Query psy17526
Match_columns 70
No_of_seqs 109 out of 361
Neff 6.3
Searched_HMMs 46136
Date Sat Aug 17 00:49:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17526.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17526hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0269|consensus 99.4 4.4E-14 9.6E-19 109.5 2.9 69 1-69 752-829 (839)
2 KOG0309|consensus 99.3 1.8E-12 4E-17 101.2 1.8 46 24-69 1032-1077(1081)
3 PF13639 zf-RING_2: Ring finge 97.6 1.6E-05 3.5E-10 41.4 0.0 37 25-61 5-42 (44)
4 PF12678 zf-rbx1: RING-H2 zinc 97.4 0.0001 2.2E-09 42.6 1.7 27 35-61 45-71 (73)
5 cd00162 RING RING-finger (Real 96.4 0.0029 6.2E-08 31.3 2.1 26 36-61 14-40 (45)
6 COG5194 APC11 Component of SCF 95.9 0.0064 1.4E-07 36.6 2.0 23 39-61 53-75 (88)
7 PF13923 zf-C3HC4_2: Zinc fing 95.8 0.0035 7.5E-08 31.7 0.6 36 25-61 3-38 (39)
8 smart00184 RING Ring finger. E 95.6 0.014 2.9E-07 27.7 2.3 25 37-61 13-38 (39)
9 PHA02929 N1R/p28-like protein; 95.4 0.017 3.7E-07 40.4 3.0 27 35-61 195-221 (238)
10 KOG2930|consensus 94.8 0.017 3.6E-07 36.3 1.4 24 38-61 79-102 (114)
11 COG5243 HRD1 HRD ubiquitin lig 94.5 0.026 5.7E-07 42.4 2.1 24 38-61 316-339 (491)
12 PF12861 zf-Apc11: Anaphase-pr 93.9 0.047 1E-06 32.9 2.0 23 39-61 51-76 (85)
13 PF13248 zf-ribbon_3: zinc-rib 93.8 0.042 9E-07 25.8 1.3 21 1-21 1-21 (26)
14 PF13719 zinc_ribbon_5: zinc-r 93.2 0.03 6.5E-07 28.4 0.3 35 1-44 1-35 (37)
15 KOG0802|consensus 92.9 0.061 1.3E-06 40.9 1.7 25 37-61 311-335 (543)
16 PF11793 FANCL_C: FANCL C-term 92.8 0.016 3.5E-07 33.1 -1.1 23 33-55 19-43 (70)
17 KOG4628|consensus 92.6 0.07 1.5E-06 39.3 1.6 41 24-65 233-275 (348)
18 PF12773 DZR: Double zinc ribb 92.2 0.057 1.2E-06 28.4 0.6 17 5-21 1-17 (50)
19 PF00097 zf-C3HC4: Zinc finger 91.7 0.13 2.9E-06 25.6 1.6 26 36-61 13-40 (41)
20 PF13717 zinc_ribbon_4: zinc-r 91.5 0.062 1.3E-06 27.2 0.2 34 1-43 1-34 (36)
21 PF11789 zf-Nse: Zinc-finger o 90.5 0.099 2.1E-06 28.9 0.4 27 38-64 28-57 (57)
22 PF13240 zinc_ribbon_2: zinc-r 89.4 0.22 4.8E-06 22.9 1.1 17 4-20 1-17 (23)
23 KOG0827|consensus 87.9 0.32 6.9E-06 36.8 1.6 24 38-61 24-50 (465)
24 COG5540 RING-finger-containing 87.5 0.3 6.5E-06 35.9 1.3 38 24-61 327-366 (374)
25 smart00504 Ubox Modified RING 87.0 0.38 8.2E-06 25.8 1.2 24 38-61 17-40 (63)
26 PF13920 zf-C3HC4_3: Zinc fing 86.8 0.41 8.9E-06 25.1 1.2 26 36-61 16-42 (50)
27 PF14634 zf-RING_5: zinc-RING 86.1 0.73 1.6E-05 23.6 2.0 27 35-61 15-41 (44)
28 PLN03208 E3 ubiquitin-protein 85.9 0.6 1.3E-05 31.9 2.0 29 24-54 22-50 (193)
29 COG5219 Uncharacterized conser 84.6 0.68 1.5E-05 38.8 2.1 27 35-61 1489-1517(1525)
30 smart00744 RINGv The RING-vari 84.5 0.88 1.9E-05 24.2 1.9 21 41-61 25-47 (49)
31 TIGR00599 rad18 DNA repair pro 83.9 1.1 2.4E-05 33.6 2.7 36 24-61 30-65 (397)
32 PF09889 DUF2116: Uncharacteri 80.9 0.84 1.8E-05 25.6 0.9 19 3-21 4-22 (59)
33 PHA02926 zinc finger-like prot 80.6 1.5 3.3E-05 30.9 2.3 29 33-61 190-224 (242)
34 KOG0317|consensus 80.4 1.5 3.2E-05 31.8 2.2 26 36-61 253-278 (293)
35 TIGR02098 MJ0042_CXXC MJ0042 f 75.9 1.2 2.6E-05 22.0 0.6 12 1-12 1-12 (38)
36 PF06906 DUF1272: Protein of u 75.4 2.4 5.3E-05 23.7 1.7 43 1-43 4-50 (57)
37 PF04606 Ogr_Delta: Ogr/Delta- 75.3 1.4 3E-05 23.2 0.7 34 4-43 1-36 (47)
38 PF01096 TFIIS_C: Transcriptio 74.2 1.3 2.9E-05 22.5 0.4 13 31-43 25-37 (39)
39 PRK14559 putative protein seri 74.1 1.3 2.9E-05 34.9 0.6 43 3-45 2-52 (645)
40 KOG0320|consensus 73.7 2.5 5.4E-05 28.8 1.8 41 24-65 135-175 (187)
41 PF15227 zf-C3HC4_4: zinc fing 73.1 2.8 6E-05 21.5 1.5 24 38-61 14-41 (42)
42 PRK14890 putative Zn-ribbon RN 72.9 1.9 4.1E-05 24.3 0.9 9 4-12 9-17 (59)
43 PF10571 UPF0547: Uncharacteri 72.1 2.5 5.4E-05 19.9 1.1 16 4-19 2-17 (26)
44 KOG1493|consensus 71.5 1.1 2.3E-05 26.8 -0.3 23 39-61 50-75 (84)
45 smart00661 RPOL9 RNA polymeras 70.4 3.3 7.1E-05 21.5 1.5 11 4-14 2-12 (52)
46 PF07649 C1_3: C1-like domain; 69.5 2 4.4E-05 20.3 0.4 25 25-49 5-30 (30)
47 PF09297 zf-NADH-PPase: NADH p 69.1 2.2 4.9E-05 20.5 0.6 11 2-12 3-13 (32)
48 smart00440 ZnF_C2C2 C2C2 Zinc 68.7 3.5 7.6E-05 21.0 1.3 16 27-43 22-37 (40)
49 KOG0828|consensus 65.4 3.1 6.7E-05 32.6 1.0 25 37-61 603-628 (636)
50 PRK05654 acetyl-CoA carboxylas 60.4 9.1 0.0002 27.4 2.6 33 29-65 22-54 (292)
51 TIGR01206 lysW lysine biosynth 60.0 5.2 0.00011 22.0 1.0 12 1-12 1-12 (54)
52 TIGR00515 accD acetyl-CoA carb 58.5 10 0.00023 27.1 2.6 32 30-65 22-53 (285)
53 PF08209 Sgf11: Sgf11 (transcr 57.4 3 6.4E-05 20.8 -0.3 11 2-12 4-14 (33)
54 PF14353 CpXC: CpXC protein 57.2 5.4 0.00012 24.5 0.9 46 3-48 2-52 (128)
55 PF14392 zf-CCHC_4: Zinc knuck 56.2 5.5 0.00012 20.9 0.7 17 31-47 28-44 (49)
56 PF12906 RINGv: RING-variant d 54.7 5.4 0.00012 20.9 0.5 19 43-61 26-46 (47)
57 KOG2691|consensus 54.7 6.5 0.00014 24.8 0.9 16 28-43 95-110 (113)
58 PF06677 Auto_anti-p27: Sjogre 54.7 5.6 0.00012 20.6 0.5 14 1-14 16-29 (41)
59 cd04476 RPA1_DBD_C RPA1_DBD_C: 53.5 6 0.00013 25.3 0.6 22 2-23 34-58 (166)
60 CHL00174 accD acetyl-CoA carbo 52.2 9.8 0.00021 27.5 1.6 38 24-65 28-65 (296)
61 PF14803 Nudix_N_2: Nudix N-te 52.2 6 0.00013 19.7 0.4 9 4-12 2-10 (34)
62 PF06827 zf-FPG_IleRS: Zinc fi 51.8 4.9 0.00011 18.9 0.0 12 3-14 2-13 (30)
63 COG1645 Uncharacterized Zn-fin 51.2 5.4 0.00012 25.7 0.2 12 2-13 28-39 (131)
64 KOG0823|consensus 50.8 9.7 0.00021 26.8 1.4 38 24-64 51-91 (230)
65 COG1885 Uncharacterized protei 50.0 8.8 0.00019 24.2 0.9 13 2-14 49-61 (115)
66 smart00834 CxxC_CXXC_SSSS Puta 48.8 8.7 0.00019 18.8 0.7 11 3-13 27-37 (41)
67 COG2888 Predicted Zn-ribbon RN 47.1 9.3 0.0002 21.7 0.7 10 3-12 10-19 (61)
68 COG1571 Predicted DNA-binding 46.1 13 0.00027 28.3 1.4 22 2-23 350-374 (421)
69 KOG2041|consensus 45.5 6.2 0.00013 32.6 -0.3 55 3-61 1118-1179(1189)
70 PF04981 NMD3: NMD3 family ; 45.0 9.3 0.0002 26.1 0.6 38 5-42 1-43 (236)
71 PF04032 Rpr2: RNAse P Rpr2/Rp 44.6 7.1 0.00015 22.1 -0.1 39 2-42 46-85 (85)
72 PHA00626 hypothetical protein 44.0 11 0.00025 21.1 0.7 17 3-20 1-18 (59)
73 KOG1952|consensus 43.4 7.4 0.00016 32.2 -0.1 32 24-55 195-228 (950)
74 PF01927 Mut7-C: Mut7-C RNAse 43.1 28 0.0006 22.1 2.5 49 2-51 91-145 (147)
75 PF03884 DUF329: Domain of unk 43.0 6.9 0.00015 21.8 -0.3 13 1-13 1-13 (57)
76 PF07754 DUF1610: Domain of un 42.7 12 0.00026 17.4 0.6 7 4-10 18-24 (24)
77 PF13445 zf-RING_UBOX: RING-ty 42.4 15 0.00033 19.0 1.0 19 38-56 17-35 (43)
78 COG2816 NPY1 NTP pyrophosphohy 42.2 20 0.00043 25.8 1.9 11 2-12 111-121 (279)
79 PF01530 zf-C2HC: Zinc finger, 42.1 13 0.00028 18.3 0.7 8 57-64 2-10 (31)
80 PRK02048 4-hydroxy-3-methylbut 42.1 10 0.00022 30.1 0.4 11 2-12 518-528 (611)
81 PF04423 Rad50_zn_hook: Rad50 40.8 7.6 0.00016 20.6 -0.3 12 4-15 22-33 (54)
82 PF10122 Mu-like_Com: Mu-like 40.7 7.4 0.00016 21.3 -0.4 13 3-15 5-17 (51)
83 PRK14810 formamidopyrimidine-D 40.5 14 0.00031 25.8 1.0 9 4-12 246-254 (272)
84 PF01396 zf-C4_Topoisom: Topoi 40.3 13 0.00027 18.8 0.5 10 3-12 2-11 (39)
85 KOG0826|consensus 40.2 22 0.00048 26.4 1.9 24 33-64 320-344 (357)
86 KOG1734|consensus 40.1 15 0.00032 26.9 1.0 27 35-61 247-275 (328)
87 PRK00420 hypothetical protein; 40.1 16 0.00034 22.9 1.0 21 1-21 22-45 (112)
88 PHA02862 5L protein; Provision 39.9 28 0.00061 23.1 2.2 21 41-61 25-47 (156)
89 PRK13945 formamidopyrimidine-D 39.8 16 0.00034 25.7 1.1 10 4-13 256-265 (282)
90 PF04475 DUF555: Protein of un 39.7 17 0.00036 22.6 1.0 14 2-15 47-60 (102)
91 PF08746 zf-RING-like: RING-li 39.0 23 0.00051 18.2 1.4 27 35-61 12-42 (43)
92 TIGR03826 YvyF flagellar opero 38.6 16 0.00034 23.6 0.9 22 1-23 80-101 (137)
93 PF07282 OrfB_Zn_ribbon: Putat 38.2 30 0.00065 18.8 1.9 20 32-51 44-63 (69)
94 PRK14811 formamidopyrimidine-D 37.9 18 0.00038 25.4 1.1 28 4-43 237-264 (269)
95 PF13408 Zn_ribbon_recom: Reco 37.5 12 0.00027 19.3 0.2 10 3-12 6-15 (58)
96 PF06750 DiS_P_DiS: Bacterial 37.3 25 0.00055 20.9 1.6 11 2-12 33-43 (92)
97 PF14260 zf-C4pol: C4-type zin 37.3 21 0.00046 19.8 1.2 37 5-41 1-52 (73)
98 PF03942 DTW: DTW domain; Int 36.5 24 0.00051 23.3 1.5 19 1-21 1-19 (203)
99 PRK03922 hypothetical protein; 36.4 20 0.00043 22.6 1.0 14 2-15 49-62 (113)
100 PF03119 DNA_ligase_ZBD: NAD-d 36.3 13 0.00028 17.6 0.1 10 4-13 1-10 (28)
101 COG1997 RPL43A Ribosomal prote 36.2 22 0.00047 21.6 1.1 20 4-23 37-60 (89)
102 PF13005 zf-IS66: zinc-finger 35.9 17 0.00036 18.4 0.5 14 3-16 3-16 (47)
103 PRK00398 rpoP DNA-directed RNA 35.4 15 0.00033 18.8 0.4 10 3-12 22-31 (46)
104 PF09723 Zn-ribbon_8: Zinc rib 34.7 18 0.00039 18.4 0.6 8 3-10 27-34 (42)
105 PRK01103 formamidopyrimidine/5 34.2 21 0.00045 24.9 0.9 10 4-13 247-256 (274)
106 smart00290 ZnF_UBP Ubiquitin C 34.1 29 0.00062 17.6 1.3 22 34-55 11-36 (50)
107 PRK10445 endonuclease VIII; Pr 33.8 22 0.00047 24.8 1.0 11 3-13 236-246 (263)
108 PF13453 zf-TFIIB: Transcripti 33.5 19 0.00041 18.0 0.5 11 4-14 1-11 (41)
109 COG4068 Uncharacterized protei 33.4 21 0.00046 20.2 0.7 19 3-21 9-27 (64)
110 COG5432 RAD18 RING-finger-cont 33.0 37 0.00081 25.2 2.1 24 38-61 41-64 (391)
111 PF07227 DUF1423: Protein of u 32.7 18 0.00038 27.8 0.4 30 24-53 132-165 (446)
112 PRK12366 replication factor A; 32.3 17 0.00037 28.6 0.3 23 1-23 531-555 (637)
113 COG0777 AccD Acetyl-CoA carbox 32.3 32 0.0007 25.0 1.7 31 31-65 25-55 (294)
114 KOG2906|consensus 32.3 18 0.00038 22.6 0.3 10 3-12 2-11 (105)
115 PRK09678 DNA-binding transcrip 32.1 43 0.00094 19.3 1.9 35 3-43 2-38 (72)
116 PF10892 DUF2688: Protein of u 31.7 13 0.00029 20.8 -0.3 11 2-12 10-20 (60)
117 PRK00694 4-hydroxy-3-methylbut 31.2 18 0.0004 28.7 0.3 13 1-13 509-521 (606)
118 PF14787 zf-CCHC_5: GAG-polypr 30.9 24 0.00051 18.0 0.6 10 3-12 3-12 (36)
119 PF15288 zf-CCHC_6: Zinc knuck 30.3 30 0.00064 18.0 0.9 19 36-61 3-21 (40)
120 PRK11088 rrmA 23S rRNA methylt 30.1 31 0.00068 23.6 1.3 21 1-21 1-23 (272)
121 PRK05767 rpl44e 50S ribosomal 30.1 26 0.00056 21.3 0.8 12 2-13 8-19 (92)
122 COG4830 RPS26B Ribosomal prote 29.9 25 0.00055 21.9 0.7 20 2-21 20-39 (108)
123 PTZ00157 60S ribosomal protein 29.8 27 0.00057 21.0 0.8 12 2-13 9-20 (84)
124 PTZ00166 DNA polymerase delta 29.7 41 0.00088 28.2 2.0 43 2-45 960-1017(1054)
125 PHA02825 LAP/PHD finger-like p 29.6 64 0.0014 21.6 2.6 23 39-61 24-53 (162)
126 KOG4718|consensus 28.8 51 0.0011 23.2 2.1 27 35-61 195-221 (235)
127 PHA02776 E7 protein; Provision 28.0 34 0.00073 21.1 1.0 38 3-41 59-98 (101)
128 COG2023 RPR2 RNase P subunit R 27.8 25 0.00054 21.9 0.4 36 2-44 56-92 (105)
129 PRK02935 hypothetical protein; 27.2 26 0.00056 22.0 0.4 11 2-12 70-80 (110)
130 PF06524 NOA36: NOA36 protein; 27.1 33 0.00072 25.0 1.0 39 4-45 173-220 (314)
131 TIGR00577 fpg formamidopyrimid 27.0 22 0.00048 24.8 0.1 9 4-12 247-255 (272)
132 PRK13130 H/ACA RNA-protein com 26.9 43 0.00094 18.5 1.3 11 2-12 17-27 (56)
133 KOG2612|consensus 26.9 31 0.00067 21.2 0.7 12 1-12 73-84 (103)
134 TIGR03037 anthran_nbaC 3-hydro 26.6 62 0.0013 21.4 2.2 33 29-61 109-156 (159)
135 PRK13264 3-hydroxyanthranilate 26.3 60 0.0013 21.9 2.1 35 29-64 115-164 (177)
136 PF08646 Rep_fac-A_C: Replicat 26.0 28 0.00061 21.7 0.5 22 2-23 18-44 (146)
137 PF11023 DUF2614: Protein of u 25.6 27 0.00059 22.1 0.3 11 2-12 69-79 (114)
138 PF13913 zf-C2HC_2: zinc-finge 25.3 37 0.00081 15.3 0.7 10 3-12 3-12 (25)
139 TIGR03823 FliZ flagellar regul 25.2 24 0.00053 23.6 0.1 19 2-21 22-40 (168)
140 TIGR00570 cdk7 CDK-activating 25.2 93 0.002 22.8 3.0 25 39-64 25-50 (309)
141 PLN02925 4-hydroxy-3-methylbut 25.0 31 0.00067 28.1 0.6 14 1-14 633-646 (733)
142 PF02150 RNA_POL_M_15KD: RNA p 24.9 26 0.00056 17.3 0.1 10 3-12 2-11 (35)
143 PF02148 zf-UBP: Zn-finger in 24.7 15 0.00032 20.1 -0.9 24 32-55 9-36 (63)
144 PRK11582 flagella biosynthesis 24.3 27 0.00059 23.4 0.2 19 2-21 22-40 (169)
145 PRK08402 replication factor A; 24.2 26 0.00056 25.8 0.0 21 1-21 211-235 (355)
146 PF12677 DUF3797: Domain of un 24.2 31 0.00067 18.7 0.3 12 1-12 12-23 (49)
147 KOG1941|consensus 24.2 40 0.00086 26.0 1.0 25 37-61 384-410 (518)
148 KOG2114|consensus 24.0 36 0.00078 28.4 0.8 20 39-61 858-877 (933)
149 PRK07218 replication factor A; 23.9 41 0.00089 25.4 1.1 18 2-21 297-314 (423)
