VGIWGCKDSSK 17 (47)
Q Consensus 7 vGIW~C~~C~~ 17 (47)
-||=+|.+||-
T Consensus 9 RGirkCp~CGt 19 (44)
T PF14952_consen 9 RGIRKCPKCGT 19 (44)
T ss_pred hccccCCcCcC
Confidence 37888999974
No 133
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=27.09 E-value=25 Score=22.07 Aligned_cols=12 Identities=25% Similarity=0.515 Sum_probs=10.3
Q ss_pred eeCCCCeeEEcc
Q 040416 11 GCKDSSKVKAGG 22 (47)
Q Consensus 11 ~C~~C~~~~AGG 22 (47)
.|.+||..|+-|
T Consensus 4 ~CtrCG~vf~~g 15 (112)
T COG3364 4 QCTRCGEVFDDG 15 (112)
T ss_pred eecccccccccc
Confidence 689999999876
No 134
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=26.12 E-value=12 Score=26.51 Aligned_cols=14 Identities=21% Similarity=0.150 Sum_probs=9.7
Q ss_pred EeeCCCCeeEEccc
Q 040416 10 WGCKDSSKVKAGGA 23 (47)
Q Consensus 10 W~C~~C~~~~AGGA 23 (47)
.+|+.|+|+||==.
T Consensus 244 ~qC~~C~KsFsl~S 257 (279)
T KOG2462|consen 244 HQCPRCGKSFALKS 257 (279)
T ss_pred ccCcchhhHHHHHH
Confidence 46888888876433
No 135
>PHA02942 putative transposase; Provisional
Probab=25.60 E-value=44 Score=23.78 Aligned_cols=14 Identities=14% Similarity=0.230 Sum_probs=11.2
Q ss_pred EEEEEeeCCCCeeE
Q 040416 6 AVGIWGCKDSSKVK 19 (47)
Q Consensus 6 avGIW~C~~C~~~~ 19 (47)
+..+|.|..||...
T Consensus 339 ~~r~f~C~~CG~~~ 352 (383)
T PHA02942 339 AHRYFHCPSCGYEN 352 (383)
T ss_pred CCCEEECCCCCCEe
Confidence 34589999999975
No 136
>KOG1873 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=25.60 E-value=41 Score=27.38 Aligned_cols=20 Identities=20% Similarity=0.375 Sum_probs=16.4
Q ss_pred EEEeeCCCCeeEEccccccc
Q 040416 8 GIWGCKDSSKVKAGGAYTLN 27 (47)
Q Consensus 8 GIW~C~~C~~~~AGGAy~~~ 27 (47)
-||-|=+||+.+-|+-=.++
T Consensus 92 ~iWLCLkCG~q~CG~~~~~~ 111 (877)
T KOG1873|consen 92 AIWLCLKCGYQGCGRNSESQ 111 (877)
T ss_pred ceeeecccCCeeeCCCcccc
Confidence 49999999999999854443
No 137
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=25.59 E-value=13 Score=19.55 Aligned_cols=13 Identities=23% Similarity=0.363 Sum_probs=8.9
Q ss_pred eEEEEEeeCCCCee
Q 040416 5 KAVGIWGCKDSSKV 18 (47)
Q Consensus 5 ~avGIW~C~~C~~~ 18 (47)
.-+||. |..||-|
T Consensus 6 ~ltG~~-CPgCG~t 18 (52)
T PF10825_consen 6 ALTGIP-CPGCGMT 18 (52)
T ss_pred hhhCCC-CCCCcHH
Confidence 345655 9999865
No 138
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=25.47 E-value=28 Score=22.23 Aligned_cols=11 Identities=9% Similarity=0.057 Sum_probs=7.7
Q ss_pred EeeCCCCeeEE
Q 040416 10 WGCKDSSKVKA 20 (47)
Q Consensus 10 W~C~~C~~~~A 20 (47)
..|.+||++|-
T Consensus 10 r~Cp~cg~kFY 20 (129)
T TIGR02300 10 RICPNTGSKFY 20 (129)
T ss_pred ccCCCcCcccc
Confidence 35788888773
No 139
>PHA02611 51 baseplate hub assembly protein; Provisional
Probab=25.32 E-value=35 Score=23.84 Aligned_cols=9 Identities=22% Similarity=0.571 Sum_probs=8.6
Q ss_pred EeeCCCCee
Q 040416 10 WGCKDSSKV 18 (47)
Q Consensus 10 W~C~~C~~~ 18 (47)
|.|++||++
T Consensus 83 ~tCp~Cg~e 91 (249)
T PHA02611 83 FTCPKCKKE 91 (249)
T ss_pred EECCCCCCc
Confidence 999999998
No 140
>PRK13552 frdB fumarate reductase iron-sulfur subunit; Provisional
Probab=25.31 E-value=23 Score=23.58 Aligned_cols=12 Identities=25% Similarity=0.620 Sum_probs=9.8
Q ss_pred EEEEeeCCCCee
Q 040416 7 VGIWGCKDSSKV 18 (47)
Q Consensus 7 vGIW~C~~C~~~ 18 (47)
.|||.|..|+.=
T Consensus 203 ~gi~~C~~C~~C 214 (239)
T PRK13552 203 DGVFGCMSLLGC 214 (239)
T ss_pred CCcCCCcCcCcc
Confidence 589999988764
No 141
