Query psy4412
Match_columns 39
No_of_seqs 111 out of 1995
Neff 12.7
Searched_HMMs 46136
Date Sat Aug 17 00:52:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4412.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4412hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.7 1.8E-17 3.8E-22 63.7 2.7 38 1-38 210-247 (279)
2 KOG3623|consensus 99.6 1.2E-15 2.6E-20 64.7 1.4 38 1-38 917-954 (1007)
3 KOG2462|consensus 99.5 1.1E-14 2.4E-19 56.2 1.2 34 5-38 186-219 (279)
4 PHA00616 hypothetical protein 99.4 9.2E-14 2E-18 41.7 1.1 33 6-38 1-33 (44)
5 KOG3623|consensus 99.3 5E-13 1.1E-17 57.2 1.1 35 4-38 279-313 (1007)
6 PHA02768 hypothetical protein; 99.2 3.3E-11 7.2E-16 37.6 2.1 30 6-37 5-34 (55)
7 PF13465 zf-H2C2_2: Zinc-finge 98.9 1.1E-09 2.4E-14 29.7 1.9 19 21-39 1-19 (26)
8 KOG1074|consensus 98.9 5.5E-10 1.2E-14 48.7 1.1 33 1-33 628-660 (958)
9 KOG3576|consensus 98.9 2.2E-10 4.7E-15 43.7 -0.2 33 6-38 145-177 (267)
10 KOG1074|consensus 98.9 8.3E-10 1.8E-14 48.2 1.1 33 7-39 354-386 (958)
11 PF13465 zf-H2C2_2: Zinc-finge 98.8 1.1E-09 2.3E-14 29.8 0.7 17 1-17 9-25 (26)
12 PF00096 zf-C2H2: Zinc finger, 98.8 1.3E-08 2.7E-13 26.7 1.9 23 7-29 1-23 (23)
13 PF13912 zf-C2H2_6: C2H2-type 98.7 1.4E-08 3.1E-13 27.5 1.5 25 6-30 1-25 (27)
14 PHA00733 hypothetical protein 98.6 1.1E-07 2.4E-12 34.1 2.6 34 3-38 70-103 (128)
15 PF13894 zf-C2H2_4: C2H2-type 98.4 3.9E-07 8.5E-12 23.6 2.1 23 7-29 1-23 (24)
16 KOG3576|consensus 98.4 1.3E-07 2.8E-12 36.4 1.0 30 1-30 168-197 (267)
17 smart00355 ZnF_C2H2 zinc finge 98.3 1.2E-06 2.5E-11 22.9 1.9 24 7-30 1-24 (26)
18 PF09237 GAGA: GAGA factor; I 98.3 4E-06 8.7E-11 26.1 2.9 32 3-34 21-52 (54)
19 KOG3608|consensus 98.1 4.2E-06 9.2E-11 34.7 2.0 37 1-38 287-323 (467)
20 PF12874 zf-met: Zinc-finger o 98.0 4.9E-06 1.1E-10 21.9 1.5 23 7-29 1-23 (25)
21 PHA00732 hypothetical protein 98.0 6.2E-06 1.3E-10 27.6 2.0 26 6-31 1-27 (79)
22 PRK04860 hypothetical protein; 97.8 4.2E-05 9.1E-10 28.6 2.6 29 6-38 119-147 (160)
23 PF13909 zf-H2C2_5: C2H2-type 97.5 0.00014 3.1E-09 18.9 1.7 22 7-29 1-22 (24)
24 PF12171 zf-C2H2_jaz: Zinc-fin 97.4 3.9E-05 8.4E-10 20.7 -0.1 22 7-28 2-23 (27)
25 KOG3608|consensus 97.3 0.00032 7E-09 29.5 2.3 33 6-38 263-296 (467)
26 PLN03086 PRLI-interacting fact 97.3 0.00037 8E-09 30.7 2.2 31 6-38 478-508 (567)
27 smart00451 ZnF_U1 U1-like zinc 97.1 0.00056 1.2E-08 19.2 1.6 22 6-27 3-24 (35)
28 PF05605 zf-Di19: Drought indu 97.0 0.0018 3.8E-08 20.2 2.6 33 6-39 2-36 (54)
29 PF12756 zf-C2H2_2: C2H2 type 96.9 0.0018 4E-08 21.8 2.1 24 6-29 50-73 (100)
30 COG5189 SFP1 Putative transcri 96.8 0.0003 6.5E-09 29.2 -0.2 24 3-26 395-418 (423)
31 PLN03086 PRLI-interacting fact 96.5 0.0059 1.3E-07 27.3 2.6 36 2-38 500-545 (567)
32 PF13913 zf-C2HC_2: zinc-finge 96.4 0.0042 9.2E-08 16.5 1.5 20 7-27 3-22 (25)
33 KOG3993|consensus 95.7 0.0067 1.5E-07 26.4 1.0 25 6-30 295-319 (500)
34 PF04959 ARS2: Arsenite-resist 95.3 0.0069 1.5E-07 24.0 0.4 28 4-31 75-102 (214)
35 KOG3993|consensus 95.0 0.014 3E-07 25.5 0.9 26 5-30 355-380 (500)
36 COG4049 Uncharacterized protei 95.0 0.019 4.1E-07 18.4 1.0 25 3-27 14-38 (65)
37 PF12013 DUF3505: Protein of u 94.0 0.091 2E-06 18.6 1.9 26 6-31 80-109 (109)
38 PF05443 ROS_MUCR: ROS/MUCR tr 93.6 0.076 1.6E-06 19.8 1.4 23 7-32 73-95 (132)
39 PF08790 zf-LYAR: LYAR-type C2 92.2 0.04 8.7E-07 15.2 -0.0 19 7-26 1-19 (28)
40 KOG2482|consensus 91.5 0.19 4.2E-06 21.8 1.5 23 7-29 196-218 (423)
41 cd00350 rubredoxin_like Rubred 91.3 0.2 4.2E-06 14.0 1.4 9 7-15 2-10 (33)
42 KOG3408|consensus 90.3 0.26 5.6E-06 18.3 1.2 24 5-28 56-79 (129)
43 COG1592 Rubrerythrin [Energy p 90.2 0.33 7.2E-06 18.9 1.5 10 6-15 134-143 (166)
44 KOG4167|consensus 89.4 0.08 1.7E-06 25.0 -0.4 25 6-30 792-816 (907)
45 COG5048 FOG: Zn-finger [Genera 88.4 0.2 4.4E-06 20.9 0.5 32 7-38 290-325 (467)
46 smart00834 CxxC_CXXC_SSSS Puta 88.3 0.29 6.2E-06 14.0 0.7 15 6-20 5-19 (41)
47 PF09723 Zn-ribbon_8: Zinc rib 87.2 0.36 7.7E-06 14.3 0.6 16 6-21 5-20 (42)
48 PF10571 UPF0547: Uncharacteri 85.3 0.48 1E-05 12.7 0.5 10 8-17 16-25 (26)
49 TIGR02605 CxxC_CxxC_SSSS putat 84.7 0.56 1.2E-05 14.3 0.6 15 6-20 5-19 (52)
50 COG4957 Predicted transcriptio 84.5 0.83 1.8E-05 17.4 1.1 24 8-34 78-101 (148)
51 PF01428 zf-AN1: AN1-like Zinc 84.1 0.5 1.1E-05 14.0 0.4 15 5-19 12-26 (43)
52 smart00154 ZnF_AN1 AN1-like Zi 83.6 0.76 1.6E-05 13.5 0.7 14 6-19 12-25 (39)
53 smart00614 ZnF_BED BED zinc fi 82.9 1.2 2.5E-05 13.6 2.0 21 7-27 19-44 (50)
54 cd00924 Cyt_c_Oxidase_Vb Cytoc 82.7 0.96 2.1E-05 16.1 0.9 13 5-17 78-90 (97)
55 PLN02294 cytochrome c oxidase 81.7 1.1 2.4E-05 17.7 1.0 15 4-18 139-153 (174)
56 PF09845 DUF2072: Zn-ribbon co 81.6 0.72 1.6E-05 17.4 0.5 15 6-20 1-15 (131)
57 PF07754 DUF1610: Domain of un 81.0 0.99 2.2E-05 12.0 0.6 9 6-14 16-24 (24)
58 PF09986 DUF2225: Uncharacteri 80.8 1 2.2E-05 18.1 0.8 19 4-22 3-21 (214)
59 PF13451 zf-trcl: Probable zin 79.1 1.3 2.8E-05 13.9 0.7 17 4-20 2-18 (49)
60 PF01286 XPA_N: XPA protein N- 77.6 1.3 2.8E-05 12.8 0.5 12 8-19 5-16 (34)
61 PF06397 Desulfoferrod_N: Desu 77.5 1.3 2.7E-05 13.0 0.5 11 6-16 6-16 (36)
62 PHA00626 hypothetical protein 76.4 2.2 4.8E-05 13.9 0.9 14 5-18 22-35 (59)
63 PF11789 zf-Nse: Zinc-finger o 76.0 2.4 5.2E-05 13.5 1.0 16 5-20 23-38 (57)
64 KOG2071|consensus 75.8 3.2 7E-05 19.6 1.6 26 5-30 417-442 (579)
65 cd00729 rubredoxin_SM Rubredox 75.8 1.9 4E-05 12.2 0.7 12 6-17 2-13 (34)
66 KOG2893|consensus 74.9 0.42 9.2E-06 19.9 -0.9 17 7-23 35-51 (341)
67 PF04423 Rad50_zn_hook: Rad50 74.1 1.5 3.2E-05 13.6 0.4 12 8-19 22-33 (54)
68 KOG0717|consensus 73.4 3.5 7.5E-05 19.1 1.4 21 7-27 293-313 (508)
69 smart00734 ZnF_Rad18 Rad18-lik 73.2 2.2 4.7E-05 11.3 1.3 18 8-26 3-20 (26)
70 PTZ00448 hypothetical protein; 72.5 3.9 8.5E-05 18.3 1.4 23 6-28 314-336 (373)
71 PF02892 zf-BED: BED zinc fing 72.4 2.8 6E-05 12.2 2.0 22 5-26 15-40 (45)
72 COG2331 Uncharacterized protei 71.5 1.6 3.4E-05 15.1 0.2 12 6-17 12-23 (82)
73 PF13878 zf-C2H2_3: zinc-finge 70.7 3.2 7E-05 12.3 1.7 24 7-30 14-39 (41)
74 PF10013 DUF2256: Uncharacteri 70.0 2.3 5E-05 12.9 0.4 14 8-21 10-23 (42)
75 COG3364 Zn-ribbon containing p 69.6 2.4 5.1E-05 15.5 0.5 14 6-19 2-15 (112)
76 COG1773 Rubredoxin [Energy pro 69.3 2.6 5.7E-05 13.6 0.5 13 6-18 3-15 (55)
77 TIGR00622 ssl1 transcription f 69.2 5.9 0.00013 14.7 1.6 24 6-29 81-104 (112)
78 PF01215 COX5B: Cytochrome c o 68.5 3.1 6.8E-05 15.9 0.7 14 5-18 111-124 (136)
79 PLN02748 tRNA dimethylallyltra 68.3 5.5 0.00012 18.3 1.5 24 4-27 416-440 (468)
80 PTZ00043 cytochrome c oxidase 67.5 3.7 8.1E-05 17.2 0.9 15 4-18 179-193 (268)
81 PF07975 C1_4: TFIIH C1-like d 67.2 0.7 1.5E-05 14.6 -0.9 23 5-27 20-42 (51)
82 PF09538 FYDLN_acid: Protein o 66.9 4.1 8.9E-05 14.9 0.9 17 3-19 23-39 (108)
83 PRK06266 transcription initiat 66.0 5 0.00011 15.9 1.0 15 6-20 117-131 (178)
84 PF00301 Rubredoxin: Rubredoxi 66.0 4 8.6E-05 12.6 0.7 11 7-17 2-12 (47)
85 PF01096 TFIIS_C: Transcriptio 64.6 3.6 7.8E-05 12.0 0.5 10 7-16 29-38 (39)
86 KOG2186|consensus 64.4 3.5 7.7E-05 17.5 0.5 21 6-27 29-49 (276)
87 TIGR00373 conserved hypothetic 63.2 9.1 0.0002 14.8 1.5 17 6-22 109-125 (158)
88 PF14353 CpXC: CpXC protein 63.1 4.7 0.0001 14.7 0.7 15 6-20 38-52 (128)
89 PF02148 zf-UBP: Zn-finger in 63.0 4.4 9.6E-05 12.9 0.6 16 4-19 9-24 (63)
90 KOG2785|consensus 62.8 8.8 0.00019 17.4 1.5 24 6-29 217-243 (390)
91 COG2888 Predicted Zn-ribbon RN 62.3 5.2 0.00011 13.2 0.7 9 5-13 49-57 (61)
92 cd00730 rubredoxin Rubredoxin; 61.9 3.7 8.1E-05 12.8 0.3 11 7-17 2-12 (50)
93 smart00659 RPOLCX RNA polymera 61.8 5.5 0.00012 12.1 0.7 12 7-18 3-14 (44)
94 PRK00464 nrdR transcriptional 61.7 4.1 8.9E-05 15.8 0.5 15 6-20 28-42 (154)
95 TIGR00319 desulf_FeS4 desulfof 61.6 5 0.00011 11.1 0.7 11 6-16 7-17 (34)
96 KOG1994|consensus 61.5 7.2 0.00016 16.5 1.1 22 6-27 239-260 (268)
97 TIGR03831 YgiT_finger YgiT-typ 61.5 4.5 9.8E-05 11.6 0.5 11 7-17 33-43 (46)
98 PF01927 Mut7-C: Mut7-C RNAse 61.1 8.8 0.00019 14.6 1.3 15 7-21 125-139 (147)
99 PF04780 DUF629: Protein of un 60.5 10 0.00022 17.6 1.6 22 6-27 57-78 (466)
100 PRK00398 rpoP DNA-directed RNA 60.4 5.9 0.00013 11.8 0.7 12 6-17 3-14 (46)
101 cd00974 DSRD Desulforedoxin (D 60.0 5.4 0.00012 11.1 0.6 11 6-16 4-14 (34)
102 KOG1146|consensus 59.5 12 0.00025 20.0 1.7 25 4-28 516-540 (1406)
103 COG1655 Uncharacterized protei 59.3 1 2.2E-05 18.7 -1.2 27 5-31 18-44 (267)
104 PF13719 zinc_ribbon_5: zinc-r 59.3 6 0.00013 11.3 1.0 11 6-16 25-35 (37)
105 PRK14890 putative Zn-ribbon RN 57.7 7 0.00015 12.8 0.7 9 5-13 47-55 (59)
106 PF14369 zf-RING_3: zinc-finge 56.9 5.6 0.00012 11.4 0.4 10 8-17 23-32 (35)
107 KOG2857|consensus 56.9 6.9 0.00015 15.3 0.7 22 6-27 17-38 (157)
108 smart00440 ZnF_C2C2 C2C2 Zinc 56.4 7.3 0.00016 11.4 0.7 10 7-16 29-38 (40)
109 PRK08222 hydrogenase 4 subunit 55.9 11 0.00024 14.9 1.2 17 6-22 114-130 (181)
110 KOG0978|consensus 55.7 3.5 7.6E-05 20.0 -0.1 17 7-23 679-695 (698)
111 KOG2593|consensus 55.3 8.4 0.00018 17.7 0.9 19 4-22 126-144 (436)
112 PF02176 zf-TRAF: TRAF-type zi 55.3 8.5 0.00018 11.8 1.8 32 6-37 9-41 (60)
113 PF08792 A2L_zn_ribbon: A2L zi 52.8 8.2 0.00018 10.9 0.6 10 7-16 22-31 (33)
114 COG3677 Transposase and inacti 52.4 8.5 0.00018 14.5 0.6 15 5-19 52-66 (129)
115 COG5152 Uncharacterized conser 51.4 9 0.0002 15.9 0.7 16 4-19 194-209 (259)
116 COG1996 RPC10 DNA-directed RNA 51.2 7.8 0.00017 12.2 0.4 12 5-16 5-16 (49)
117 TIGR00244 transcriptional regu 50.5 7.8 0.00017 15.1 0.4 14 7-20 29-42 (147)
118 KOG2636|consensus 49.9 23 0.0005 16.7 1.7 23 4-26 399-422 (497)
119 KOG0562|consensus 49.8 20 0.00043 14.5 1.8 25 5-29 152-176 (184)
120 PF05191 ADK_lid: Adenylate ki 49.8 9.8 0.00021 11.0 0.9 10 8-17 23-32 (36)
121 KOG0782|consensus 49.4 3 6.5E-05 20.0 -0.8 14 7-20 254-267 (1004)
122 PRK12387 formate hydrogenlyase 49.2 11 0.00024 14.8 0.8 16 6-21 114-129 (180)
123 TIGR02098 MJ0042_CXXC MJ0042 f 49.1 9.6 0.00021 10.6 0.8 14 7-20 3-16 (38)
124 COG1997 RPL43A Ribosomal prote 48.7 11 0.00024 13.5 0.7 11 7-17 54-64 (89)
125 COG1327 Predicted transcriptio 48.6 8.6 0.00019 15.1 0.4 13 8-20 30-42 (156)
126 KOG4727|consensus 48.5 16 0.00034 14.8 1.1 21 6-26 75-95 (193)
127 smart00132 LIM Zinc-binding do 47.2 8.7 0.00019 10.2 0.3 9 7-15 28-36 (39)
128 PF13717 zinc_ribbon_4: zinc-r 47.0 11 0.00024 10.7 1.0 10 7-16 26-35 (36)
129 COG5112 UFD2 U1-like Zn-finger 47.0 11 0.00023 14.0 0.5 22 6-27 55-76 (126)
130 PF03811 Zn_Tnp_IS1: InsA N-te 47.0 2.1 4.5E-05 12.4 -1.0 28 7-38 6-33 (36)
131 PF06170 DUF983: Protein of un 46.4 11 0.00023 13.2 0.5 12 8-19 10-21 (86)
132 PF10083 DUF2321: Uncharacteri 45.1 12 0.00025 14.9 0.5 18 4-21 66-83 (158)
133 PF09965 DUF2199: Uncharacteri 45.1 11 0.00023 14.7 0.4 13 7-19 1-13 (148)
134 PF14447 Prok-RING_4: Prokaryo 44.9 11 0.00025 12.2 0.4 13 5-17 38-50 (55)
135 TIGR03829 YokU_near_AblA uncha 44.1 18 0.0004 12.9 0.9 16 7-22 36-51 (89)
136 COG3091 SprT Zn-dependent meta 44.1 14 0.00029 14.7 0.6 27 6-37 117-143 (156)
137 PF13240 zinc_ribbon_2: zinc-r 44.1 8.6 0.00019 9.8 0.1 6 9-14 16-21 (23)
138 PF10367 Vps39_2: Vacuolar sor 44.1 14 0.0003 12.8 0.6 12 8-19 80-91 (109)
139 COG4306 Uncharacterized protei 44.0 15 0.00033 14.1 0.7 16 4-19 66-81 (160)
140 COG4888 Uncharacterized Zn rib 43.8 16 0.00034 13.5 0.7 9 6-14 22-30 (104)
141 KOG3362|consensus 43.8 7 0.00015 15.3 -0.1 20 6-25 129-148 (156)
142 PF03604 DNA_RNApol_7kD: DNA d 43.7 13 0.00028 10.5 0.6 10 7-16 1-10 (32)
143 smart00531 TFIIE Transcription 43.6 23 0.00051 13.5 1.2 16 5-20 98-113 (147)
144 COG1631 RPL42A Ribosomal prote 43.0 12 0.00026 13.5 0.4 11 7-17 69-79 (94)
145 PF14690 zf-ISL3: zinc-finger 42.7 14 0.00031 10.7 0.5 9 6-14 2-10 (47)
146 KOG3183|consensus 42.5 12 0.00025 16.0 0.4 14 6-19 23-36 (250)
147 COG1594 RPB9 DNA-directed RNA 42.5 14 0.00031 13.6 0.6 10 7-16 101-110 (113)
148 PLN03238 probable histone acet 42.3 35 0.00075 15.1 2.3 24 5-28 47-70 (290)
149 PF03107 C1_2: C1 domain; Int 42.2 12 0.00026 10.0 0.3 7 8-14 2-8 (30)
150 TIGR01206 lysW lysine biosynth 41.8 13 0.00028 11.9 0.4 11 7-17 3-13 (54)
151 COG3357 Predicted transcriptio 41.7 13 0.00028 13.4 0.4 14 5-18 57-70 (97)
152 PF06353 DUF1062: Protein of u 41.3 15 0.00033 14.2 0.6 10 7-16 14-23 (142)
153 PLN00104 MYST -like histone ac 40.7 36 0.00078 16.1 1.7 23 5-27 197-219 (450)
154 TIGR02300 FYDLN_acid conserved 40.6 22 0.00047 13.7 0.9 16 4-19 24-39 (129)
155 PF13824 zf-Mss51: Zinc-finger 40.5 18 0.00039 11.7 0.6 14 4-17 12-25 (55)
156 PF15269 zf-C2H2_7: Zinc-finge 40.1 18 0.00039 11.2 1.2 21 7-27 21-41 (54)
157 PF07295 DUF1451: Protein of u 38.9 14 0.00031 14.3 0.4 11 6-16 112-122 (146)
158 COG4338 Uncharacterized protei 38.5 11 0.00024 11.9 0.1 13 8-20 14-26 (54)
159 PF09855 DUF2082: Nucleic-acid 38.5 15 0.00032 12.2 0.3 7 8-14 2-8 (64)
160 PF14787 zf-CCHC_5: GAG-polypr 37.5 18 0.00039 10.7 0.4 13 8-20 4-16 (36)
161 PF01780 Ribosomal_L37ae: Ribo 37.4 21 0.00047 12.8 0.7 8 7-14 36-43 (90)
162 PF10276 zf-CHCC: Zinc-finger 37.1 19 0.00042 10.7 0.7 11 6-16 29-39 (40)
163 PF09943 DUF2175: Uncharacteri 37.0 17 0.00038 13.3 0.4 9 7-15 3-11 (101)
164 PRK03824 hypA hydrogenase nick 36.6 22 0.00047 13.5 0.7 14 6-19 70-83 (135)
165 PF14354 Lar_restr_allev: Rest 36.4 22 0.00047 11.1 0.6 6 8-13 5-10 (61)
166 KOG4124|consensus 36.3 5 0.00011 18.0 -1.0 20 4-23 396-415 (442)
167 KOG0402|consensus 36.3 11 0.00023 13.4 -0.1 8 7-14 37-44 (92)
168 PF01363 FYVE: FYVE zinc finge 36.3 22 0.00047 11.4 0.6 12 6-17 25-36 (69)
169 smart00661 RPOL9 RNA polymeras 35.8 21 0.00045 10.6 0.8 14 6-19 20-33 (52)
170 KOG1842|consensus 35.7 28 0.00061 16.5 1.0 25 6-30 15-39 (505)
171 PF13696 zf-CCHC_2: Zinc knuck 35.6 19 0.00041 10.3 0.4 9 6-14 8-16 (32)
172 COG1885 Uncharacterized protei 35.5 19 0.00042 13.3 0.5 10 7-16 50-59 (115)
173 COG4530 Uncharacterized protei 35.1 26 0.00056 13.2 0.7 14 3-16 23-36 (129)
174 PF08209 Sgf11: Sgf11 (transcr 34.7 20 0.00044 10.2 0.6 20 6-26 4-23 (33)
175 TIGR03830 CxxCG_CxxCG_HTH puta 34.5 32 0.00068 12.4 1.8 17 7-23 32-48 (127)
176 PF01194 RNA_pol_N: RNA polyme 34.4 19 0.00042 11.9 0.4 15 5-19 3-17 (60)
177 PF08271 TF_Zn_Ribbon: TFIIB z 34.4 21 0.00046 10.4 0.5 7 8-14 2-8 (43)