150 PF06676 DUF1178: Protein of u 23.9 29 0.00063 22.7 0.2 28 34-65 2-40 (148)
151 PRK05978 hypothetical protein; 23.4 47 0.001 21.7 1.2 34 27-64 26-59 (148)
152 PF14446 Prok-RING_1: Prokaryo 23.1 60 0.0013 17.8 1.4 26 24-49 9-36 (54)
153 PF03107 C1_2: C1 domain; Int 22.8 12 0.00027 17.6 -1.3 23 25-47 5-28 (30)
154 PF03811 Zn_Tnp_IS1: InsA N-te 22.8 42 0.0009 16.8 0.6 11 2-12 5-15 (36)
155 PF14690 zf-ISL3: zinc-finger 22.6 44 0.00096 16.6 0.7 10 3-12 3-12 (47)
156 PF00098 zf-CCHC: Zinc knuckle 22.3 36 0.00078 14.3 0.3 11 36-46 2-12 (18)
157 COG1631 RPL42A Ribosomal prote 21.9 40 0.00087 20.6 0.5 11 2-12 8-18 (94)
158 COG1998 RPS31 Ribosomal protei 21.9 44 0.00096 18.3 0.7 9 2-10 19-27 (51)
159 PF08271 TF_Zn_Ribbon: TFIIB z 21.8 46 0.00099 16.7 0.7 9 4-12 2-10 (43)
160 KOG0825|consensus 21.6 65 0.0014 27.1 1.8 31 31-61 135-165 (1134)
161 PRK00418 DNA gyrase inhibitor; 21.4 53 0.0012 18.5 0.9 10 3-12 7-16 (62)
162 PF12760 Zn_Tnp_IS1595: Transp 21.3 49 0.0011 16.9 0.7 9 3-11 19-27 (46)
163 PF04828 GFA: Glutathione-depe 21.2 21 0.00045 19.8 -0.8 12 2-13 48-59 (92)
164 PRK11866 2-oxoacid ferredoxin 21.2 59 0.0013 23.1 1.4 25 30-54 3-27 (279)
165 cd02340 ZZ_NBR1_like Zinc fing 20.6 77 0.0017 16.2 1.4 21 3-23 1-21 (43)
166 PRK09628 oorB 2-oxoglutarate-a 20.5 80 0.0017 22.3 1.9 22 34-55 16-37 (277)
167 PF01286 XPA_N: XPA protein N- 20.4 40 0.00087 16.8 0.3 12 2-13 3-14 (34)
168 PF04564 U-box: U-box domain; 20.3 62 0.0013 18.0 1.1 23 39-61 21-44 (73)
169 COG3024 Uncharacterized protei 20.1 60 0.0013 18.6 1.0 13 2-14 7-19 (65)
170 COG3791 Uncharacterized conser 20.1 49 0.0011 20.7 0.7 11 2-12 69-79 (133)
No 1
>KOG0269|consensus
Probab=99.44 E-value=4.4e-14 Score=109.54 Aligned_cols=69 Identities=28% Similarity=0.624 Sum_probs=61.7
Q ss_pred CcccCccCCCCCCcC-ccccccch-------HHHHhhhhcccccccCCCCCChHHHHHHHHhCCCCCCC-CCCccccC
Q psy17526 1 MNAHSDRCQHGLGNF-GKLEGKIQ-------MLVFCLVSGLYSWCQGCSHGGHLSHMQEWFMKNNVCPT-GCGHYCES 69 (70)
Q Consensus 1 ~~~~C~~C~~~l~~~-~~~C~~~~-------~iC~~~v~~l~~~C~~C~HggH~~h~~~Wf~~~~~CP~-gC~c~C~~ 69 (70)
|.+.|++|++++... .|+|+++. ++|+++|+|+++||+.|+|+||.+|++.||..+..||. +||+.|.+
T Consensus 752 i~~~~~nc~a~~~~~~~~~c~rc~s~a~~~CtVC~~vi~G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~~~C~~~c~~ 829 (839)
T KOG0269|consen 752 IHYACPNCDAPMVLTKLWQCDRCESRASAKCTVCDLVIRGVDVWCQVCGHGGHDSHLKSWFFKASPCAKSICPHLCHY 829 (839)
T ss_pred eeccccccCCccccccceeechHHHHhhcCceeecceeeeeEeecccccccccHHHHHHHHhcCCCCccccCCccccc
Confidence 346899999999544 38999954 78999999999999999999999999999999999998 79999975
No 2
>KOG0309|consensus
Probab=99.25 E-value=1.8e-12 Score=101.21 Aligned_cols=46 Identities=41% Similarity=0.917 Sum_probs=44.5
Q ss_pred HHHHhhhhcccccccCCCCCChHHHHHHHHhCCCCCCCCCCccccC
Q psy17526 24 MLVFCLVSGLYSWCQGCSHGGHLSHMQEWFMKNNVCPTGCGHYCES 69 (70)
Q Consensus 24 ~iC~~~v~~l~~~C~~C~HggH~~h~~~Wf~~~~~CP~gC~c~C~~ 69 (70)
+||+..|+|+..+|.+|+|+||.+|++|||....+||+||||.|.+
T Consensus 1032 ~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~gd~CpsGCGC~C~~ 1077 (1081)
T KOG0309|consen 1032 AICHLAVRGSSNFCGTCGHVGHTSCMMEWFRTGDVCPSGCGCHCLL 1077 (1081)
T ss_pred eeEeeEeeccchhhccccccccHHHHHHHHhcCCcCCCCCCcCchh
Confidence 8999999999999999999999999999999999999999999964
No 3
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=97.57 E-value=1.6e-05 Score=41.38 Aligned_cols=37 Identities=30% Similarity=0.508 Sum_probs=27.0
Q ss_pred HHHhhhh-cccccccCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 25 LVFCLVS-GLYSWCQGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 25 iC~~~v~-~l~~~C~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
||.+.+. +-.+.-+.|+|..|.+++++|++++..||+
T Consensus 5 IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~ 42 (44)
T PF13639_consen 5 ICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPV 42 (44)
T ss_dssp TTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TT
T ss_pred CCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCc
Confidence 4544442 334445569999999999999999999997
No 4
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=97.38 E-value=0.0001 Score=42.62 Aligned_cols=27 Identities=30% Similarity=0.652 Sum_probs=22.9
Q ss_pred ccccCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 35 SWCQGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 35 ~~C~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
+.=..|+|..|.++|++|+..+.+||+
T Consensus 45 i~~~~C~H~FH~~Ci~~Wl~~~~~CP~ 71 (73)
T PF12678_consen 45 IVWGPCGHIFHFHCISQWLKQNNTCPL 71 (73)
T ss_dssp EEEETTSEEEEHHHHHHHHTTSSB-TT
T ss_pred eEecccCCCEEHHHHHHHHhcCCcCCC
Confidence 334569999999999999999999997
No 5
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=96.42 E-value=0.0029 Score=31.31 Aligned_cols=26 Identities=27% Similarity=0.531 Sum_probs=22.4
Q ss_pred cccCCCCCChHHHHHHHHhC-CCCCCC
Q psy17526 36 WCQGCSHGGHLSHMQEWFMK-NNVCPT 61 (70)
Q Consensus 36 ~C~~C~HggH~~h~~~Wf~~-~~~CP~ 61 (70)
.-..|+|..|.+++++|++. ...||.
T Consensus 14 ~~~~C~H~~c~~C~~~~~~~~~~~Cp~ 40 (45)
T cd00162 14 VLLPCGHVFCRSCIDKWLKSGKNTCPL 40 (45)
T ss_pred EecCCCChhcHHHHHHHHHhCcCCCCC
Confidence 34569999999999999998 778997
No 6
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=95.88 E-value=0.0064 Score=36.59 Aligned_cols=23 Identities=30% Similarity=0.693 Sum_probs=21.5
Q ss_pred CCCCCChHHHHHHHHhCCCCCCC
Q psy17526 39 GCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 39 ~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
.|.|..|.+++..|++...+||.
T Consensus 53 ~CnHaFH~HCI~rWL~Tk~~CPl 75 (88)
T COG5194 53 VCNHAFHDHCIYRWLDTKGVCPL 75 (88)
T ss_pred ecchHHHHHHHHHHHhhCCCCCC
Confidence 39999999999999999999995
No 7
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=95.82 E-value=0.0035 Score=31.72 Aligned_cols=36 Identities=17% Similarity=0.314 Sum_probs=26.8
Q ss_pred HHHhhhhcccccccCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 25 LVFCLVSGLYSWCQGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 25 iC~~~v~~l~~~C~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
||.+.++. .+.-..|||....+++++|+++...||+
T Consensus 3 iC~~~~~~-~~~~~~CGH~fC~~C~~~~~~~~~~CP~ 38 (39)
T PF13923_consen 3 ICLDELRD-PVVVTPCGHSFCKECIEKYLEKNPKCPV 38 (39)
T ss_dssp TTTSB-SS-EEEECTTSEEEEHHHHHHHHHCTSB-TT
T ss_pred CCCCcccC-cCEECCCCCchhHHHHHHHHHCcCCCcC
Confidence 34444444 3457899999999999999999888986
No 8
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=95.57 E-value=0.014 Score=27.73 Aligned_cols=25 Identities=32% Similarity=0.678 Sum_probs=21.1
Q ss_pred ccCCCCCChHHHHHHHHh-CCCCCCC
Q psy17526 37 CQGCSHGGHLSHMQEWFM-KNNVCPT 61 (70)
Q Consensus 37 C~~C~HggH~~h~~~Wf~-~~~~CP~ 61 (70)
-+.|+|..|.+++++|++ ....||+
T Consensus 13 ~~~C~H~~c~~C~~~~~~~~~~~CP~ 38 (39)
T smart00184 13 VLPCGHTFCRSCIRKWLKSGNNTCPI 38 (39)
T ss_pred EecCCChHHHHHHHHHHHhCcCCCCC
Confidence 356999999999999998 5667885
No 9
>PHA02929 N1R/p28-like protein; Provisional
Probab=95.37 E-value=0.017 Score=40.37 Aligned_cols=27 Identities=22% Similarity=0.533 Sum_probs=24.2
Q ss_pred ccccCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 35 SWCQGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 35 ~~C~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
..=..|+|..|..|+.+|.....+||+
T Consensus 195 ~vl~~C~H~FC~~CI~~Wl~~~~tCPl 221 (238)
T PHA02929 195 GILSNCNHVFCIECIDIWKKEKNTCPV 221 (238)
T ss_pred eecCCCCCcccHHHHHHHHhcCCCCCC
Confidence 345689999999999999999999998
No 10
>KOG2930|consensus
Probab=94.75 E-value=0.017 Score=36.29 Aligned_cols=24 Identities=33% Similarity=0.822 Sum_probs=22.5
Q ss_pred cCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 38 QGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 38 ~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
..|.|..|.++|..|+.+..+||.
T Consensus 79 G~CNHaFH~hCisrWlktr~vCPL 102 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLKTRNVCPL 102 (114)
T ss_pred eecchHHHHHHHHHHHhhcCcCCC
Confidence 469999999999999999999996
No 11
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=94.48 E-value=0.026 Score=42.39 Aligned_cols=24 Identities=29% Similarity=0.782 Sum_probs=22.8
Q ss_pred cCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 38 QGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 38 ~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
+.|||..|.+|++.|.++..+||.
T Consensus 316 LpCGHilHl~CLknW~ERqQTCPI 339 (491)
T COG5243 316 LPCGHILHLHCLKNWLERQQTCPI 339 (491)
T ss_pred ccccceeeHHHHHHHHHhccCCCc
Confidence 579999999999999999999997
No 12
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=93.90 E-value=0.047 Score=32.88 Aligned_cols=23 Identities=30% Similarity=0.816 Sum_probs=20.1
Q ss_pred CCCCCChHHHHHHHHhC---CCCCCC
Q psy17526 39 GCSHGGHLSHMQEWFMK---NNVCPT 61 (70)
Q Consensus 39 ~C~HggH~~h~~~Wf~~---~~~CP~ 61 (70)
.|+|..|.+++.+|+++ ...||.
T Consensus 51 ~C~H~FH~hCI~kWl~~~~~~~~CPm 76 (85)
T PF12861_consen 51 KCSHNFHMHCILKWLSTQSSKGQCPM 76 (85)
T ss_pred cCccHHHHHHHHHHHccccCCCCCCC
Confidence 49999999999999997 367885
No 13
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=93.76 E-value=0.042 Score=25.83 Aligned_cols=21 Identities=14% Similarity=0.199 Sum_probs=15.3
Q ss_pred CcccCccCCCCCCcCcccccc
Q psy17526 1 MNAHSDRCQHGLGNFGKLEGK 21 (70)
Q Consensus 1 ~~~~C~~C~~~l~~~~~~C~~ 21 (70)
|-+.||+||+.++....+|..
T Consensus 1 m~~~Cp~Cg~~~~~~~~fC~~ 21 (26)
T PF13248_consen 1 MEMFCPNCGAEIDPDAKFCPN 21 (26)
T ss_pred CcCCCcccCCcCCcccccChh
Confidence 567899999988666555543
No 14
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.21 E-value=0.03 Score=28.39 Aligned_cols=35 Identities=20% Similarity=0.172 Sum_probs=22.8
Q ss_pred CcccCccCCCCCCcCccccccchHHHHhhhhcccccccCCCCCC
Q psy17526 1 MNAHSDRCQHGLGNFGKLEGKIQMLVFCLVSGLYSWCQGCSHGG 44 (70)
Q Consensus 1 ~~~~C~~C~~~l~~~~~~C~~~~~iC~~~v~~l~~~C~~C~Hgg 44 (70)
|.+.||+|+....-.. -..+..+..+-|.+|+|..
T Consensus 1 M~i~CP~C~~~f~v~~---------~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPD---------DKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred CEEECCCCCceEEcCH---------HHcccCCcEEECCCCCcEe
Confidence 7899999998773221 0023456677788888753
No 15
>KOG0802|consensus
Probab=92.88 E-value=0.061 Score=40.93 Aligned_cols=25 Identities=36% Similarity=0.735 Sum_probs=23.3
Q ss_pred ccCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 37 CQGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 37 C~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
=+.|+|..|.+++++||++...||+
T Consensus 311 rL~C~Hifh~~CL~~W~er~qtCP~ 335 (543)
T KOG0802|consen 311 RLPCGHIFHDSCLRSWFERQQTCPT 335 (543)
T ss_pred eeecccchHHHHHHHHHHHhCcCCc
Confidence 3679999999999999999999997
No 16
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=92.83 E-value=0.016 Score=33.14 Aligned_cols=23 Identities=30% Similarity=0.674 Sum_probs=12.9
Q ss_pred cccccc--CCCCCChHHHHHHHHhC
Q psy17526 33 LYSWCQ--GCSHGGHLSHMQEWFMK 55 (70)
Q Consensus 33 l~~~C~--~C~HggH~~h~~~Wf~~ 55 (70)
..++|. +|+...|..+|.+||++
T Consensus 19 p~~~C~n~~C~~~fH~~CL~~wf~~ 43 (70)
T PF11793_consen 19 PDVVCPNPSCGKKFHLLCLSEWFLS 43 (70)
T ss_dssp --B--S-TT----B-SGGGHHHHHH
T ss_pred CceEcCCcccCCHHHHHHHHHHHHH
Confidence 457787 99999999999999996
No 17
>KOG4628|consensus
Probab=92.58 E-value=0.07 Score=39.26 Aligned_cols=41 Identities=22% Similarity=0.516 Sum_probs=29.6
Q ss_pred HHHH-hhhhcccccccCCCCCChHHHHHHHHhCCC-CCCCCCCc
Q psy17526 24 MLVF-CLVSGLYSWCQGCSHGGHLSHMQEWFMKNN-VCPTGCGH 65 (70)
Q Consensus 24 ~iC~-~~v~~l~~~C~~C~HggH~~h~~~Wf~~~~-~CP~gC~c 65 (70)
+||- +-..|--+-=+.|.|-.|.+|+.-|+.+.+ .||+ |..
T Consensus 233 aIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPv-CK~ 275 (348)
T KOG4628|consen 233 AICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPV-CKR 275 (348)
T ss_pred EEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCC-CCC
Confidence 5662 333344444489999999999999999985 5998 543
No 18
>PF12773 DZR: Double zinc ribbon
Probab=92.20 E-value=0.057 Score=28.39 Aligned_cols=17 Identities=12% Similarity=0.069 Sum_probs=10.0
Q ss_pred CccCCCCCCcCcccccc
Q psy17526 5 SDRCQHGLGNFGKLEGK 21 (70)
Q Consensus 5 C~~C~~~l~~~~~~C~~ 21 (70)
||+||++++....+|..