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=25.22 E-value=44 Score=18.80 Aligned_cols=11 Identities=27% Similarity=0.353 Sum_probs=9.1
Q ss_pred EeeCCCCeeEE
Q 040416 10 WGCKDSSKVKA 20 (47)
Q Consensus 10 W~C~~C~~~~A 20 (47)
-.|.+||+.+-
T Consensus 74 ~~C~~Cg~i~~ 84 (116)
T cd07153 74 LICTKCGKVID 84 (116)
T ss_pred eEeCCCCCEEE
Confidence 46999999876
No 142
>PRK04351 hypothetical protein; Provisional
Probab=24.70 E-value=49 Score=20.85 Aligned_cols=11 Identities=9% Similarity=0.546 Sum_probs=9.2
Q ss_pred EEeeCCCCeeE
Q 040416 9 IWGCKDSSKVK 19 (47)
Q Consensus 9 IW~C~~C~~~~ 19 (47)
+|.|..|+..+
T Consensus 112 ~Y~C~~Cg~~~ 122 (149)
T PRK04351 112 LYECQSCGQQY 122 (149)
T ss_pred EEECCCCCCEe
Confidence 69999999765
No 143
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PRK05950 sdhB succinate dehydrogenase iron-sulfur subunit; Reviewed
Probab=24.53 E-value=27 Score=22.74 Aligned_cols=32 Identities=9% Similarity=0.269 Sum_probs=19.5
Q ss_pred EEEEeeCCCCeeEEcccccccccHHHHHHHHHHHHHhh
Q 040416 7 VGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLREQ 44 (47)
Q Consensus 7 vGIW~C~~C~~~~AGGAy~~~T~~a~tvk~~irrl~e~ 44 (47)
.|||.|-.|+.-.. .=|.+.-....|.+||+.
T Consensus 195 ~~i~~C~~Cg~C~~------~CP~gi~~~~~I~~lR~~ 226 (232)
T PRK05950 195 FGVFRCHTIMNCVE------VCPKGLNPTKAIGEIKRM 226 (232)
T ss_pred cccccCcCcCCcCc------cccCCCCHHHHHHHHHHH
Confidence 38999888876542 223344455566666654
No 145
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=24.49 E-value=68 Score=18.97 Aligned_cols=18 Identities=11% Similarity=0.222 Sum_probs=11.7
Q ss_pred EEEeeCCCCeeEEccccc
Q 040416 8 GIWGCKDSSKVKAGGAYT 25 (47)
Q Consensus 8 GIW~C~~C~~~~AGGAy~ 25 (47)
..-.|..||+.|.-..+.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~ 86 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEFD 86 (113)
T ss_dssp -EEEETTTS-EEECHHCC
T ss_pred CcEECCCCCCEEecCCCC
Confidence 456899999998755443
No 146
>PF01831 Peptidase_C16: Peptidase C16 family; InterPro: IPR002705 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This entry contains coronavirus cysteine endopeptidases that belong to MEROPS peptidase families C30 (clan PA) and C16 (subfamiles C16A and C16B, clan CA). These peptidase are involved in viral polyprotein processing. All coronaviruses encodes between one and two accessory cysteine proteinases that recognise and process one or two sites in the amino-terminal half of the replicase polyprotein during assembly of the viral replication complex. MHV, HCoV and TGEV encode two accesssory proteinases, called coronavirus papain-like proteinase 1 and 2 (PL1-PRO and PL2-PRO). IBV and SARS encodes only one called PL-PRO []. Coronavirus papain-like proteinases 1 and 2 have restricted specificities, cleaving respectively two and one bond(s)in the polyprotein. This restricted activity may be due to extended specificity sites: Arg or Lys at the cleavage site position P5 are required for PL1-PRO [], and Phe at the cleavage site position P6 is required for PL2-PRO []. PL1-PRO releases p28 and p65 from the N terminus of the polyprotein; PL2-PRO cleaves between p210 and p150. ; GO: 0003968 RNA-directed RNA polymerase activity, 0008234 cysteine-type peptidase activity, 0006508 proteolysis
Probab=24.38 E-value=16 Score=25.45 Aligned_cols=14 Identities=21% Similarity=0.491 Sum_probs=11.3
Q ss_pred eEEEEEeeCCCCee
Q 040416 5 KAVGIWGCKDSSKV 18 (47)
Q Consensus 5 ~avGIW~C~~C~~~ 18 (47)
+++-+|.|.+|+-.