178 PF12907 zf-met2: Zinc-binding 34.3 17 0.00036 10.9 0.2 21 7-27 2-25 (40)
179 PF00412 LIM: LIM domain; Int 34.3 23 0.00049 10.6 0.7 12 7-18 27-38 (58)
180 PTZ00064 histone acetyltransfe 34.3 63 0.0014 15.8 2.0 24 5-28 279-302 (552)
181 PRK11823 DNA repair protein Ra 34.1 29 0.00063 16.0 0.9 12 6-17 7-18 (446)
182 KOG4173|consensus 34.0 18 0.0004 15.2 0.3 19 8-26 108-126 (253)
183 PF13408 Zn_ribbon_recom: Reco 34.0 19 0.00041 10.9 0.3 12 7-18 6-17 (58)
184 COG1656 Uncharacterized conser 33.9 41 0.0009 13.6 1.5 16 7-22 131-146 (165)
185 PHA02998 RNA polymerase subuni 33.9 32 0.0007 14.2 1.0 13 7-19 172-184 (195)
186 PRK04016 DNA-directed RNA poly 33.6 26 0.00056 11.7 0.6 14 5-18 3-16 (62)
187 PF13821 DUF4187: Domain of un 33.5 23 0.0005 11.3 0.5 19 7-25 28-46 (55)
188 PF00935 Ribosomal_L44: Riboso 33.2 24 0.00053 12.2 0.5 10 7-16 54-63 (77)
189 PF07503 zf-HYPF: HypF finger; 32.6 23 0.00049 10.2 0.6 11 7-17 22-32 (35)
190 PF02998 Lentiviral_Tat: Lenti 32.4 28 0.0006 12.3 0.6 11 5-15 73-83 (86)
191 KOG3214|consensus 32.3 16 0.00034 13.5 0.0 13 7-19 48-60 (109)
192 COG5188 PRP9 Splicing factor 3 32.3 21 0.00046 16.3 0.4 21 7-27 239-259 (470)
193 COG4847 Uncharacterized protei 32.0 23 0.00051 12.9 0.4 11 5-15 5-15 (103)
194 PRK01343 zinc-binding protein; 31.8 25 0.00055 11.5 0.5 12 6-17 9-20 (57)
195 PF14803 Nudix_N_2: Nudix N-te 31.7 22 0.00047 10.2 0.3 8 9-16 3-10 (34)
196 PF03286 Pox_Ag35: Pox virus A 31.5 46 0.00099 13.9 1.2 21 11-31 9-29 (200)
197 PF06689 zf-C4_ClpX: ClpX C4-t 31.2 24 0.00051 10.4 0.4 9 8-16 3-11 (41)
198 PF15499 Peptidase_C98: Ubiqui 30.8 15 0.00033 15.9 -0.1 12 5-16 133-144 (275)
199 PF09889 DUF2116: Uncharacteri 30.8 32 0.00069 11.3 0.8 9 8-16 5-13 (59)
200 PRK11032 hypothetical protein; 30.5 23 0.0005 14.1 0.3 8 7-14 125-132 (160)
201 PF03194 LUC7: LUC7 N_terminus 30.4 28 0.0006 14.8 0.6 10 7-16 191-200 (254)
202 PF04438 zf-HIT: HIT zinc fing 29.8 24 0.00053 9.7 0.6 12 6-17 13-24 (30)
203 PF05290 Baculo_IE-1: Baculovi 29.5 32 0.0007 13.4 0.6 15 5-19 79-93 (140)
204 PF01844 HNH: HNH endonuclease 29.4 24 0.00053 10.0 0.3 7 10-16 2-8 (47)
205 PF05741 zf-nanos: Nanos RNA b 29.3 25 0.00055 11.4 0.3 9 6-14 33-41 (55)
206 PF03691 UPF0167: Uncharacteri 28.8 33 0.00071 13.9 0.6 11 6-16 160-170 (176)
207 PLN03239 histone acetyltransfe 28.7 58 0.0013 14.9 1.3 23 5-27 105-127 (351)
208 PF14311 DUF4379: Domain of un 28.7 32 0.00069 10.6 1.0 13 7-19 29-41 (55)
209 PF01155 HypA: Hydrogenase exp 28.7 31 0.00068 12.6 0.6 12 7-18 71-82 (113)
210 PF04810 zf-Sec23_Sec24: Sec23 28.4 29 0.00063 10.1 0.8 10 5-14 23-32 (40)
211 PF07649 C1_3: C1-like domain; 28.4 25 0.00054 9.3 0.5 10 5-14 14-23 (30)
212 KOG3014|consensus 28.4 65 0.0014 14.1 1.6 24 7-30 38-63 (257)
213 COG4640 Predicted membrane pro 28.4 68 0.0015 15.2 1.5 19 5-23 14-32 (465)
214 TIGR00416 sms DNA repair prote 28.2 42 0.0009 15.6 0.9 11 6-16 7-17 (454)
215 COG5151 SSL1 RNA polymerase II 28.0 68 0.0015 14.6 1.5 24 6-29 388-411 (421)
216 KOG3352|consensus 27.8 31 0.00066 13.7 0.5 13 5-17 132-144 (153)
217 cd07153 Fur_like Ferric uptake 27.6 35 0.00075 12.1 0.6 12 7-18 74-85 (116)
218 PF04988 AKAP95: A-kinase anch 27.6 49 0.0011 13.4 1.0 20 7-26 1-20 (165)
219 COG4855 Uncharacterized protei 27.5 33 0.00073 11.7 0.5 11 8-18 25-35 (76)
220 PF14446 Prok-RING_1: Prokaryo 27.4 26 0.00056 11.3 0.2 11 7-17 6-16 (54)
221 TIGR00280 L37a ribosomal prote 27.2 38 0.00082 12.2 0.6 10 7-16 54-63 (91)
222 PF14445 Prok-RING_2: Prokaryo 27.1 15 0.00032 11.8 -0.3 11 7-17 8-18 (57)
223 TIGR00320 dfx_rbo desulfoferro 27.1 39 0.00084 12.8 0.7 11 6-16 7-17 (125)
224 PF12230 PRP21_like_P: Pre-mRN 26.6 22 0.00047 14.6 0.0 26 7-33 169-194 (229)
225 PF03884 DUF329: Domain of unk 26.6 35 0.00077 11.1 0.5 12 7-18 3-14 (57)
226 TIGR02986 restrict_Alw26I type 25.9 19 0.00042 16.6 -0.2 9 9-17 85-93 (424)
227 cd00065 FYVE FYVE domain; Zinc 25.9 36 0.00078 10.3 0.6 12 6-17 18-29 (57)
228 PF14255 Cys_rich_CPXG: Cystei 25.7 34 0.00073 10.9 0.4 8 9-16 3-10 (52)
229 PF10955 DUF2757: Protein of u 25.6 41 0.00088 11.7 0.6 11 6-16 4-14 (76)
230 PF01475 FUR: Ferric uptake re 25.6 38 0.00083 12.2 0.6 13 7-19 81-93 (120)
231 PRK09678 DNA-binding transcrip 25.5 44 0.00095 11.4 0.6 16 6-21 27-44 (72)
232 PTZ00255 60S ribosomal protein 24.8 45 0.00098 12.0 0.6 11 6-16 54-64 (90)
233 PF08394 Arc_trans_TRASH: Arch 24.7 37 0.0008 10.0 0.5 6 9-14 1-6 (37)
234 PF13453 zf-TFIIB: Transcripti 24.5 36 0.00077 9.8 1.3 17 7-23 20-36 (41)
235 PF11931 DUF3449: Domain of un 24.5 25 0.00054 14.5 0.0 21 5-25 100-121 (196)
236 PF12523 DUF3725: Protein of u 24.5 49 0.0011 11.3 0.7 12 4-15 57-68 (74)
237 PF10588 NADH-G_4Fe-4S_3: NADH 24.3 37 0.00081 10.0 0.4 9 6-14 13-21 (41)
238 COG4830 RPS26B Ribosomal prote 24.3 56 0.0012 12.1 0.8 12 6-17 20-31 (108)
239 KOG1280|consensus 24.2 93 0.002 14.5 1.9 25 6-30 79-103 (381)
240 KOG0227|consensus 24.1 49 0.0011 13.9 0.7 21 6-26 53-73 (222)
241 smart00064 FYVE Protein presen 24.0 44 0.00095 10.6 0.6 12 6-17 26-37 (68)
242 PHA00689 hypothetical protein 24.0 43 0.00094 10.6 0.6 13 5-17 16-28 (62)
243 PF02891 zf-MIZ: MIZ/SP-RING z 24.0 33 0.00072 10.5 0.2 7 7-13 42-48 (50)
244 PF08274 PhnA_Zn_Ribbon: PhnA 24.0 35 0.00076 9.5 0.5 8 7-14 20-27 (30)
245 KOG4118|consensus 23.9 50 0.0011 11.2 1.1 21 7-27 39-59 (74)
246 PF05180 zf-DNL: DNL zinc fing 23.6 46 0.00099 11.2 0.5 9 7-15 5-13 (66)
247 PF10609 ParA: ParA/MinD ATPas 23.6 43 0.00092 11.7 0.5 10 6-15 65-74 (81)
248 PRK03976 rpl37ae 50S ribosomal 23.5 49 0.0011 11.9 0.6 10 7-16 55-64 (90)
249 PF06524 NOA36: NOA36 protein; 23.5 13 0.00027 16.2 -0.9 24 5-28 208-231 (314)
250 PLN00032 DNA-directed RNA poly 23.3 49 0.0011 11.4 0.6 15 5-19 3-17 (71)
251 KOG3456|consensus 23.0 38 0.00083 12.7 0.3 13 6-18 104-116 (120)
252 PF00130 C1_1: Phorbol esters/ 22.7 42 0.00091 10.0 0.9 12 5-16 10-21 (53)
253 COG4068 Uncharacterized protei 22.6 42 0.0009 11.1 0.4 10 8-17 10-19 (64)
254 PF11672 DUF3268: Protein of u 22.5 46 0.001 12.2 0.5 9 6-14 2-10 (102)
255 cd02336 ZZ_RSC8 Zinc finger, Z 22.5 41 0.0009 10.2 0.3 7 8-14 2-8 (45)
256 PRK12860 transcriptional activ 22.4 80 0.0017 13.1 1.3 10 8-17 136-145 (189)
257 TIGR03826 YvyF flagellar opero 22.1 31 0.00068 13.3 0.1 11 8-18 5-15 (137)
258 PF10058 DUF2296: Predicted in 21.9 50 0.0011 10.5 0.6 8 6-13 44-51 (54)
259 PF04032 Rpr2: RNAse P Rpr2/Rp 21.9 50 0.0011 11.0 0.5 7 7-13 78-84 (85)
260 PRK00564 hypA hydrogenase nick 21.8 48 0.001 12.3 0.5 12 7-18 72-83 (117)
261 PF03966 Trm112p: Trm112p-like 21.8 52 0.0011 10.7 0.7 12 6-17 53-64 (68)
262 PF09665 RE_Alw26IDE: Type II 21.8 43 0.00093 16.1 0.4 8 9-16 85-92 (511)
263 PRK12380 hydrogenase nickel in 21.7 54 0.0012 12.1 0.6 12 7-18 71-82 (113)
264 PTZ00157 60S ribosomal protein 21.2 52 0.0011 11.7 0.5 10 7-16 70-79 (84)
265 COG3024 Uncharacterized protei 21.2 50 0.0011 11.2 0.4 11 7-17 8-18 (65)
266 KOG1813|consensus 21.1 50 0.0011 14.8 0.5 14 5-18 240-253 (313)
267 TIGR02159 PA_CoA_Oxy4 phenylac 21.0 23 0.0005 13.7 -0.4 10 7-16 131-140 (146)
268 PRK05767 rpl44e 50S ribosomal 21.0 49 0.0011 12.0 0.4 10 7-16 68-77 (92)
269 PF02591 DUF164: Putative zinc 21.0 50 0.0011 10.2 1.1 9 6-14 46-54 (56)
270 COG1571 Predicted DNA-binding 20.8 75 0.0016 15.0 1.0 15 4-18 365-379 (421)
271 COG1644 RPB10 DNA-directed RNA 20.8 56 0.0012 11.0 0.5 15 5-19 3-17 (63)
272 PF04570 DUF581: Protein of un 20.8 26 0.00057 11.4 -0.2 10 8-17 18-27 (58)
273 TIGR00340 zpr1_rel ZPR1-relate 20.7 61 0.0013 13.0 0.7 10 6-15 28-37 (163)
274 PF05864 Chordopox_RPO7: Chord 20.7 53 0.0012 10.8 0.5 14 6-19 4-17 (63)
275 PF01396 zf-C4_Topoisom: Topoi 20.7 33 0.00072 9.9 0.0 8 8-15 3-10 (39)
276 KOG3497|consensus 20.4 60 0.0013 10.9 0.7 15 5-19 3-17 (69)
277 PRK12722 transcriptional activ 20.4 91 0.002 12.9 1.3 8 9-16 137-144 (187)
278 PF05766 NinG: Bacteriophage L 20.3 36 0.00078 14.0 0.1 15 5-19 5-19 (189)
279 COG4332 Uncharacterized protei 20.1 62 0.0014 13.5 0.7 10 7-16 50-59 (203)
280 TIGR01384 TFS_arch transcripti 20.0 61 0.0013 11.4 0.6 9 7-15 91-99 (104)
No 1
>KOG2462|consensus
Probab=99.70 E-value=1.8e-17 Score=63.68 Aligned_cols=38 Identities=21% Similarity=0.517 Sum_probs=35.7
Q ss_pred CCCCcceeccccccccccchhHHHHhHHhcCCCCccCC
Q psy4412 1 MDPTYLYACLWCDYHTLNSGHMRDHIRRHTGEKPFVCP 38 (39)
Q Consensus 1 h~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~c~ 38 (39)
|+||+||.|..|+++|..+++|+.|+++|.+.|+|+|.
T Consensus 210 HTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~ 247 (279)
T KOG2462|consen 210 HTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCP 247 (279)
T ss_pred ccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCc
Confidence 78999999999999999999999999999999999985
No 2
>KOG3623|consensus
Probab=99.56 E-value=1.2e-15 Score=64.69 Aligned_cols=38 Identities=34% Similarity=0.709 Sum_probs=36.6
Q ss_pred CCCCcceeccccccccccchhHHHHhHHhcCCCCccCC
Q psy4412 1 MDPTYLYACLWCDYHTLNSGHMRDHIRRHTGEKPFVCP 38 (39)
Q Consensus 1 h~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~c~ 38 (39)
|+|++||.|..|.++|.++-.|..|.|.|.|||||.|.
T Consensus 917 HsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCd 954 (1007)
T KOG3623|consen 917 HSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCD 954 (1007)
T ss_pred hcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhh
Confidence 78999999999999999999999999999999999984
No 3
>KOG2462|consensus
Probab=99.49 E-value=1.1e-14 Score=56.24 Aligned_cols=34 Identities=41% Similarity=0.737 Sum_probs=32.1
Q ss_pred cceeccccccccccchhHHHHhHHhcCCCCccCC
Q psy4412 5 YLYACLWCDYHTLNSGHMRDHIRRHTGEKPFVCP 38 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~c~ 38 (39)
-++.|..|++.|....-|+.|+|+|+|||||.|.
T Consensus 186 l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~ 219 (279)
T KOG2462|consen 186 LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCP 219 (279)
T ss_pred CCcccccccccccchHHhhcccccccCCCCccCC
Confidence 4789999999999999999999999999999996
No 4
>PHA00616 hypothetical protein
Probab=99.41 E-value=9.2e-14 Score=41.69 Aligned_cols=33 Identities=15% Similarity=0.328 Sum_probs=30.9
Q ss_pred ceeccccccccccchhHHHHhHHhcCCCCccCC
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRRHTGEKPFVCP 38 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~c~ 38 (39)
||.|..|++.|.+.+.+..|++.+++++++.|.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 688999999999999999999999999998775
No 5
>KOG3623|consensus
Probab=99.32 E-value=5e-13 Score=57.16 Aligned_cols=35 Identities=37% Similarity=0.794 Sum_probs=32.8
Q ss_pred CcceeccccccccccchhHHHHhHHhcCCCCccCC
Q psy4412 4 TYLYACLWCDYHTLNSGHMRDHIRRHTGEKPFVCP 38 (39)
Q Consensus 4 ~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~c~ 38 (39)
-+.|.|.+|+++|..+-.|..|.|+|.|||||.|+
T Consensus 279 lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCp 313 (1007)
T KOG3623|consen 279 LRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECP 313 (1007)
T ss_pred hccccccccchhhhhHHHHHhhheeecCCCCcCCc
Confidence 35689999999999999999999999999999996
No 6
>PHA02768 hypothetical protein; Provisional
Probab=99.17 E-value=3.3e-11 Score=37.65 Aligned_cols=30 Identities=23% Similarity=0.449 Sum_probs=25.8
Q ss_pred ceeccccccccccchhHHHHhHHhcCCCCccC
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRRHTGEKPFVC 37 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~c 37 (39)
.|.|..|++.|.....|..|++.|+ ++++|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc 34 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKL 34 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccC
Confidence 4789999999999999999999999 34444
No 7
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.95 E-value=1.1e-09 Score=29.72 Aligned_cols=19 Identities=58% Similarity=1.375 Sum_probs=16.6
Q ss_pred hHHHHhHHhcCCCCccCCC
Q psy4412 21 HMRDHIRRHTGEKPFVCPF 39 (39)
Q Consensus 21 ~~~~~~~~~~~~~~~~c~~ 39 (39)
+|..|++.|++++||.|++
T Consensus 1 ~l~~H~~~H~~~k~~~C~~ 19 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPY 19 (26)
T ss_dssp HHHHHHHHHSSSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCC
Confidence 4788999999999999974
No 8
>KOG1074|consensus
Probab=98.90 E-value=5.5e-10 Score=48.73 Aligned_cols=33 Identities=15% Similarity=0.383 Sum_probs=27.4
Q ss_pred CCCCcceeccccccccccchhHHHHhHHhcCCC
Q psy4412 1 MDPTYLYACLWCDYHTLNSGHMRDHIRRHTGEK 33 (39)
Q Consensus 1 h~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~ 33 (39)
|+|++||.|..|+++|..+.+|+.|+.+|...-
T Consensus 628 HtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p 660 (958)
T KOG1074|consen 628 HTGERPFKCKICGRAFTTKGNLKAHMSVHKAKP 660 (958)
T ss_pred ccCcCccccccccchhccccchhhcccccccCc
Confidence 678889999999999988888888888776553
No 9
>KOG3576|consensus
Probab=98.89 E-value=2.2e-10 Score=43.68 Aligned_cols=33 Identities=27% Similarity=0.646 Sum_probs=23.7
Q ss_pred ceeccccccccccchhHHHHhHHhcCCCCccCC
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRRHTGEKPFVCP 38 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~c~ 38 (39)
-+-|..|+++|...-+|..|.++|+|.+||+|.
T Consensus 145 r~lct~cgkgfndtfdlkrh~rthtgvrpykc~ 177 (267)
T KOG3576|consen 145 RHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCS 177 (267)
T ss_pred HHHHhhccCcccchhhhhhhhccccCccccchh
Confidence 355667777777777777777777777777774
No 10
>KOG1074|consensus
Probab=98.87 E-value=8.3e-10 Score=48.22 Aligned_cols=33 Identities=33% Similarity=0.715 Sum_probs=28.9
Q ss_pred eeccccccccccchhHHHHhHHhcCCCCccCCC
Q psy4412 7 YACLWCDYHTLNSGHMRDHIRRHTGEKPFVCPF 39 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~c~~ 39 (39)
.+|..|.+.|...+.|..|.|.|+||+||+|.+
T Consensus 354 hkCr~CakvfgS~SaLqiHlRSHTGERPfqCnv 386 (958)
T KOG1074|consen 354 HKCRFCAKVFGSDSALQIHLRSHTGERPFQCNV 386 (958)
T ss_pred chhhhhHhhcCchhhhhhhhhccCCCCCeeecc
Confidence 578899999999999999999999999999864
No 11
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.84 E-value=1.1e-09 Score=29.77 Aligned_cols=17 Identities=18% Similarity=0.360 Sum_probs=15.4
Q ss_pred CCCCcceeccccccccc
Q psy4412 1 MDPTYLYACLWCDYHTL 17 (39)
Q Consensus 1 h~~~~~~~c~~c~~~~~ 17 (39)
|++++||.|..|++.|.