T Consensus 1 Cp~Cg~~~~~~~~fC~~ 17 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPH 17 (50)
T ss_pred CCCcCCcCCccccCChh
Confidence 56677776555445543
No 19
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=91.71 E-value=0.13 Score=25.64 Aligned_cols=26 Identities=19% Similarity=0.459 Sum_probs=22.1
Q ss_pred cccCCCCCChHHHHHHHHh--CCCCCCC
Q psy17526 36 WCQGCSHGGHLSHMQEWFM--KNNVCPT 61 (70)
Q Consensus 36 ~C~~C~HggH~~h~~~Wf~--~~~~CP~ 61 (70)
.-..|+|....+++++|++ ....||.
T Consensus 13 ~~~~C~H~fC~~C~~~~~~~~~~~~CP~ 40 (41)
T PF00097_consen 13 ILLPCGHSFCRDCLRKWLENSGSVKCPL 40 (41)
T ss_dssp EETTTSEEEEHHHHHHHHHHTSSSBTTT
T ss_pred EEecCCCcchHHHHHHHHHhcCCccCCc
Confidence 4578999999999999999 4567885
No 20
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=91.49 E-value=0.062 Score=27.17 Aligned_cols=34 Identities=21% Similarity=0.188 Sum_probs=21.6
Q ss_pred CcccCccCCCCCCcCccccccchHHHHhhhhcccccccCCCCC
Q psy17526 1 MNAHSDRCQHGLGNFGKLEGKIQMLVFCLVSGLYSWCQGCSHG 43 (70)
Q Consensus 1 ~~~~C~~C~~~l~~~~~~C~~~~~iC~~~v~~l~~~C~~C~Hg 43 (70)
|.+.||+|++...-.. -..+-.+..+-|.+|+|.
T Consensus 1 M~i~Cp~C~~~y~i~d---------~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDD---------EKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred CEEECCCCCCEEeCCH---------HHCCCCCcEEECCCCCCE
Confidence 7889999988762221 002335567778888875
No 21
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=90.53 E-value=0.099 Score=28.94 Aligned_cols=27 Identities=22% Similarity=0.696 Sum_probs=18.6
Q ss_pred cCCCCCChHHHHHHHHhC--CCCCCC-CCC
Q psy17526 38 QGCSHGGHLSHMQEWFMK--NNVCPT-GCG 64 (70)
Q Consensus 38 ~~C~HggH~~h~~~Wf~~--~~~CP~-gC~ 64 (70)
..|+|..=.+.+.+|+++ ...||+ ||.
T Consensus 28 ~~C~H~fek~aI~~~i~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 28 KKCGHTFEKEAILQYIQRNGSKRCPVAGCN 57 (57)
T ss_dssp SSS--EEEHHHHHHHCTTTS-EE-SCCC-S
T ss_pred CCCCCeecHHHHHHHHHhcCCCCCCCCCCC
Confidence 389999999999999944 578998 884
No 22
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=89.41 E-value=0.22 Score=22.87 Aligned_cols=17 Identities=12% Similarity=0.143 Sum_probs=12.2
Q ss_pred cCccCCCCCCcCccccc
Q psy17526 4 HSDRCQHGLGNFGKLEG 20 (70)
Q Consensus 4 ~C~~C~~~l~~~~~~C~ 20 (70)
.||+||+.++.....|.
T Consensus 1 ~Cp~CG~~~~~~~~fC~ 17 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCP 17 (23)
T ss_pred CCcccCCCCCCcCcchh
Confidence 48899999876654554
No 23
>KOG0827|consensus
Probab=87.85 E-value=0.32 Score=36.77 Aligned_cols=24 Identities=33% Similarity=0.735 Sum_probs=20.0
Q ss_pred cCCCCCChHHHHHHHHhC---CCCCCC
Q psy17526 38 QGCSHGGHLSHMQEWFMK---NNVCPT 61 (70)
Q Consensus 38 ~~C~HggH~~h~~~Wf~~---~~~CP~ 61 (70)
..|||..|..++.+||+. ++.||.
T Consensus 24 ~~cGhifh~~cl~qwfe~~Ps~R~cpi 50 (465)
T KOG0827|consen 24 GTCGHIFHTTCLTQWFEGDPSNRGCPI 50 (465)
T ss_pred cchhhHHHHHHHHHHHccCCccCCCCc
Confidence 459999999999999987 256774
No 24
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.54 E-value=0.3 Score=35.94 Aligned_cols=38 Identities=18% Similarity=0.464 Sum_probs=30.2
Q ss_pred HHH-HhhhhcccccccCCCCCChHHHHHHHHhC-CCCCCC
Q psy17526 24 MLV-FCLVSGLYSWCQGCSHGGHLSHMQEWFMK-NNVCPT 61 (70)
Q Consensus 24 ~iC-~~~v~~l~~~C~~C~HggH~~h~~~Wf~~-~~~CP~ 61 (70)
+|| .+.+++-.+.-+-|.|..|..|+..|... ...||+
T Consensus 327 aICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPv 366 (374)
T COG5540 327 AICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPV 366 (374)
T ss_pred EEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCc
Confidence 455 24456666778899999999999999995 578998
No 25
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=87.05 E-value=0.38 Score=25.79 Aligned_cols=24 Identities=8% Similarity=0.295 Sum_probs=21.7
Q ss_pred cCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 38 QGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 38 ~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
..+||..-.+++.+|++++..||.
T Consensus 17 ~~~G~v~~~~~i~~~~~~~~~cP~ 40 (63)
T smart00504 17 LPSGQTYERRAIEKWLLSHGTDPV 40 (63)
T ss_pred CCCCCEEeHHHHHHHHHHCCCCCC
Confidence 468899999999999999889997
No 26
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=86.75 E-value=0.41 Score=25.06 Aligned_cols=26 Identities=15% Similarity=0.235 Sum_probs=23.2
Q ss_pred cccCCCCC-ChHHHHHHHHhCCCCCCC
Q psy17526 36 WCQGCSHG-GHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 36 ~C~~C~Hg-gH~~h~~~Wf~~~~~CP~ 61 (70)
.-..|+|. .-..++.+|+++...||+
T Consensus 16 ~~~pCgH~~~C~~C~~~~~~~~~~CP~ 42 (50)
T PF13920_consen 16 VLLPCGHLCFCEECAERLLKRKKKCPI 42 (50)
T ss_dssp EEETTCEEEEEHHHHHHHHHTTSBBTT
T ss_pred EEeCCCChHHHHHHhHHhcccCCCCCc
Confidence 34579999 999999999999999997
No 27
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=86.08 E-value=0.73 Score=23.60 Aligned_cols=27 Identities=19% Similarity=0.215 Sum_probs=23.6
Q ss_pred ccccCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 35 SWCQGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 35 ~~C~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
.+=..|+|....+++.........||+
T Consensus 15 ~~l~~CgH~~C~~C~~~~~~~~~~CP~ 41 (44)
T PF14634_consen 15 PRLTSCGHIFCEKCLKKLKGKSVKCPI 41 (44)
T ss_pred eEEcccCCHHHHHHHHhhcCCCCCCcC
Confidence 566789999999999999877788997
No 28
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=85.87 E-value=0.6 Score=31.89 Aligned_cols=29 Identities=14% Similarity=0.167 Sum_probs=22.2
Q ss_pred HHHHhhhhcccccccCCCCCChHHHHHHHHh
Q psy17526 24 MLVFCLVSGLYSWCQGCSHGGHLSHMQEWFM 54 (70)
Q Consensus 24 ~iC~~~v~~l~~~C~~C~HggH~~h~~~Wf~ 54 (70)
.||.+.++...+ ..|+|.....|+.+|+.
T Consensus 22 pICld~~~dPVv--T~CGH~FC~~CI~~wl~ 50 (193)
T PLN03208 22 NICLDQVRDPVV--TLCGHLFCWPCIHKWTY 50 (193)
T ss_pred ccCCCcCCCcEE--cCCCchhHHHHHHHHHH
Confidence 566666555444 57999999999999975
No 29
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=84.65 E-value=0.68 Score=38.78 Aligned_cols=27 Identities=26% Similarity=0.717 Sum_probs=24.5
Q ss_pred ccccCCCCCChHHHHHHHHhC--CCCCCC
Q psy17526 35 SWCQGCSHGGHLSHMQEWFMK--NNVCPT 61 (70)
Q Consensus 35 ~~C~~C~HggH~~h~~~Wf~~--~~~CP~ 61 (70)
--|..|.|-.|+.|+..||+. +..||.
T Consensus 1489 krC~TCknKFH~~CLyKWf~Ss~~s~CPl 1517 (1525)
T COG5219 1489 KRCATCKNKFHTRCLYKWFASSARSNCPL 1517 (1525)
T ss_pred cccchhhhhhhHHHHHHHHHhcCCCCCCc
Confidence 459999999999999999998 478997
No 30
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=84.53 E-value=0.88 Score=24.22 Aligned_cols=21 Identities=14% Similarity=0.409 Sum_probs=17.2
Q ss_pred CCCChHHHHHHHHhCC--CCCCC
Q psy17526 41 SHGGHLSHMQEWFMKN--NVCPT 61 (70)
Q Consensus 41 ~HggH~~h~~~Wf~~~--~~CP~ 61 (70)
.|--|.++|+.|++.. ..||+
T Consensus 25 ~~~vH~~Cl~~W~~~~~~~~C~i 47 (49)
T smart00744 25 LKYVHQECLERWINESGNKTCEI 47 (49)
T ss_pred hhHHHHHHHHHHHHHcCCCcCCC
Confidence 3778999999999764 47887
No 31
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.85 E-value=1.1 Score=33.55 Aligned_cols=36 Identities=14% Similarity=0.155 Sum_probs=28.2
Q ss_pred HHHHhhhhcccccccCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 24 MLVFCLVSGLYSWCQGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 24 ~iC~~~v~~l~~~C~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
.||.+.+..-++ ..|+|-....|+++|+.....||+
T Consensus 30 ~IC~d~~~~Pvi--tpCgH~FCs~CI~~~l~~~~~CP~ 65 (397)
T TIGR00599 30 HICKDFFDVPVL--TSCSHTFCSLCIRRCLSNQPKCPL 65 (397)
T ss_pred CcCchhhhCccC--CCCCCchhHHHHHHHHhCCCCCCC
Confidence 455555544332 689999999999999999888997
No 32
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=80.93 E-value=0.84 Score=25.64 Aligned_cols=19 Identities=11% Similarity=0.114 Sum_probs=15.6
Q ss_pred ccCccCCCCCCcCcccccc
Q psy17526 3 AHSDRCQHGLGNFGKLEGK 21 (70)
Q Consensus 3 ~~C~~C~~~l~~~~~~C~~ 21 (70)
-+|+.||+++|..-..|+.
T Consensus 4 kHC~~CG~~Ip~~~~fCS~ 22 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSP 22 (59)
T ss_pred CcCCcCCCcCCcchhhhCH
Confidence 3799999999877667864
No 33
>PHA02926 zinc finger-like protein; Provisional
Probab=80.60 E-value=1.5 Score=30.85 Aligned_cols=29 Identities=17% Similarity=0.539 Sum_probs=23.4
Q ss_pred ccccccCCCCCChHHHHHHHHhCC------CCCCC
Q psy17526 33 LYSWCQGCSHGGHLSHMQEWFMKN------NVCPT 61 (70)
Q Consensus 33 l~~~C~~C~HggH~~h~~~Wf~~~------~~CP~ 61 (70)
.+-.=.+|+|.....|+++|.+.. ..||.
T Consensus 190 rFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPi 224 (242)
T PHA02926 190 YFGLLDSCNHIFCITCINIWHRTRRETGASDNCPI 224 (242)
T ss_pred cccccCCCCchHHHHHHHHHHHhccccCcCCcCCC
Confidence 455667999999999999999863 34986
No 34
>KOG0317|consensus
Probab=80.42 E-value=1.5 Score=31.79 Aligned_cols=26 Identities=27% Similarity=0.473 Sum_probs=24.0
Q ss_pred cccCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 36 WCQGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 36 ~C~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
.|.-|||..--+|+.+|.....+||.
T Consensus 253 SaTpCGHiFCWsCI~~w~~ek~eCPl 278 (293)
T KOG0317|consen 253 SATPCGHIFCWSCILEWCSEKAECPL 278 (293)
T ss_pred CcCcCcchHHHHHHHHHHccccCCCc
Confidence 47789999999999999999999997
No 35
>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=75.91 E-value=1.2 Score=21.99 Aligned_cols=12 Identities=17% Similarity=0.551 Sum_probs=10.0
Q ss_pred CcccCccCCCCC
Q psy17526 1 MNAHSDRCQHGL 12 (70)
Q Consensus 1 ~~~~C~~C~~~l 12 (70)
|++.||+|+...
T Consensus 1 M~~~CP~C~~~~ 12 (38)
T TIGR02098 1 MRIQCPNCKTSF 12 (38)
T ss_pred CEEECCCCCCEE
Confidence 788999999865
No 36
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=75.37 E-value=2.4 Score=23.72 Aligned_cols=43 Identities=9% Similarity=0.155 Sum_probs=28.7
Q ss_pred CcccCccCCCCCCcC---ccccccchHHHHhhhhcc-cccccCCCCC
Q psy17526 1 MNAHSDRCQHGLGNF---GKLEGKIQMLVFCLVSGL-YSWCQGCSHG 43 (70)
Q Consensus 1 ~~~~C~~C~~~l~~~---~~~C~~~~~iC~~~v~~l-~~~C~~C~Hg 43 (70)
|+..|..|++.|+.. ..||+-=-+.|.+-+..+ ...|+|||-.
T Consensus 4 lrpnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGe 50 (57)
T PF06906_consen 4 LRPNCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGE 50 (57)
T ss_pred cCCCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCc
Confidence 678899999999653 367875224444433333 5689999865
No 37
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=75.27 E-value=1.4 Score=23.18 Aligned_cols=34 Identities=24% Similarity=0.376 Sum_probs=19.7
Q ss_pred cCccCCCCCCcCccccccchHHHHhhhhcccccccC--CCCC
Q psy17526 4 HSDRCQHGLGNFGKLEGKIQMLVFCLVSGLYSWCQG--CSHG 43 (70)
Q Consensus 4 ~C~~C~~~l~~~~~~C~~~~~iC~~~v~~l~~~C~~--C~Hg 43 (70)
.||.||.++---. ...+ ...++.++..|.| |||-
T Consensus 1 ~CP~Cg~~a~ir~-----S~~~-s~~~~~~Y~qC~N~~Cg~t 36 (47)
T PF04606_consen 1 RCPHCGSKARIRT-----SRQL-SPLTRELYCQCTNPECGHT 36 (47)
T ss_pred CcCCCCCeeEEEE-----chhh-CcceEEEEEEECCCcCCCE
Confidence 4888888771100 0000 2455778888888 8875
No 38
>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=74.24 E-value=1.3 Score=22.50 Aligned_cols=13 Identities=31% Similarity=0.731 Sum_probs=8.8
Q ss_pred hcccccccCCCCC
Q psy17526 31 SGLYSWCQGCSHG 43 (70)
Q Consensus 31 ~~l~~~C~~C~Hg 43 (70)
..++..|.+|+|-
T Consensus 25 ~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 25 MTLFYVCCNCGHR 37 (39)
T ss_dssp SEEEEEESSSTEE
T ss_pred CeEEEEeCCCCCe
Confidence 3456668888873
No 39
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=74.07 E-value=1.3 Score=34.90 Aligned_cols=43 Identities=16% Similarity=0.081 Sum_probs=29.0
Q ss_pred ccCccCCCCCCcCccccccch--------HHHHhhhhcccccccCCCCCCh
Q psy17526 3 AHSDRCQHGLGNFGKLEGKIQ--------MLVFCLVSGLYSWCQGCSHGGH 45 (70)
Q Consensus 3 ~~C~~C~~~l~~~~~~C~~~~--------~iC~~~v~~l~~~C~~C~HggH 45 (70)
..||+||...+.....|.++. .-|...+..-.-||.+||+-..
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGTSLTHKPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred CcCCCCCCcCCCCCccccccCCCCCCCcCCCCCCCCCcccccccccCCccc
Confidence 478888888876666676643 2345566666677888877643
No 40
>KOG0320|consensus
Probab=73.65 E-value=2.5 Score=28.81 Aligned_cols=41 Identities=22% Similarity=0.328 Sum_probs=32.5
Q ss_pred HHHHhhhhcccccccCCCCCChHHHHHHHHhCCCCCCCCCCc
Q psy17526 24 MLVFCLVSGLYSWCQGCSHGGHLSHMQEWFMKNNVCPTGCGH 65 (70)
Q Consensus 24 ~iC~~~v~~l~~~C~~C~HggH~~h~~~Wf~~~~~CP~gC~c 65 (70)
-||-+.+.--..+=.+|||..-..|+++=......||+ |.+
T Consensus 135 PiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~-C~k 175 (187)
T KOG0320|consen 135 PICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPT-CRK 175 (187)
T ss_pred CceecchhhccccccccchhHHHHHHHHHHHhCCCCCC-ccc
Confidence 35555555555567899999999999999999999999 443
No 41
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=73.09 E-value=2.8 Score=21.47 Aligned_cols=24 Identities=21% Similarity=0.403 Sum_probs=17.9
Q ss_pred cCCCCCChHHHHHHHHhCC----CCCCC
Q psy17526 38 QGCSHGGHLSHMQEWFMKN----NVCPT 61 (70)
Q Consensus 38 ~~C~HggH~~h~~~Wf~~~----~~CP~ 61 (70)
+.|||..-.+++.+|+++. ..||.