T Consensus 108 qaya~w~ClkC~~e 121 (249)
T PF01831_consen 108 QAYANWRCLKCQME 121 (249)
T ss_pred hhhhhhhHhhcCce
Confidence 46789999999854
No 147
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=24.36 E-value=90 Score=17.74 Aligned_cols=20 Identities=10% Similarity=-0.024 Sum_probs=12.8
Q ss_pred EEEEeeCCCCeeEEccccccccc
Q 040416 7 VGIWGCKDSSKVKAGGAYTLNIG 29 (47)
Q Consensus 7 vGIW~C~~C~~~~AGGAy~~~T~ 29 (47)
..+|.|.+|+. .|.|.++-+
T Consensus 25 ~~~v~C~~CgA---~~~~~~te~ 44 (64)
T PRK09710 25 YYRAKCNGCES---RTGYGGSEK 44 (64)
T ss_pred eEEEEcCCCCc---CcccccCHH
Confidence 34678999987 355555444
No 148
>TIGR02453 conserved hypothetical protein TIGR02453. Members of this family are widely (though sparsely) distributed bacterial proteins about 230 residues in length. All members have a motif RxxRDxRFxxx[DN]KxxY. The function of this protein family is unknown. In several fungi, this model identifies a conserved region of a longer protein. Therefore, it may be incorrect to speculate that all members share a common function.
Probab=24.32 E-value=69 Score=21.15 Aligned_cols=24 Identities=17% Similarity=0.315 Sum_probs=19.2
Q ss_pred CeeEEcccccccccHHHHHHHHHH
Q 040416 16 SKVKAGGAYTLNIGSAVTARVTIR 39 (47)
Q Consensus 16 ~~~~AGGAy~~~T~~a~tvk~~ir 39 (47)
+--++||-|.|+.+.-..+|..|.
T Consensus 107 ~~~~g~G~~~p~~~~L~~iR~~I~ 130 (217)
T TIGR02453 107 GSFAGGGLWGPEAETLAAVRAAIA 130 (217)
T ss_pred CeEEEEEeCCCCHHHHHHHHHHHH
Confidence 346788999999888888887774
No 149
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=24.24 E-value=38 Score=24.31 Aligned_cols=13 Identities=23% Similarity=0.851 Sum_probs=8.6
Q ss_pred EEEE-eeCCCCeeE
Q 040416 7 VGIW-GCKDSSKVK 19 (47)
Q Consensus 7 vGIW-~C~~C~~~~ 19 (47)
-|+| +|.+|+..+
T Consensus 25 e~lw~KCp~c~~~~ 38 (294)
T COG0777 25 EGLWTKCPSCGEML 38 (294)
T ss_pred CCceeECCCcccee
Confidence 4677 577777654
No 150
>PRK08640 sdhB succinate dehydrogenase iron-sulfur subunit; Reviewed
Probab=24.15 E-value=31 Score=23.15 Aligned_cols=32 Identities=13% Similarity=0.223 Sum_probs=17.8
Q ss_pred EEEEEeeCCCCeeEEcccccccccHHHHHHHHHHHHHh
Q 040416 6 AVGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLRE 43 (47)
Q Consensus 6 avGIW~C~~C~~~~AGGAy~~~T~~a~tvk~~irrl~e 43 (47)
..|+|.|..|+.=.. .=|.+.-....|.+||.