T Consensus 9 H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 9 HTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HSSSSSEEESSSSEEES
T ss_pred cCCCCCCCCCCCcCeeC
Confidence 67999999999999885
No 12
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.76 E-value=1.3e-08 Score=26.65 Aligned_cols=23 Identities=30% Similarity=0.746 Sum_probs=20.6
Q ss_pred eeccccccccccchhHHHHhHHh
Q psy4412 7 YACLWCDYHTLNSGHMRDHIRRH 29 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~~~ 29 (39)
|.|..|++.|.....|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 57999999999999999998764
No 13
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.70 E-value=1.4e-08 Score=27.50 Aligned_cols=25 Identities=24% Similarity=0.446 Sum_probs=22.5
Q ss_pred ceeccccccccccchhHHHHhHHhc
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRRHT 30 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~~~ 30 (39)
|+.|..|++.|.....+..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 5889999999999999999988764
No 14
>PHA00733 hypothetical protein
Probab=98.58 E-value=1.1e-07 Score=34.13 Aligned_cols=34 Identities=32% Similarity=0.557 Sum_probs=27.6
Q ss_pred CCcceeccccccccccchhHHHHhHHhcCCCCccCC
Q psy4412 3 PTYLYACLWCDYHTLNSGHMRDHIRRHTGEKPFVCP 38 (39)
Q Consensus 3 ~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~c~ 38 (39)
+.+||.|..|++.|.....+..|++.+ +.++.|.
T Consensus 70 ~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~ 103 (128)
T PHA00733 70 AVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCP 103 (128)
T ss_pred CCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCC
Confidence 467899999999999999999998865 3456664
No 15
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.44 E-value=3.9e-07 Score=23.59 Aligned_cols=23 Identities=26% Similarity=0.673 Sum_probs=18.7
Q ss_pred eeccccccccccchhHHHHhHHh
Q psy4412 7 YACLWCDYHTLNSGHMRDHIRRH 29 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~~~ 29 (39)
|.|..|+..|.....+..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 57999999999999999998765
No 16
>KOG3576|consensus
Probab=98.40 E-value=1.3e-07 Score=36.43 Aligned_cols=30 Identities=13% Similarity=0.343 Sum_probs=26.1
Q ss_pred CCCCcceeccccccccccchhHHHHhHHhc
Q psy4412 1 MDPTYLYACLWCDYHTLNSGHMRDHIRRHT 30 (39)
Q Consensus 1 h~~~~~~~c~~c~~~~~~~~~~~~~~~~~~ 30 (39)
|+|.+||.|..|+++|.++-.|..|.+...
T Consensus 168 htgvrpykc~~c~kaftqrcsleshl~kvh 197 (267)
T KOG3576|consen 168 HTGVRPYKCSLCEKAFTQRCSLESHLKKVH 197 (267)
T ss_pred ccCccccchhhhhHHHHhhccHHHHHHHHc
Confidence 679999999999999999999988876443
No 17
>smart00355 ZnF_C2H2 zinc finger.
Probab=98.29 E-value=1.2e-06 Score=22.91 Aligned_cols=24 Identities=25% Similarity=0.549 Sum_probs=20.6
Q ss_pred eeccccccccccchhHHHHhHHhc
Q psy4412 7 YACLWCDYHTLNSGHMRDHIRRHT 30 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~~~~ 30 (39)
+.|..|++.|.....+..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 468999999999999999988654
No 18
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=98.25 E-value=4e-06 Score=26.06 Aligned_cols=32 Identities=22% Similarity=0.323 Sum_probs=23.0
Q ss_pred CCcceeccccccccccchhHHHHhHHhcCCCC
Q psy4412 3 PTYLYACLWCDYHTLNSGHMRDHIRRHTGEKP 34 (39)
Q Consensus 3 ~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~ 34 (39)
.+.|-.|..|+..+.+..+|..|+....+.||
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 45678999999999999999999988887775
No 19
>KOG3608|consensus
Probab=98.06 E-value=4.2e-06 Score=34.67 Aligned_cols=37 Identities=16% Similarity=0.474 Sum_probs=24.7
Q ss_pred CCCCcceeccccccccccchhHHHHhHHhcCCCCccCC
Q psy4412 1 MDPTYLYACLWCDYHTLNSGHMRDHIRRHTGEKPFVCP 38 (39)
Q Consensus 1 h~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~c~ 38 (39)
|+..+|+.|+.|...+...++|..|...|+ +..|.|.
T Consensus 287 Hs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~ 323 (467)
T KOG3608|consen 287 HSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCE 323 (467)
T ss_pred hccCCCccccchhhhhccHHHHHHHHHhcc-ccceecC
Confidence 345677777777777777777777776665 4445553
No 20
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.05 E-value=4.9e-06 Score=21.93 Aligned_cols=23 Identities=22% Similarity=0.570 Sum_probs=20.0
Q ss_pred eeccccccccccchhHHHHhHHh
Q psy4412 7 YACLWCDYHTLNSGHMRDHIRRH 29 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~~~ 29 (39)
|.|..|...|.....+..|.+.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 57999999999999999998654
No 21
>PHA00732 hypothetical protein
Probab=98.05 E-value=6.2e-06 Score=27.62 Aligned_cols=26 Identities=31% Similarity=0.681 Sum_probs=21.8
Q ss_pred ceeccccccccccchhHHHHhHH-hcC
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRR-HTG 31 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~-~~~ 31 (39)
||.|..|++.|.....+..|++. |.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~ 27 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL 27 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC
Confidence 57899999999999999999874 543
No 22
>PRK04860 hypothetical protein; Provisional
Probab=97.82 E-value=4.2e-05 Score=28.63 Aligned_cols=29 Identities=31% Similarity=0.599 Sum_probs=24.7
Q ss_pred ceeccccccccccchhHHHHhHHhcCCCCccCC
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRRHTGEKPFVCP 38 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~c~ 38 (39)
+|.|. |+. ....+..|.+++.++++|.|.
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~ 147 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCR 147 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECC
Confidence 68897 876 566789999999999999985
No 23
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.52 E-value=0.00014 Score=18.91 Aligned_cols=22 Identities=36% Similarity=0.982 Sum_probs=15.8
Q ss_pred eeccccccccccchhHHHHhHHh
Q psy4412 7 YACLWCDYHTLNSGHMRDHIRRH 29 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~~~ 29 (39)
|.|..|..... ...+..|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 57889987776 77888888765
No 24
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.35 E-value=3.9e-05 Score=20.67 Aligned_cols=22 Identities=18% Similarity=0.523 Sum_probs=18.2
Q ss_pred eeccccccccccchhHHHHhHH
Q psy4412 7 YACLWCDYHTLNSGHMRDHIRR 28 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~~ 28 (39)
|.|..|++.|.....+..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 5799999999999888877653
No 25
>KOG3608|consensus
Probab=97.34 E-value=0.00032 Score=29.53 Aligned_cols=33 Identities=39% Similarity=0.885 Sum_probs=25.7
Q ss_pred ceeccccccccccchhHHHHhH-HhcCCCCccCC
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIR-RHTGEKPFVCP 38 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~-~~~~~~~~~c~ 38 (39)
.|.|..|.-+....++|..|++ -|...+||+|.
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd 296 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCD 296 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhccCCCcccc
Confidence 4678888888888888888887 45567899885
No 26
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.28 E-value=0.00037 Score=30.66 Aligned_cols=31 Identities=16% Similarity=0.309 Sum_probs=14.1
Q ss_pred ceeccccccccccchhHHHHhHHhcCCCCccCC
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRRHTGEKPFVCP 38 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~c~ 38 (39)
++.|. |+..+ ....+..|...+...+++.|.
T Consensus 478 pv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~ 508 (567)
T PLN03086 478 PLQCP-CGVVL-EKEQMVQHQASTCPLRLITCR 508 (567)
T ss_pred CccCC-CCCCc-chhHHHhhhhccCCCCceeCC
Confidence 33444 44322 334444555555555555553
No 27
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=97.14 E-value=0.00056 Score=19.17 Aligned_cols=22 Identities=14% Similarity=0.409 Sum_probs=18.2
Q ss_pred ceeccccccccccchhHHHHhH
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIR 27 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~ 27 (39)
++.|..|...|.....+..|..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 5789999999998887777764
No 28
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.02 E-value=0.0018 Score=20.15 Aligned_cols=33 Identities=27% Similarity=0.735 Sum_probs=21.8
Q ss_pred ceeccccccccccchhHHHHhHH-hcCC-CCccCCC
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRR-HTGE-KPFVCPF 39 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~-~~~~-~~~~c~~ 39 (39)
.|.|+.|++ ......|..|... |..+ +.+.|++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPi 36 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPI 36 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCC
Confidence 477888998 5556778888654 3332 4567753
No 29
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.85 E-value=0.0018 Score=21.84 Aligned_cols=24 Identities=17% Similarity=0.588 Sum_probs=20.7
Q ss_pred ceeccccccccccchhHHHHhHHh
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRRH 29 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~~ 29 (39)
.+.|..|+..|.....+..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 478999999999999999999865
No 30
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.75 E-value=0.0003 Score=29.24 Aligned_cols=24 Identities=25% Similarity=0.362 Sum_probs=20.5
Q ss_pred CCcceeccccccccccchhHHHHh
Q psy4412 3 PTYLYACLWCDYHTLNSGHMRDHI 26 (39)
Q Consensus 3 ~~~~~~c~~c~~~~~~~~~~~~~~ 26 (39)
..+||.|.+|++.+.....|..|.
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCCceeccccchhhccCccceecc
Confidence 358999999999999988887764
No 31
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.46 E-value=0.0059 Score=27.26 Aligned_cols=36 Identities=22% Similarity=0.387 Sum_probs=27.1
Q ss_pred CCCcceecccccccccc----------chhHHHHhHHhcCCCCccCC
Q psy4412 2 DPTYLYACLWCDYHTLN----------SGHMRDHIRRHTGEKPFVCP 38 (39)
Q Consensus 2 ~~~~~~~c~~c~~~~~~----------~~~~~~~~~~~~~~~~~~c~ 38 (39)
..++++.|..|+..+.. ...+..|.... +.+++.|.
T Consensus 500 Cp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~ 545 (567)
T PLN03086 500 CPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCD 545 (567)
T ss_pred CCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEcc
Confidence 35788999999988742 24688887774 88888884
No 32
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.43 E-value=0.0042 Score=16.51 Aligned_cols=20 Identities=15% Similarity=0.378 Sum_probs=14.5
Q ss_pred eeccccccccccchhHHHHhH
Q psy4412 7 YACLWCDYHTLNSGHMRDHIR 27 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~ 27 (39)
..|..|+..|. ...+..|..
T Consensus 3 ~~C~~CgR~F~-~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKFN-PDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEEC-HHHHHHHHH
Confidence 46889999994 555777754
No 33
>KOG3993|consensus
Probab=95.66 E-value=0.0067 Score=26.39 Aligned_cols=25 Identities=28% Similarity=0.440 Sum_probs=22.3
Q ss_pred ceeccccccccccchhHHHHhHHhc
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRRHT 30 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~~~ 30 (39)
-|.|.+|++.|.-..+|..|.|.|.
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred eecCCcccccccCchhhhhhhcccC
Confidence 5899999999999999999988774
No 34
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=95.26 E-value=0.0069 Score=23.99 Aligned_cols=28 Identities=18% Similarity=0.273 Sum_probs=20.7
Q ss_pred CcceeccccccccccchhHHHHhHHhcC
Q psy4412 4 TYLYACLWCDYHTLNSGHMRDHIRRHTG 31 (39)
Q Consensus 4 ~~~~~c~~c~~~~~~~~~~~~~~~~~~~ 31 (39)
+..|.|..|++.|.-...+.+|+..-+.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 3458999999999999999999875543
No 35
>KOG3993|consensus
Probab=95.03 E-value=0.014 Score=25.53 Aligned_cols=26 Identities=19% Similarity=0.402 Sum_probs=22.3
Q ss_pred cceeccccccccccchhHHHHhHHhc
Q psy4412 5 YLYACLWCDYHTLNSGHMRDHIRRHT 30 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~~~~~~~~~~~~ 30 (39)
.-|.|..|++.|.....|+.|+..|.
T Consensus 355 gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 355 GIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred ceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 46899999999999999999976654
No 36
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=95.01 E-value=0.019 Score=18.39 Aligned_cols=25 Identities=12% Similarity=0.208 Sum_probs=20.7
Q ss_pred CCcceeccccccccccchhHHHHhH
Q psy4412 3 PTYLYACLWCDYHTLNSGHMRDHIR 27 (39)
Q Consensus 3 ~~~~~~c~~c~~~~~~~~~~~~~~~ 27 (39)
|+.-+.|..|+..|....+...|..
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhh
Confidence 6667899999999988888877754
No 37
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=94.04 E-value=0.091 Score=18.56 Aligned_cols=26 Identities=38% Similarity=0.719 Sum_probs=21.1
Q ss_pred ceec----cccccccccchhHHHHhHHhcC
Q psy4412 6 LYAC----LWCDYHTLNSGHMRDHIRRHTG 31 (39)
Q Consensus 6 ~~~c----~~c~~~~~~~~~~~~~~~~~~~ 31 (39)
.|.| ..|+........+..|.+...+
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3678 8899988999999999886643
No 38
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=93.57 E-value=0.076 Score=19.78 Aligned_cols=23 Identities=30% Similarity=0.638 Sum_probs=14.4
Q ss_pred eeccccccccccchhHHHHhHHhcCC
Q psy4412 7 YACLWCDYHTLNSGHMRDHIRRHTGE 32 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~~~~~~ 32 (39)
..|.+||+.|.. |..|.+.|.|-
T Consensus 73 i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-S
T ss_pred eEEccCCcccch---HHHHHHHccCC
Confidence 579999998866 57888888654
No 39
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=92.20 E-value=0.04 Score=15.23 Aligned_cols=19 Identities=16% Similarity=0.494 Sum_probs=11.2
Q ss_pred eeccccccccccchhHHHHh
Q psy4412 7 YACLWCDYHTLNSGHMRDHI 26 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~ 26 (39)
+.|..|++.|. ......|.
T Consensus 1 ~sCiDC~~~F~-~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDFD-GDSYKSHT 19 (28)
T ss_dssp EEETTTTEEEE-GGGTTT--
T ss_pred CeeecCCCCcC-cCCcCCCC
Confidence 46888999884 33344443
No 40
>KOG2482|consensus
Probab=91.49 E-value=0.19 Score=21.80 Aligned_cols=23 Identities=22% Similarity=0.748 Sum_probs=20.3
Q ss_pred eeccccccccccchhHHHHhHHh
Q psy4412 7 YACLWCDYHTLNSGHMRDHIRRH 29 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~~~ 29 (39)
+.|.-|.+.|..+..|..|++..
T Consensus 196 ~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred heeeeeccccCCcHHHHHHHHhc
Confidence 57999999999999999998743
No 41
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=91.33 E-value=0.2 Score=14.05 Aligned_cols=9 Identities=44% Similarity=1.173 Sum_probs=4.2
Q ss_pred eeccccccc
Q psy4412 7 YACLWCDYH 15 (39)
Q Consensus 7 ~~c~~c~~~ 15 (39)
|.|..|+..
T Consensus 2 ~~C~~CGy~ 10 (33)
T cd00350 2 YVCPVCGYI 10 (33)
T ss_pred EECCCCCCE
Confidence 345555543
No 42
>KOG3408|consensus
Probab=90.32 E-value=0.26 Score=18.32 Aligned_cols=24 Identities=13% Similarity=0.439 Sum_probs=20.0
Q ss_pred cceeccccccccccchhHHHHhHH
Q psy4412 5 YLYACLWCDYHTLNSGHMRDHIRR 28 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~~~~~~~~~~ 28 (39)
..|-|..|.+-|.....+..|.++
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhc
Confidence 357899999999999999888664
No 43
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=90.23 E-value=0.33 Score=18.87 Aligned_cols=10 Identities=30% Similarity=1.055 Sum_probs=6.8
Q ss_pred ceeccccccc
Q psy4412 6 LYACLWCDYH 15 (39)
Q Consensus 6 ~~~c~~c~~~ 15 (39)
-|.|.+||..
T Consensus 134 ~~vC~vCGy~ 143 (166)
T COG1592 134 VWVCPVCGYT 143 (166)
T ss_pred EEEcCCCCCc
Confidence 3678888753
No 44
>KOG4167|consensus
Probab=89.38 E-value=0.08 Score=24.96 Aligned_cols=25 Identities=16% Similarity=0.445 Sum_probs=20.9
Q ss_pred ceeccccccccccchhHHHHhHHhc
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRRHT 30 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~~~ 30 (39)
-|.|.+|++-|..-.++..|++.|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 3789999999988888888888775
No 45
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=88.37 E-value=0.2 Score=20.92 Aligned_cols=32 Identities=38% Similarity=0.773 Sum_probs=16.5
Q ss_pred eeccccccccccchhHHHHhH--HhcCC--CCccCC
Q psy4412 7 YACLWCDYHTLNSGHMRDHIR--RHTGE--KPFVCP 38 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~--~~~~~--~~~~c~ 38 (39)
+.|..|...+.....+..|.+ .|.++ +++.|.
T Consensus 290 ~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p 325 (467)
T COG5048 290 IKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCP 325 (467)
T ss_pred CCCccccCCccccccccccccccccccccCCceeee
Confidence 344455555555555555555 45555 555443
No 46
>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=88.33 E-value=0.29 Score=14.00 Aligned_cols=15 Identities=20% Similarity=0.151 Sum_probs=10.7
Q ss_pred ceeccccccccccch
Q psy4412 6 LYACLWCDYHTLNSG 20 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~ 20 (39)
.|.|..|+..|....
T Consensus 5 ~y~C~~Cg~~fe~~~ 19 (41)
T smart00834 5 EYRCEDCGHTFEVLQ 19 (41)
T ss_pred EEEcCCCCCEEEEEE
Confidence 378999998775443
No 47
>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=87.22 E-value=0.36 Score=14.30 Aligned_cols=16 Identities=19% Similarity=0.171 Sum_probs=11.3
Q ss_pred ceeccccccccccchh
Q psy4412 6 LYACLWCDYHTLNSGH 21 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~ 21 (39)
.|.|..|+..|.....
T Consensus 5 ey~C~~Cg~~fe~~~~ 20 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQS 20 (42)
T ss_pred EEEeCCCCCEEEEEEE
Confidence 3789999987765443
No 48
>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=85.34 E-value=0.48 Score=12.72 Aligned_cols=10 Identities=30% Similarity=0.697 Sum_probs=6.8
Q ss_pred eccccccccc
Q psy4412 8 ACLWCDYHTL 17 (39)
Q Consensus 8 ~c~~c~~~~~ 17 (39)
.|..||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5777877664
No 49
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=84.67 E-value=0.56 Score=14.26 Aligned_cols=15 Identities=20% Similarity=0.239 Sum_probs=10.4
Q ss_pred ceeccccccccccch
Q psy4412 6 LYACLWCDYHTLNSG 20 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~ 20 (39)
-|.|..|+..|....
T Consensus 5 ey~C~~Cg~~fe~~~ 19 (52)
T TIGR02605 5 EYRCTACGHRFEVLQ 19 (52)
T ss_pred EEEeCCCCCEeEEEE
Confidence 367888888775543
No 50
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=84.54 E-value=0.83 Score=17.40 Aligned_cols=24 Identities=25% Similarity=0.425 Sum_probs=17.6
Q ss_pred eccccccccccchhHHHHhHHhcCCCC
Q psy4412 8 ACLWCDYHTLNSGHMRDHIRRHTGEKP 34 (39)
Q Consensus 8 ~c~~c~~~~~~~~~~~~~~~~~~~~~~ 34 (39)
.|.++|+.|. +|..|..+|.+..|
T Consensus 78 icLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 78 ICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEeccCcchH---HHHHHHhcccCCCH
Confidence 5888888775 48888888776543
No 51
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=84.07 E-value=0.5 Score=14.00 Aligned_cols=15 Identities=13% Similarity=0.306 Sum_probs=9.1
Q ss_pred cceeccccccccccc
Q psy4412 5 YLYACLWCDYHTLNS 19 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~ 19 (39)
.|+.|..|+..|-..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 478899999888643
No 52
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=83.64 E-value=0.76 Score=13.47 Aligned_cols=14 Identities=14% Similarity=0.335 Sum_probs=10.9
Q ss_pred ceeccccccccccc
Q psy4412 6 LYACLWCDYHTLNS 19 (39)
Q Consensus 6 ~~~c~~c~~~~~~~ 19 (39)
|+.|..|+..|...
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78899998887643
No 53
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=82.93 E-value=1.2 Score=13.58 Aligned_cols=21 Identities=29% Similarity=0.673 Sum_probs=14.8
Q ss_pred eeccccccccccc-----hhHHHHhH
Q psy4412 7 YACLWCDYHTLNS-----GHMRDHIR 27 (39)
Q Consensus 7 ~~c~~c~~~~~~~-----~~~~~~~~ 27 (39)
-.|..|++.+... +.|..|+.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 4688898877554 46777776
No 54
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=82.74 E-value=0.96 Score=16.12 Aligned_cols=13 Identities=15% Similarity=0.026 Sum_probs=10.6
Q ss_pred cceeccccccccc
Q psy4412 5 YLYACLWCDYHTL 17 (39)
Q Consensus 5 ~~~~c~~c~~~~~ 17 (39)
.+..|..|+.-|.
T Consensus 78 ~~~rC~eCG~~fk 90 (97)
T cd00924 78 KPKRCPECGHVFK 90 (97)
T ss_pred CceeCCCCCcEEE
Confidence 5789999998775
No 55
>PLN02294 cytochrome c oxidase subunit Vb
Probab=81.72 E-value=1.1 Score=17.68 Aligned_cols=15 Identities=13% Similarity=0.135 Sum_probs=11.6
Q ss_pred Ccceecccccccccc
Q psy4412 4 TYLYACLWCDYHTLN 18 (39)
Q Consensus 4 ~~~~~c~~c~~~~~~ 18 (39)
.+|..|.+|+.-|.-
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 468899999987753
No 56
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=81.58 E-value=0.72 Score=17.38 Aligned_cols=15 Identities=13% Similarity=0.175 Sum_probs=10.3
Q ss_pred ceeccccccccccch
Q psy4412 6 LYACLWCDYHTLNSG 20 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~ 20 (39)
|+.|..|++.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 456788888776544
No 57
>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=81.00 E-value=0.99 Score=11.99 Aligned_cols=9 Identities=22% Similarity=0.940 Sum_probs=6.3
Q ss_pred ceecccccc
Q psy4412 6 LYACLWCDY 14 (39)
Q Consensus 6 ~~~c~~c~~ 14 (39)
.|.|..|++
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 577887763
No 58
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=80.81 E-value=1 Score=18.10 Aligned_cols=19 Identities=11% Similarity=0.067 Sum_probs=14.0
Q ss_pred CcceeccccccccccchhH
Q psy4412 4 TYLYACLWCDYHTLNSGHM 22 (39)
Q Consensus 4 ~~~~~c~~c~~~~~~~~~~ 22 (39)
++...|+.|++.|....-.