T Consensus 14 l~CGH~FC~~Cl~~~~~~~~~~~~~CP~ 41 (42)
T PF15227_consen 14 LPCGHSFCRSCLERLWKEPSGSGFSCPE 41 (42)
T ss_dssp -SSSSEEEHHHHHHHHCCSSSST---SS
T ss_pred cCCcCHHHHHHHHHHHHccCCcCCCCcC
Confidence 5899999999999999884 34764
No 42
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=72.88 E-value=1.9 Score=24.33 Aligned_cols=9 Identities=11% Similarity=0.401 Sum_probs=5.1
Q ss_pred cCccCCCCC
Q psy17526 4 HSDRCQHGL 12 (70)
Q Consensus 4 ~C~~C~~~l 12 (70)
.|..||++|
T Consensus 9 ~CtSCg~~i 17 (59)
T PRK14890 9 KCTSCGIEI 17 (59)
T ss_pred cccCCCCcc
Confidence 355566555
No 43
>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=72.05 E-value=2.5 Score=19.89 Aligned_cols=16 Identities=13% Similarity=0.198 Sum_probs=9.3
Q ss_pred cCccCCCCCCcCcccc
Q psy17526 4 HSDRCQHGLGNFGKLE 19 (70)
Q Consensus 4 ~C~~C~~~l~~~~~~C 19 (70)
.||.|++.++.....|
T Consensus 2 ~CP~C~~~V~~~~~~C 17 (26)
T PF10571_consen 2 TCPECGAEVPESAKFC 17 (26)
T ss_pred cCCCCcCCchhhcCcC
Confidence 4677777665554344
No 44
>KOG1493|consensus
Probab=71.51 E-value=1.1 Score=26.82 Aligned_cols=23 Identities=26% Similarity=0.642 Sum_probs=18.9
Q ss_pred CCCCCChHHHHHHHHhC---CCCCCC
Q psy17526 39 GCSHGGHLSHMQEWFMK---NNVCPT 61 (70)
Q Consensus 39 ~C~HggH~~h~~~Wf~~---~~~CP~ 61 (70)
.|.|-.|++++.+|.+. ...||.
T Consensus 50 ~C~h~fh~hCI~~wl~~~tsq~~CPm 75 (84)
T KOG1493|consen 50 YCLHAFHAHCILKWLNTPTSQGQCPM 75 (84)
T ss_pred HHHHHHHHHHHHHHhcCccccccCCc
Confidence 46799999999999987 356885
No 45
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=70.37 E-value=3.3 Score=21.47 Aligned_cols=11 Identities=18% Similarity=0.268 Sum_probs=8.5
Q ss_pred cCccCCCCCCc
Q psy17526 4 HSDRCQHGLGN 14 (70)
Q Consensus 4 ~C~~C~~~l~~ 14 (70)
+||+||..|..
T Consensus 2 FCp~Cg~~l~~ 12 (52)
T smart00661 2 FCPKCGNMLIP 12 (52)
T ss_pred CCCCCCCcccc
Confidence 68999988843
No 46
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=69.48 E-value=2 Score=20.34 Aligned_cols=25 Identities=16% Similarity=0.262 Sum_probs=10.4
Q ss_pred HHHhhhhc-ccccccCCCCCChHHHH
Q psy17526 25 LVFCLVSG-LYSWCQGCSHGGHLSHM 49 (70)
Q Consensus 25 iC~~~v~~-l~~~C~~C~HggH~~h~ 49 (70)
+|.+++.+ ++..|..|.-..|.+++
T Consensus 5 ~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 5 ACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp TTS----S--EEE-TTT-----HHHH
T ss_pred cCCCcCCCCceEECccCCCccChhcC
Confidence 45667777 78889999988888764
No 47
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=69.12 E-value=2.2 Score=20.50 Aligned_cols=11 Identities=18% Similarity=0.371 Sum_probs=5.7
Q ss_pred cccCccCCCCC
Q psy17526 2 NAHSDRCQHGL 12 (70)
Q Consensus 2 ~~~C~~C~~~l 12 (70)
+-.|++||.++
T Consensus 3 ~rfC~~CG~~t 13 (32)
T PF09297_consen 3 HRFCGRCGAPT 13 (32)
T ss_dssp TSB-TTT--BE
T ss_pred CcccCcCCccc
Confidence 34688888887
No 48
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=68.74 E-value=3.5 Score=21.03 Aligned_cols=16 Identities=19% Similarity=0.480 Sum_probs=11.6
Q ss_pred HhhhhcccccccCCCCC
Q psy17526 27 FCLVSGLYSWCQGCSHG 43 (70)
Q Consensus 27 ~~~v~~l~~~C~~C~Hg 43 (70)
+++|. ++..|.+|+|-
T Consensus 22 DE~mT-~fy~C~~C~~~ 37 (40)
T smart00440 22 DEPMT-VFYVCTKCGHR 37 (40)
T ss_pred CCCCe-EEEEeCCCCCE
Confidence 45554 78889999984
No 49
>KOG0828|consensus
Probab=65.42 E-value=3.1 Score=32.58 Aligned_cols=25 Identities=24% Similarity=0.595 Sum_probs=21.5
Q ss_pred ccCCCCCChHHHHHHHHhCCC-CCCC
Q psy17526 37 CQGCSHGGHLSHMQEWFMKNN-VCPT 61 (70)
Q Consensus 37 C~~C~HggH~~h~~~Wf~~~~-~CP~ 61 (70)
-.-|.|..|..+++.|-...+ +||+
T Consensus 603 ~tPC~HifH~~CL~~WMd~ykl~CPv 628 (636)
T KOG0828|consen 603 LTPCHHIFHRQCLLQWMDTYKLICPV 628 (636)
T ss_pred ccchHHHHHHHHHHHHHhhhcccCCc
Confidence 446889999999999999655 9998
No 50
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=60.41 E-value=9.1 Score=27.42 Aligned_cols=33 Identities=36% Similarity=0.744 Sum_probs=23.3
Q ss_pred hhhcccccccCCCCCChHHHHHHHHhCCCCCCCCCCc
Q psy17526 29 LVSGLYSWCQGCSHGGHLSHMQEWFMKNNVCPTGCGH 65 (70)
Q Consensus 29 ~v~~l~~~C~~C~HggH~~h~~~Wf~~~~~CP~gC~c 65 (70)
+-.++|+-|+.|+.--+. +++..+..+||. |++
T Consensus 22 ~~~~~~~~c~~c~~~~~~---~~l~~~~~vc~~-c~~ 54 (292)
T PRK05654 22 VPEGLWTKCPSCGQVLYR---KELEANLNVCPK-CGH 54 (292)
T ss_pred CCCCCeeECCCccchhhH---HHHHhcCCCCCC-CCC
Confidence 346788888888876554 666666778887 554
No 51
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=59.98 E-value=5.2 Score=21.98 Aligned_cols=12 Identities=17% Similarity=0.387 Sum_probs=9.7
Q ss_pred CcccCccCCCCC
Q psy17526 1 MNAHSDRCQHGL 12 (70)
Q Consensus 1 ~~~~C~~C~~~l 12 (70)
|...||.||..+
T Consensus 1 ~~~~CP~CG~~i 12 (54)
T TIGR01206 1 MQFECPDCGAEI 12 (54)
T ss_pred CccCCCCCCCEE
Confidence 456899999987
No 52
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=58.45 E-value=10 Score=27.06 Aligned_cols=32 Identities=28% Similarity=0.612 Sum_probs=20.5
Q ss_pred hhcccccccCCCCCChHHHHHHHHhCCCCCCCCCCc
Q psy17526 30 VSGLYSWCQGCSHGGHLSHMQEWFMKNNVCPTGCGH 65 (70)
Q Consensus 30 v~~l~~~C~~C~HggH~~h~~~Wf~~~~~CP~gC~c 65 (70)
-.++|+-|+.|+.--+. +++..+..+||. |++
T Consensus 22 ~~~~~~~c~~c~~~~~~---~~l~~~~~vc~~-c~~ 53 (285)
T TIGR00515 22 PEGVWTKCPKCGQVLYT---KELERNLEVCPK-CDH 53 (285)
T ss_pred CCCCeeECCCCcchhhH---HHHHhhCCCCCC-CCC
Confidence 35577777777766444 556666677776 554
No 53
>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=57.36 E-value=3 Score=20.81 Aligned_cols=11 Identities=9% Similarity=0.308 Sum_probs=8.3
Q ss_pred cccCccCCCCC
Q psy17526 2 NAHSDRCQHGL 12 (70)
Q Consensus 2 ~~~C~~C~~~l 12 (70)
+..||+|+|++
T Consensus 4 ~~~C~nC~R~v 14 (33)
T PF08209_consen 4 YVECPNCGRPV 14 (33)
T ss_dssp EEE-TTTSSEE
T ss_pred eEECCCCcCCc
Confidence 46799999987
No 54
>PF14353 CpXC: CpXC protein
Probab=57.17 E-value=5.4 Score=24.55 Aligned_cols=46 Identities=17% Similarity=0.118 Sum_probs=26.9
Q ss_pred ccCccCCCCCCcCcccccc---chHHHHhhhhccc--ccccCCCCCChHHH
Q psy17526 3 AHSDRCQHGLGNFGKLEGK---IQMLVFCLVSGLY--SWCQGCSHGGHLSH 48 (70)
Q Consensus 3 ~~C~~C~~~l~~~~~~C~~---~~~iC~~~v~~l~--~~C~~C~HggH~~h 48 (70)
+.||+|+++..-..|.=-. -+.+=..++.|-+ +.|++||+.+..++
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEY 52 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCC
Confidence 6799999988544321111 1133344554443 55999999876643
No 55
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=56.22 E-value=5.5 Score=20.93 Aligned_cols=17 Identities=29% Similarity=0.589 Sum_probs=13.7
Q ss_pred hcccccccCCCCCChHH
Q psy17526 31 SGLYSWCQGCSHGGHLS 47 (70)
Q Consensus 31 ~~l~~~C~~C~HggH~~ 47 (70)
.++-.+|..|+.-||..
T Consensus 28 E~lp~~C~~C~~~gH~~ 44 (49)
T PF14392_consen 28 ERLPRFCFHCGRIGHSD 44 (49)
T ss_pred CCcChhhcCCCCcCcCH
Confidence 45667899999999974
No 56
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=54.67 E-value=5.4 Score=20.90 Aligned_cols=19 Identities=26% Similarity=0.524 Sum_probs=13.4
Q ss_pred CChHHHHHHHHhC--CCCCCC
Q psy17526 43 GGHLSHMQEWFMK--NNVCPT 61 (70)
Q Consensus 43 ggH~~h~~~Wf~~--~~~CP~ 61 (70)
--|.++|++|+.. +..|++
T Consensus 26 ~vH~~CL~~W~~~~~~~~C~~ 46 (47)
T PF12906_consen 26 YVHRSCLERWIRESGNRKCEI 46 (47)
T ss_dssp SEECCHHHHHHHHHT-SB-TT
T ss_pred hhHHHHHHHHHHhcCCCcCCC
Confidence 4599999999985 456664
No 57
>KOG2691|consensus
Probab=54.67 E-value=6.5 Score=24.79 Aligned_cols=16 Identities=25% Similarity=0.474 Sum_probs=12.8
Q ss_pred hhhhcccccccCCCCC
Q psy17526 28 CLVSGLYSWCQGCSHG 43 (70)
Q Consensus 28 ~~v~~l~~~C~~C~Hg 43 (70)
+..-+|+..|.+|+|-
T Consensus 95 d~~m~l~yvC~~C~h~ 110 (113)
T KOG2691|consen 95 DEAMRLFYVCCSCGHR 110 (113)
T ss_pred cceEEEEEEecccccc
Confidence 5666788889999985
No 58
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=54.65 E-value=5.6 Score=20.65 Aligned_cols=14 Identities=21% Similarity=0.465 Sum_probs=10.9
Q ss_pred CcccCccCCCCCCc
Q psy17526 1 MNAHSDRCQHGLGN 14 (70)
Q Consensus 1 ~~~~C~~C~~~l~~ 14 (70)
+...||+|+-||-+
T Consensus 16 L~~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 16 LDEHCPDCGTPLMR 29 (41)
T ss_pred hcCccCCCCCeeEE
Confidence 35689999999943
No 59
>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=53.47 E-value=6 Score=25.28 Aligned_cols=22 Identities=9% Similarity=-0.038 Sum_probs=16.3
Q ss_pred cccCccCCCCCCcC---ccccccch
Q psy17526 2 NAHSDRCQHGLGNF---GKLEGKIQ 23 (70)
Q Consensus 2 ~~~C~~C~~~l~~~---~~~C~~~~ 23 (70)
|.+||+|+|.+... .+.|.++.
T Consensus 34 Y~aC~~C~kkv~~~~~~~~~C~~C~ 58 (166)
T cd04476 34 YPACPGCNKKVVEEGNGTYRCEKCN 58 (166)
T ss_pred EccccccCcccEeCCCCcEECCCCC
Confidence 78999999999432 36787744
No 60
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=52.24 E-value=9.8 Score=27.53 Aligned_cols=38 Identities=21% Similarity=0.278 Sum_probs=26.1
Q ss_pred HHHHhhhhcccccccCCCCCChHHHHHHHHhCCCCCCCCCCc
Q psy17526 24 MLVFCLVSGLYSWCQGCSHGGHLSHMQEWFMKNNVCPTGCGH 65 (70)
Q Consensus 24 ~iC~~~v~~l~~~C~~C~HggH~~h~~~Wf~~~~~CP~gC~c 65 (70)
+++.++-.++|+-|++|+.--.. +++-.+..+||. |++
T Consensus 28 ~~~~~~p~~lw~kc~~C~~~~~~---~~l~~~~~vcp~-c~~ 65 (296)
T CHL00174 28 SWNTQKYKHLWVQCENCYGLNYK---KFLKSKMNICEQ-CGY 65 (296)
T ss_pred ccCCCCCCCCeeECCCccchhhH---HHHHHcCCCCCC-CCC
Confidence 45555667888889888877655 455555678886 554
No 61
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=52.24 E-value=6 Score=19.72 Aligned_cols=9 Identities=22% Similarity=0.456 Sum_probs=4.3
Q ss_pred cCccCCCCC
Q psy17526 4 HSDRCQHGL 12 (70)
Q Consensus 4 ~C~~C~~~l 12 (70)
+||+||.+|
T Consensus 2 fC~~CG~~l 10 (34)
T PF14803_consen 2 FCPQCGGPL 10 (34)
T ss_dssp B-TTT--B-
T ss_pred ccccccChh
Confidence 589999998
No 62
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=51.78 E-value=4.9 Score=18.89 Aligned_cols=12 Identities=17% Similarity=0.415 Sum_probs=6.2
Q ss_pred ccCccCCCCCCc
Q psy17526 3 AHSDRCQHGLGN 14 (70)
Q Consensus 3 ~~C~~C~~~l~~ 14 (70)
..|++|+..+++
T Consensus 2 ~~C~rC~~~~~~ 13 (30)
T PF06827_consen 2 EKCPRCWNYIED 13 (30)
T ss_dssp SB-TTT--BBEE
T ss_pred CcCccCCCcceE
Confidence 358888888843
No 63
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=51.18 E-value=5.4 Score=25.73 Aligned_cols=12 Identities=25% Similarity=0.412 Sum_probs=10.4
Q ss_pred cccCccCCCCCC
Q psy17526 2 NAHSDRCQHGLG 13 (70)
Q Consensus 2 ~~~C~~C~~~l~ 13 (70)
..+||+||.||-
T Consensus 28 ~~hCp~Cg~PLF 39 (131)
T COG1645 28 AKHCPKCGTPLF 39 (131)
T ss_pred HhhCcccCCcce
Confidence 568999999994
No 64
>KOG0823|consensus
Probab=50.81 E-value=9.7 Score=26.75 Aligned_cols=38 Identities=18% Similarity=0.414 Sum_probs=28.3
Q ss_pred HHHHhhhhcccccccCCCCCChHHHHHHHHhC---CCCCCCCCC
Q psy17526 24 MLVFCLVSGLYSWCQGCSHGGHLSHMQEWFMK---NNVCPTGCG 64 (70)
Q Consensus 24 ~iC~~~v~~l~~~C~~C~HggH~~h~~~Wf~~---~~~CP~gC~ 64 (70)
.||-+..+.-++-+ |||=.--.|+.+|... ..+||+ |.
T Consensus 51 NICLd~akdPVvTl--CGHLFCWpClyqWl~~~~~~~~cPV-CK 91 (230)
T KOG0823|consen 51 NICLDLAKDPVVTL--CGHLFCWPCLYQWLQTRPNSKECPV-CK 91 (230)
T ss_pred eeeccccCCCEEee--cccceehHHHHHHHhhcCCCeeCCc-cc
Confidence 57766665555443 8999999999999987 367898 44
No 65
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=49.96 E-value=8.8 Score=24.17 Aligned_cols=13 Identities=8% Similarity=0.381 Sum_probs=10.9
Q ss_pred cccCccCCCCCCc
Q psy17526 2 NAHSDRCQHGLGN 14 (70)
Q Consensus 2 ~~~C~~C~~~l~~ 14 (70)
++.||+||.++..
T Consensus 49 ~t~CP~Cg~~~e~ 61 (115)
T COG1885 49 STSCPKCGEPFES 61 (115)
T ss_pred cccCCCCCCccce
Confidence 5899999999843
No 66
>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=48.78 E-value=8.7 Score=18.77 Aligned_cols=11 Identities=18% Similarity=0.362 Sum_probs=6.5
Q ss_pred ccCccCCCCCC
Q psy17526 3 AHSDRCQHGLG 13 (70)
Q Consensus 3 ~~C~~C~~~l~ 13 (70)
+.||.||..+.
T Consensus 27 ~~CP~Cg~~~~ 37 (41)
T smart00834 27 ATCPECGGDVR 37 (41)
T ss_pred CCCCCCCCcce
Confidence 45666666543
No 67
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=47.13 E-value=9.3 Score=21.66 Aligned_cols=10 Identities=10% Similarity=0.378 Sum_probs=6.0
Q ss_pred ccCccCCCCC
Q psy17526 3 AHSDRCQHGL 12 (70)
Q Consensus 3 ~~C~~C~~~l 12 (70)
..|..||..|
T Consensus 10 ~~CtSCg~~i 19 (61)
T COG2888 10 PVCTSCGREI 19 (61)
T ss_pred ceeccCCCEe
Confidence 3566666666
No 68
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=46.13 E-value=13 Score=28.30 Aligned_cols=22 Identities=27% Similarity=0.289 Sum_probs=16.7
Q ss_pred cccCccCCCCC---CcCccccccch
Q psy17526 2 NAHSDRCQHGL---GNFGKLEGKIQ 23 (70)
Q Consensus 2 ~~~C~~C~~~l---~~~~~~C~~~~ 23 (70)
+..||.||+.| ++.++-|+++.