T Consensus 205 ~~g~~~C~~Cg~C~~------vCPkgI~~~~~I~~lr~ 236 (249)
T PRK08640 205 DGGIADCGNAQNCVR------VCPKGIPLTTSIAAMNR 236 (249)
T ss_pred CCCeeCCcCcCcccc------cCCCCCCHHHHHHHHHH
Confidence 358999998765321 12333444445555544
No 151
>PF12322 T4_baseplate: T4 bacteriophage base plate protein; InterPro: IPR024364 Proteins in this family are found in T4-like viruses. They have a single completely conserved residue S that may be functionally important. The family includes the two base plate proteins from bacteriophage T4: Gp51 and Gp26, encoded by late genes []. Gp26 is a structural component of central hub of the baseplate. It associates with Gp25 (tail lysozyme) in the assembly process. Gp51 is essential for the formation of the central hub of the phage baseplate, playing a catalytic role for the central hub formation. It may be also a structural component of the hub.
Probab=24.04 E-value=48 Score=21.92 Aligned_cols=11 Identities=18% Similarity=0.422 Sum_probs=9.1
Q ss_pred EEeeCCCCeeE
Q 040416 9 IWGCKDSSKVK 19 (47)
Q Consensus 9 IW~C~~C~~~~ 19 (47)
.|.|..||+.+
T Consensus 78 ~~~C~~cg~~~ 88 (205)
T PF12322_consen 78 NYTCPDCGEEV 88 (205)
T ss_pred EEECCCCCcEE
Confidence 49999999865
No 152
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=23.86 E-value=20 Score=24.34 Aligned_cols=12 Identities=25% Similarity=0.598 Sum_probs=9.2
Q ss_pred EEEEeeCCCCee
Q 040416 7 VGIWGCKDSSKV 18 (47)
Q Consensus 7 vGIW~C~~C~~~ 18 (47)
.|.|.|..|...
T Consensus 257 kgkWyC~~C~~~ 268 (274)
T KOG1973|consen 257 KGKWYCPRCKAE 268 (274)
T ss_pred CCcccchhhhhh
Confidence 367999999753
No 153
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=23.79 E-value=70 Score=15.62 Aligned_cols=13 Identities=23% Similarity=0.302 Sum_probs=9.3
Q ss_pred EEEEEeeCCCCee
Q 040416 6 AVGIWGCKDSSKV 18 (47)
Q Consensus 6 avGIW~C~~C~~~ 18 (47)
.+=|..|.+|+=.
T Consensus 16 ~~~id~C~~C~G~ 28 (41)
T PF13453_consen 16 DVEIDVCPSCGGI 28 (41)
T ss_pred CEEEEECCCCCeE
Confidence 3568899999643
No 154
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=23.64 E-value=37 Score=29.21 Aligned_cols=35 Identities=11% Similarity=0.209 Sum_probs=20.0
Q ss_pred EEEEEeeCCCCeeEEcccccccccH-HHHHHHHHHHHH
Q 040416 6 AVGIWGCKDSSKVKAGGAYTLNIGS-AVTARVTIRRLR 42 (47)
Q Consensus 6 avGIW~C~~C~~~~AGGAy~~~T~~-a~tvk~~irrl~ 42 (47)
..|+|+|..||.. |..+.+--.. +..++.+++.++
T Consensus 1602 ~~G~w~c~~~G~~--Gd~~dli~~~~g~~F~EA~~~~~ 1637 (1960)
T TIGR02760 1602 YRGLWHDFSTGEK--GTLIQLIEAKKGLSFKEALNQAA 1637 (1960)
T ss_pred cCCeEeccCCCCC--CCHHHHHHHHhCCCHHHHHHHHH
Confidence 3699999999963 5554443211 223555555444
No 155
>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]
Probab=23.23 E-value=18 Score=25.81 Aligned_cols=33 Identities=30% Similarity=0.620 Sum_probs=18.6
Q ss_pred EEeeCCCCeeEEcccccccccHHHHHHHHHHHHHhhhh
Q 040416 9 IWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLREQTE 46 (47)
Q Consensus 9 IW~C~~C~~~~AGGAy~~~T~~a~tvk~~irrl~e~~e 46 (47)
+|-||-|+++.+- .+---|.|.+ -=||||+..|
T Consensus 103 ~wackackrks~s----vDRRKAATMR-ERRRLkKVNE 135 (284)
T KOG3960|consen 103 LWACKACKRKSTS----VDRRKAATMR-ERRRLKKVNE 135 (284)
T ss_pred HHhhhhccccccc----hhHHHHHHHH-HHHHHHHHHH
Confidence 6999999987541 2222233433 3456666543
No 156
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This 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.