T Consensus 3 ~k~~~CPvC~~~F~~~~vr 21 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVR 21 (214)
T ss_pred CCceECCCCCCeeeeeEEE
Confidence 3567899999988766433
No 59
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=79.14 E-value=1.3 Score=13.87 Aligned_cols=17 Identities=12% Similarity=0.192 Sum_probs=12.1
Q ss_pred Ccceeccccccccccch
Q psy4412 4 TYLYACLWCDYHTLNSG 20 (39)
Q Consensus 4 ~~~~~c~~c~~~~~~~~ 20 (39)
.+.+.|..|+..|.-..
T Consensus 2 Dk~l~C~dCg~~FvfTa 18 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTA 18 (49)
T ss_pred CeeEEcccCCCeEEEeh
Confidence 35678999998775544
No 60
>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=77.62 E-value=1.3 Score=12.78 Aligned_cols=12 Identities=25% Similarity=0.451 Sum_probs=5.7
Q ss_pred eccccccccccc
Q psy4412 8 ACLWCDYHTLNS 19 (39)
Q Consensus 8 ~c~~c~~~~~~~ 19 (39)
.|..|++.|..+
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 688888877543
No 61
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=77.45 E-value=1.3 Score=12.98 Aligned_cols=11 Identities=27% Similarity=0.767 Sum_probs=6.0
Q ss_pred ceecccccccc
Q psy4412 6 LYACLWCDYHT 16 (39)
Q Consensus 6 ~~~c~~c~~~~ 16 (39)
-|.|..|++..
T Consensus 6 ~YkC~~CGniV 16 (36)
T PF06397_consen 6 FYKCEHCGNIV 16 (36)
T ss_dssp EEE-TTT--EE
T ss_pred EEEccCCCCEE
Confidence 47899998754
No 62
>PHA00626 hypothetical protein
Probab=76.40 E-value=2.2 Score=13.86 Aligned_cols=14 Identities=29% Similarity=0.601 Sum_probs=11.0
Q ss_pred cceecccccccccc
Q psy4412 5 YLYACLWCDYHTLN 18 (39)
Q Consensus 5 ~~~~c~~c~~~~~~ 18 (39)
..|.|..|+..|..
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 46899999987754
No 63
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=75.96 E-value=2.4 Score=13.50 Aligned_cols=16 Identities=6% Similarity=-0.132 Sum_probs=8.7
Q ss_pred cceeccccccccccch
Q psy4412 5 YLYACLWCDYHTLNSG 20 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~~ 20 (39)
.|+....|+..|....
T Consensus 23 ~PV~s~~C~H~fek~a 38 (57)
T PF11789_consen 23 DPVKSKKCGHTFEKEA 38 (57)
T ss_dssp SEEEESSS--EEEHHH
T ss_pred CCcCcCCCCCeecHHH
Confidence 4666677777775443
No 64
>KOG2071|consensus
Probab=75.81 E-value=3.2 Score=19.59 Aligned_cols=26 Identities=19% Similarity=0.267 Sum_probs=19.9
Q ss_pred cceeccccccccccchhHHHHhHHhc
Q psy4412 5 YLYACLWCDYHTLNSGHMRDHIRRHT 30 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~~~~~~~~~~~~ 30 (39)
.|-.|..||..|........++..|.
T Consensus 417 ~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 417 SPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CcchhcccccccccchhhhhHhhhhh
Confidence 45679999999988887777666553
No 65
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=75.75 E-value=1.9 Score=12.22 Aligned_cols=12 Identities=25% Similarity=0.742 Sum_probs=8.2
Q ss_pred ceeccccccccc
Q psy4412 6 LYACLWCDYHTL 17 (39)
Q Consensus 6 ~~~c~~c~~~~~ 17 (39)
.|.|..|+..+.
T Consensus 2 ~~~C~~CG~i~~ 13 (34)
T cd00729 2 VWVCPVCGYIHE 13 (34)
T ss_pred eEECCCCCCEeE
Confidence 367888887543
No 66
>KOG2893|consensus
Probab=74.91 E-value=0.42 Score=19.86 Aligned_cols=17 Identities=12% Similarity=0.481 Sum_probs=7.2
Q ss_pred eeccccccccccchhHH
Q psy4412 7 YACLWCDYHTLNSGHMR 23 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~ 23 (39)
|.|..|.+-+..-..|.
T Consensus 35 fkchichkkl~sgpgls 51 (341)
T KOG2893|consen 35 FKCHICHKKLFSGPGLS 51 (341)
T ss_pred ceeeeehhhhccCCCce
Confidence 44444444443333333
No 67
>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=74.05 E-value=1.5 Score=13.58 Aligned_cols=12 Identities=17% Similarity=0.376 Sum_probs=6.0
Q ss_pred eccccccccccc
Q psy4412 8 ACLWCDYHTLNS 19 (39)
Q Consensus 8 ~c~~c~~~~~~~ 19 (39)
.|++|+..|...
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 799999887543
No 68
>KOG0717|consensus
Probab=73.45 E-value=3.5 Score=19.08 Aligned_cols=21 Identities=14% Similarity=0.447 Sum_probs=17.3
Q ss_pred eeccccccccccchhHHHHhH
Q psy4412 7 YACLWCDYHTLNSGHMRDHIR 27 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~ 27 (39)
+-|..|.++|.....+..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 569999999998888877754
No 69
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=73.17 E-value=2.2 Score=11.32 Aligned_cols=18 Identities=17% Similarity=0.407 Sum_probs=10.8
Q ss_pred eccccccccccchhHHHHh
Q psy4412 8 ACLWCDYHTLNSGHMRDHI 26 (39)
Q Consensus 8 ~c~~c~~~~~~~~~~~~~~ 26 (39)
.|..|.+.+ ....+..|.
T Consensus 3 ~CPiC~~~v-~~~~in~HL 20 (26)
T smart00734 3 QCPVCFREV-PENLINSHL 20 (26)
T ss_pred cCCCCcCcc-cHHHHHHHH
Confidence 577888776 334444543
No 70
>PTZ00448 hypothetical protein; Provisional
Probab=72.50 E-value=3.9 Score=18.26 Aligned_cols=23 Identities=17% Similarity=0.576 Sum_probs=17.0
Q ss_pred ceeccccccccccchhHHHHhHH
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRR 28 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~ 28 (39)
.+.|..|.-.|......+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 46799999888766666666553
No 71
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=72.44 E-value=2.8 Score=12.20 Aligned_cols=22 Identities=18% Similarity=0.424 Sum_probs=12.3
Q ss_pred cceeccccccccccc----hhHHHHh
Q psy4412 5 YLYACLWCDYHTLNS----GHMRDHI 26 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~----~~~~~~~ 26 (39)
.-..|..|++.+... +.|..|+
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHH
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 345789999877553 4566666
No 72
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.46 E-value=1.6 Score=15.05 Aligned_cols=12 Identities=25% Similarity=0.451 Sum_probs=9.0
Q ss_pred ceeccccccccc
Q psy4412 6 LYACLWCDYHTL 17 (39)
Q Consensus 6 ~~~c~~c~~~~~ 17 (39)
.|.|..|+..|-
T Consensus 12 ~Y~c~~cg~~~d 23 (82)
T COG2331 12 SYECTECGNRFD 23 (82)
T ss_pred EEeecccchHHH
Confidence 478999987653
No 73
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=70.73 E-value=3.2 Score=12.27 Aligned_cols=24 Identities=17% Similarity=0.231 Sum_probs=15.3
Q ss_pred eecccccccccc--chhHHHHhHHhc
Q psy4412 7 YACLWCDYHTLN--SGHMRDHIRRHT 30 (39)
Q Consensus 7 ~~c~~c~~~~~~--~~~~~~~~~~~~ 30 (39)
-.|..|+-.+.. ..+...|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 478899876643 345566666553
No 74
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=70.03 E-value=2.3 Score=12.94 Aligned_cols=14 Identities=14% Similarity=0.162 Sum_probs=10.2
Q ss_pred eccccccccccchh
Q psy4412 8 ACLWCDYHTLNSGH 21 (39)
Q Consensus 8 ~c~~c~~~~~~~~~ 21 (39)
.|..|+..|.-...
T Consensus 10 ~C~~C~rpf~WRKK 23 (42)
T PF10013_consen 10 ICPVCGRPFTWRKK 23 (42)
T ss_pred cCcccCCcchHHHH
Confidence 58899988865443
No 75
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=69.57 E-value=2.4 Score=15.48 Aligned_cols=14 Identities=14% Similarity=0.173 Sum_probs=10.2
Q ss_pred ceeccccccccccc
Q psy4412 6 LYACLWCDYHTLNS 19 (39)
Q Consensus 6 ~~~c~~c~~~~~~~ 19 (39)
|..|..|+..|..-
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 56788888877663
No 76
>COG1773 Rubredoxin [Energy production and conversion]
Probab=69.32 E-value=2.6 Score=13.57 Aligned_cols=13 Identities=23% Similarity=0.480 Sum_probs=8.9
Q ss_pred ceecccccccccc
Q psy4412 6 LYACLWCDYHTLN 18 (39)
Q Consensus 6 ~~~c~~c~~~~~~ 18 (39)
.+.|..|+..|--
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 4678888876643
No 77
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=69.23 E-value=5.9 Score=14.69 Aligned_cols=24 Identities=21% Similarity=0.243 Sum_probs=15.2
Q ss_pred ceeccccccccccchhHHHHhHHh
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRRH 29 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~~ 29 (39)
.|.|..|.+.|...-++-.|...|
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred ceeCCCCCCccccccchhhhhhcc
Confidence 366777777777666666555444
No 78
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=68.47 E-value=3.1 Score=15.86 Aligned_cols=14 Identities=14% Similarity=-0.026 Sum_probs=10.8
Q ss_pred cceecccccccccc
Q psy4412 5 YLYACLWCDYHTLN 18 (39)
Q Consensus 5 ~~~~c~~c~~~~~~ 18 (39)
++..|..|+..|.-
T Consensus 111 ~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 111 KPQRCPECGQVFKL 124 (136)
T ss_dssp SEEEETTTEEEEEE
T ss_pred CccCCCCCCeEEEE
Confidence 57889999987753
No 79
>PLN02748 tRNA dimethylallyltransferase
Probab=68.33 E-value=5.5 Score=18.33 Aligned_cols=24 Identities=17% Similarity=0.237 Sum_probs=17.3
Q ss_pred Ccceecccccc-ccccchhHHHHhH
Q psy4412 4 TYLYACLWCDY-HTLNSGHMRDHIR 27 (39)
Q Consensus 4 ~~~~~c~~c~~-~~~~~~~~~~~~~ 27 (39)
++.|.|..|+. .+.....+..|..
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlk 440 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQ 440 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhc
Confidence 35678999997 6776666666654
No 80
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=67.48 E-value=3.7 Score=17.20 Aligned_cols=15 Identities=33% Similarity=0.620 Sum_probs=11.3
Q ss_pred Ccceecccccccccc
Q psy4412 4 TYLYACLWCDYHTLN 18 (39)
Q Consensus 4 ~~~~~c~~c~~~~~~ 18 (39)
.++..|..|+.-|.-
T Consensus 179 GkpqRCpECGqVFKL 193 (268)
T PTZ00043 179 GFLYRCGECDQIFML 193 (268)
T ss_pred CCCccCCCCCcEEEE
Confidence 457889999987754
No 81
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=67.25 E-value=0.7 Score=14.55 Aligned_cols=23 Identities=22% Similarity=0.226 Sum_probs=11.0
Q ss_pred cceeccccccccccchhHHHHhH
Q psy4412 5 YLYACLWCDYHTLNSGHMRDHIR 27 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~~~~~~~~~ 27 (39)
..|.|..|.+.|...-++-.|..
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTT
T ss_pred CeEECCCCCCccccCcChhhhcc
Confidence 35888888888876555444433
No 82
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=66.94 E-value=4.1 Score=14.86 Aligned_cols=17 Identities=12% Similarity=0.083 Sum_probs=12.1
Q ss_pred CCcceeccccccccccc
Q psy4412 3 PTYLYACLWCDYHTLNS 19 (39)
Q Consensus 3 ~~~~~~c~~c~~~~~~~ 19 (39)
++.|-.|..|+..|...
T Consensus 23 nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 23 NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCCCccCCCCCCccCcc
Confidence 34577788888877655
No 83
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=66.04 E-value=5 Score=15.88 Aligned_cols=15 Identities=13% Similarity=0.341 Sum_probs=9.1
Q ss_pred ceeccccccccccch
Q psy4412 6 LYACLWCDYHTLNSG 20 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~ 20 (39)
-|.|..|+..|....
T Consensus 117 ~Y~Cp~C~~rytf~e 131 (178)
T PRK06266 117 FFFCPNCHIRFTFDE 131 (178)
T ss_pred EEECCCCCcEEeHHH
Confidence 366777776665444
No 84
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=65.96 E-value=4 Score=12.60 Aligned_cols=11 Identities=36% Similarity=0.779 Sum_probs=7.3
Q ss_pred eeccccccccc
Q psy4412 7 YACLWCDYHTL 17 (39)
Q Consensus 7 ~~c~~c~~~~~ 17 (39)
|.|..|+..+-
T Consensus 2 y~C~~CgyvYd 12 (47)
T PF00301_consen 2 YQCPVCGYVYD 12 (47)
T ss_dssp EEETTTSBEEE
T ss_pred cCCCCCCEEEc
Confidence 56777876553
No 85
>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=64.56 E-value=3.6 Score=11.97 Aligned_cols=10 Identities=30% Similarity=0.694 Sum_probs=5.9
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
|.|..|++.+
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 5666666543
No 86
>KOG2186|consensus
Probab=64.43 E-value=3.5 Score=17.52 Aligned_cols=21 Identities=14% Similarity=0.463 Sum_probs=14.1
Q ss_pred ceeccccccccccchhHHHHhH
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIR 27 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~ 27 (39)
-|.|..|++.|.. .+...|..
T Consensus 29 ~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 29 YFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred eeEEeeccccccc-chhhhhhh
Confidence 3678888888876 44555543
No 87
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=63.24 E-value=9.1 Score=14.83 Aligned_cols=17 Identities=12% Similarity=0.086 Sum_probs=10.6
Q ss_pred ceeccccccccccchhH
Q psy4412 6 LYACLWCDYHTLNSGHM 22 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~ 22 (39)
-|.|..|+..|.....+
T Consensus 109 ~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAM 125 (158)
T ss_pred eEECCCCCcEeeHHHHH
Confidence 46777777666554444
No 88
>PF14353 CpXC: CpXC protein
Probab=63.07 E-value=4.7 Score=14.74 Aligned_cols=15 Identities=13% Similarity=0.186 Sum_probs=10.3
Q ss_pred ceeccccccccccch
Q psy4412 6 LYACLWCDYHTLNSG 20 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~ 20 (39)
.+.|..|+..+....
T Consensus 38 ~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEY 52 (128)
T ss_pred EEECCCCCCceecCC
Confidence 468999998665443
No 89
>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=63.04 E-value=4.4 Score=12.94 Aligned_cols=16 Identities=31% Similarity=0.708 Sum_probs=11.0
Q ss_pred Ccceeccccccccccc
Q psy4412 4 TYLYACLWCDYHTLNS 19 (39)
Q Consensus 4 ~~~~~c~~c~~~~~~~ 19 (39)
...+.|..|+..+...
T Consensus 9 ~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 9 SNLWLCLTCGYVGCGR 24 (63)
T ss_dssp SSEEEETTTS-EEETT
T ss_pred CceEEeCCCCcccccC
Confidence 4578899998877554
No 90
>KOG2785|consensus
Probab=62.76 E-value=8.8 Score=17.39 Aligned_cols=24 Identities=25% Similarity=0.587 Sum_probs=18.5
Q ss_pred ceeccccc---cccccchhHHHHhHHh
Q psy4412 6 LYACLWCD---YHTLNSGHMRDHIRRH 29 (39)
Q Consensus 6 ~~~c~~c~---~~~~~~~~~~~~~~~~ 29 (39)
.+.|..|. ..|.....++.|+...
T Consensus 217 ~~~CL~CN~~~~~f~sleavr~HM~~K 243 (390)
T KOG2785|consen 217 GFICLFCNELGRPFSSLEAVRAHMRDK 243 (390)
T ss_pred CceEEEeccccCcccccHHHHHHHhhc
Confidence 35677777 8888889999998643
No 91
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=62.27 E-value=5.2 Score=13.19 Aligned_cols=9 Identities=33% Similarity=0.770 Sum_probs=5.8
Q ss_pred cceeccccc
Q psy4412 5 YLYACLWCD 13 (39)
Q Consensus 5 ~~~~c~~c~ 13 (39)
.+|.|..|+
T Consensus 49 ~~Y~Cp~CG 57 (61)
T COG2888 49 NPYRCPKCG 57 (61)
T ss_pred CceECCCcC
Confidence 357777765
No 92
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=61.91 E-value=3.7 Score=12.82 Aligned_cols=11 Identities=36% Similarity=0.806 Sum_probs=7.5
Q ss_pred eeccccccccc
Q psy4412 7 YACLWCDYHTL 17 (39)
Q Consensus 7 ~~c~~c~~~~~ 17 (39)
|.|..|+..+-
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 56778876654
No 93
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=61.77 E-value=5.5 Score=12.05 Aligned_cols=12 Identities=25% Similarity=0.415 Sum_probs=8.1
Q ss_pred eecccccccccc
Q psy4412 7 YACLWCDYHTLN 18 (39)
Q Consensus 7 ~~c~~c~~~~~~ 18 (39)
|.|..|+..+..
T Consensus 3 Y~C~~Cg~~~~~ 14 (44)
T smart00659 3 YICGECGRENEI 14 (44)
T ss_pred EECCCCCCEeec
Confidence 677888775543
No 94
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=61.74 E-value=4.1 Score=15.82 Aligned_cols=15 Identities=20% Similarity=0.255 Sum_probs=11.5
Q ss_pred ceeccccccccccch
Q psy4412 6 LYACLWCDYHTLNSG 20 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~ 20 (39)
-+.|..|+..|....
T Consensus 28 ~~~c~~c~~~f~~~e 42 (154)
T PRK00464 28 RRECLACGKRFTTFE 42 (154)
T ss_pred eeeccccCCcceEeE
Confidence 378999999887654
No 95
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=61.55 E-value=5 Score=11.12 Aligned_cols=11 Identities=27% Similarity=0.706 Sum_probs=8.1
Q ss_pred ceecccccccc
Q psy4412 6 LYACLWCDYHT 16 (39)
Q Consensus 6 ~~~c~~c~~~~ 16 (39)
-|.|..|+...
T Consensus 7 ~ykC~~Cgniv 17 (34)
T TIGR00319 7 VYKCEVCGNIV 17 (34)
T ss_pred EEEcCCCCcEE
Confidence 47888888755
No 96
>KOG1994|consensus
Probab=61.52 E-value=7.2 Score=16.45 Aligned_cols=22 Identities=18% Similarity=0.576 Sum_probs=17.9
Q ss_pred ceeccccccccccchhHHHHhH
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIR 27 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~ 27 (39)
-|-|..|+--|.....|..|..
T Consensus 239 h~YC~fCG~~y~~~edl~ehCP 260 (268)
T KOG1994|consen 239 HYYCFFCGIKYKDEEDLYEHCP 260 (268)
T ss_pred ceEEEEeccccCCHHHHHHhCC
Confidence 4679999999998888887743
No 97
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=61.51 E-value=4.5 Score=11.62 Aligned_cols=11 Identities=27% Similarity=0.546 Sum_probs=7.0
Q ss_pred eeccccccccc
Q psy4412 7 YACLWCDYHTL 17 (39)
Q Consensus 7 ~~c~~c~~~~~ 17 (39)
+.|..|+..+.
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 35777776553
No 98
>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=61.06 E-value=8.8 Score=14.55 Aligned_cols=15 Identities=20% Similarity=0.470 Sum_probs=10.5
Q ss_pred eeccccccccccchh
Q psy4412 7 YACLWCDYHTLNSGH 21 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~ 21 (39)
+.|..|++.|..-+.
T Consensus 125 ~~C~~C~kiyW~GsH 139 (147)
T PF01927_consen 125 WRCPGCGKIYWEGSH 139 (147)
T ss_pred EECCCCCCEeccccc
Confidence 578888887765443
No 99
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=60.53 E-value=10 Score=17.65 Aligned_cols=22 Identities=14% Similarity=0.421 Sum_probs=18.7
Q ss_pred ceeccccccccccchhHHHHhH
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIR 27 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~ 27 (39)
=+.|..|.+.|.....+..|+.
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~ 78 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHME 78 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHH
Confidence 3579999999999999998876
No 100
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=60.45 E-value=5.9 Score=11.79 Aligned_cols=12 Identities=25% Similarity=0.576 Sum_probs=7.6
Q ss_pred ceeccccccccc
Q psy4412 6 LYACLWCDYHTL 17 (39)
Q Consensus 6 ~~~c~~c~~~~~ 17 (39)
.|.|..|+..+.
T Consensus 3 ~y~C~~CG~~~~ 14 (46)
T PRK00398 3 EYKCARCGREVE 14 (46)
T ss_pred EEECCCCCCEEE
Confidence 466777776553
No 101
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=60.01 E-value=5.4 Score=11.06 Aligned_cols=11 Identities=27% Similarity=0.730 Sum_probs=7.7
Q ss_pred ceecccccccc
Q psy4412 6 LYACLWCDYHT 16 (39)
Q Consensus 6 ~~~c~~c~~~~ 16 (39)
-|.|..|+...