T Consensus 350 ~p~Cp~Cg~~m~S~G~~g~rC~kCg 374 (421)
T COG1571 350 NPVCPRCGGRMKSAGRNGFRCKKCG 374 (421)
T ss_pred CCCCCccCCchhhcCCCCccccccc
Confidence 56899999999 34366788754
No 69
>KOG2041|consensus
Probab=45.54 E-value=6.2 Score=32.60 Aligned_cols=55 Identities=18% Similarity=0.379 Sum_probs=38.4
Q ss_pred ccCccCCCCCCcCccccccch---HHH---Hhh-hhcccccccCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 3 AHSDRCQHGLGNFGKLEGKIQ---MLV---FCL-VSGLYSWCQGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 3 ~~C~~C~~~l~~~~~~C~~~~---~iC---~~~-v~~l~~~C~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
..|..||-++++..-.|+.++ -+| ..| ....+..|+.|.|+.|.+-+ ++++.||.
T Consensus 1118 vdc~~cg~~i~~~~~~c~ec~~kfP~CiasG~pIt~~~fWlC~~CkH~a~~~EI----s~y~~CPL 1179 (1189)
T KOG2041|consen 1118 VDCSVCGAKIDPYDLQCSECQTKFPVCIASGRPITDNIFWLCPRCKHRAHQHEI----SKYNCCPL 1179 (1189)
T ss_pred eeeeecCCcCCccCCCChhhcCcCceeeccCCccccceEEEccccccccccccc----cccccCcc
Confidence 457788888877666777755 233 334 45557779999999988654 44678886
No 70
>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=45.04 E-value=9.3 Score=26.11 Aligned_cols=38 Identities=13% Similarity=0.178 Sum_probs=21.3
Q ss_pred CccCCCCCCcC-ccccccch----HHHHhhhhcccccccCCCC
Q psy17526 5 SDRCQHGLGNF-GKLEGKIQ----MLVFCLVSGLYSWCQGCSH 42 (70)
Q Consensus 5 C~~C~~~l~~~-~~~C~~~~----~iC~~~v~~l~~~C~~C~H 42 (70)
|++||++..+- ..+|..+- .+-..+-.--..+|..||=
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~ 43 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGR 43 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCC
Confidence 89999988442 23776632 2222222224667877763
No 71
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=44.55 E-value=7.1 Score=22.11 Aligned_cols=39 Identities=18% Similarity=0.036 Sum_probs=16.3
Q ss_pred cccCccCCCCCCcCcccccc-chHHHHhhhhcccccccCCCC
Q psy17526 2 NAHSDRCQHGLGNFGKLEGK-IQMLVFCLVSGLYSWCQGCSH 42 (70)
Q Consensus 2 ~~~C~~C~~~l~~~~~~C~~-~~~iC~~~v~~l~~~C~~C~H 42 (70)
++.|.+|+..|-+.. .|.- .. -=......+.+-|..|+|
T Consensus 46 r~~Ck~C~~~liPG~-~~~vri~-~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 46 RTICKKCGSLLIPGV-NCSVRIR-KKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp CTB-TTT--B--CTT-TEEEEEE----SSS-EEEEEETTTTE
T ss_pred cccccCCCCEEeCCC-ccEEEEE-ecCCCCCEEEEEccccCC
Confidence 567888888883331 2322 00 001223455666888876
No 72
>PHA00626 hypothetical protein
Probab=43.97 E-value=11 Score=21.14 Aligned_cols=17 Identities=12% Similarity=0.255 Sum_probs=11.5
Q ss_pred ccCccCCCC-CCcCccccc
Q psy17526 3 AHSDRCQHG-LGNFGKLEG 20 (70)
Q Consensus 3 ~~C~~C~~~-l~~~~~~C~ 20 (70)
+.||+||+. +-+++ +|.
T Consensus 1 m~CP~CGS~~Ivrcg-~cr 18 (59)
T PHA00626 1 MSCPKCGSGNIAKEK-TMR 18 (59)
T ss_pred CCCCCCCCceeeeec-eec
Confidence 469999994 56665 443
No 73
>KOG1952|consensus
Probab=43.36 E-value=7.4 Score=32.15 Aligned_cols=32 Identities=22% Similarity=0.402 Sum_probs=25.2
Q ss_pred HHHHhhhhcc--cccccCCCCCChHHHHHHHHhC
Q psy17526 24 MLVFCLVSGL--YSWCQGCSHGGHLSHMQEWFMK 55 (70)
Q Consensus 24 ~iC~~~v~~l--~~~C~~C~HggH~~h~~~Wf~~ 55 (70)
.||.+.|++. .+.|.+|-|..|++++++|-.+
T Consensus 195 mIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs 228 (950)
T KOG1952|consen 195 MICTERIKRTAPVWSCKSCYHVFHLNCIKKWARS 228 (950)
T ss_pred EEeeeeccccCCceecchhhhhhhHHHHHHHHHH
Confidence 5676666444 3459999999999999999765
No 74
>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=43.14 E-value=28 Score=22.09 Aligned_cols=49 Identities=22% Similarity=0.506 Sum_probs=25.7
Q ss_pred cccCccCCCCCCcCcc--ccccchHHHHhhhhcccccccCCC----CCChHHHHHH
Q psy17526 2 NAHSDRCQHGLGNFGK--LEGKIQMLVFCLVSGLYSWCQGCS----HGGHLSHMQE 51 (70)
Q Consensus 2 ~~~C~~C~~~l~~~~~--~C~~~~~iC~~~v~~l~~~C~~C~----HggH~~h~~~ 51 (70)
.+.|+.||.+|-.... +=.+.+..=.+. ..-|..|+.|+ .|.|...|++
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~-~~~f~~C~~C~kiyW~GsH~~~~~~ 145 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYET-YDEFWRCPGCGKIYWEGSHWRRMEE 145 (147)
T ss_pred CCccCCCCcEeeechhhccccccCcccccc-CCeEEECCCCCCEecccccHHHHHh
Confidence 3678888888843320 000111000011 12277899998 5778777654
No 75
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=43.03 E-value=6.9 Score=21.78 Aligned_cols=13 Identities=15% Similarity=0.335 Sum_probs=7.5
Q ss_pred CcccCccCCCCCC
Q psy17526 1 MNAHSDRCQHGLG 13 (70)
Q Consensus 1 ~~~~C~~C~~~l~ 13 (70)
|.+.||.|+|+..
T Consensus 1 m~v~CP~C~k~~~ 13 (57)
T PF03884_consen 1 MTVKCPICGKPVE 13 (57)
T ss_dssp -EEE-TTT--EEE
T ss_pred CcccCCCCCCeec
Confidence 6788999999983
No 76
>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=42.69 E-value=12 Score=17.39 Aligned_cols=7 Identities=14% Similarity=0.430 Sum_probs=5.3
Q ss_pred cCccCCC
Q psy17526 4 HSDRCQH 10 (70)
Q Consensus 4 ~C~~C~~ 10 (70)
.||+||+
T Consensus 18 ~CPnCG~ 24 (24)
T PF07754_consen 18 PCPNCGF 24 (24)
T ss_pred eCCCCCC
Confidence 5888874
No 77
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=42.37 E-value=15 Score=18.95 Aligned_cols=19 Identities=21% Similarity=0.141 Sum_probs=14.7
Q ss_pred cCCCCCChHHHHHHHHhCC
Q psy17526 38 QGCSHGGHLSHMQEWFMKN 56 (70)
Q Consensus 38 ~~C~HggH~~h~~~Wf~~~ 56 (70)
+.|||..-.++++.+.++.
T Consensus 17 L~CGH~~c~~cl~~l~~~~ 35 (43)
T PF13445_consen 17 LPCGHVFCKDCLQKLSKKS 35 (43)
T ss_dssp -SSS-EEEHHHHHHHHHH-
T ss_pred EeCccHHHHHHHHHHHhcC
Confidence 6699999999999999854
No 78
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=42.22 E-value=20 Score=25.84 Aligned_cols=11 Identities=18% Similarity=0.401 Sum_probs=8.7
Q ss_pred cccCccCCCCC
Q psy17526 2 NAHSDRCQHGL 12 (70)
Q Consensus 2 ~~~C~~C~~~l 12 (70)
+-.|++||.++
T Consensus 111 ~RFCg~CG~~~ 121 (279)
T COG2816 111 HRFCGRCGTKT 121 (279)
T ss_pred CcCCCCCCCcC
Confidence 34789999888
No 79
>PF01530 zf-C2HC: Zinc finger, C2HC type; InterPro: IPR002515 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 CysCysHisCys (C2HC) type zinc finger domain found in eukaryotes. Proteins containing these domains include: MYST family histone acetyltransferases [, [] Myelin transcription factor Myt1 [] Suppressor of tumourigenicity protein 18 (ST18) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2CS8_A 1PXE_A 2JX1_A 2JYD_A.
Probab=42.12 E-value=13 Score=18.34 Aligned_cols=8 Identities=63% Similarity=1.460 Sum_probs=4.8
Q ss_pred CCCCC-CCC
Q psy17526 57 NVCPT-GCG 64 (70)
Q Consensus 57 ~~CP~-gC~ 64 (70)
..||+ ||+
T Consensus 2 ~~CPtpGCd 10 (31)
T PF01530_consen 2 LKCPTPGCD 10 (31)
T ss_dssp TSSSSTT--
T ss_pred CcCCCCCCC
Confidence 57998 886
No 80
>PRK02048 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional
Probab=42.05 E-value=10 Score=30.10 Aligned_cols=11 Identities=18% Similarity=0.305 Sum_probs=10.3
Q ss_pred cccCccCCCCC
Q psy17526 2 NAHSDRCQHGL 12 (70)
Q Consensus 2 ~~~C~~C~~~l 12 (70)
|++||.|||.|
T Consensus 518 yISCPsCGRTL 528 (611)
T PRK02048 518 YISCPGCGRTL 528 (611)
T ss_pred EEECCCCCcch
Confidence 78999999999
No 81
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=40.84 E-value=7.6 Score=20.64 Aligned_cols=12 Identities=17% Similarity=0.182 Sum_probs=6.2
Q ss_pred cCccCCCCCCcC
Q psy17526 4 HSDRCQHGLGNF 15 (70)
Q Consensus 4 ~C~~C~~~l~~~ 15 (70)
.||-|+|+|..-
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 799999998643
No 82
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=40.72 E-value=7.4 Score=21.33 Aligned_cols=13 Identities=15% Similarity=0.309 Sum_probs=10.2
Q ss_pred ccCccCCCCCCcC
Q psy17526 3 AHSDRCQHGLGNF 15 (70)
Q Consensus 3 ~~C~~C~~~l~~~ 15 (70)
+.|++|+|-|.+.
T Consensus 5 iRC~~CnklLa~~ 17 (51)
T PF10122_consen 5 IRCGHCNKLLAKA 17 (51)
T ss_pred eeccchhHHHhhh
Confidence 5788999888664
No 83
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=40.50 E-value=14 Score=25.83 Aligned_cols=9 Identities=11% Similarity=0.342 Sum_probs=6.8
Q ss_pred cCccCCCCC
Q psy17526 4 HSDRCQHGL 12 (70)
Q Consensus 4 ~C~~C~~~l 12 (70)
.||+||.++
T Consensus 246 pCprCG~~I 254 (272)
T PRK14810 246 PCLNCKTPI 254 (272)
T ss_pred cCCCCCCee
Confidence 577888777
No 84
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=40.27 E-value=13 Score=18.79 Aligned_cols=10 Identities=20% Similarity=0.474 Sum_probs=8.6
Q ss_pred ccCccCCCCC
Q psy17526 3 AHSDRCQHGL 12 (70)
Q Consensus 3 ~~C~~C~~~l 12 (70)
..||+||.+|
T Consensus 2 ~~CP~Cg~~l 11 (39)
T PF01396_consen 2 EKCPKCGGPL 11 (39)
T ss_pred cCCCCCCcee
Confidence 3699999998
No 85
>KOG0826|consensus
Probab=40.23 E-value=22 Score=26.44 Aligned_cols=24 Identities=21% Similarity=0.610 Sum_probs=19.6
Q ss_pred ccccccCCCCCChHHHHHHHHhCCCCCCC-CCC
Q psy17526 33 LYSWCQGCSHGGHLSHMQEWFMKNNVCPT-GCG 64 (70)
Q Consensus 33 l~~~C~~C~HggH~~h~~~Wf~~~~~CP~-gC~ 64 (70)
-+++| ..|+-.+..++..||+ |++
T Consensus 320 GyVfC--------Y~Ci~~Yv~~~~~CPVT~~p 344 (357)
T KOG0826|consen 320 GYVFC--------YPCIFSYVVNYGHCPVTGYP 344 (357)
T ss_pred ceEEe--------HHHHHHHHHhcCCCCccCCc
Confidence 36677 6778889899999998 876
No 86
>KOG1734|consensus
Probab=40.10 E-value=15 Score=26.89 Aligned_cols=27 Identities=22% Similarity=0.577 Sum_probs=22.0
Q ss_pred ccccCCCCCChHHHHHHHHhC--CCCCCC
Q psy17526 35 SWCQGCSHGGHLSHMQEWFMK--NNVCPT 61 (70)
Q Consensus 35 ~~C~~C~HggH~~h~~~Wf~~--~~~CP~ 61 (70)
++=+.|+|..|..|++-|-.- -.+||-
T Consensus 247 ty~LsCnHvFHEfCIrGWcivGKkqtCPY 275 (328)
T KOG1734|consen 247 TYKLSCNHVFHEFCIRGWCIVGKKQTCPY 275 (328)
T ss_pred heeeecccchHHHhhhhheeecCCCCCch
Confidence 456789999999999999654 467884
No 87
>PRK00420 hypothetical protein; Validated
Probab=40.05 E-value=16 Score=22.94 Aligned_cols=21 Identities=19% Similarity=0.150 Sum_probs=14.7
Q ss_pred CcccCccCCCCCCc--Cc-ccccc
Q psy17526 1 MNAHSDRCQHGLGN--FG-KLEGK 21 (70)
Q Consensus 1 ~~~~C~~C~~~l~~--~~-~~C~~ 21 (70)
+...||.||.||.+ .+ .+|..
T Consensus 22 l~~~CP~Cg~pLf~lk~g~~~Cp~ 45 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDGEVVCPV 45 (112)
T ss_pred ccCCCCCCCCcceecCCCceECCC
Confidence 35789999999954 33 45654
No 88
>PHA02862 5L protein; Provisional
Probab=39.86 E-value=28 Score=23.11 Aligned_cols=21 Identities=24% Similarity=0.381 Sum_probs=15.8
Q ss_pred CCCChHHHHHHHHhCC--CCCCC
Q psy17526 41 SHGGHLSHMQEWFMKN--NVCPT 61 (70)
Q Consensus 41 ~HggH~~h~~~Wf~~~--~~CP~ 61 (70)
-.--|.+||++|.+.+ ..||.
T Consensus 25 ~K~VHq~CL~~WIn~S~k~~CeL 47 (156)
T PHA02862 25 YKVVHIKCMQLWINYSKKKECNL 47 (156)
T ss_pred chhHHHHHHHHHHhcCCCcCccC
Confidence 3445999999999764 56776
No 89
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=39.85 E-value=16 Score=25.74 Aligned_cols=10 Identities=10% Similarity=0.401 Sum_probs=6.9
Q ss_pred cCccCCCCCC
Q psy17526 4 HSDRCQHGLG 13 (70)
Q Consensus 4 ~C~~C~~~l~ 13 (70)
.|++||.++.
T Consensus 256 pC~~Cg~~I~ 265 (282)
T PRK13945 256 PCRKCGTPIE 265 (282)
T ss_pred CCCcCCCeeE
Confidence 5777777773
No 90
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=39.72 E-value=17 Score=22.60 Aligned_cols=14 Identities=14% Similarity=0.370 Sum_probs=11.6
Q ss_pred cccCccCCCCCCcC
Q psy17526 2 NAHSDRCQHGLGNF 15 (70)
Q Consensus 2 ~~~C~~C~~~l~~~ 15 (70)
.+.||.||.+|...
T Consensus 47 ~~~cP~Cge~~~~a 60 (102)
T PF04475_consen 47 DTICPKCGEELDSA 60 (102)
T ss_pred cccCCCCCCccCce
Confidence 57899999999654
No 91
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=39.03 E-value=23 Score=18.15 Aligned_cols=27 Identities=22% Similarity=0.618 Sum_probs=16.3
Q ss_pred cccc--CCCCCChHHHHHHHHhCCC--CCCC
Q psy17526 35 SWCQ--GCSHGGHLSHMQEWFMKNN--VCPT 61 (70)
Q Consensus 35 ~~C~--~C~HggH~~h~~~Wf~~~~--~CP~ 61 (70)
+-|. .|+=..|..+++.+|...+ .||.
T Consensus 12 ~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~ 42 (43)
T PF08746_consen 12 QRCSNRDCNVRLHDDCFKKYFRHRSNPKCPN 42 (43)
T ss_dssp EE-SS--S--EE-HHHHHHHTTT-SS-B-TT
T ss_pred ccCCCCccCchHHHHHHHHHHhcCCCCCCcC
Confidence 3466 4777899999999999865 6986
No 92
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=38.56 E-value=16 Score=23.59 Aligned_cols=22 Identities=14% Similarity=0.276 Sum_probs=17.0
Q ss_pred CcccCccCCCCCCcCccccccch
Q psy17526 1 MNAHSDRCQHGLGNFGKLEGKIQ 23 (70)
Q Consensus 1 ~~~~C~~C~~~l~~~~~~C~~~~ 23 (70)
+...|.+||+++... ++|+++.