Probab=22.85 E-value=1.3e+02 Score=19.58 Aligned_cols=34 Identities=9% Similarity=0.042 Sum_probs=24.7
Q ss_pred EEeeCCCCeeEEcccccccccHHHHHHHHHHHHHh
Q 040416 9 IWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLRE 43 (47)
Q Consensus 9 IW~C~~C~~~~AGGAy~~~T~~a~tvk~~irrl~e 43 (47)
.|.|..|+..+- =.|-.-+-...-++..|.....
T Consensus 114 ~wyc~~c~~~~~-e~~f~~~d~~~~~~~~~~~f~~ 147 (159)
T TIGR03037 114 QWFCPQCGHKLH-RAEVQLENIVTDLPPVFEHFYS 147 (159)
T ss_pred EEECCCCCCeEE-EEEEEecChhhhhHHHHHHHhC
Confidence 499999998887 5555556666777777766544
No 157
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=22.09 E-value=52 Score=18.82 Aligned_cols=12 Identities=25% Similarity=0.393 Sum_probs=8.7
Q ss_pred EEeeCCCCeeEE
Q 040416 9 IWGCKDSSKVKA 20 (47)
Q Consensus 9 IW~C~~C~~~~A 20 (47)
-..|..||+.+-
T Consensus 80 h~iC~~Cg~v~~ 91 (120)
T PF01475_consen 80 HFICTQCGKVID 91 (120)
T ss_dssp EEEETTTS-EEE
T ss_pred EEEECCCCCEEE
Confidence 357999999873
No 158
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=21.94 E-value=37 Score=17.01 Aligned_cols=17 Identities=6% Similarity=0.299 Sum_probs=11.3
Q ss_pred eeCCCCeeEEccccccc
Q 040416 11 GCKDSSKVKAGGAYTLN 27 (47)
Q Consensus 11 ~C~~C~~~~AGGAy~~~ 27 (47)
+|+.||+.|=+......
T Consensus 20 ~Cr~Cg~~~C~~C~~~~ 36 (57)
T cd00065 20 HCRNCGRIFCSKCSSNR 36 (57)
T ss_pred ccCcCcCCcChHHcCCe
Confidence 68888888766554433
No 159
>PRK12575 succinate dehydrogenase iron-sulfur subunit; Provisional
Probab=21.33 E-value=33 Score=22.96 Aligned_cols=31 Identities=10% Similarity=0.231 Sum_probs=18.1
Q ss_pred EEEEeeCCCCeeEEcccccccccHHHHHHHHHHHHHh
Q 040416 7 VGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLRE 43 (47)
Q Consensus 7 vGIW~C~~C~~~~AGGAy~~~T~~a~tvk~~irrl~e 43 (47)
.|+|.|-.|+.=.. .=|.+.-....|.+||+
T Consensus 198 ~gl~~C~~C~~C~~------vCPkgI~~~~~I~~lR~ 228 (235)
T PRK12575 198 YRLFRCRTIMNCVD------VCPKGLNPARAIGQIRT 228 (235)
T ss_pred CCcccccCcchhcc------ccCCCCcHHHHHHHHHH
Confidence 48999988875322 12334445555666654
No 160
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=21.23 E-value=48 Score=21.86 Aligned_cols=36 Identities=14% Similarity=0.137 Sum_probs=21.4
Q ss_pred eeeEEEEEeeCCCCeeEEcccccccccHHHHHHHHHHHHHh
Q 040416 3 VRKAVGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLRE 43 (47)
Q Consensus 3 ~R~avGIW~C~~C~~~~AGGAy~~~T~~a~tvk~~irrl~e 43 (47)
.+...-.|.|.+||+.+= +-..-...++.-++.+++
T Consensus 124 ~~~~~~f~~C~~CgkiYW-----~GsHw~~m~~~~~~~~~~ 159 (165)
T COG1656 124 YRNYEEFYRCPKCGKIYW-----KGSHWRRMVERIVENLRP 159 (165)
T ss_pred hhcccceeECCCCccccc-----CchHHHHHHHHHHHHhcc
Confidence 345566899999999853 223444444444444444
No 161
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=21.12 E-value=68 Score=19.13 Aligned_cols=18 Identities=17% Similarity=0.063 Sum_probs=13.3
Q ss_pred EEEeeCCCCeeEEccccc
Q 040416 8 GIWGCKDSSKVKAGGAYT 25 (47)
Q Consensus 8 GIW~C~~C~~~~AGGAy~ 25 (47)
+...|+.|++.|.-..+.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~ 86 (115)
T TIGR00100 69 VECECEDCSEEVSPEIDL 86 (115)
T ss_pred cEEEcccCCCEEecCCcC
Confidence 457899999888776543
No 162
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=21.09 E-value=34 Score=21.17 Aligned_cols=16 Identities=19% Similarity=0.119 Sum_probs=12.7
Q ss_pred eeEEEEEeeCCCCeeE
Q 040416 4 RKAVGIWGCKDSSKVK 19 (47)
Q Consensus 4 R~avGIW~C~~C~~~~ 19 (47)
..-+|...|.+||.-+
T Consensus 42 eIevG~~~cP~Cge~~ 57 (102)
T PF04475_consen 42 EIEVGDTICPKCGEEL 57 (102)
T ss_pred EEecCcccCCCCCCcc
Confidence 3568999999999754
No 163
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=20.98 E-value=63 Score=16.04 Aligned_cols=11 Identities=27% Similarity=0.289 Sum_probs=6.4
Q ss_pred eeCCCCeeEEc
Q 040416 11 GCKDSSKVKAG 21 (47)
Q Consensus 11 ~C~~C~~~~AG 21 (47)
.|+.|++.|=.