T Consensus 4 ~ykC~~CGniv 14 (34)
T cd00974 4 VYKCEICGNIV 14 (34)
T ss_pred EEEcCCCCcEE
Confidence 36788887655
No 102
>KOG1146|consensus
Probab=59.49 E-value=12 Score=20.04 Aligned_cols=25 Identities=28% Similarity=0.652 Sum_probs=21.0
Q ss_pred CcceeccccccccccchhHHHHhHH
Q psy4412 4 TYLYACLWCDYHTLNSGHMRDHIRR 28 (39)
Q Consensus 4 ~~~~~c~~c~~~~~~~~~~~~~~~~ 28 (39)
.++|.|..|..++.....+..|+..
T Consensus 516 ~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 516 GKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CCcccceeeeeeeecchHHHHHHHH
Confidence 4678999999999988888888764
No 103
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.34 E-value=1 Score=18.73 Aligned_cols=27 Identities=19% Similarity=0.229 Sum_probs=18.1
Q ss_pred cceeccccccccccchhHHHHhHHhcC
Q psy4412 5 YLYACLWCDYHTLNSGHMRDHIRRHTG 31 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~~~~~~~~~~~~~ 31 (39)
+...|++|+-.|.....+....|+.++
T Consensus 18 k~ieCPvC~tkFkkeev~tgsiRiiag 44 (267)
T COG1655 18 KTIECPVCNTKFKKEEVKTGSIRIIAG 44 (267)
T ss_pred ceeccCcccchhhhhheeccceeEecc
Confidence 457899999888776655554454444
No 104
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=59.26 E-value=6 Score=11.32 Aligned_cols=11 Identities=18% Similarity=0.217 Sum_probs=7.4
Q ss_pred ceecccccccc
Q psy4412 6 LYACLWCDYHT 16 (39)
Q Consensus 6 ~~~c~~c~~~~ 16 (39)
...|..|+..|
T Consensus 25 ~vrC~~C~~~f 35 (37)
T PF13719_consen 25 KVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCcEe
Confidence 45677777665
No 105
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=57.66 E-value=7 Score=12.82 Aligned_cols=9 Identities=33% Similarity=0.815 Sum_probs=5.8
Q ss_pred cceeccccc
Q psy4412 5 YLYACLWCD 13 (39)
Q Consensus 5 ~~~~c~~c~ 13 (39)
.+|.|..|+
T Consensus 47 ~~Y~CP~CG 55 (59)
T PRK14890 47 NPYTCPKCG 55 (59)
T ss_pred CceECCCCC
Confidence 356777665
No 106
>PF14369 zf-RING_3: zinc-finger
Probab=56.90 E-value=5.6 Score=11.36 Aligned_cols=10 Identities=30% Similarity=0.537 Sum_probs=6.9
Q ss_pred eccccccccc
Q psy4412 8 ACLWCDYHTL 17 (39)
Q Consensus 8 ~c~~c~~~~~ 17 (39)
.|..|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4777877764
No 107
>KOG2857|consensus
Probab=56.86 E-value=6.9 Score=15.25 Aligned_cols=22 Identities=18% Similarity=0.267 Sum_probs=17.3
Q ss_pred ceeccccccccccchhHHHHhH
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIR 27 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~ 27 (39)
.|.|..|.-.+....-++.|.-
T Consensus 17 KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 17 KYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hccCCCCCCccccchhhhhccC
Confidence 5888888888888877777754
No 108
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=56.45 E-value=7.3 Score=11.41 Aligned_cols=10 Identities=30% Similarity=0.704 Sum_probs=6.0
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 5666676543
No 109
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=55.91 E-value=11 Score=14.92 Aligned_cols=17 Identities=18% Similarity=0.333 Sum_probs=12.6
Q ss_pred ceeccccccccccchhH
Q psy4412 6 LYACLWCDYHTLNSGHM 22 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~ 22 (39)
...|..|++.|.....+
T Consensus 114 ~~~C~~Cg~~f~~~k~i 130 (181)
T PRK08222 114 LQRCSRCERPFAPQKTV 130 (181)
T ss_pred cCcCcccCCccCcHhHH
Confidence 56799999999755443
No 110
>KOG0978|consensus
Probab=55.67 E-value=3.5 Score=19.96 Aligned_cols=17 Identities=18% Similarity=0.192 Sum_probs=11.5
Q ss_pred eeccccccccccchhHH
Q psy4412 7 YACLWCDYHTLNSGHMR 23 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~ 23 (39)
-.|+.|+.+|.....+.
T Consensus 679 RKCP~Cn~aFganDv~~ 695 (698)
T KOG0978|consen 679 RKCPKCNAAFGANDVHR 695 (698)
T ss_pred CCCCCCCCCCCcccccc
Confidence 36888888887655433
No 111
>KOG2593|consensus
Probab=55.29 E-value=8.4 Score=17.74 Aligned_cols=19 Identities=16% Similarity=0.258 Sum_probs=13.7
Q ss_pred CcceeccccccccccchhH
Q psy4412 4 TYLYACLWCDYHTLNSGHM 22 (39)
Q Consensus 4 ~~~~~c~~c~~~~~~~~~~ 22 (39)
...|.|..|.+.|.....+
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~ 144 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEAL 144 (436)
T ss_pred cccccCCccccchhhhHHH
Confidence 4568899999888765543
No 112
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=55.25 E-value=8.5 Score=11.83 Aligned_cols=32 Identities=19% Similarity=0.485 Sum_probs=14.5
Q ss_pred ceeccc-cccccccchhHHHHhHHhcCCCCccC
Q psy4412 6 LYACLW-CDYHTLNSGHMRDHIRRHTGEKPFVC 37 (39)
Q Consensus 6 ~~~c~~-c~~~~~~~~~~~~~~~~~~~~~~~~c 37 (39)
+..|.. |......+..+..|....-..++..|
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C 41 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECPKRPVPC 41 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCCCCcEEC
Confidence 445665 33333345567777764444444444
No 113
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=52.84 E-value=8.2 Score=10.92 Aligned_cols=10 Identities=20% Similarity=0.753 Sum_probs=6.0
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
+.|..|+..+
T Consensus 22 ~~C~~Cg~~~ 31 (33)
T PF08792_consen 22 EVCIFCGSSF 31 (33)
T ss_pred EEcccCCcEe
Confidence 3566676654
No 114
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=52.43 E-value=8.5 Score=14.48 Aligned_cols=15 Identities=20% Similarity=0.301 Sum_probs=11.1
Q ss_pred cceeccccccccccc
Q psy4412 5 YLYACLWCDYHTLNS 19 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~ 19 (39)
.-|.|..|++.|...
T Consensus 52 qRyrC~~C~~tf~~~ 66 (129)
T COG3677 52 QRYKCKSCGSTFTVE 66 (129)
T ss_pred cccccCCcCcceeee
Confidence 357899999887554
No 115
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=51.42 E-value=9 Score=15.87 Aligned_cols=16 Identities=13% Similarity=0.277 Sum_probs=11.2
Q ss_pred Ccceeccccccccccc
Q psy4412 4 TYLYACLWCDYHTLNS 19 (39)
Q Consensus 4 ~~~~~c~~c~~~~~~~ 19 (39)
..||.|..|-+.|...
T Consensus 194 ~IPF~C~iCKkdy~sp 209 (259)
T COG5152 194 KIPFLCGICKKDYESP 209 (259)
T ss_pred CCceeehhchhhccch
Confidence 4688888887766543
No 116
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=51.22 E-value=7.8 Score=12.21 Aligned_cols=12 Identities=25% Similarity=0.648 Sum_probs=9.2
Q ss_pred cceecccccccc
Q psy4412 5 YLYACLWCDYHT 16 (39)
Q Consensus 5 ~~~~c~~c~~~~ 16 (39)
..|.|..|+..+
T Consensus 5 ~~Y~C~~Cg~~~ 16 (49)
T COG1996 5 MEYKCARCGREV 16 (49)
T ss_pred EEEEhhhcCCee
Confidence 357888888876
No 117
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=50.53 E-value=7.8 Score=15.11 Aligned_cols=14 Identities=21% Similarity=0.302 Sum_probs=10.3
Q ss_pred eeccccccccccch
Q psy4412 7 YACLWCDYHTLNSG 20 (39)
Q Consensus 7 ~~c~~c~~~~~~~~ 20 (39)
-.|..|++.|....
T Consensus 29 ReC~~C~~RFTTyE 42 (147)
T TIGR00244 29 RECLECHERFTTFE 42 (147)
T ss_pred ccCCccCCccceee
Confidence 36888998887654
No 118
>KOG2636|consensus
Probab=49.92 E-value=23 Score=16.72 Aligned_cols=23 Identities=22% Similarity=0.444 Sum_probs=15.8
Q ss_pred Ccceeccccc-cccccchhHHHHh
Q psy4412 4 TYLYACLWCD-YHTLNSGHMRDHI 26 (39)
Q Consensus 4 ~~~~~c~~c~-~~~~~~~~~~~~~ 26 (39)
.+.|.|..|+ ..+.-+..+..|.
T Consensus 399 ~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 399 DIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred CcccceeeccCccccCcHHHHHHh
Confidence 3468999999 5666666666663
No 119
>KOG0562|consensus
Probab=49.78 E-value=20 Score=14.52 Aligned_cols=25 Identities=16% Similarity=0.345 Sum_probs=17.7
Q ss_pred cceeccccccccccchhHHHHhHHh
Q psy4412 5 YLYACLWCDYHTLNSGHMRDHIRRH 29 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~~~~~~~~~~~ 29 (39)
.+..|-.|.......+.+..|.+.+
T Consensus 152 ~dLrC~~Cq~~~~~~~kLK~Hl~~~ 176 (184)
T KOG0562|consen 152 EDLRCWRCQTFGPHFPKLKAHLREE 176 (184)
T ss_pred cceeehhhhhcccccHHHHHHHHHH
Confidence 4567888886556667788887654
No 120
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=49.75 E-value=9.8 Score=10.96 Aligned_cols=10 Identities=20% Similarity=0.418 Sum_probs=5.0
Q ss_pred eccccccccc
Q psy4412 8 ACLWCDYHTL 17 (39)
Q Consensus 8 ~c~~c~~~~~ 17 (39)
.|+.|+..+.
T Consensus 23 ~Cd~cg~~L~ 32 (36)
T PF05191_consen 23 VCDNCGGELV 32 (36)
T ss_dssp BCTTTTEBEB
T ss_pred ccCCCCCeeE
Confidence 4555555443
No 121
>KOG0782|consensus
Probab=49.36 E-value=3 Score=19.97 Aligned_cols=14 Identities=14% Similarity=0.014 Sum_probs=10.0
Q ss_pred eeccccccccccch
Q psy4412 7 YACLWCDYHTLNSG 20 (39)
Q Consensus 7 ~~c~~c~~~~~~~~ 20 (39)
..|..|+++|.++-
T Consensus 254 GkC~~CgKgFQQKf 267 (1004)
T KOG0782|consen 254 GKCNTCGKGFQQKF 267 (1004)
T ss_pred cccchhhhhhhhhe
Confidence 46888888877654
No 122
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=49.19 E-value=11 Score=14.76 Aligned_cols=16 Identities=19% Similarity=0.262 Sum_probs=12.1
Q ss_pred ceeccccccccccchh
Q psy4412 6 LYACLWCDYHTLNSGH 21 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~ 21 (39)
+..|..|++.|.....
T Consensus 114 ~~~C~~CG~~f~~~~~ 129 (180)
T PRK12387 114 LCNCRVCGRPFAVQKE 129 (180)
T ss_pred cccchhhCCccccHHH
Confidence 5689999998875543
No 123
>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=49.05 E-value=9.6 Score=10.65 Aligned_cols=14 Identities=14% Similarity=0.171 Sum_probs=9.2
Q ss_pred eeccccccccccch
Q psy4412 7 YACLWCDYHTLNSG 20 (39)
Q Consensus 7 ~~c~~c~~~~~~~~ 20 (39)
..|..|+..|....
T Consensus 3 ~~CP~C~~~~~v~~ 16 (38)
T TIGR02098 3 IQCPNCKTSFRVVD 16 (38)
T ss_pred EECCCCCCEEEeCH
Confidence 46778887765544
No 124
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=48.72 E-value=11 Score=13.46 Aligned_cols=11 Identities=18% Similarity=0.489 Sum_probs=7.8
Q ss_pred eeccccccccc
Q psy4412 7 YACLWCDYHTL 17 (39)
Q Consensus 7 ~~c~~c~~~~~ 17 (39)
+.|..|+..|.
T Consensus 54 W~C~kCg~~fA 64 (89)
T COG1997 54 WKCRKCGAKFA 64 (89)
T ss_pred EEcCCCCCeec
Confidence 67888887664
No 125
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=48.55 E-value=8.6 Score=15.15 Aligned_cols=13 Identities=23% Similarity=0.363 Sum_probs=9.7
Q ss_pred eccccccccccch
Q psy4412 8 ACLWCDYHTLNSG 20 (39)
Q Consensus 8 ~c~~c~~~~~~~~ 20 (39)
.|..|+..|....
T Consensus 30 eC~~C~~RFTTfE 42 (156)
T COG1327 30 ECLECGERFTTFE 42 (156)
T ss_pred cccccccccchhh
Confidence 6888888886654
No 126
>KOG4727|consensus
Probab=48.53 E-value=16 Score=14.84 Aligned_cols=21 Identities=38% Similarity=0.523 Sum_probs=16.2
Q ss_pred ceeccccccccccchhHHHHh
Q psy4412 6 LYACLWCDYHTLNSGHMRDHI 26 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~ 26 (39)
.|-|.+|.-.+...-.+..|+
T Consensus 75 GyyCdVCdcvvKDSinflDHi 95 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHI 95 (193)
T ss_pred ceeeeecceeehhhHHHHHHh
Confidence 478999998887777777664
No 127
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=47.22 E-value=8.7 Score=10.22 Aligned_cols=9 Identities=22% Similarity=0.704 Sum_probs=4.6
Q ss_pred eeccccccc
Q psy4412 7 YACLWCDYH 15 (39)
Q Consensus 7 ~~c~~c~~~ 15 (39)
+.|..|+..
T Consensus 28 f~C~~C~~~ 36 (39)
T smart00132 28 FKCSKCGKP 36 (39)
T ss_pred CCCcccCCc
Confidence 445555544
No 128
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=47.02 E-value=11 Score=10.75 Aligned_cols=10 Identities=20% Similarity=0.315 Sum_probs=6.0
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
..|..|+..|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 4666666544
No 129
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=46.97 E-value=11 Score=14.01 Aligned_cols=22 Identities=14% Similarity=0.320 Sum_probs=16.8
Q ss_pred ceeccccccccccchhHHHHhH
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIR 27 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~ 27 (39)
.+-|.+|.+-|.....|..|.+
T Consensus 55 qhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhc
Confidence 3568889988888877777755
No 130
>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=46.96 E-value=2.1 Score=12.42 Aligned_cols=28 Identities=14% Similarity=0.482 Sum_probs=15.4
Q ss_pred eeccccccccccchhHHHHhHHhcCCCCccCC
Q psy4412 7 YACLWCDYHTLNSGHMRDHIRRHTGEKPFVCP 38 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~c~ 38 (39)
..|..|...- .+..|.....|...|.|.
T Consensus 6 v~CP~C~s~~----~v~k~G~~~~G~qryrC~ 33 (36)
T PF03811_consen 6 VHCPRCQSTE----GVKKNGKSPSGHQRYRCK 33 (36)
T ss_pred eeCCCCCCCC----cceeCCCCCCCCEeEecC
Confidence 4566665422 144555566666677664
No 131
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=46.42 E-value=11 Score=13.24 Aligned_cols=12 Identities=17% Similarity=0.504 Sum_probs=8.4
Q ss_pred eccccccccccc
Q psy4412 8 ACLWCDYHTLNS 19 (39)
Q Consensus 8 ~c~~c~~~~~~~ 19 (39)
.|..|+..+...
T Consensus 10 ~C~~CG~d~~~~ 21 (86)
T PF06170_consen 10 RCPHCGLDYSHA 21 (86)
T ss_pred cccccCCccccC
Confidence 688888766543
No 132
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=45.11 E-value=12 Score=14.86 Aligned_cols=18 Identities=11% Similarity=-0.001 Sum_probs=12.9
Q ss_pred Ccceeccccccccccchh
Q psy4412 4 TYLYACLWCDYHTLNSGH 21 (39)
Q Consensus 4 ~~~~~c~~c~~~~~~~~~ 21 (39)
..|.-|..||+.|..-..
T Consensus 66 ~~PsYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPWTEN 83 (158)
T ss_pred CCChhHHhCCCCCchHHH
Confidence 356778999998865543
No 133
>PF09965 DUF2199: Uncharacterized protein conserved in bacteria (DUF2199); InterPro: IPR018697 This domain has no known function.
Probab=45.08 E-value=11 Score=14.69 Aligned_cols=13 Identities=23% Similarity=0.547 Sum_probs=7.6
Q ss_pred eeccccccccccc
Q psy4412 7 YACLWCDYHTLNS 19 (39)
Q Consensus 7 ~~c~~c~~~~~~~ 19 (39)
|.|..|+..+...
T Consensus 1 y~C~~Cg~~h~~~ 13 (148)
T PF09965_consen 1 YTCSCCGEEHEGL 13 (148)
T ss_pred CCCCcCCccCCCC
Confidence 4577777655443
No 134
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=44.88 E-value=11 Score=12.18 Aligned_cols=13 Identities=15% Similarity=0.353 Sum_probs=7.9
Q ss_pred cceeccccccccc
Q psy4412 5 YLYACLWCDYHTL 17 (39)
Q Consensus 5 ~~~~c~~c~~~~~ 17 (39)
+-..|..|+..|.
T Consensus 38 rYngCPfC~~~~~ 50 (55)
T PF14447_consen 38 RYNGCPFCGTPFE 50 (55)
T ss_pred hccCCCCCCCccc
Confidence 3346777776654
No 135
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=44.13 E-value=18 Score=12.91 Aligned_cols=16 Identities=13% Similarity=0.422 Sum_probs=11.2
Q ss_pred eeccccccccccchhH
Q psy4412 7 YACLWCDYHTLNSGHM 22 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~ 22 (39)
..|..||..+......
T Consensus 36 ~~C~~CGe~y~~dev~ 51 (89)
T TIGR03829 36 ISCSHCGMEYQDDTTV 51 (89)
T ss_pred ccccCCCcEeecHHHH
Confidence 4688899887665543
No 136
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=44.13 E-value=14 Score=14.66 Aligned_cols=27 Identities=37% Similarity=0.805 Sum_probs=13.6
Q ss_pred ceeccccccccccchhHHHHhHHhcCCCCccC
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRRHTGEKPFVC 37 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~c 37 (39)
+|.|. |+..+.. .+.|-.+-.|+ .|.|
T Consensus 117 ~Y~C~-C~q~~l~---~RRhn~~~~g~-~YrC 143 (156)
T COG3091 117 PYRCQ-CQQHYLR---IRRHNTVRRGE-VYRC 143 (156)
T ss_pred eEEee-cCCccch---hhhcccccccc-eEEe
Confidence 57777 7765433 23333344444 5555
No 137
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=44.12 E-value=8.6 Score=9.82 Aligned_cols=6 Identities=33% Similarity=0.850 Sum_probs=3.1
Q ss_pred cccccc
Q psy4412 9 CLWCDY 14 (39)
Q Consensus 9 c~~c~~ 14 (39)
|..|+.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 555553
No 138
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=44.06 E-value=14 Score=12.75 Aligned_cols=12 Identities=33% Similarity=0.421 Sum_probs=8.9
Q ss_pred eccccccccccc
Q psy4412 8 ACLWCDYHTLNS 19 (39)
Q Consensus 8 ~c~~c~~~~~~~ 19 (39)
.|..|++.+...
T Consensus 80 ~C~vC~k~l~~~ 91 (109)
T PF10367_consen 80 KCSVCGKPLGNS 91 (109)
T ss_pred CccCcCCcCCCc
Confidence 588899877653
No 139
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.95 E-value=15 Score=14.08 Aligned_cols=16 Identities=13% Similarity=0.002 Sum_probs=11.3
Q ss_pred Ccceeccccccccccc
Q psy4412 4 TYLYACLWCDYHTLNS 19 (39)
Q Consensus 4 ~~~~~c~~c~~~~~~~ 19 (39)
+.|.-|..|++.|...
T Consensus 66 e~psfchncgs~fpwt 81 (160)
T COG4306 66 EPPSFCHNCGSRFPWT 81 (160)
T ss_pred CCcchhhcCCCCCCcH
Confidence 4466788898887644
No 140
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=43.77 E-value=16 Score=13.47 Aligned_cols=9 Identities=22% Similarity=0.792 Sum_probs=6.0
Q ss_pred ceecccccc
Q psy4412 6 LYACLWCDY 14 (39)
Q Consensus 6 ~~~c~~c~~ 14 (39)
.|.|..|+.
T Consensus 22 ~FtCp~Cgh 30 (104)
T COG4888 22 TFTCPRCGH 30 (104)
T ss_pred eEecCccCC
Confidence 467777765
No 141
>KOG3362|consensus
Probab=43.76 E-value=7 Score=15.27 Aligned_cols=20 Identities=20% Similarity=0.542 Sum_probs=10.7
Q ss_pred ceeccccccccccchhHHHH
Q psy4412 6 LYACLWCDYHTLNSGHMRDH 25 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~ 25 (39)
+|.|.-||..+....-+..|
T Consensus 129 ~ysC~~CG~kyCsv~C~~~H 148 (156)
T KOG3362|consen 129 KYSCVNCGTKYCSVRCLKTH 148 (156)
T ss_pred hhHHHhcCCceeechhhhhc
Confidence 35555566655555544444
No 142
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=43.70 E-value=13 Score=10.49 Aligned_cols=10 Identities=30% Similarity=0.654 Sum_probs=5.1
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
|.|..|+..+
T Consensus 1 Y~C~~Cg~~~ 10 (32)
T PF03604_consen 1 YICGECGAEV 10 (32)
T ss_dssp EBESSSSSSE
T ss_pred CCCCcCCCee
Confidence 3455665543
No 143
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=43.57 E-value=23 Score=13.50 Aligned_cols=16 Identities=19% Similarity=0.266 Sum_probs=11.6
Q ss_pred cceeccccccccccch
Q psy4412 5 YLYACLWCDYHTLNSG 20 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~~ 20 (39)
.-|.|+.|+..|....