T Consensus 80 l~~~CE~CG~~I~~G-r~C~~C~ 101 (137)
T TIGR03826 80 LGYPCERCGTSIREG-RLCDSCA 101 (137)
T ss_pred CcCcccccCCcCCCC-CccHHHH
Confidence 456799999988665 6888855
No 93
>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=38.16 E-value=30 Score=18.79 Aligned_cols=20 Identities=15% Similarity=0.177 Sum_probs=11.8
Q ss_pred cccccccCCCCCChHHHHHH
Q psy17526 32 GLYSWCQGCSHGGHLSHMQE 51 (70)
Q Consensus 32 ~l~~~C~~C~HggH~~h~~~ 51 (70)
+....|++||+..|.+.-.+
T Consensus 44 ~r~~~C~~Cg~~~~rD~naA 63 (69)
T PF07282_consen 44 GRVFTCPNCGFEMDRDVNAA 63 (69)
T ss_pred cceEEcCCCCCEECcHHHHH
Confidence 34566777777666554443
No 94
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=37.88 E-value=18 Score=25.39 Aligned_cols=28 Identities=14% Similarity=0.283 Sum_probs=15.1
Q ss_pred cCccCCCCCCcCccccccchHHHHhhhhcccccccCCCCC
Q psy17526 4 HSDRCQHGLGNFGKLEGKIQMLVFCLVSGLYSWCQGCSHG 43 (70)
Q Consensus 4 ~C~~C~~~l~~~~~~C~~~~~iC~~~v~~l~~~C~~C~Hg 43 (70)
.||+||.++.+.. +-.+-..||++|...
T Consensus 237 pC~~Cg~~I~~~~------------~~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 237 PCPRCGTPIEKIV------------VGGRGTHFCPQCQPL 264 (269)
T ss_pred CCCcCCCeeEEEE------------ECCCCcEECCCCcCC
Confidence 4777777663321 123445666666654
No 95
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=37.51 E-value=12 Score=19.33 Aligned_cols=10 Identities=10% Similarity=0.408 Sum_probs=8.9
Q ss_pred ccCccCCCCC
Q psy17526 3 AHSDRCQHGL 12 (70)
Q Consensus 3 ~~C~~C~~~l 12 (70)
+.|+.||+.|
T Consensus 6 l~C~~CG~~m 15 (58)
T PF13408_consen 6 LRCGHCGSKM 15 (58)
T ss_pred EEcccCCcEe
Confidence 5799999999
No 96
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=37.34 E-value=25 Score=20.89 Aligned_cols=11 Identities=36% Similarity=0.797 Sum_probs=9.6
Q ss_pred cccCccCCCCC
Q psy17526 2 NAHSDRCQHGL 12 (70)
Q Consensus 2 ~~~C~~C~~~l 12 (70)
+..|++|+++|
T Consensus 33 rS~C~~C~~~L 43 (92)
T PF06750_consen 33 RSHCPHCGHPL 43 (92)
T ss_pred CCcCcCCCCcC
Confidence 46899999999
No 97
>PF14260 zf-C4pol: C4-type zinc-finger of DNA polymerase delta
Probab=37.27 E-value=21 Score=19.80 Aligned_cols=37 Identities=19% Similarity=0.205 Sum_probs=25.9
Q ss_pred CccCCCCCCcCc-cccccch--------------HHHHhhhhcccccccCCC
Q psy17526 5 SDRCQHGLGNFG-KLEGKIQ--------------MLVFCLVSGLYSWCQGCS 41 (70)
Q Consensus 5 C~~C~~~l~~~~-~~C~~~~--------------~iC~~~v~~l~~~C~~C~ 41 (70)
|..|++.+.... .+|+.+. ..-+..+..++..|++|.
T Consensus 1 C~~C~~~~~~~~~~lC~~C~~~~~~~~~~l~~~~~~~E~~~~~l~~iC~~C~ 52 (73)
T PF14260_consen 1 CLVCGAKTQEGESPLCSNCRSDPQQTIYNLLSRLRELERRFNELWTICQSCS 52 (73)
T ss_pred CCCCCCcCCCCCCCcCcccCcChHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 678999886532 4666632 122677888899999998
No 98
>PF03942 DTW: DTW domain; InterPro: IPR005636 This presumed domain is found in bacterial and eukaryotic proteins. Its function is unknown. The domain contains multiple conserved motifs including a DTXW motif that this domain has been named after.
Probab=36.49 E-value=24 Score=23.31 Aligned_cols=19 Identities=16% Similarity=0.134 Sum_probs=15.3
Q ss_pred CcccCccCCCCCCcCcccccc
Q psy17526 1 MNAHSDRCQHGLGNFGKLEGK 21 (70)
Q Consensus 1 ~~~~C~~C~~~l~~~~~~C~~ 21 (70)
++..|++|++++.-+ +|+.
T Consensus 1 rr~~C~~C~~~~~~C--~C~~ 19 (203)
T PF03942_consen 1 RRFRCPRCWRPLSLC--ICSL 19 (203)
T ss_pred CCCcCcCCCCccccC--CCcC
Confidence 578999999998665 5766
No 99
>PRK03922 hypothetical protein; Provisional
Probab=36.40 E-value=20 Score=22.63 Aligned_cols=14 Identities=7% Similarity=0.180 Sum_probs=11.6
Q ss_pred cccCccCCCCCCcC
Q psy17526 2 NAHSDRCQHGLGNF 15 (70)
Q Consensus 2 ~~~C~~C~~~l~~~ 15 (70)
.+.||.||.++...
T Consensus 49 ~~~cP~cge~~~~a 62 (113)
T PRK03922 49 LTICPKCGEPFDSA 62 (113)
T ss_pred cccCCCCCCcCCcE
Confidence 57899999999653
No 100
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=36.34 E-value=13 Score=17.58 Aligned_cols=10 Identities=20% Similarity=0.235 Sum_probs=5.4
Q ss_pred cCccCCCCCC
Q psy17526 4 HSDRCQHGLG 13 (70)
Q Consensus 4 ~C~~C~~~l~ 13 (70)
.||.||.+|-
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 4899999983
No 101
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=36.20 E-value=22 Score=21.59 Aligned_cols=20 Identities=15% Similarity=-0.077 Sum_probs=14.2
Q ss_pred cCccCCCCCC---cCc-cccccch
Q psy17526 4 HSDRCQHGLG---NFG-KLEGKIQ 23 (70)
Q Consensus 4 ~C~~C~~~l~---~~~-~~C~~~~ 23 (70)
.||.|+++.- ..+ |.|+++.
T Consensus 37 ~Cp~C~~~~VkR~a~GIW~C~kCg 60 (89)
T COG1997 37 VCPFCGRTTVKRIATGIWKCRKCG 60 (89)
T ss_pred cCCCCCCcceeeeccCeEEcCCCC
Confidence 6999999862 223 8888843
No 102
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=35.90 E-value=17 Score=18.44 Aligned_cols=14 Identities=21% Similarity=0.415 Sum_probs=11.0
Q ss_pred ccCccCCCCCCcCc
Q psy17526 3 AHSDRCQHGLGNFG 16 (70)
Q Consensus 3 ~~C~~C~~~l~~~~ 16 (70)
..|+.||..|.+.+
T Consensus 3 ~~C~~Cg~~l~~ig 16 (47)
T PF13005_consen 3 RACPDCGGELKEIG 16 (47)
T ss_pred CcCCCCCceeeECC
Confidence 57999999996544
No 103
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=35.44 E-value=15 Score=18.78 Aligned_cols=10 Identities=10% Similarity=0.281 Sum_probs=6.1
Q ss_pred ccCccCCCCC
Q psy17526 3 AHSDRCQHGL 12 (70)
Q Consensus 3 ~~C~~C~~~l 12 (70)
+.||.||.++
T Consensus 22 ~~Cp~CG~~~ 31 (46)
T PRK00398 22 VRCPYCGYRI 31 (46)
T ss_pred eECCCCCCeE
Confidence 4566666655
No 104
>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=34.75 E-value=18 Score=18.36 Aligned_cols=8 Identities=13% Similarity=0.380 Sum_probs=5.7
Q ss_pred ccCccCCC
Q psy17526 3 AHSDRCQH 10 (70)
Q Consensus 3 ~~C~~C~~ 10 (70)
+.||+||.
T Consensus 27 ~~CP~Cg~ 34 (42)
T PF09723_consen 27 VPCPECGS 34 (42)
T ss_pred CcCCCCCC
Confidence 56777777
No 105
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=34.18 E-value=21 Score=24.95 Aligned_cols=10 Identities=20% Similarity=0.468 Sum_probs=6.8
Q ss_pred cCccCCCCCC
Q psy17526 4 HSDRCQHGLG 13 (70)
Q Consensus 4 ~C~~C~~~l~ 13 (70)
.||+||.++.
T Consensus 247 pC~~Cg~~I~ 256 (274)
T PRK01103 247 PCRRCGTPIE 256 (274)
T ss_pred CCCCCCCeeE
Confidence 4777777773
No 106
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=34.14 E-value=29 Score=17.64 Aligned_cols=22 Identities=32% Similarity=0.561 Sum_probs=16.1
Q ss_pred cccccCCCCCCh----HHHHHHHHhC
Q psy17526 34 YSWCQGCSHGGH----LSHMQEWFMK 55 (70)
Q Consensus 34 ~~~C~~C~HggH----~~h~~~Wf~~ 55 (70)
...|+.|+|++. .+|+.+.|.+
T Consensus 11 l~~CL~C~~~~c~~~~~~h~~~H~~~ 36 (50)
T smart00290 11 LWLCLTCGQVGCGRYQLGHALEHFEE 36 (50)
T ss_pred eEEecCCCCcccCCCCCcHHHHHhhh
Confidence 557888888776 4678887765
No 107
>PRK10445 endonuclease VIII; Provisional
Probab=33.78 E-value=22 Score=24.81 Aligned_cols=11 Identities=18% Similarity=0.404 Sum_probs=7.6
Q ss_pred ccCccCCCCCC
Q psy17526 3 AHSDRCQHGLG 13 (70)
Q Consensus 3 ~~C~~C~~~l~ 13 (70)
..||+||.++.
T Consensus 236 ~~Cp~Cg~~I~ 246 (263)
T PRK10445 236 EACERCGGIIE 246 (263)
T ss_pred CCCCCCCCEeE
Confidence 35788887773
No 108
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=33.47 E-value=19 Score=18.02 Aligned_cols=11 Identities=27% Similarity=0.498 Sum_probs=8.3
Q ss_pred cCccCCCCCCc
Q psy17526 4 HSDRCQHGLGN 14 (70)
Q Consensus 4 ~C~~C~~~l~~ 14 (70)
.||+|+..|..
T Consensus 1 ~CP~C~~~l~~ 11 (41)
T PF13453_consen 1 KCPRCGTELEP 11 (41)
T ss_pred CcCCCCcccce
Confidence 38999988843
No 109
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=33.36 E-value=21 Score=20.25 Aligned_cols=19 Identities=11% Similarity=0.162 Sum_probs=15.6
Q ss_pred ccCccCCCCCCcCcccccc
Q psy17526 3 AHSDRCQHGLGNFGKLEGK 21 (70)
Q Consensus 3 ~~C~~C~~~l~~~~~~C~~ 21 (70)
-+|+-||+++|..-..|+.
T Consensus 9 ~HC~VCg~aIp~de~~CSe 27 (64)
T COG4068 9 RHCVVCGKAIPPDEQVCSE 27 (64)
T ss_pred ccccccCCcCCCccchHHH
Confidence 4799999999887667776
No 110
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=33.03 E-value=37 Score=25.19 Aligned_cols=24 Identities=17% Similarity=0.347 Sum_probs=22.3
Q ss_pred cCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 38 QGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 38 ~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
..|||+.-.-|++..+..+..||+
T Consensus 41 TtCgHtFCslCIR~hL~~qp~CP~ 64 (391)
T COG5432 41 TTCGHTFCSLCIRRHLGTQPFCPV 64 (391)
T ss_pred cccccchhHHHHHHHhcCCCCCcc
Confidence 369999999999999999999997
No 111
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=32.68 E-value=18 Score=27.78 Aligned_cols=30 Identities=17% Similarity=0.139 Sum_probs=23.0
Q ss_pred HHHH----hhhhcccccccCCCCCChHHHHHHHH
Q psy17526 24 MLVF----CLVSGLYSWCQGCSHGGHLSHMQEWF 53 (70)
Q Consensus 24 ~iC~----~~v~~l~~~C~~C~HggH~~h~~~Wf 53 (70)
.||. ..-..+|+.|-.|+|..|++|+..=.
T Consensus 132 ~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~ 165 (446)
T PF07227_consen 132 CICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHE 165 (446)
T ss_pred cccCCcccCCCCeeEEeccCCCceehhhhhcccc
Confidence 6773 33456788899999999999987643
No 112
>PRK12366 replication factor A; Reviewed
Probab=32.32 E-value=17 Score=28.58 Aligned_cols=23 Identities=4% Similarity=-0.068 Sum_probs=16.7
Q ss_pred CcccCccCCCCCCc--Cccccccch
Q psy17526 1 MNAHSDRCQHGLGN--FGKLEGKIQ 23 (70)
Q Consensus 1 ~~~~C~~C~~~l~~--~~~~C~~~~ 23 (70)
+|.+||.|+|.+.. ..|.|.++.
T Consensus 531 ~y~aCp~CnkKv~~~~g~~~C~~c~ 555 (637)
T PRK12366 531 ILYLCPNCRKRVEEVDGEYICEFCG 555 (637)
T ss_pred EEecccccCeEeEcCCCcEECCCCC
Confidence 47899999999943 226787754
No 113
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=32.30 E-value=32 Score=25.01 Aligned_cols=31 Identities=32% Similarity=0.790 Sum_probs=22.7
Q ss_pred hcccccccCCCCCChHHHHHHHHhCCCCCCCCCCc
Q psy17526 31 SGLYSWCQGCSHGGHLSHMQEWFMKNNVCPTGCGH 65 (70)
Q Consensus 31 ~~l~~~C~~C~HggH~~h~~~Wf~~~~~CP~gC~c 65 (70)
.++|+-|+.|++..+..-+. ++..+||. |++
T Consensus 25 e~lw~KCp~c~~~~y~~eL~---~n~~vcp~-c~~ 55 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELE---SNLKVCPK-CGH 55 (294)
T ss_pred CCceeECCCccceeeHHHHH---hhhhcccc-cCc
Confidence 68899999999988874444 44568887 554
No 114
>KOG2906|consensus
Probab=32.27 E-value=18 Score=22.55 Aligned_cols=10 Identities=20% Similarity=0.338 Sum_probs=8.8
Q ss_pred ccCccCCCCC
Q psy17526 3 AHSDRCQHGL 12 (70)
Q Consensus 3 ~~C~~C~~~l 12 (70)
+.||.||..|
T Consensus 2 ~FCP~Cgn~L 11 (105)
T KOG2906|consen 2 LFCPTCGNML 11 (105)
T ss_pred cccCCCCCEE
Confidence 5799999998
No 115
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=32.10 E-value=43 Score=19.33 Aligned_cols=35 Identities=26% Similarity=0.405 Sum_probs=20.2
Q ss_pred ccCccCCCCCCcCccccccchHHHHhhhhccccccc--CCCCC
Q psy17526 3 AHSDRCQHGLGNFGKLEGKIQMLVFCLVSGLYSWCQ--GCSHG 43 (70)
Q Consensus 3 ~~C~~C~~~l~~~~~~C~~~~~iC~~~v~~l~~~C~--~C~Hg 43 (70)
+.||.||... +.- +.+.+ .+.++.++..|. .|||-
T Consensus 2 m~CP~Cg~~a-~ir----tSr~~-s~~~~~~Y~qC~N~eCg~t 38 (72)
T PRK09678 2 FHCPLCQHAA-HAR----TSRYI-TDTTKERYHQCQNVNCSAT 38 (72)
T ss_pred ccCCCCCCcc-EEE----EChhc-ChhhheeeeecCCCCCCCE
Confidence 5688888776 110 00011 133777788887 78875
No 116
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=31.69 E-value=13 Score=20.85 Aligned_cols=11 Identities=18% Similarity=0.582 Sum_probs=9.4
Q ss_pred cccCccCCCCC
Q psy17526 2 NAHSDRCQHGL 12 (70)
Q Consensus 2 ~~~C~~C~~~l 12 (70)
.|.|.+|||++
T Consensus 10 ~t~CrRCGk~i 20 (60)
T PF10892_consen 10 ETPCRRCGKSI 20 (60)
T ss_pred eehhhhhCccH
Confidence 36899999998
No 117
>PRK00694 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated
Probab=31.22 E-value=18 Score=28.68 Aligned_cols=13 Identities=15% Similarity=0.074 Sum_probs=11.0
Q ss_pred CcccCccCCCCCC
Q psy17526 1 MNAHSDRCQHGLG 13 (70)
Q Consensus 1 ~~~~C~~C~~~l~ 13 (70)
.|++||.|||.|-
T Consensus 509 e~isCP~CgRtlf 521 (606)
T PRK00694 509 EYISCPGCGRTLF 521 (606)
T ss_pred eEEECCCCCceee
Confidence 3789999999983
No 118
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=30.92 E-value=24 Score=18.00 Aligned_cols=10 Identities=30% Similarity=0.747 Sum_probs=5.2
Q ss_pred ccCccCCCCC
Q psy17526 3 AHSDRCQHGL 12 (70)
Q Consensus 3 ~~C~~C~~~l 12 (70)
+.||+|+|.-
T Consensus 3 ~~CprC~kg~ 12 (36)
T PF14787_consen 3 GLCPRCGKGF 12 (36)
T ss_dssp -C-TTTSSSC
T ss_pred ccCcccCCCc
Confidence 4577777654
No 119
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=30.33 E-value=30 Score=17.98 Aligned_cols=19 Identities=37% Similarity=0.889 Sum_probs=14.9
Q ss_pred cccCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 36 WCQGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 36 ~C~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
-|.+||=-||. ..+..||.
T Consensus 3 kC~~CG~~GH~-------~t~k~CP~ 21 (40)
T PF15288_consen 3 KCKNCGAFGHM-------RTNKRCPM 21 (40)
T ss_pred ccccccccccc-------ccCccCCC
Confidence 47889988887 56778885
No 120
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=30.14 E-value=31 Score=23.56 Aligned_cols=21 Identities=14% Similarity=0.177 Sum_probs=15.3
Q ss_pred CcccCccCCCCCC--cCcccccc
Q psy17526 1 MNAHSDRCQHGLG--NFGKLEGK 21 (70)
Q Consensus 1 ~~~~C~~C~~~l~--~~~~~C~~ 21 (70)
|...||.|+.+|. ...|.|..