T Consensus 15 ~C~~C~~~FC~ 25 (43)
T PF01428_consen 15 KCKHCGKSFCL 25 (43)
T ss_dssp E-TTTS-EE-T
T ss_pred ECCCCCcccCc
Confidence 68889988854
No 164
>PF08134 cIII: cIII protein family; InterPro: IPR012995 This family consists of the CIII family of regulatory proteins. The lambda CIII protein has 54 amino acids and it forms an amphipathic helix within its amino acid sequence. Lambda CIII stabilises the lambda CII protein and the host sigma factor 32, responsible for transcribing genes of the heat shock regulon [].
Probab=20.43 E-value=1.3e+02 Score=16.00 Aligned_cols=28 Identities=29% Similarity=0.277 Sum_probs=18.7
Q ss_pred eEEccc-----ccccccHHHHHHHHHHHHHhhh
Q 040416 18 VKAGGA-----YTLNIGSAVTARVTIRRLREQT 45 (47)
Q Consensus 18 ~~AGGA-----y~~~T~~a~tvk~~irrl~e~~ 45 (47)
.+|||. |.++....+-+++-||..++.-
T Consensus 5 ~laG~gvmSAyYP~ESELskr~rrLIRaa~k~l 37 (44)
T PF08134_consen 5 QLAGSGVMSAYYPTESELSKRIRRLIRAARKQL 37 (44)
T ss_pred EecCceeeeeecCcHHHHHHHHHHHHHHHHHHH
Confidence 456653 4556677788888888776653
No 165
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=20.38 E-value=71 Score=19.24 Aligned_cols=11 Identities=9% Similarity=0.250 Sum_probs=8.4
Q ss_pred EEeeCCCCeeE
Q 040416 9 IWGCKDSSKVK 19 (47)
Q Consensus 9 IW~C~~C~~~~ 19 (47)
...|.+||++|
T Consensus 100 Fy~C~~Cg~~w 110 (113)
T COG1594 100 FYKCTRCGYRW 110 (113)
T ss_pred EEEecccCCEe
Confidence 46788888876
No 166
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=20.11 E-value=54 Score=19.86 Aligned_cols=13 Identities=8% Similarity=0.115 Sum_probs=10.1
Q ss_pred EEEEeeCCCCeeE
Q 040416 7 VGIWGCKDSSKVK 19 (47)
Q Consensus 7 vGIW~C~~C~~~~ 19 (47)
.=.|.|.+|+..+
T Consensus 110 ~~~y~C~~C~~~~ 122 (146)
T smart00731 110 KYPYRCTGCGQRY 122 (146)
T ss_pred eEEEECCCCCCCC
Confidence 3589999998765
No 167
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=20.02 E-value=71 Score=20.26 Aligned_cols=19 Identities=16% Similarity=0.413 Sum_probs=9.5
Q ss_pred EEeeCCCCeeE----Eccccccc
Q 040416 9 IWGCKDSSKVK----AGGAYTLN 27 (47)
Q Consensus 9 IW~C~~C~~~~----AGGAy~~~ 27 (47)
-+.|.+||++. .+|+..|.
T Consensus 30 sf~C~~CGyk~~ev~~~~~~~~~ 52 (161)
T PF03367_consen 30 SFECEHCGYKNNEVKSGGQIQPK 52 (161)
T ss_dssp EEE-TTT--EEEEEEEECSS-SS
T ss_pred EeECCCCCCEeeeEEECccCCCC
Confidence 37899999864 35655543
Done!