T Consensus 98 ~~Y~Cp~C~~~y~~~e 113 (147)
T smart00531 98 AYYKCPNCQSKYTFLE 113 (147)
T ss_pred cEEECcCCCCEeeHHH
Confidence 3578999998777543
No 144
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=42.98 E-value=12 Score=13.48 Aligned_cols=11 Identities=18% Similarity=0.368 Sum_probs=8.3
Q ss_pred eeccccccccc
Q psy4412 7 YACLWCDYHTL 17 (39)
Q Consensus 7 ~~c~~c~~~~~ 17 (39)
+.|..|+++-.
T Consensus 69 ~~Ct~Cgkah~ 79 (94)
T COG1631 69 LRCTECGKAHQ 79 (94)
T ss_pred EEehhhccccc
Confidence 68999987644
No 145
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=42.71 E-value=14 Score=10.74 Aligned_cols=9 Identities=22% Similarity=0.449 Sum_probs=5.6
Q ss_pred ceecccccc
Q psy4412 6 LYACLWCDY 14 (39)
Q Consensus 6 ~~~c~~c~~ 14 (39)
|..|..|+.
T Consensus 2 ~~~Cp~Cg~ 10 (47)
T PF14690_consen 2 PPRCPHCGS 10 (47)
T ss_pred CccCCCcCC
Confidence 456777774
No 146
>KOG3183|consensus
Probab=42.53 E-value=12 Score=15.96 Aligned_cols=14 Identities=14% Similarity=0.126 Sum_probs=10.3
Q ss_pred ceeccccccccccc
Q psy4412 6 LYACLWCDYHTLNS 19 (39)
Q Consensus 6 ~~~c~~c~~~~~~~ 19 (39)
|+.|+.|...|...
T Consensus 23 Pf~Cd~C~~~FC~e 36 (250)
T KOG3183|consen 23 PFKCDGCSGIFCLE 36 (250)
T ss_pred ceeeCCccchhhhc
Confidence 78888888777543
No 147
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=42.49 E-value=14 Score=13.57 Aligned_cols=10 Identities=40% Similarity=1.082 Sum_probs=6.4
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
|.|..|+..+
T Consensus 101 y~C~~Cg~~w 110 (113)
T COG1594 101 YKCTRCGYRW 110 (113)
T ss_pred EEecccCCEe
Confidence 5677776654
No 148
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=42.26 E-value=35 Score=15.10 Aligned_cols=24 Identities=21% Similarity=0.458 Sum_probs=20.0
Q ss_pred cceeccccccccccchhHHHHhHH
Q psy4412 5 YLYACLWCDYHTLNSGHMRDHIRR 28 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~~~~~~~~~~ 28 (39)
..|.|..|-+-|.....+..|...
T Consensus 47 ~lyiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 47 KLYICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred eEEEcCCCcchhCCHHHHHHHHHh
Confidence 458899999999999999988763
No 149
>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=42.15 E-value=12 Score=10.05 Aligned_cols=7 Identities=29% Similarity=0.510 Sum_probs=3.2
Q ss_pred ecccccc
Q psy4412 8 ACLWCDY 14 (39)
Q Consensus 8 ~c~~c~~ 14 (39)
.|..|++
T Consensus 2 ~C~~C~~ 8 (30)
T PF03107_consen 2 WCDVCRR 8 (30)
T ss_pred CCCCCCC
Confidence 3444543
No 150
>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=41.78 E-value=13 Score=11.89 Aligned_cols=11 Identities=18% Similarity=0.471 Sum_probs=6.6
Q ss_pred eeccccccccc
Q psy4412 7 YACLWCDYHTL 17 (39)
Q Consensus 7 ~~c~~c~~~~~ 17 (39)
+.|..|+..+.
T Consensus 3 ~~CP~CG~~ie 13 (54)
T TIGR01206 3 FECPDCGAEIE 13 (54)
T ss_pred cCCCCCCCEEe
Confidence 45777776543
No 151
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=41.70 E-value=13 Score=13.43 Aligned_cols=14 Identities=14% Similarity=0.332 Sum_probs=9.5
Q ss_pred cceecccccccccc
Q psy4412 5 YLYACLWCDYHTLN 18 (39)
Q Consensus 5 ~~~~c~~c~~~~~~ 18 (39)
+|-.|..||.-|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 35578888876654
No 152
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=41.32 E-value=15 Score=14.19 Aligned_cols=10 Identities=50% Similarity=1.086 Sum_probs=7.6
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
|.|..|+.+.
T Consensus 14 YrC~~C~~Tw 23 (142)
T PF06353_consen 14 YRCEKCDYTW 23 (142)
T ss_pred EEcccCcCcc
Confidence 7888888654
No 153
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=40.65 E-value=36 Score=16.05 Aligned_cols=23 Identities=22% Similarity=0.556 Sum_probs=19.8
Q ss_pred cceeccccccccccchhHHHHhH
Q psy4412 5 YLYACLWCDYHTLNSGHMRDHIR 27 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~~~~~~~~~ 27 (39)
..|.|..|-+-|.....+..|+.
T Consensus 197 ~lyiCe~Cl~y~~~~~~~~~H~~ 219 (450)
T PLN00104 197 KLYFCEFCLKFMKRKEQLQRHMK 219 (450)
T ss_pred eEEEchhhhhhhcCHHHHHHHHh
Confidence 46889999999999999999875
No 154
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=40.61 E-value=22 Score=13.68 Aligned_cols=16 Identities=0% Similarity=-0.238 Sum_probs=9.5
Q ss_pred Ccceeccccccccccc
Q psy4412 4 TYLYACLWCDYHTLNS 19 (39)
Q Consensus 4 ~~~~~c~~c~~~~~~~ 19 (39)
+.|-.|..|+..+...
T Consensus 24 k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 24 RRPAVSPYTGEQFPPE 39 (129)
T ss_pred CCCccCCCcCCccCcc
Confidence 4466677777665443
No 155
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=40.51 E-value=18 Score=11.72 Aligned_cols=14 Identities=21% Similarity=0.361 Sum_probs=9.7
Q ss_pred Ccceeccccccccc
Q psy4412 4 TYLYACLWCDYHTL 17 (39)
Q Consensus 4 ~~~~~c~~c~~~~~ 17 (39)
...|.|..||-..-
T Consensus 12 ~v~~~Cp~cGipth 25 (55)
T PF13824_consen 12 HVNFECPDCGIPTH 25 (55)
T ss_pred ccCCcCCCCCCcCc
Confidence 45688998886543
No 156
>PF15269 zf-C2H2_7: Zinc-finger
Probab=40.15 E-value=18 Score=11.23 Aligned_cols=21 Identities=24% Similarity=0.804 Sum_probs=11.3
Q ss_pred eeccccccccccchhHHHHhH
Q psy4412 7 YACLWCDYHTLNSGHMRDHIR 27 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~ 27 (39)
|.|-+|.-.-...+.+-.|+.
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 456666544444455555554
No 157
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=38.90 E-value=14 Score=14.29 Aligned_cols=11 Identities=18% Similarity=0.416 Sum_probs=7.1
Q ss_pred ceecccccccc
Q psy4412 6 LYACLWCDYHT 16 (39)
Q Consensus 6 ~~~c~~c~~~~ 16 (39)
.+.|..|+...
T Consensus 112 ~l~C~~Cg~~~ 122 (146)
T PF07295_consen 112 TLVCENCGHEV 122 (146)
T ss_pred eEecccCCCEE
Confidence 46777777533
No 158
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.52 E-value=11 Score=11.88 Aligned_cols=13 Identities=15% Similarity=0.158 Sum_probs=9.3
Q ss_pred eccccccccccch
Q psy4412 8 ACLWCDYHTLNSG 20 (39)
Q Consensus 8 ~c~~c~~~~~~~~ 20 (39)
.|..|...|....
T Consensus 14 ICpvCqRPFsWRk 26 (54)
T COG4338 14 ICPVCQRPFSWRK 26 (54)
T ss_pred hhhhhcCchHHHH
Confidence 5888888876543
No 159
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=38.51 E-value=15 Score=12.21 Aligned_cols=7 Identities=29% Similarity=0.738 Sum_probs=3.7
Q ss_pred ecccccc
Q psy4412 8 ACLWCDY 14 (39)
Q Consensus 8 ~c~~c~~ 14 (39)
.|+.|+.
T Consensus 2 ~C~KCg~ 8 (64)
T PF09855_consen 2 KCPKCGN 8 (64)
T ss_pred CCCCCCC
Confidence 4555554
No 160
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=37.53 E-value=18 Score=10.67 Aligned_cols=13 Identities=15% Similarity=0.215 Sum_probs=7.0
Q ss_pred eccccccccccch
Q psy4412 8 ACLWCDYHTLNSG 20 (39)
Q Consensus 8 ~c~~c~~~~~~~~ 20 (39)
.|..|++.+-..+
T Consensus 4 ~CprC~kg~Hwa~ 16 (36)
T PF14787_consen 4 LCPRCGKGFHWAS 16 (36)
T ss_dssp C-TTTSSSCS-TT
T ss_pred cCcccCCCcchhh
Confidence 4777877765443
No 161
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=37.36 E-value=21 Score=12.79 Aligned_cols=8 Identities=38% Similarity=1.277 Sum_probs=4.1
Q ss_pred eecccccc
Q psy4412 7 YACLWCDY 14 (39)
Q Consensus 7 ~~c~~c~~ 14 (39)
|.|..|++
T Consensus 36 y~Cp~Cgk 43 (90)
T PF01780_consen 36 YTCPFCGK 43 (90)
T ss_dssp BEESSSSS
T ss_pred CcCCCCCC
Confidence 45555554
No 162
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=37.06 E-value=19 Score=10.73 Aligned_cols=11 Identities=18% Similarity=0.558 Sum_probs=7.1
Q ss_pred ceecccccccc
Q psy4412 6 LYACLWCDYHT 16 (39)
Q Consensus 6 ~~~c~~c~~~~ 16 (39)
+..|..|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 45677777654
No 163
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=36.95 E-value=17 Score=13.31 Aligned_cols=9 Identities=22% Similarity=0.807 Sum_probs=6.1
Q ss_pred eeccccccc
Q psy4412 7 YACLWCDYH 15 (39)
Q Consensus 7 ~~c~~c~~~ 15 (39)
+.|..|++.
T Consensus 3 WkC~iCg~~ 11 (101)
T PF09943_consen 3 WKCYICGKP 11 (101)
T ss_pred eEEEecCCe
Confidence 567777763
No 164
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.57 E-value=22 Score=13.50 Aligned_cols=14 Identities=14% Similarity=0.221 Sum_probs=10.2
Q ss_pred ceeccccccccccc
Q psy4412 6 LYACLWCDYHTLNS 19 (39)
Q Consensus 6 ~~~c~~c~~~~~~~ 19 (39)
.+.|..|+..|...
T Consensus 70 ~~~C~~CG~~~~~~ 83 (135)
T PRK03824 70 VLKCRNCGNEWSLK 83 (135)
T ss_pred EEECCCCCCEEecc
Confidence 36899999776543
No 165
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=36.42 E-value=22 Score=11.08 Aligned_cols=6 Identities=33% Similarity=1.370 Sum_probs=2.8
Q ss_pred eccccc
Q psy4412 8 ACLWCD 13 (39)
Q Consensus 8 ~c~~c~ 13 (39)
.|..||
T Consensus 5 PCPFCG 10 (61)
T PF14354_consen 5 PCPFCG 10 (61)
T ss_pred CCCCCC
Confidence 345554
No 166
>KOG4124|consensus
Probab=36.32 E-value=5 Score=18.01 Aligned_cols=20 Identities=20% Similarity=0.370 Sum_probs=14.4
Q ss_pred CcceeccccccccccchhHH
Q psy4412 4 TYLYACLWCDYHTLNSGHMR 23 (39)
Q Consensus 4 ~~~~~c~~c~~~~~~~~~~~ 23 (39)
.+++.|..|.+.+.....|.
T Consensus 396 nk~~r~~i~~~~~k~~~~l~ 415 (442)
T KOG4124|consen 396 NKPYRCEVCSKRYKNLNGLK 415 (442)
T ss_pred cCcccChhhhhhhccCCCCC
Confidence 57889999988776655443
No 167
>KOG0402|consensus
Probab=36.30 E-value=11 Score=13.39 Aligned_cols=8 Identities=38% Similarity=1.286 Sum_probs=5.5
Q ss_pred eecccccc
Q psy4412 7 YACLWCDY 14 (39)
Q Consensus 7 ~~c~~c~~ 14 (39)
|.|..|++
T Consensus 37 y~CsfCGK 44 (92)
T KOG0402|consen 37 YTCSFCGK 44 (92)
T ss_pred hhhhhcch
Confidence 56777775
No 168
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=36.26 E-value=22 Score=11.36 Aligned_cols=12 Identities=17% Similarity=0.191 Sum_probs=4.9
Q ss_pred ceeccccccccc
Q psy4412 6 LYACLWCDYHTL 17 (39)
Q Consensus 6 ~~~c~~c~~~~~ 17 (39)
.+.|..||..+.
T Consensus 25 rhhCr~CG~~vC 36 (69)
T PF01363_consen 25 RHHCRNCGRVVC 36 (69)
T ss_dssp EEE-TTT--EEE
T ss_pred eEccCCCCCEEC
Confidence 355666666553
No 169
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=35.82 E-value=21 Score=10.63 Aligned_cols=14 Identities=21% Similarity=0.563 Sum_probs=9.4
Q ss_pred ceeccccccccccc
Q psy4412 6 LYACLWCDYHTLNS 19 (39)
Q Consensus 6 ~~~c~~c~~~~~~~ 19 (39)
-+.|..|+..+...
T Consensus 20 ~~vC~~Cg~~~~~~ 33 (52)
T smart00661 20 RFVCRKCGYEEPIE 33 (52)
T ss_pred EEECCcCCCeEECC
Confidence 46788888765443
No 170
>KOG1842|consensus
Probab=35.72 E-value=28 Score=16.47 Aligned_cols=25 Identities=20% Similarity=0.360 Sum_probs=20.3
Q ss_pred ceeccccccccccchhHHHHhHHhc
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRRHT 30 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~~~ 30 (39)
.+.|+.|..-|.....|..|.-..+
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH 39 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEH 39 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhc
Confidence 5789999999999888888875433
No 171
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=35.58 E-value=19 Score=10.27 Aligned_cols=9 Identities=33% Similarity=0.792 Sum_probs=6.1
Q ss_pred ceecccccc
Q psy4412 6 LYACLWCDY 14 (39)
Q Consensus 6 ~~~c~~c~~ 14 (39)
.|.|..|+.
T Consensus 8 ~Y~C~~C~~ 16 (32)
T PF13696_consen 8 GYVCHRCGQ 16 (32)
T ss_pred CCEeecCCC
Confidence 367777764
No 172
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=35.52 E-value=19 Score=13.34 Aligned_cols=10 Identities=20% Similarity=0.351 Sum_probs=6.8
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
..|+.|+..|
T Consensus 50 t~CP~Cg~~~ 59 (115)
T COG1885 50 TSCPKCGEPF 59 (115)
T ss_pred ccCCCCCCcc
Confidence 4688888654
No 173
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.06 E-value=26 Score=13.19 Aligned_cols=14 Identities=0% Similarity=-0.223 Sum_probs=10.4
Q ss_pred CCcceecccccccc
Q psy4412 3 PTYLYACLWCDYHT 16 (39)
Q Consensus 3 ~~~~~~c~~c~~~~ 16 (39)
+..|..|..|+++|
T Consensus 23 NrdPiVsPytG~s~ 36 (129)
T COG4530 23 NRDPIVSPYTGKSY 36 (129)
T ss_pred CCCccccCcccccc
Confidence 34577788888887
No 174
>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=34.74 E-value=20 Score=10.22 Aligned_cols=20 Identities=20% Similarity=0.368 Sum_probs=11.0
Q ss_pred ceeccccccccccchhHHHHh
Q psy4412 6 LYACLWCDYHTLNSGHMRDHI 26 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~ 26 (39)
.+.|..|+....... +..|.
T Consensus 4 ~~~C~nC~R~v~a~R-fA~HL 23 (33)
T PF08209_consen 4 YVECPNCGRPVAASR-FAPHL 23 (33)
T ss_dssp EEE-TTTSSEEEGGG-HHHHH
T ss_pred eEECCCCcCCcchhh-hHHHH
Confidence 467888987654432 44443
No 175
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=34.46 E-value=32 Score=12.38 Aligned_cols=17 Identities=18% Similarity=0.452 Sum_probs=11.3
Q ss_pred eeccccccccccchhHH
Q psy4412 7 YACLWCDYHTLNSGHMR 23 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~ 23 (39)
+.|..|+..+.......
T Consensus 32 ~~C~~CGe~~~~~e~~~ 48 (127)
T TIGR03830 32 WYCPACGEELLDPEESK 48 (127)
T ss_pred eECCCCCCEEEcHHHHH
Confidence 56888888776655433
No 176
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=34.44 E-value=19 Score=11.86 Aligned_cols=15 Identities=20% Similarity=0.262 Sum_probs=9.2
Q ss_pred cceeccccccccccc
Q psy4412 5 YLYACLWCDYHTLNS 19 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~ 19 (39)
.|..|-.||+...+.
T Consensus 3 iPVRCFTCGkvi~~~ 17 (60)
T PF01194_consen 3 IPVRCFTCGKVIGNK 17 (60)
T ss_dssp -SSS-STTTSBTCGH
T ss_pred CceecCCCCCChhHh
Confidence 366788888866544
No 177
>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=34.36 E-value=21 Score=10.39 Aligned_cols=7 Identities=29% Similarity=0.710 Sum_probs=3.2
Q ss_pred ecccccc
Q psy4412 8 ACLWCDY 14 (39)
Q Consensus 8 ~c~~c~~ 14 (39)
.|..|+.
T Consensus 2 ~Cp~Cg~ 8 (43)
T PF08271_consen 2 KCPNCGS 8 (43)
T ss_dssp SBTTTSS
T ss_pred CCcCCcC
Confidence 3445544
No 178
>PF12907 zf-met2: Zinc-binding
Probab=34.34 E-value=17 Score=10.91 Aligned_cols=21 Identities=14% Similarity=0.501 Sum_probs=12.3
Q ss_pred eeccccccccccc---hhHHHHhH
Q psy4412 7 YACLWCDYHTLNS---GHMRDHIR 27 (39)
Q Consensus 7 ~~c~~c~~~~~~~---~~~~~~~~ 27 (39)
+.|..|...|... ..|..|-.
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~e 25 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAE 25 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHH
Confidence 3577777666443 44666654
No 179
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=34.31 E-value=23 Score=10.64 Aligned_cols=12 Identities=17% Similarity=0.471 Sum_probs=7.3
Q ss_pred eecccccccccc
Q psy4412 7 YACLWCDYHTLN 18 (39)
Q Consensus 7 ~~c~~c~~~~~~ 18 (39)
+.|..|+..+..
T Consensus 27 f~C~~C~~~l~~ 38 (58)
T PF00412_consen 27 FKCSKCGKPLND 38 (58)
T ss_dssp SBETTTTCBTTT
T ss_pred cccCCCCCccCC
Confidence 567777765543
No 180
>PTZ00064 histone acetyltransferase; Provisional
Probab=34.29 E-value=63 Score=15.79 Aligned_cols=24 Identities=21% Similarity=0.311 Sum_probs=19.9
Q ss_pred cceeccccccccccchhHHHHhHH
Q psy4412 5 YLYACLWCDYHTLNSGHMRDHIRR 28 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~~~~~~~~~~ 28 (39)
..|.|..|-+-|.....+..|+..
T Consensus 279 ~LYICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 279 TLHFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred eEEEccchhhhhCCHHHHHHHHhc
Confidence 458899999988888889988663
No 181
>PRK11823 DNA repair protein RadA; Provisional
Probab=34.08 E-value=29 Score=15.99 Aligned_cols=12 Identities=25% Similarity=0.592 Sum_probs=8.2
Q ss_pred ceeccccccccc
Q psy4412 6 LYACLWCDYHTL 17 (39)
Q Consensus 6 ~~~c~~c~~~~~ 17 (39)
.|.|..|+....
T Consensus 7 ~y~C~~Cg~~~~ 18 (446)
T PRK11823 7 AYVCQECGAESP 18 (446)
T ss_pred eEECCcCCCCCc
Confidence 478888886543
No 182
>KOG4173|consensus
Probab=34.04 E-value=18 Score=15.18 Aligned_cols=19 Identities=21% Similarity=0.506 Sum_probs=14.2
Q ss_pred eccccccccccchhHHHHh
Q psy4412 8 ACLWCDYHTLNSGHMRDHI 26 (39)
Q Consensus 8 ~c~~c~~~~~~~~~~~~~~ 26 (39)
.|..|.+.|....-|..|+
T Consensus 108 sCs~C~r~~Pt~hLLd~HI 126 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHI 126 (253)
T ss_pred hhHHHHHhCCchhhhhHHH
Confidence 6888888887776666664
No 183
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=33.99 E-value=19 Score=10.86 Aligned_cols=12 Identities=17% Similarity=0.401 Sum_probs=7.9
Q ss_pred eecccccccccc
Q psy4412 7 YACLWCDYHTLN 18 (39)
Q Consensus 7 ~~c~~c~~~~~~ 18 (39)
..|..|+..+..
T Consensus 6 l~C~~CG~~m~~ 17 (58)
T PF13408_consen 6 LRCGHCGSKMTR 17 (58)
T ss_pred EEcccCCcEeEE
Confidence 357778876654
No 184
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=33.94 E-value=41 Score=13.58 Aligned_cols=16 Identities=25% Similarity=0.505 Sum_probs=11.1
Q ss_pred eeccccccccccchhH
Q psy4412 7 YACLWCDYHTLNSGHM 22 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~ 22 (39)
+.|..|++.|-.-+.+
T Consensus 131 ~~C~~CgkiYW~GsHw 146 (165)
T COG1656 131 YRCPKCGKIYWKGSHW 146 (165)
T ss_pred eECCCCcccccCchHH
Confidence 5689999877655443
No 185
>PHA02998 RNA polymerase subunit; Provisional
Probab=33.89 E-value=32 Score=14.15 Aligned_cols=13 Identities=31% Similarity=0.396 Sum_probs=9.2
Q ss_pred eeccccccccccc
Q psy4412 7 YACLWCDYHTLNS 19 (39)
Q Consensus 7 ~~c~~c~~~~~~~ 19 (39)
|.|..|++.+...