T Consensus 1 ~~~~CP~C~~~l~~~~~~~~C~~ 23 (272)
T PRK11088 1 MSYQCPLCHQPLTLEENSWICPQ 23 (272)
T ss_pred CcccCCCCCcchhcCCCEEEcCC
Confidence 4468999999993 23477776
No 121
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=30.08 E-value=26 Score=21.32 Aligned_cols=12 Identities=8% Similarity=0.155 Sum_probs=10.3
Q ss_pred cccCccCCCCCC
Q psy17526 2 NAHSDRCQHGLG 13 (70)
Q Consensus 2 ~~~C~~C~~~l~ 13 (70)
+|.||+|+++-+
T Consensus 8 ~tyCp~CkkHt~ 19 (92)
T PRK05767 8 RTYCPYCKTHTE 19 (92)
T ss_pred cccCcCCCCccc
Confidence 689999999883
No 122
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=29.93 E-value=25 Score=21.88 Aligned_cols=20 Identities=10% Similarity=0.237 Sum_probs=16.6
Q ss_pred cccCccCCCCCCcCcccccc
Q psy17526 2 NAHSDRCQHGLGNFGKLEGK 21 (70)
Q Consensus 2 ~~~C~~C~~~l~~~~~~C~~ 21 (70)
++.|.+||+.+|+.-.++.-
T Consensus 20 ~v~CdnCg~~vPkdKAikr~ 39 (108)
T COG4830 20 YVRCDNCGKAVPKDKAIKRT 39 (108)
T ss_pred ceeeccccccCCccceeeEe
Confidence 67899999999988766655
No 123
>PTZ00157 60S ribosomal protein L36a; Provisional
Probab=29.80 E-value=27 Score=20.97 Aligned_cols=12 Identities=8% Similarity=0.315 Sum_probs=10.3
Q ss_pred cccCccCCCCCC
Q psy17526 2 NAHSDRCQHGLG 13 (70)
Q Consensus 2 ~~~C~~C~~~l~ 13 (70)
+|.||+|+++-+
T Consensus 9 ~tyC~~C~kHt~ 20 (84)
T PTZ00157 9 KTYCKKCGKHTS 20 (84)
T ss_pred cccCcCCCCCcc
Confidence 689999999883
No 124
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=29.70 E-value=41 Score=28.18 Aligned_cols=43 Identities=21% Similarity=0.242 Sum_probs=31.3
Q ss_pred cccCccCCCCCCcCccccccc-h-----H---------HHHhhhhcccccccCCCCCCh
Q psy17526 2 NAHSDRCQHGLGNFGKLEGKI-Q-----M---------LVFCLVSGLYSWCQGCSHGGH 45 (70)
Q Consensus 2 ~~~C~~C~~~l~~~~~~C~~~-~-----~---------iC~~~v~~l~~~C~~C~HggH 45 (70)
...|..|++++... .+|..+ . . .-+....++++.|+.|.+..|
T Consensus 960 ~~~c~~c~~~~~~~-~~c~~c~~~~~~~~~~~~~~~~~~~e~~~~~~~~~c~~c~g~~~ 1017 (1054)
T PTZ00166 960 QLQCLGCKSVIKEG-ALCDNCNQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLH 1017 (1054)
T ss_pred CcccCCCCCCCCCC-CcCccccCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCC
Confidence 35799999999543 477665 1 1 225677889999999998776
No 125
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=29.61 E-value=64 Score=21.57 Aligned_cols=23 Identities=22% Similarity=0.601 Sum_probs=17.3
Q ss_pred CCCCCC-----hHHHHHHHHhCC--CCCCC
Q psy17526 39 GCSHGG-----HLSHMQEWFMKN--NVCPT 61 (70)
Q Consensus 39 ~C~Hgg-----H~~h~~~Wf~~~--~~CP~ 61 (70)
-|.=-| |.++++.|.... ..|+.
T Consensus 24 PC~CkGs~k~VH~sCL~rWi~~s~~~~Cei 53 (162)
T PHA02825 24 YCNCKNENKIVHKECLEEWINTSKNKSCKI 53 (162)
T ss_pred CcccCCCchHHHHHHHHHHHhcCCCCcccc
Confidence 455555 999999998874 56775
No 126
>KOG4718|consensus
Probab=28.80 E-value=51 Score=23.21 Aligned_cols=27 Identities=22% Similarity=0.653 Sum_probs=24.9
Q ss_pred ccccCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 35 SWCQGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 35 ~~C~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
+-|.+|+--.|..+++++|++...||.
T Consensus 195 ~rCg~c~i~~h~~c~qty~q~~~~cph 221 (235)
T KOG4718|consen 195 IRCGSCNIQYHRGCIQTYLQRRDICPH 221 (235)
T ss_pred eccCcccchhhhHHHHHHhcccCcCCc
Confidence 559999999999999999999999997
No 127
>PHA02776 E7 protein; Provisional
Probab=27.98 E-value=34 Score=21.09 Aligned_cols=38 Identities=21% Similarity=0.216 Sum_probs=21.2
Q ss_pred ccCccCCCCCCcCcccccc--chHHHHhhhhcccccccCCC
Q psy17526 3 AHSDRCQHGLGNFGKLEGK--IQMLVFCLVSGLYSWCQGCS 41 (70)
Q Consensus 3 ~~C~~C~~~l~~~~~~C~~--~~~iC~~~v~~l~~~C~~C~ 41 (70)
+.|.+|++.+-=.. .++. ++.+=.+.+..+.+.|+.|.
T Consensus 59 t~C~~C~~~lRL~V-~st~~~IR~lqqLLl~~L~ivCp~Ca 98 (101)
T PHA02776 59 TCCCGCDNNVRLVV-ECTEPDIQELHNLLLGSLNIVCPICA 98 (101)
T ss_pred eECCCCCCeEEEEE-EcChhhHHHHHHHhcCCeEEECCCCC
Confidence 34666666553332 2322 22333566678888888885
No 128
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=27.85 E-value=25 Score=21.92 Aligned_cols=36 Identities=14% Similarity=0.076 Sum_probs=20.3
Q ss_pred cccCccCCCCCCcCccccccchHHHHhhhh-cccccccCCCCCC
Q psy17526 2 NAHSDRCQHGLGNFGKLEGKIQMLVFCLVS-GLYSWCQGCSHGG 44 (70)
Q Consensus 2 ~~~C~~C~~~l~~~~~~C~~~~~iC~~~v~-~l~~~C~~C~Hgg 44 (70)
++.|.+|..+|-+.. .+.- .... .+.+-|+.||+.-
T Consensus 56 R~~CkkC~t~Lvpg~-n~rv------R~~~~~v~vtC~~CG~~~ 92 (105)
T COG2023 56 RTICKKCYTPLVPGK-NARV------RLRKGRVVVTCLECGTIR 92 (105)
T ss_pred HHhccccCcccccCc-ceEE------EEcCCeEEEEecCCCcEE
Confidence 467999999883322 1211 1111 1667788888753
No 129
>PRK02935 hypothetical protein; Provisional
Probab=27.23 E-value=26 Score=22.03 Aligned_cols=11 Identities=9% Similarity=0.265 Sum_probs=8.9
Q ss_pred cccCccCCCCC
Q psy17526 2 NAHSDRCQHGL 12 (70)
Q Consensus 2 ~~~C~~C~~~l 12 (70)
+..||+|+|+-
T Consensus 70 qV~CP~C~K~T 80 (110)
T PRK02935 70 QVICPSCEKPT 80 (110)
T ss_pred eeECCCCCchh
Confidence 46799999976
No 130
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=27.08 E-value=33 Score=24.96 Aligned_cols=39 Identities=15% Similarity=0.155 Sum_probs=23.8
Q ss_pred cCccCCCCCCcCccccccch-HHHHhhhhc--------ccccccCCCCCCh
Q psy17526 4 HSDRCQHGLGNFGKLEGKIQ-MLVFCLVSG--------LYSWCQGCSHGGH 45 (70)
Q Consensus 4 ~C~~C~~~l~~~~~~C~~~~-~iC~~~v~~--------l~~~C~~C~HggH 45 (70)
.|..|+| |+. +.|.++. .+|++-|++ -.+.|+.|+|...
T Consensus 173 KC~SCNr-lGq--~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg~et~ 220 (314)
T PF06524_consen 173 KCQSCNR-LGQ--YSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKCGYETQ 220 (314)
T ss_pred ccccccc-ccc--hhhhheeeeehhhhhhhcccccccCCCCCCCCCCCccc
Confidence 3555555 211 3566665 677776655 3456999999753
No 131
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.95 E-value=22 Score=24.85 Aligned_cols=9 Identities=22% Similarity=0.549 Sum_probs=6.5
Q ss_pred cCccCCCCC
Q psy17526 4 HSDRCQHGL 12 (70)
Q Consensus 4 ~C~~C~~~l 12 (70)
.||+||.++
T Consensus 247 pC~~Cg~~I 255 (272)
T TIGR00577 247 PCRRCGTPI 255 (272)
T ss_pred CCCCCCCee
Confidence 577777777
No 132
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=26.91 E-value=43 Score=18.46 Aligned_cols=11 Identities=9% Similarity=0.084 Sum_probs=8.5
Q ss_pred cccCccCCCCC
Q psy17526 2 NAHSDRCQHGL 12 (70)
Q Consensus 2 ~~~C~~C~~~l 12 (70)
...||.||.++
T Consensus 17 k~~CP~CG~~t 27 (56)
T PRK13130 17 KEICPVCGGKT 27 (56)
T ss_pred cccCcCCCCCC
Confidence 45788888887
No 133
>KOG2612|consensus
Probab=26.89 E-value=31 Score=21.16 Aligned_cols=12 Identities=25% Similarity=0.861 Sum_probs=9.0
Q ss_pred CcccCccCCCCC
Q psy17526 1 MNAHSDRCQHGL 12 (70)
Q Consensus 1 ~~~~C~~C~~~l 12 (70)
|+..|++|+|-.
T Consensus 73 ~~~hCeNC~RdV 84 (103)
T KOG2612|consen 73 MDCHCENCDRDV 84 (103)
T ss_pred ccccCCCCccHH
Confidence 677888888754
No 134
>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=26.55 E-value=62 Score=21.41 Aligned_cols=33 Identities=18% Similarity=0.553 Sum_probs=22.5
Q ss_pred hhhcccccccCCCCCCh-------------HHHHHHHHhC--CCCCCC
Q psy17526 29 LVSGLYSWCQGCSHGGH-------------LSHMQEWFMK--NNVCPT 61 (70)
Q Consensus 29 ~v~~l~~~C~~C~HggH-------------~~h~~~Wf~~--~~~CP~ 61 (70)
...++..||.+|.+--| ...+.+|+++ .++|+.
T Consensus 109 ~~d~~~wyc~~c~~~~~e~~f~~~d~~~~~~~~~~~f~~~~~~rtC~~ 156 (159)
T TIGR03037 109 ELDGFQWFCPQCGHKLHRAEVQLENIVTDLPPVFEHFYSNEDARTCKN 156 (159)
T ss_pred CCcceEEECCCCCCeEEEEEEEecChhhhhHHHHHHHhCChhhccCCc
Confidence 35677777888877766 3456677766 467876
No 135
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=26.34 E-value=60 Score=21.87 Aligned_cols=35 Identities=23% Similarity=0.677 Sum_probs=23.6
Q ss_pred hhhcccccccCCCCCCh-------------HHHHHHHHhC--CCCCCCCCC
Q psy17526 29 LVSGLYSWCQGCSHGGH-------------LSHMQEWFMK--NNVCPTGCG 64 (70)
Q Consensus 29 ~v~~l~~~C~~C~HggH-------------~~h~~~Wf~~--~~~CP~gC~ 64 (70)
...++-.||.+|.+--| ...+.+|+++ .++|+. ||
T Consensus 115 ~~d~~~wyc~~c~~~~~e~~f~~~d~~~~~~~~~~~f~~~~e~rtC~~-CG 164 (177)
T PRK13264 115 ELDGFQWYCDECNHKVHEVEVQLTDIETDLPPVFAAFYASEELRTCDN-CG 164 (177)
T ss_pred CccceEEECCCCCCeEEEEEEEecChhhhhHHHHHHHhcCHhhccCCc-CC
Confidence 45677778888887766 3456677766 467876 44
No 136
>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=26.00 E-value=28 Score=21.68 Aligned_cols=22 Identities=9% Similarity=0.086 Sum_probs=12.4
Q ss_pred cccCc--cCCCCCCcC---ccccccch
Q psy17526 2 NAHSD--RCQHGLGNF---GKLEGKIQ 23 (70)
Q Consensus 2 ~~~C~--~C~~~l~~~---~~~C~~~~ 23 (70)
|.+|| .|+|.+... .+.|.++.
T Consensus 18 Y~aC~~~~C~kKv~~~~~~~y~C~~C~ 44 (146)
T PF08646_consen 18 YPACPNEKCNKKVTENGDGSYRCEKCN 44 (146)
T ss_dssp EEE-TSTTTS-B-EEETTTEEEETTTT
T ss_pred ECCCCCccCCCEeecCCCcEEECCCCC
Confidence 67899 999988322 25776643
No 137
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=25.56 E-value=27 Score=22.05 Aligned_cols=11 Identities=9% Similarity=0.295 Sum_probs=8.3
Q ss_pred cccCccCCCCC
Q psy17526 2 NAHSDRCQHGL 12 (70)
Q Consensus 2 ~~~C~~C~~~l 12 (70)
+..||+|+|+-
T Consensus 69 ~V~CP~C~K~T 79 (114)
T PF11023_consen 69 QVECPNCGKQT 79 (114)
T ss_pred eeECCCCCChH
Confidence 35799999875
No 138
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=25.27 E-value=37 Score=15.35 Aligned_cols=10 Identities=10% Similarity=0.268 Sum_probs=7.7
Q ss_pred ccCccCCCCC
Q psy17526 3 AHSDRCQHGL 12 (70)
Q Consensus 3 ~~C~~C~~~l 12 (70)
..|+.|||..
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 5688888876
No 139
>TIGR03823 FliZ flagellar regulatory protein FliZ. FliZ is involved in the regulation of flagellar assembly and possibly also the down-regulation of the motile phenotype. FliZ interacts with the flagellar translational activator FlhCD complex.
Probab=25.22 E-value=24 Score=23.63 Aligned_cols=19 Identities=21% Similarity=0.401 Sum_probs=15.0
Q ss_pred cccCccCCCCCCcCcccccc
Q psy17526 2 NAHSDRCQHGLGNFGKLEGK 21 (70)
Q Consensus 2 ~~~C~~C~~~l~~~~~~C~~ 21 (70)
.|.|.+|+|.|.|.. ...+
T Consensus 22 QthCshC~K~LDRis-LV~~ 40 (168)
T TIGR03823 22 QTHCSHCHKLLDRIS-LVFR 40 (168)
T ss_pred cchhhhhcchhhhee-eeec
Confidence 589999999998875 4544
No 140
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.18 E-value=93 Score=22.77 Aligned_cols=25 Identities=28% Similarity=0.622 Sum_probs=20.7
Q ss_pred CCCCCChHHHHHHHHhCC-CCCCCCCC
Q psy17526 39 GCSHGGHLSHMQEWFMKN-NVCPTGCG 64 (70)
Q Consensus 39 ~C~HggH~~h~~~Wf~~~-~~CP~gC~ 64 (70)
.|||-.-.+|+...|... ..||. |+
T Consensus 25 ~CGH~~C~sCv~~l~~~~~~~CP~-C~ 50 (309)
T TIGR00570 25 VCGHTLCESCVDLLFVRGSGSCPE-CD 50 (309)
T ss_pred CCCCcccHHHHHHHhcCCCCCCCC-CC
Confidence 799999999999988764 57995 54
No 141
>PLN02925 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
Probab=25.04 E-value=31 Score=28.06 Aligned_cols=14 Identities=14% Similarity=0.162 Sum_probs=11.5
Q ss_pred CcccCccCCCCCCc
Q psy17526 1 MNAHSDRCQHGLGN 14 (70)
Q Consensus 1 ~~~~C~~C~~~l~~ 14 (70)
.+++||.|||.+..
T Consensus 633 e~isCPgCGRT~~d 646 (733)
T PLN02925 633 EYVSCPSCGRTLFD 646 (733)
T ss_pred eEEECCCCCCcccc
Confidence 37899999999843
No 142
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=24.90 E-value=26 Score=17.26 Aligned_cols=10 Identities=20% Similarity=0.348 Sum_probs=8.0
Q ss_pred ccCccCCCCC
Q psy17526 3 AHSDRCQHGL 12 (70)
Q Consensus 3 ~~C~~C~~~l 12 (70)
..||+||.-|
T Consensus 2 ~FCp~C~nlL 11 (35)
T PF02150_consen 2 RFCPECGNLL 11 (35)
T ss_dssp -BETTTTSBE
T ss_pred eeCCCCCccc
Confidence 4799999988
No 143
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=24.71 E-value=15 Score=20.05 Aligned_cols=24 Identities=17% Similarity=0.256 Sum_probs=16.2
Q ss_pred cccccccCCCCCChHH----HHHHHHhC
Q psy17526 32 GLYSWCQGCSHGGHLS----HMQEWFMK 55 (70)
Q Consensus 32 ~l~~~C~~C~HggH~~----h~~~Wf~~ 55 (70)
.-...|+.|++.|-.. |+++.+++
T Consensus 9 ~~lw~CL~Cg~~~C~~~~~~Ha~~H~~~ 36 (63)
T PF02148_consen 9 SNLWLCLTCGYVGCGRYSNGHALKHYKE 36 (63)
T ss_dssp SSEEEETTTS-EEETTTSTSHHHHHHHH
T ss_pred CceEEeCCCCcccccCCcCcHHHHhhcc
Confidence 3445588888887765 77887765
No 144
>PRK11582 flagella biosynthesis protein FliZ; Provisional
Probab=24.31 E-value=27 Score=23.41 Aligned_cols=19 Identities=21% Similarity=0.366 Sum_probs=15.1
Q ss_pred cccCccCCCCCCcCcccccc
Q psy17526 2 NAHSDRCQHGLGNFGKLEGK 21 (70)
Q Consensus 2 ~~~C~~C~~~l~~~~~~C~~ 21 (70)
.|+|.+|+|.|.|.. ...+
T Consensus 22 QthCshC~K~LDRis-LV~~ 40 (169)
T PRK11582 22 QTHCAHCRKLLDRIT-LVFR 40 (169)
T ss_pred ccchhhhccchhhee-eeec
Confidence 589999999998875 5544
No 145
>PRK08402 replication factor A; Reviewed
Probab=24.25 E-value=26 Score=25.84 Aligned_cols=21 Identities=5% Similarity=0.067 Sum_probs=15.8
Q ss_pred CcccCccCCCCCC----cCcccccc
Q psy17526 1 MNAHSDRCQHGLG----NFGKLEGK 21 (70)
Q Consensus 1 ~~~~C~~C~~~l~----~~~~~C~~ 21 (70)
+|.+||.|+|.+. ...|.|..