T Consensus 172 YkC~~CG~~wkpp 184 (195)
T PHA02998 172 HACRDCKKHFKPP 184 (195)
T ss_pred EEcCCCCCccCCc
Confidence 6788888776543
No 186
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=33.64 E-value=26 Score=11.68 Aligned_cols=14 Identities=14% Similarity=0.285 Sum_probs=10.2
Q ss_pred cceecccccccccc
Q psy4412 5 YLYACLWCDYHTLN 18 (39)
Q Consensus 5 ~~~~c~~c~~~~~~ 18 (39)
.|..|-.||+....
T Consensus 3 iPvRCFTCGkvi~~ 16 (62)
T PRK04016 3 IPVRCFTCGKVIAE 16 (62)
T ss_pred CCeEecCCCCChHH
Confidence 36778889886654
No 187
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=33.51 E-value=23 Score=11.29 Aligned_cols=19 Identities=16% Similarity=0.608 Sum_probs=12.6
Q ss_pred eeccccccccccchhHHHH
Q psy4412 7 YACLWCDYHTLNSGHMRDH 25 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~ 25 (39)
+-|..|+-.+.....|..+
T Consensus 28 ~YC~~Cg~~Y~d~~dL~~~ 46 (55)
T PF13821_consen 28 NYCFWCGTKYDDEEDLERN 46 (55)
T ss_pred ceeeeeCCccCCHHHHHhC
Confidence 3477888777776666543
No 188
>PF00935 Ribosomal_L44: Ribosomal protein L44; InterPro: IPR000552 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of mammalian [], Trypanosoma brucei, Caenorhabditis elegans and fungal L44, and Haloarcula marismortui LA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_r 1S1I_Z 3O5H_f 3O58_f 3IZR_r 1M1K_4 3CCQ_3 3CCL_3 3CME_3 1K73_4 ....
Probab=33.21 E-value=24 Score=12.24 Aligned_cols=10 Identities=20% Similarity=0.478 Sum_probs=6.7
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
+.|..|+...
T Consensus 54 l~C~~C~~~~ 63 (77)
T PF00935_consen 54 LECTECGKAH 63 (77)
T ss_dssp EEETTTS-EE
T ss_pred EEeCCCCccc
Confidence 6788888654
No 189
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=32.65 E-value=23 Score=10.19 Aligned_cols=11 Identities=18% Similarity=0.368 Sum_probs=5.4
Q ss_pred eeccccccccc
Q psy4412 7 YACLWCDYHTL 17 (39)
Q Consensus 7 ~~c~~c~~~~~ 17 (39)
-.|..||..+.
T Consensus 22 isC~~CGPr~~ 32 (35)
T PF07503_consen 22 ISCTNCGPRYS 32 (35)
T ss_dssp --BTTCC-SCC
T ss_pred ccCCCCCCCEE
Confidence 35777876553
No 190
>PF02998 Lentiviral_Tat: Lentiviral Tat protein; InterPro: IPR004247 This family contains retroviral transactivating (Tat) proteins, from a variety of lentiviruses. The Tat protein may have a role in trans-activation of the viral long terminal repeat [].; GO: 0045893 positive regulation of transcription, DNA-dependent
Probab=32.38 E-value=28 Score=12.26 Aligned_cols=11 Identities=18% Similarity=0.416 Sum_probs=7.4
Q ss_pred cceeccccccc
Q psy4412 5 YLYACLWCDYH 15 (39)
Q Consensus 5 ~~~~c~~c~~~ 15 (39)
++..|..|..+
T Consensus 73 R~CGCRlCNPG 83 (86)
T PF02998_consen 73 RPCGCRLCNPG 83 (86)
T ss_pred cCCCccccCCC
Confidence 46777777654
No 191
>KOG3214|consensus
Probab=32.34 E-value=16 Score=13.47 Aligned_cols=13 Identities=15% Similarity=0.409 Sum_probs=9.4
Q ss_pred eeccccccccccc
Q psy4412 7 YACLWCDYHTLNS 19 (39)
Q Consensus 7 ~~c~~c~~~~~~~ 19 (39)
..|..|+.+|...
T Consensus 48 ~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 48 ASCRICEESFQTT 60 (109)
T ss_pred eeeeehhhhhccc
Confidence 4688888888654
No 192
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=32.30 E-value=21 Score=16.31 Aligned_cols=21 Identities=19% Similarity=0.322 Sum_probs=16.6
Q ss_pred eeccccccccccchhHHHHhH
Q psy4412 7 YACLWCDYHTLNSGHMRDHIR 27 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~ 27 (39)
+-|..|++.|.....+..|..
T Consensus 239 ~YC~~C~r~f~~~~VFe~Hl~ 259 (470)
T COG5188 239 VYCVKCGREFSRSKVFEYHLE 259 (470)
T ss_pred eeeHhhhhHhhhhHHHHHHHh
Confidence 569999999988877777754
No 193
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.02 E-value=23 Score=12.91 Aligned_cols=11 Identities=18% Similarity=0.455 Sum_probs=7.5
Q ss_pred cceeccccccc
Q psy4412 5 YLYACLWCDYH 15 (39)
Q Consensus 5 ~~~~c~~c~~~ 15 (39)
+.|.|..|+..
T Consensus 5 kewkC~VCg~~ 15 (103)
T COG4847 5 KEWKCYVCGGT 15 (103)
T ss_pred ceeeEeeeCCE
Confidence 45778888763
No 194
>PRK01343 zinc-binding protein; Provisional
Probab=31.81 E-value=25 Score=11.48 Aligned_cols=12 Identities=17% Similarity=0.299 Sum_probs=8.6
Q ss_pred ceeccccccccc
Q psy4412 6 LYACLWCDYHTL 17 (39)
Q Consensus 6 ~~~c~~c~~~~~ 17 (39)
...|..|++.+.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 356899998654
No 195
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=31.68 E-value=22 Score=10.17 Aligned_cols=8 Identities=25% Similarity=0.488 Sum_probs=2.6
Q ss_pred cccccccc
Q psy4412 9 CLWCDYHT 16 (39)
Q Consensus 9 c~~c~~~~ 16 (39)
|..|+...
T Consensus 3 C~~CG~~l 10 (34)
T PF14803_consen 3 CPQCGGPL 10 (34)
T ss_dssp -TTT--B-
T ss_pred cccccChh
Confidence 66676654
No 196
>PF03286 Pox_Ag35: Pox virus Ag35 surface protein; InterPro: IPR004966 The Pox virus Ag35 surface protein is an evelope protein known as protein H5.; GO: 0019031 viral envelope
Probab=31.54 E-value=46 Score=13.88 Aligned_cols=21 Identities=14% Similarity=0.117 Sum_probs=16.7
Q ss_pred ccccccccchhHHHHhHHhcC
Q psy4412 11 WCDYHTLNSGHMRDHIRRHTG 31 (39)
Q Consensus 11 ~c~~~~~~~~~~~~~~~~~~~ 31 (39)
-++-.|.....++.|.+.-+.
T Consensus 9 ~~~~~f~tl~eiR~hlrs~ae 29 (200)
T PF03286_consen 9 NGGSNFKTLEEIRAHLRSTAE 29 (200)
T ss_pred CCCccceeHHHHHHHHhhhcc
Confidence 367789999999999886654
No 197
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=31.21 E-value=24 Score=10.39 Aligned_cols=9 Identities=22% Similarity=0.778 Sum_probs=3.4
Q ss_pred ecccccccc
Q psy4412 8 ACLWCDYHT 16 (39)
Q Consensus 8 ~c~~c~~~~ 16 (39)
.|..|++.-
T Consensus 3 ~CSFCgr~~ 11 (41)
T PF06689_consen 3 RCSFCGRPE 11 (41)
T ss_dssp B-TTT--BT
T ss_pred CccCCCCCH
Confidence 466676644
No 198
>PF15499 Peptidase_C98: Ubiquitin-specific peptidase-like, SUMO isopeptidase
Probab=30.84 E-value=15 Score=15.88 Aligned_cols=12 Identities=17% Similarity=0.589 Sum_probs=7.6
Q ss_pred cceecccccccc
Q psy4412 5 YLYACLWCDYHT 16 (39)
Q Consensus 5 ~~~~c~~c~~~~ 16 (39)
..|.|..|+..+
T Consensus 133 WeFeC~~Cg~~~ 144 (275)
T PF15499_consen 133 WEFECSQCGHKY 144 (275)
T ss_pred EEEEccccCChh
Confidence 346777777544
No 199
>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=30.82 E-value=32 Score=11.28 Aligned_cols=9 Identities=22% Similarity=0.505 Sum_probs=5.5
Q ss_pred ecccccccc
Q psy4412 8 ACLWCDYHT 16 (39)
Q Consensus 8 ~c~~c~~~~ 16 (39)
.|..||++.
T Consensus 5 HC~~CG~~I 13 (59)
T PF09889_consen 5 HCPVCGKPI 13 (59)
T ss_pred cCCcCCCcC
Confidence 467777544
No 200
>PRK11032 hypothetical protein; Provisional
Probab=30.54 E-value=23 Score=14.08 Aligned_cols=8 Identities=25% Similarity=0.625 Sum_probs=4.4
Q ss_pred eecccccc
Q psy4412 7 YACLWCDY 14 (39)
Q Consensus 7 ~~c~~c~~ 14 (39)
..|..|+.
T Consensus 125 LvC~~Cg~ 132 (160)
T PRK11032 125 LVCEKCHH 132 (160)
T ss_pred EEecCCCC
Confidence 45666654
No 201
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=30.38 E-value=28 Score=14.83 Aligned_cols=10 Identities=20% Similarity=0.385 Sum_probs=6.8
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
-.|.+||...
T Consensus 191 ~VCeVCGA~L 200 (254)
T PF03194_consen 191 EVCEVCGAFL 200 (254)
T ss_pred cchhhhhhHH
Confidence 4688888533
No 202
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=29.78 E-value=24 Score=9.66 Aligned_cols=12 Identities=25% Similarity=0.537 Sum_probs=4.9
Q ss_pred ceeccccccccc
Q psy4412 6 LYACLWCDYHTL 17 (39)
Q Consensus 6 ~~~c~~c~~~~~ 17 (39)
.|.|..|+..+-
T Consensus 13 kY~Cp~C~~~~C 24 (30)
T PF04438_consen 13 KYRCPRCGARYC 24 (30)
T ss_dssp SEE-TTT--EES
T ss_pred EEECCCcCCcee
Confidence 456666665443
No 203
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=29.47 E-value=32 Score=13.43 Aligned_cols=15 Identities=27% Similarity=0.596 Sum_probs=10.1
Q ss_pred cceeccccccccccc
Q psy4412 5 YLYACLWCDYHTLNS 19 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~ 19 (39)
+.|+|+.|..++...
T Consensus 79 ~lYeCnIC~etS~ee 93 (140)
T PF05290_consen 79 KLYECNICKETSAEE 93 (140)
T ss_pred CceeccCcccccchh
Confidence 568888887655433
No 204
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=29.39 E-value=24 Score=10.03 Aligned_cols=7 Identities=14% Similarity=0.468 Sum_probs=1.8
Q ss_pred ccccccc
Q psy4412 10 LWCDYHT 16 (39)
Q Consensus 10 ~~c~~~~ 16 (39)
..|+..+
T Consensus 2 ~~C~~~~ 8 (47)
T PF01844_consen 2 QYCGKPG 8 (47)
T ss_dssp TTT--B-
T ss_pred CCCCCcC
Confidence 3454443
No 205
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=29.33 E-value=25 Score=11.36 Aligned_cols=9 Identities=33% Similarity=0.837 Sum_probs=2.7
Q ss_pred ceecccccc
Q psy4412 6 LYACLWCDY 14 (39)
Q Consensus 6 ~~~c~~c~~ 14 (39)
.|.|..|+.
T Consensus 33 ~y~Cp~CgA 41 (55)
T PF05741_consen 33 KYVCPICGA 41 (55)
T ss_dssp G---TTT--
T ss_pred cCcCCCCcC
Confidence 367777764
No 206
>PF03691 UPF0167: Uncharacterised protein family (UPF0167); InterPro: IPR005363 The proteins in this family are about 200 amino acids long and each contain 3 CXXC motifs.
Probab=28.77 E-value=33 Score=13.91 Aligned_cols=11 Identities=45% Similarity=1.165 Sum_probs=8.3
Q ss_pred ceecccccccc
Q psy4412 6 LYACLWCDYHT 16 (39)
Q Consensus 6 ~~~c~~c~~~~ 16 (39)
.|.|..|++-.
T Consensus 160 lFrClhCgk~~ 170 (176)
T PF03691_consen 160 LFRCLHCGKHR 170 (176)
T ss_pred EEEcCcCCcEE
Confidence 47899998743
No 207
>PLN03239 histone acetyltransferase; Provisional
Probab=28.75 E-value=58 Score=14.94 Aligned_cols=23 Identities=13% Similarity=0.148 Sum_probs=18.3
Q ss_pred cceeccccccccccchhHHHHhH
Q psy4412 5 YLYACLWCDYHTLNSGHMRDHIR 27 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~~~~~~~~~ 27 (39)
..|.|..|-+-|.....+..|+.
T Consensus 105 ~lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 105 VLYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred eEEEeccchhhhcCHHHHHHHHH
Confidence 46889999988888888887764
No 208
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=28.74 E-value=32 Score=10.61 Aligned_cols=13 Identities=23% Similarity=0.399 Sum_probs=8.9
Q ss_pred eeccccccccccc
Q psy4412 7 YACLWCDYHTLNS 19 (39)
Q Consensus 7 ~~c~~c~~~~~~~ 19 (39)
+.|..|+..+...
T Consensus 29 W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 29 WKCPKCGHEWKAS 41 (55)
T ss_pred EECCCCCCeeEcc
Confidence 5788887766543
No 209
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=28.70 E-value=31 Score=12.58 Aligned_cols=12 Identities=17% Similarity=0.146 Sum_probs=7.7
Q ss_pred eecccccccccc
Q psy4412 7 YACLWCDYHTLN 18 (39)
Q Consensus 7 ~~c~~c~~~~~~ 18 (39)
..|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 568888877653
No 210
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=28.43 E-value=29 Score=10.06 Aligned_cols=10 Identities=20% Similarity=0.723 Sum_probs=5.6
Q ss_pred cceecccccc
Q psy4412 5 YLYACLWCDY 14 (39)
Q Consensus 5 ~~~~c~~c~~ 14 (39)
+.+.|..|+.
T Consensus 23 ~~w~C~~C~~ 32 (40)
T PF04810_consen 23 KTWICNFCGT 32 (40)
T ss_dssp TEEEETTT--
T ss_pred CEEECcCCCC
Confidence 4567887765
No 211
>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=28.38 E-value=25 Score=9.30 Aligned_cols=10 Identities=40% Similarity=1.321 Sum_probs=4.7
Q ss_pred cceecccccc
Q psy4412 5 YLYACLWCDY 14 (39)
Q Consensus 5 ~~~~c~~c~~ 14 (39)
..|.|..|.-
T Consensus 14 ~~Y~C~~Cdf 23 (30)
T PF07649_consen 14 WFYRCSECDF 23 (30)
T ss_dssp -EEE-TTT--
T ss_pred ceEECccCCC
Confidence 4678888864
No 212
>KOG3014|consensus
Probab=28.35 E-value=65 Score=14.09 Aligned_cols=24 Identities=17% Similarity=0.224 Sum_probs=16.0
Q ss_pred eeccccccccc--cchhHHHHhHHhc
Q psy4412 7 YACLWCDYHTL--NSGHMRDHIRRHT 30 (39)
Q Consensus 7 ~~c~~c~~~~~--~~~~~~~~~~~~~ 30 (39)
..|..|+-.+. ...+...|...|.
T Consensus 38 ~~C~~Cgm~Yt~~s~EDe~~H~~fH~ 63 (257)
T KOG3014|consen 38 VKCKECGMKYTVTSPEDEALHEKFHN 63 (257)
T ss_pred eehhhcCceecCCCHHHHHHHHHHHH
Confidence 47888986554 3455667777775
No 213
>COG4640 Predicted membrane protein [Function unknown]
Probab=28.35 E-value=68 Score=15.19 Aligned_cols=19 Identities=11% Similarity=0.069 Sum_probs=13.0
Q ss_pred cceeccccccccccchhHH
Q psy4412 5 YLYACLWCDYHTLNSGHMR 23 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~~~~~ 23 (39)
-...|.+||..+.......
T Consensus 14 d~~qC~qCG~~~t~~~sqa 32 (465)
T COG4640 14 DDVQCTQCGHKFTSRQSQA 32 (465)
T ss_pred ccccccccCCcCCchhhhh
Confidence 3456999998887665443
No 214
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=28.20 E-value=42 Score=15.63 Aligned_cols=11 Identities=18% Similarity=0.712 Sum_probs=6.7
Q ss_pred ceecccccccc
Q psy4412 6 LYACLWCDYHT 16 (39)
Q Consensus 6 ~~~c~~c~~~~ 16 (39)
.|.|..|+...
T Consensus 7 ~y~C~~Cg~~~ 17 (454)
T TIGR00416 7 KFVCQHCGADS 17 (454)
T ss_pred eEECCcCCCCC
Confidence 36777777533
No 215
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=27.98 E-value=68 Score=14.64 Aligned_cols=24 Identities=21% Similarity=0.290 Sum_probs=16.2
Q ss_pred ceeccccccccccchhHHHHhHHh
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRRH 29 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~~ 29 (39)
.|.|..|...|..--+.-.|...|
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ceechhhhhhhhhhhHHHHHHHHh
Confidence 477888877777766666665444
No 216
>KOG3352|consensus
Probab=27.79 E-value=31 Score=13.73 Aligned_cols=13 Identities=15% Similarity=0.041 Sum_probs=8.7
Q ss_pred cceeccccccccc
Q psy4412 5 YLYACLWCDYHTL 17 (39)
Q Consensus 5 ~~~~c~~c~~~~~ 17 (39)
+...|.+|+.-|.
T Consensus 132 e~~rc~eCG~~fk 144 (153)
T KOG3352|consen 132 ETQRCPECGHYFK 144 (153)
T ss_pred CcccCCcccceEE
Confidence 3456888887664
No 217
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=27.65 E-value=35 Score=12.06 Aligned_cols=12 Identities=17% Similarity=0.160 Sum_probs=8.9
Q ss_pred eecccccccccc
Q psy4412 7 YACLWCDYHTLN 18 (39)
Q Consensus 7 ~~c~~c~~~~~~ 18 (39)
+.|..|++.+-.
T Consensus 74 ~~C~~Cg~i~~~ 85 (116)
T cd07153 74 LICTKCGKVIDF 85 (116)
T ss_pred eEeCCCCCEEEe
Confidence 678889986643
No 218
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=27.61 E-value=49 Score=13.39 Aligned_cols=20 Identities=20% Similarity=0.891 Sum_probs=10.4
Q ss_pred eeccccccccccchhHHHHh
Q psy4412 7 YACLWCDYHTLNSGHMRDHI 26 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~ 26 (39)
|.|..|.........+..|.
T Consensus 1 F~Cs~CKfrtf~~~ei~~Hl 20 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHL 20 (165)
T ss_pred CccceeeeecccHHHHHHHH
Confidence 35666665444444455543
No 219
>COG4855 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.46 E-value=33 Score=11.68 Aligned_cols=11 Identities=18% Similarity=0.483 Sum_probs=7.0
Q ss_pred ecccccccccc
Q psy4412 8 ACLWCDYHTLN 18 (39)
Q Consensus 8 ~c~~c~~~~~~ 18 (39)
.|..|+.+...
T Consensus 25 iCIVCG~GlC~ 35 (76)
T COG4855 25 ICIVCGMGLCM 35 (76)
T ss_pred EEEEeCchHHH
Confidence 57777766543
No 220
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=27.38 E-value=26 Score=11.32 Aligned_cols=11 Identities=18% Similarity=0.350 Sum_probs=7.3
Q ss_pred eeccccccccc
Q psy4412 7 YACLWCDYHTL 17 (39)
Q Consensus 7 ~~c~~c~~~~~ 17 (39)
..|..|+..|.
T Consensus 6 ~~C~~Cg~~~~ 16 (54)
T PF14446_consen 6 CKCPVCGKKFK 16 (54)
T ss_pred ccChhhCCccc
Confidence 35777777664
No 221
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=27.23 E-value=38 Score=12.24 Aligned_cols=10 Identities=20% Similarity=0.611 Sum_probs=6.4
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
+.|..|++.|
T Consensus 54 W~C~~C~~~~ 63 (91)
T TIGR00280 54 WTCRKCGAKF 63 (91)
T ss_pred EEcCCCCCEE
Confidence 5677777654
No 222
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=27.14 E-value=15 Score=11.75 Aligned_cols=11 Identities=27% Similarity=0.748 Sum_probs=7.3
Q ss_pred eeccccccccc
Q psy4412 7 YACLWCDYHTL 17 (39)
Q Consensus 7 ~~c~~c~~~~~ 17 (39)
|.|+.|..++.
T Consensus 8 y~CDLCn~~~p 18 (57)
T PF14445_consen 8 YSCDLCNSSHP 18 (57)
T ss_pred HhHHhhcccCc
Confidence 56777776554
No 223
>TIGR00320 dfx_rbo desulfoferrodoxin. This protein is described in some articles as rubredoxin oxidoreductase (rbo), and its gene shares an operon with the rubredoxin gene in Desulfovibrio vulgaris Hildenborough.
Probab=27.13 E-value=39 Score=12.78 Aligned_cols=11 Identities=27% Similarity=0.706 Sum_probs=8.2
Q ss_pred ceecccccccc
Q psy4412 6 LYACLWCDYHT 16 (39)
Q Consensus 6 ~~~c~~c~~~~ 16 (39)
-|.|..|+...