T Consensus 211 ~y~aCp~CnKkv~~~~~~~~~~Ce~ 235 (355)
T PRK08402 211 VYDACPECRRKVDYDPATDTWICPE 235 (355)
T ss_pred eEecCCCCCeEEEEecCCCCEeCCC
Confidence 4789999999994 23477876
No 146
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=24.20 E-value=31 Score=18.72 Aligned_cols=12 Identities=8% Similarity=0.282 Sum_probs=8.5
Q ss_pred CcccCccCCCCC
Q psy17526 1 MNAHSDRCQHGL 12 (70)
Q Consensus 1 ~~~~C~~C~~~l 12 (70)
+|-.||+||.-.
T Consensus 12 kY~~Cp~CGN~~ 23 (49)
T PF12677_consen 12 KYCKCPKCGNDK 23 (49)
T ss_pred hhccCcccCCcE
Confidence 366788888754
No 147
>KOG1941|consensus
Probab=24.19 E-value=40 Score=25.99 Aligned_cols=25 Identities=40% Similarity=0.622 Sum_probs=21.6
Q ss_pred ccCCCCCChHHHHHHHHhCC--CCCCC
Q psy17526 37 CQGCSHGGHLSHMQEWFMKN--NVCPT 61 (70)
Q Consensus 37 C~~C~HggH~~h~~~Wf~~~--~~CP~ 61 (70)
-+.|.|..|..++.+.+.++ +.||.
T Consensus 384 ALpCsHIfH~rCl~e~L~~n~~rsCP~ 410 (518)
T KOG1941|consen 384 ALPCSHIFHLRCLQEILENNGTRSCPN 410 (518)
T ss_pred ccchhHHHHHHHHHHHHHhCCCCCCcc
Confidence 57789999999999999885 67885
No 148
>KOG2114|consensus
Probab=24.00 E-value=36 Score=28.36 Aligned_cols=20 Identities=30% Similarity=0.635 Sum_probs=17.3
Q ss_pred CCCCCChHHHHHHHHhCCCCCCC
Q psy17526 39 GCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 39 ~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
.|+|..|.+|+. ...++||.
T Consensus 858 ~CgHsyHqhC~e---~~~~~CP~ 877 (933)
T KOG2114|consen 858 LCGHSYHQHCLE---DKEDKCPK 877 (933)
T ss_pred ecccHHHHHhhc---cCcccCCc
Confidence 589999999998 66789996
No 149
>PRK07218 replication factor A; Provisional
Probab=23.90 E-value=41 Score=25.41 Aligned_cols=18 Identities=6% Similarity=0.028 Sum_probs=13.8
Q ss_pred cccCccCCCCCCcCcccccc
Q psy17526 2 NAHSDRCQHGLGNFGKLEGK 21 (70)
Q Consensus 2 ~~~C~~C~~~l~~~~~~C~~ 21 (70)
.+.||.|+|.|.+ ++|..
T Consensus 297 i~rCP~C~r~v~~--~~C~~ 314 (423)
T PRK07218 297 IERCPECGRVIQK--GQCRS 314 (423)
T ss_pred eecCcCccccccC--CcCCC
Confidence 4689999999976 25655
No 150
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=23.89 E-value=29 Score=22.69 Aligned_cols=28 Identities=32% Similarity=0.859 Sum_probs=17.9
Q ss_pred cccccCCCCCChHHHHHHHHhC-----------CCCCCCCCCc
Q psy17526 34 YSWCQGCSHGGHLSHMQEWFMK-----------NNVCPTGCGH 65 (70)
Q Consensus 34 ~~~C~~C~HggH~~h~~~Wf~~-----------~~~CP~gC~c 65 (70)
..|=+.|.+| |. ...||.+ .-.||+ ||.
T Consensus 2 I~y~L~C~~g-H~--FEgWF~ss~~fd~Q~~~glv~CP~-Cgs 40 (148)
T PF06676_consen 2 IVYDLRCENG-HE--FEGWFRSSAAFDRQQARGLVSCPV-CGS 40 (148)
T ss_pred eeEEEecCCC-Cc--cceecCCHHHHHHHHHcCCccCCC-CCC
Confidence 3455566643 44 6899998 246998 553
No 151
>PRK05978 hypothetical protein; Provisional
Probab=23.40 E-value=47 Score=21.69 Aligned_cols=34 Identities=21% Similarity=0.649 Sum_probs=24.6
Q ss_pred HhhhhcccccccCCCCCChHHHHHHHHhCCCCCCCCCC
Q psy17526 27 FCLVSGLYSWCQGCSHGGHLSHMQEWFMKNNVCPTGCG 64 (70)
Q Consensus 27 ~~~v~~l~~~C~~C~HggH~~h~~~Wf~~~~~CP~gC~ 64 (70)
....+|+.--|++||-|-=. +.+++-+..||. ||
T Consensus 26 ~~~~rGl~grCP~CG~G~LF---~g~Lkv~~~C~~-CG 59 (148)
T PRK05978 26 RAMWRGFRGRCPACGEGKLF---RAFLKPVDHCAA-CG 59 (148)
T ss_pred HHHHHHHcCcCCCCCCCccc---ccccccCCCccc-cC
Confidence 35668888899999988433 455666888997 44
No 152
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=23.06 E-value=60 Score=17.84 Aligned_cols=26 Identities=12% Similarity=-0.003 Sum_probs=16.6
Q ss_pred HHHHhhh--hcccccccCCCCCChHHHH
Q psy17526 24 MLVFCLV--SGLYSWCQGCSHGGHLSHM 49 (70)
Q Consensus 24 ~iC~~~v--~~l~~~C~~C~HggH~~h~ 49 (70)
.+|.+++ ..-.+.|+.|+=.-|-++.
T Consensus 9 ~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 9 PVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred hhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 3455555 4556778888877766553
No 153
>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=22.82 E-value=12 Score=17.64 Aligned_cols=23 Identities=17% Similarity=0.485 Sum_probs=13.3
Q ss_pred HHHhhhhcc-cccccCCCCCChHH
Q psy17526 25 LVFCLVSGL-YSWCQGCSHGGHLS 47 (70)
Q Consensus 25 iC~~~v~~l-~~~C~~C~HggH~~ 47 (70)
+|++.+.+. +..|..|.-..|..
T Consensus 5 ~C~~~~~~~~~Y~C~~c~f~lh~~ 28 (30)
T PF03107_consen 5 VCRRKIDGFYFYHCSECCFTLHVR 28 (30)
T ss_pred CCCCCcCCCEeEEeCCCCCeEcCc
Confidence 455556666 66666666555543
No 154
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=22.77 E-value=42 Score=16.78 Aligned_cols=11 Identities=36% Similarity=0.682 Sum_probs=8.9
Q ss_pred cccCccCCCCC
Q psy17526 2 NAHSDRCQHGL 12 (70)
Q Consensus 2 ~~~C~~C~~~l 12 (70)
.+.||.|++.-
T Consensus 5 ~v~CP~C~s~~ 15 (36)
T PF03811_consen 5 DVHCPRCQSTE 15 (36)
T ss_pred eeeCCCCCCCC
Confidence 46799999876
No 155
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=22.64 E-value=44 Score=16.64 Aligned_cols=10 Identities=10% Similarity=0.252 Sum_probs=7.9
Q ss_pred ccCccCCCCC
Q psy17526 3 AHSDRCQHGL 12 (70)
Q Consensus 3 ~~C~~C~~~l 12 (70)
..||.||.+.
T Consensus 3 ~~Cp~Cg~~~ 12 (47)
T PF14690_consen 3 PRCPHCGSPS 12 (47)
T ss_pred ccCCCcCCCc
Confidence 5789999776
No 156
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=22.31 E-value=36 Score=14.34 Aligned_cols=11 Identities=36% Similarity=0.966 Sum_probs=7.7
Q ss_pred cccCCCCCChH
Q psy17526 36 WCQGCSHGGHL 46 (70)
Q Consensus 36 ~C~~C~HggH~ 46 (70)
.|-+|+=.||.
T Consensus 2 ~C~~C~~~GH~ 12 (18)
T PF00098_consen 2 KCFNCGEPGHI 12 (18)
T ss_dssp BCTTTSCSSSC
T ss_pred cCcCCCCcCcc
Confidence 36677777775
No 157
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=21.92 E-value=40 Score=20.63 Aligned_cols=11 Identities=9% Similarity=0.220 Sum_probs=9.5
Q ss_pred cccCccCCCCC
Q psy17526 2 NAHSDRCQHGL 12 (70)
Q Consensus 2 ~~~C~~C~~~l 12 (70)
+|.||.|.++-
T Consensus 8 ~tyCp~CkkhT 18 (94)
T COG1631 8 RTYCPYCKKHT 18 (94)
T ss_pred eecCcccccce
Confidence 68899999887
No 158
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=21.91 E-value=44 Score=18.25 Aligned_cols=9 Identities=33% Similarity=0.615 Sum_probs=6.2
Q ss_pred cccCccCCC
Q psy17526 2 NAHSDRCQH 10 (70)
Q Consensus 2 ~~~C~~C~~ 10 (70)
|-.||+||-
T Consensus 19 ~~~CPrCG~ 27 (51)
T COG1998 19 NRFCPRCGP 27 (51)
T ss_pred cccCCCCCC
Confidence 456888883
No 159
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=21.83 E-value=46 Score=16.71 Aligned_cols=9 Identities=11% Similarity=0.250 Sum_probs=6.6
Q ss_pred cCccCCCCC
Q psy17526 4 HSDRCQHGL 12 (70)
Q Consensus 4 ~C~~C~~~l 12 (70)
.||+||...
T Consensus 2 ~Cp~Cg~~~ 10 (43)
T PF08271_consen 2 KCPNCGSKE 10 (43)
T ss_dssp SBTTTSSSE
T ss_pred CCcCCcCCc
Confidence 688888764
No 160
>KOG0825|consensus
Probab=21.64 E-value=65 Score=27.09 Aligned_cols=31 Identities=16% Similarity=0.155 Sum_probs=26.4
Q ss_pred hcccccccCCCCCChHHHHHHHHhCCCCCCC
Q psy17526 31 SGLYSWCQGCSHGGHLSHMQEWFMKNNVCPT 61 (70)
Q Consensus 31 ~~l~~~C~~C~HggH~~h~~~Wf~~~~~CP~ 61 (70)
++|..-=..|+|..|.+++..|-....+||+
T Consensus 135 DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPi 165 (1134)
T KOG0825|consen 135 DQLEESEKHTAHYFCEECVGSWSRCAQTCPV 165 (1134)
T ss_pred HHhhccccccccccHHHHhhhhhhhcccCch
Confidence 4555556789999999999999999999996
No 161
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=21.37 E-value=53 Score=18.54 Aligned_cols=10 Identities=10% Similarity=0.394 Sum_probs=8.7
Q ss_pred ccCccCCCCC
Q psy17526 3 AHSDRCQHGL 12 (70)
Q Consensus 3 ~~C~~C~~~l 12 (70)
..||.|+|+.
T Consensus 7 v~CP~C~k~~ 16 (62)
T PRK00418 7 VNCPTCGKPV 16 (62)
T ss_pred ccCCCCCCcc
Confidence 5799999986
No 162
>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=21.34 E-value=49 Score=16.89 Aligned_cols=9 Identities=11% Similarity=0.183 Sum_probs=6.6
Q ss_pred ccCccCCCC
Q psy17526 3 AHSDRCQHG 11 (70)
Q Consensus 3 ~~C~~C~~~ 11 (70)
.+||+||..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 468888874
No 163
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=21.22 E-value=21 Score=19.80 Aligned_cols=12 Identities=17% Similarity=0.132 Sum_probs=7.5
Q ss_pred cccCccCCCCCC
Q psy17526 2 NAHSDRCQHGLG 13 (70)
Q Consensus 2 ~~~C~~C~~~l~ 13 (70)
+..|++||.+|-
T Consensus 48 r~FC~~CGs~l~ 59 (92)
T PF04828_consen 48 RYFCPTCGSPLF 59 (92)
T ss_dssp EEEETTT--EEE
T ss_pred CcccCCCCCeee
Confidence 357999999883
No 164
>PRK11866 2-oxoacid ferredoxin oxidoreductase subunit beta; Provisional
Probab=21.21 E-value=59 Score=23.08 Aligned_cols=25 Identities=28% Similarity=0.634 Sum_probs=20.0
Q ss_pred hhcccccccCCCCCChHHHHHHHHh
Q psy17526 30 VSGLYSWCQGCSHGGHLSHMQEWFM 54 (70)
Q Consensus 30 v~~l~~~C~~C~HggH~~h~~~Wf~ 54 (70)
|+|-.+||+.|+|++=..-+++=+.
T Consensus 3 ~~r~~~~CpGCg~~~il~al~~al~ 27 (279)
T PRK11866 3 VKRPPIWCPGCGNYGILEALRKALA 27 (279)
T ss_pred CCCCCCCCCCCCChHHHHHHHHHHH
Confidence 5667899999999987777777663
No 165
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=20.60 E-value=77 Score=16.15 Aligned_cols=21 Identities=14% Similarity=-0.040 Sum_probs=13.5
Q ss_pred ccCccCCCCCCcCccccccch
Q psy17526 3 AHSDRCQHGLGNFGKLEGKIQ 23 (70)
Q Consensus 3 ~~C~~C~~~l~~~~~~C~~~~ 23 (70)
+.|..|++++...-+.|..+.
T Consensus 1 v~Cd~C~~~i~G~ry~C~~C~ 21 (43)
T cd02340 1 VICDGCQGPIVGVRYKCLVCP 21 (43)
T ss_pred CCCCCCCCcCcCCeEECCCCC
Confidence 368888887755445665543
No 166
>PRK09628 oorB 2-oxoglutarate-acceptor oxidoreductase subunit OorB; Reviewed
Probab=20.46 E-value=80 Score=22.34 Aligned_cols=22 Identities=32% Similarity=0.629 Sum_probs=17.7
Q ss_pred cccccCCCCCChHHHHHHHHhC
Q psy17526 34 YSWCQGCSHGGHLSHMQEWFMK 55 (70)
Q Consensus 34 ~~~C~~C~HggH~~h~~~Wf~~ 55 (70)
-.||+.|+|+.....+.+-+.+
T Consensus 16 ~~~CpGCg~~i~~~~v~~al~e 37 (277)
T PRK09628 16 TLWCWGCGDGVILKSIIRAIDK 37 (277)
T ss_pred CCcCCCCCCchHHHHHHHHHHH
Confidence 4799999999888877776654
No 167
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=20.45 E-value=40 Score=16.81 Aligned_cols=12 Identities=17% Similarity=0.354 Sum_probs=5.9
Q ss_pred cccCccCCCCCC
Q psy17526 2 NAHSDRCQHGLG 13 (70)
Q Consensus 2 ~~~C~~C~~~l~ 13 (70)
+..|-.|+++..
T Consensus 3 ~~~C~eC~~~f~ 14 (34)
T PF01286_consen 3 YPKCDECGKPFM 14 (34)
T ss_dssp -EE-TTT--EES
T ss_pred CchHhHhCCHHH
Confidence 457888888873
No 168
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=20.28 E-value=62 Score=17.98 Aligned_cols=23 Identities=17% Similarity=0.330 Sum_probs=18.6
Q ss_pred CCCCCChHHHHHHHHhC-CCCCCC
Q psy17526 39 GCSHGGHLSHMQEWFMK-NNVCPT 61 (70)
Q Consensus 39 ~C~HggH~~h~~~Wf~~-~~~CP~ 61 (70)
..||..=-+.+.+|+++ +.+||.
T Consensus 21 ~~G~tyer~~I~~~l~~~~~~~P~ 44 (73)
T PF04564_consen 21 PSGHTYERSAIERWLEQNGGTDPF 44 (73)
T ss_dssp TTSEEEEHHHHHHHHCTTSSB-TT
T ss_pred CcCCEEcHHHHHHHHHcCCCCCCC
Confidence 45677778999999999 889996
No 169
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.12 E-value=60 Score=18.58 Aligned_cols=13 Identities=8% Similarity=0.082 Sum_probs=10.2
Q ss_pred cccCccCCCCCCc
Q psy17526 2 NAHSDRCQHGLGN 14 (70)
Q Consensus 2 ~~~C~~C~~~l~~ 14 (70)
..-||.|||+...
T Consensus 7 ~v~CP~Cgkpv~w 19 (65)
T COG3024 7 TVPCPTCGKPVVW 19 (65)
T ss_pred cccCCCCCCcccc
Confidence 3569999999954
No 170
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=20.08 E-value=49 Score=20.68 Aligned_cols=11 Identities=18% Similarity=0.383 Sum_probs=9.4
Q ss_pred cccCccCCCCC
Q psy17526 2 NAHSDRCQHGL 12 (70)
Q Consensus 2 ~~~C~~C~~~l 12 (70)
+..|++||.+|
T Consensus 69 r~FC~~CGs~l 79 (133)
T COG3791 69 RGFCPTCGSPL 79 (133)
T ss_pred CeecccCCCce
Confidence 35799999999
Done!