T Consensus 7 fYkC~~CGniv 17 (125)
T TIGR00320 7 VYKCEVCGNIV 17 (125)
T ss_pred EEECCCCCcEE
Confidence 47888888765
No 224
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=26.63 E-value=22 Score=14.61 Aligned_cols=26 Identities=15% Similarity=0.188 Sum_probs=0.0
Q ss_pred eeccccccccccchhHHHHhHHhcCCC
Q psy4412 7 YACLWCDYHTLNSGHMRDHIRRHTGEK 33 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~~~~~~~ 33 (39)
..|..||.... ...+..|+++.....
T Consensus 169 ~~cPitGe~IP-~~e~~eHmRi~LlDP 194 (229)
T PF12230_consen 169 IICPITGEMIP-ADEMDEHMRIELLDP 194 (229)
T ss_dssp ---------------------------
T ss_pred ccccccccccc-ccccccccccccccc
Confidence 46888887443 455788888766543
No 225
>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=26.62 E-value=35 Score=11.10 Aligned_cols=12 Identities=17% Similarity=0.221 Sum_probs=4.7
Q ss_pred eecccccccccc
Q psy4412 7 YACLWCDYHTLN 18 (39)
Q Consensus 7 ~~c~~c~~~~~~ 18 (39)
..|..|++....
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 357777765443
No 226
>TIGR02986 restrict_Alw26I type II restriction endonuclease, Alw26I/Eco31I/Esp3I family. Members of this family are type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family. Characterized specificities of three members are GGTCTC, CGTCTC, and the shared subsequence GTCTC.
Probab=25.95 E-value=19 Score=16.60 Aligned_cols=9 Identities=22% Similarity=0.479 Sum_probs=5.9
Q ss_pred ccccccccc
Q psy4412 9 CLWCDYHTL 17 (39)
Q Consensus 9 c~~c~~~~~ 17 (39)
|..||+.+.
T Consensus 85 C~~CG~~m~ 93 (424)
T TIGR02986 85 CQTCGKTMS 93 (424)
T ss_pred hHhcCCeee
Confidence 677777553
No 227
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=25.86 E-value=36 Score=10.28 Aligned_cols=12 Identities=17% Similarity=0.124 Sum_probs=7.2
Q ss_pred ceeccccccccc
Q psy4412 6 LYACLWCDYHTL 17 (39)
Q Consensus 6 ~~~c~~c~~~~~ 17 (39)
.+.|..|+..+.
T Consensus 18 k~~Cr~Cg~~~C 29 (57)
T cd00065 18 RHHCRNCGRIFC 29 (57)
T ss_pred ccccCcCcCCcC
Confidence 345666776654
No 228
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=25.70 E-value=34 Score=10.86 Aligned_cols=8 Identities=25% Similarity=0.854 Sum_probs=4.1
Q ss_pred cccccccc
Q psy4412 9 CLWCDYHT 16 (39)
Q Consensus 9 c~~c~~~~ 16 (39)
|..|+..+
T Consensus 3 CPyCge~~ 10 (52)
T PF14255_consen 3 CPYCGEPI 10 (52)
T ss_pred CCCCCCee
Confidence 55555543
No 229
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=25.62 E-value=41 Score=11.72 Aligned_cols=11 Identities=27% Similarity=0.664 Sum_probs=7.1
Q ss_pred ceecccccccc
Q psy4412 6 LYACLWCDYHT 16 (39)
Q Consensus 6 ~~~c~~c~~~~ 16 (39)
-|.|..|+...
T Consensus 4 ~Y~CRHCg~~I 14 (76)
T PF10955_consen 4 HYYCRHCGTKI 14 (76)
T ss_pred EEEecCCCCEE
Confidence 36788887533
No 230
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=25.59 E-value=38 Score=12.15 Aligned_cols=13 Identities=15% Similarity=0.314 Sum_probs=8.0
Q ss_pred eeccccccccccc
Q psy4412 7 YACLWCDYHTLNS 19 (39)
Q Consensus 7 ~~c~~c~~~~~~~ 19 (39)
+.|..|++...-.
T Consensus 81 ~iC~~Cg~v~~~~ 93 (120)
T PF01475_consen 81 FICTQCGKVIDLD 93 (120)
T ss_dssp EEETTTS-EEEE-
T ss_pred EEECCCCCEEEec
Confidence 5788999866443
No 231
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=25.46 E-value=44 Score=11.43 Aligned_cols=16 Identities=13% Similarity=0.243 Sum_probs=10.5
Q ss_pred ceecc--ccccccccchh
Q psy4412 6 LYACL--WCDYHTLNSGH 21 (39)
Q Consensus 6 ~~~c~--~c~~~~~~~~~ 21 (39)
-+.|. .|+..|.....
T Consensus 27 Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 27 YHQCQNVNCSATFITYES 44 (72)
T ss_pred eeecCCCCCCCEEEEEEE
Confidence 35676 78888765543
No 232
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=24.79 E-value=45 Score=12.02 Aligned_cols=11 Identities=18% Similarity=0.646 Sum_probs=6.8
Q ss_pred ceecccccccc
Q psy4412 6 LYACLWCDYHT 16 (39)
Q Consensus 6 ~~~c~~c~~~~ 16 (39)
.+.|..|++.|
T Consensus 54 IW~C~~C~~~~ 64 (90)
T PTZ00255 54 IWRCKGCKKTV 64 (90)
T ss_pred EEEcCCCCCEE
Confidence 35677777654
No 233
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=24.75 E-value=37 Score=10.02 Aligned_cols=6 Identities=33% Similarity=1.065 Sum_probs=2.6
Q ss_pred cccccc
Q psy4412 9 CLWCDY 14 (39)
Q Consensus 9 c~~c~~ 14 (39)
|+.|++
T Consensus 1 Cd~CG~ 6 (37)
T PF08394_consen 1 CDYCGG 6 (37)
T ss_pred CCccCC
Confidence 344444
No 234
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=24.52 E-value=36 Score=9.80 Aligned_cols=17 Identities=18% Similarity=0.405 Sum_probs=10.8
Q ss_pred eeccccccccccchhHH
Q psy4412 7 YACLWCDYHTLNSGHMR 23 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~ 23 (39)
..|..|+..+.....+.
T Consensus 20 d~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGELE 36 (41)
T ss_pred EECCCCCeEEccHHHHH
Confidence 45777777766555544
No 235
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=24.51 E-value=25 Score=14.51 Aligned_cols=21 Identities=19% Similarity=0.445 Sum_probs=0.0
Q ss_pred cceecccccccc-ccchhHHHH
Q psy4412 5 YLYACLWCDYHT-LNSGHMRDH 25 (39)
Q Consensus 5 ~~~~c~~c~~~~-~~~~~~~~~ 25 (39)
+.|.|..||... .-+..+..|
T Consensus 100 ~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 100 VEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp ----------------------
T ss_pred CeeeeEeCCCcceecHHHHHHh
Confidence 358899999633 233444444
No 236
>PF12523 DUF3725: Protein of unknown function (DUF3725); InterPro: IPR022199 This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with PF01577 from PFAM. There is a conserved FLE sequence motif.
Probab=24.49 E-value=49 Score=11.33 Aligned_cols=12 Identities=33% Similarity=0.769 Sum_probs=7.7
Q ss_pred Ccceeccccccc
Q psy4412 4 TYLYACLWCDYH 15 (39)
Q Consensus 4 ~~~~~c~~c~~~ 15 (39)
...+.|..|+++
T Consensus 57 ~Elw~Ch~C~~t 68 (74)
T PF12523_consen 57 SELWECHSCDNT 68 (74)
T ss_pred cceEEeecCCCc
Confidence 345677777764
No 237
>PF10588 NADH-G_4Fe-4S_3: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; InterPro: IPR019574 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes. This entry represents the iron-sulphur binding domain of the G subunit.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3.
Probab=24.35 E-value=37 Score=9.96 Aligned_cols=9 Identities=33% Similarity=0.637 Sum_probs=3.4
Q ss_pred ceecccccc
Q psy4412 6 LYACLWCDY 14 (39)
Q Consensus 6 ~~~c~~c~~ 14 (39)
|..|..|.+
T Consensus 13 ~~dC~~C~~ 21 (41)
T PF10588_consen 13 PLDCPTCDK 21 (41)
T ss_dssp ---TTT-TT
T ss_pred CCcCcCCCC
Confidence 556777764
No 238
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=24.32 E-value=56 Score=12.09 Aligned_cols=12 Identities=17% Similarity=0.241 Sum_probs=8.3
Q ss_pred ceeccccccccc
Q psy4412 6 LYACLWCDYHTL 17 (39)
Q Consensus 6 ~~~c~~c~~~~~ 17 (39)
...|+.|++...
T Consensus 20 ~v~CdnCg~~vP 31 (108)
T COG4830 20 YVRCDNCGKAVP 31 (108)
T ss_pred ceeeccccccCC
Confidence 457888887543
No 239
>KOG1280|consensus
Probab=24.16 E-value=93 Score=14.47 Aligned_cols=25 Identities=12% Similarity=0.487 Sum_probs=17.9
Q ss_pred ceeccccccccccchhHHHHhHHhc
Q psy4412 6 LYACLWCDYHTLNSGHMRDHIRRHT 30 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~~~~~ 30 (39)
.|.|..|+..-.....+..|.....
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~H 103 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQH 103 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcC
Confidence 5788888877677777777765433
No 240
>KOG0227|consensus
Probab=24.07 E-value=49 Score=13.87 Aligned_cols=21 Identities=29% Similarity=0.444 Sum_probs=13.9
Q ss_pred ceeccccccccccchhHHHHh
Q psy4412 6 LYACLWCDYHTLNSGHMRDHI 26 (39)
Q Consensus 6 ~~~c~~c~~~~~~~~~~~~~~ 26 (39)
.|.|..|.-...+..+...|.
T Consensus 53 ~yeCkLClT~H~ne~Syl~Ht 73 (222)
T KOG0227|consen 53 KYECKLCLTLHNNEGSYLAHT 73 (222)
T ss_pred ceeehhhhhhhcchhhhhhhh
Confidence 478888876666666665553
No 241
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PHA00689 hypothetical protein
Probab=23.99 E-value=43 Score=10.57 Aligned_cols=13 Identities=23% Similarity=0.422 Sum_probs=8.0
Q ss_pred cceeccccccccc
Q psy4412 5 YLYACLWCDYHTL 17 (39)
Q Consensus 5 ~~~~c~~c~~~~~ 17 (39)
+...|..|++.-.
T Consensus 16 ravtckrcgktgl 28 (62)
T PHA00689 16 RAVTCKRCGKTGL 28 (62)
T ss_pred ceeehhhccccCc
Confidence 3456777876543
No 243
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=23.96 E-value=33 Score=10.54 Aligned_cols=7 Identities=29% Similarity=1.179 Sum_probs=2.3
Q ss_pred eeccccc
Q psy4412 7 YACLWCD 13 (39)
Q Consensus 7 ~~c~~c~ 13 (39)
+.|..|+
T Consensus 42 W~CPiC~ 48 (50)
T PF02891_consen 42 WKCPICN 48 (50)
T ss_dssp -B-TTT-
T ss_pred eECcCCc
Confidence 4565554
No 244
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=23.95 E-value=35 Score=9.48 Aligned_cols=8 Identities=25% Similarity=0.601 Sum_probs=4.8
Q ss_pred eecccccc
Q psy4412 7 YACLWCDY 14 (39)
Q Consensus 7 ~~c~~c~~ 14 (39)
+.|..|+.
T Consensus 20 ~vCp~C~~ 27 (30)
T PF08274_consen 20 LVCPECGH 27 (30)
T ss_dssp EEETTTTE
T ss_pred EeCCcccc
Confidence 56666653
No 245
>KOG4118|consensus
Probab=23.88 E-value=50 Score=11.23 Aligned_cols=21 Identities=14% Similarity=0.390 Sum_probs=11.5
Q ss_pred eeccccccccccchhHHHHhH
Q psy4412 7 YACLWCDYHTLNSGHMRDHIR 27 (39)
Q Consensus 7 ~~c~~c~~~~~~~~~~~~~~~ 27 (39)
+.|.+|.-.......+..|.-
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe 59 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFE 59 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHh
Confidence 456666655554455555543
No 246
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=23.60 E-value=46 Score=11.23 Aligned_cols=9 Identities=22% Similarity=0.778 Sum_probs=5.6
Q ss_pred eeccccccc
Q psy4412 7 YACLWCDYH 15 (39)
Q Consensus 7 ~~c~~c~~~ 15 (39)
|.|..|+..
T Consensus 5 FTC~~C~~R 13 (66)
T PF05180_consen 5 FTCNKCGTR 13 (66)
T ss_dssp EEETTTTEE
T ss_pred EEcCCCCCc
Confidence 567777643
No 247
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=23.58 E-value=43 Score=11.73 Aligned_cols=10 Identities=20% Similarity=0.770 Sum_probs=4.6
Q ss_pred ceeccccccc
Q psy4412 6 LYACLWCDYH 15 (39)
Q Consensus 6 ~~~c~~c~~~ 15 (39)
.|.|..|++.
T Consensus 65 ~~~Cp~Cg~~ 74 (81)
T PF10609_consen 65 YFVCPHCGER 74 (81)
T ss_dssp EEE-TTT--E
T ss_pred ccCCCCCCCe
Confidence 3678887754
No 248
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=23.55 E-value=49 Score=11.93 Aligned_cols=10 Identities=20% Similarity=0.591 Sum_probs=6.2
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
+.|..|++.|
T Consensus 55 W~C~~C~~~~ 64 (90)
T PRK03976 55 WECRKCGAKF 64 (90)
T ss_pred EEcCCCCCEE
Confidence 5666676644
No 249
>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=23.52 E-value=13 Score=16.19 Aligned_cols=24 Identities=21% Similarity=0.371 Sum_probs=13.9
Q ss_pred cceeccccccccccchhHHHHhHH
Q psy4412 5 YLYACLWCDYHTLNSGHMRDHIRR 28 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~~~~~~~~~~ 28 (39)
+++.|+.|+........|....+.
T Consensus 208 k~~PCPKCg~et~eTkdLSmStR~ 231 (314)
T PF06524_consen 208 KPIPCPKCGYETQETKDLSMSTRS 231 (314)
T ss_pred CCCCCCCCCCcccccccceeeeec
Confidence 466788887655555555443333
No 250
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=23.30 E-value=49 Score=11.40 Aligned_cols=15 Identities=20% Similarity=0.262 Sum_probs=10.3
Q ss_pred cceeccccccccccc
Q psy4412 5 YLYACLWCDYHTLNS 19 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~ 19 (39)
.|..|-.||+.....
T Consensus 3 iPVRCFTCGkvig~~ 17 (71)
T PLN00032 3 IPVRCFTCGKVIGNK 17 (71)
T ss_pred CceeecCCCCCcHHH
Confidence 467788888866444
No 251
>KOG3456|consensus
Probab=22.97 E-value=38 Score=12.69 Aligned_cols=13 Identities=15% Similarity=0.472 Sum_probs=8.6
Q ss_pred ceecccccccccc
Q psy4412 6 LYACLWCDYHTLN 18 (39)
Q Consensus 6 ~~~c~~c~~~~~~ 18 (39)
+..|..|+..|.+
T Consensus 104 ~~~CgYCGlrf~~ 116 (120)
T KOG3456|consen 104 PHICGYCGLRFVQ 116 (120)
T ss_pred Ccccccchhhhhh
Confidence 4567778776643
No 252
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=22.73 E-value=42 Score=9.98 Aligned_cols=12 Identities=17% Similarity=0.146 Sum_probs=6.8
Q ss_pred cceecccccccc
Q psy4412 5 YLYACLWCDYHT 16 (39)
Q Consensus 5 ~~~~c~~c~~~~ 16 (39)
.|..|..|++..
T Consensus 10 ~~~~C~~C~~~i 21 (53)
T PF00130_consen 10 KPTYCDVCGKFI 21 (53)
T ss_dssp STEB-TTSSSBE
T ss_pred CCCCCcccCccc
Confidence 455677777654
No 253
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=22.58 E-value=42 Score=11.15 Aligned_cols=10 Identities=20% Similarity=0.524 Sum_probs=6.9
Q ss_pred eccccccccc
Q psy4412 8 ACLWCDYHTL 17 (39)
Q Consensus 8 ~c~~c~~~~~ 17 (39)
.|..|+++..
T Consensus 10 HC~VCg~aIp 19 (64)
T COG4068 10 HCVVCGKAIP 19 (64)
T ss_pred cccccCCcCC
Confidence 5888887543
No 254
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.55 E-value=46 Score=12.24 Aligned_cols=9 Identities=22% Similarity=0.633 Sum_probs=5.1
Q ss_pred ceecccccc
Q psy4412 6 LYACLWCDY 14 (39)
Q Consensus 6 ~~~c~~c~~ 14 (39)
|-.|..|+.
T Consensus 2 p~~CpYCg~ 10 (102)
T PF11672_consen 2 PIICPYCGG 10 (102)
T ss_pred CcccCCCCC
Confidence 445666664
No 255
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=22.53 E-value=41 Score=10.25 Aligned_cols=7 Identities=29% Similarity=0.923 Sum_probs=3.5
Q ss_pred ecccccc
Q psy4412 8 ACLWCDY 14 (39)
Q Consensus 8 ~c~~c~~ 14 (39)
.|..|+.
T Consensus 2 ~C~~Cg~ 8 (45)
T cd02336 2 HCFTCGN 8 (45)
T ss_pred cccCCCC
Confidence 3555554
No 256
>PRK12860 transcriptional activator FlhC; Provisional
Probab=22.45 E-value=80 Score=13.12 Aligned_cols=10 Identities=20% Similarity=0.521 Sum_probs=4.7
Q ss_pred eccccccccc
Q psy4412 8 ACLWCDYHTL 17 (39)
Q Consensus 8 ~c~~c~~~~~ 17 (39)
.|..|+..|.
T Consensus 136 ~C~~Cgg~fv 145 (189)
T PRK12860 136 RCCRCGGKFV 145 (189)
T ss_pred cCCCCCCCee
Confidence 3455554443
No 257
>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=22.13 E-value=31 Score=13.33 Aligned_cols=11 Identities=18% Similarity=0.416 Sum_probs=7.0
Q ss_pred ecccccccccc
Q psy4412 8 ACLWCDYHTLN 18 (39)
Q Consensus 8 ~c~~c~~~~~~ 18 (39)
.|..|++.|..
T Consensus 5 nC~~CgklF~~ 15 (137)
T TIGR03826 5 NCPKCGRLFVK 15 (137)
T ss_pred cccccchhhhh
Confidence 46777776654
No 258
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=21.91 E-value=50 Score=10.51 Aligned_cols=8 Identities=38% Similarity=1.269 Sum_probs=4.9
Q ss_pred ceeccccc
Q psy4412 6 LYACLWCD 13 (39)
Q Consensus 6 ~~~c~~c~ 13 (39)
.|.|..|+
T Consensus 44 ~y~C~~Cg 51 (54)
T PF10058_consen 44 QYRCPYCG 51 (54)
T ss_pred EEEcCCCC
Confidence 36666665
No 259
>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=21.91 E-value=50 Score=10.99 Aligned_cols=7 Identities=57% Similarity=1.516 Sum_probs=3.1
Q ss_pred eeccccc
Q psy4412 7 YACLWCD 13 (39)
Q Consensus 7 ~~c~~c~ 13 (39)
+.|..|+
T Consensus 78 ~~C~~C~ 84 (85)
T PF04032_consen 78 YTCLNCG 84 (85)
T ss_dssp EEETTTT
T ss_pred EEccccC
Confidence 3444443
No 260
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.85 E-value=48 Score=12.28 Aligned_cols=12 Identities=17% Similarity=0.191 Sum_probs=8.3
Q ss_pred eecccccccccc
Q psy4412 7 YACLWCDYHTLN 18 (39)
Q Consensus 7 ~~c~~c~~~~~~ 18 (39)
..|..|+..|..
T Consensus 72 ~~C~~Cg~~~~~ 83 (117)
T PRK00564 72 LECKDCSHVFKP 83 (117)
T ss_pred EEhhhCCCcccc
Confidence 578888866544
No 261
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=21.77 E-value=52 Score=10.70 Aligned_cols=12 Identities=17% Similarity=0.205 Sum_probs=8.2
Q ss_pred ceeccccccccc
Q psy4412 6 LYACLWCDYHTL 17 (39)
Q Consensus 6 ~~~c~~c~~~~~ 17 (39)
-..|..|+..|.
T Consensus 53 ~L~Cp~c~r~YP 64 (68)
T PF03966_consen 53 ELICPECGREYP 64 (68)
T ss_dssp EEEETTTTEEEE
T ss_pred EEEcCCCCCEEe
Confidence 356788877664
No 262
>PF09665 RE_Alw26IDE: Type II restriction endonuclease (RE_Alw26IDE); InterPro: IPR014328 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family [], whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I).
Probab=21.76 E-value=43 Score=16.06 Aligned_cols=8 Identities=25% Similarity=0.526 Sum_probs=5.4
Q ss_pred cccccccc
Q psy4412 9 CLWCDYHT 16 (39)
Q Consensus 9 c~~c~~~~ 16 (39)
|..||+.+
T Consensus 85 Ck~CG~~m 92 (511)
T PF09665_consen 85 CKTCGKIM 92 (511)
T ss_pred hHhcCCee
Confidence 67777654
No 263
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=21.73 E-value=54 Score=12.06 Aligned_cols=12 Identities=17% Similarity=0.072 Sum_probs=8.2
Q ss_pred eecccccccccc
Q psy4412 7 YACLWCDYHTLN 18 (39)
Q Consensus 7 ~~c~~c~~~~~~ 18 (39)
..|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PRK12380 71 AWCWDCSQVVEI 82 (113)
T ss_pred EEcccCCCEEec
Confidence 568888866543
No 264
>PTZ00157 60S ribosomal protein L36a; Provisional
Probab=21.19 E-value=52 Score=11.73 Aligned_cols=10 Identities=20% Similarity=0.574 Sum_probs=6.9
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
+.|..|++..
T Consensus 70 l~C~~C~~~~ 79 (84)
T PTZ00157 70 LECTKCKSKR 79 (84)
T ss_pred EEecccCcee
Confidence 6788887643
No 265
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.18 E-value=50 Score=11.16 Aligned_cols=11 Identities=18% Similarity=0.459 Sum_probs=7.5
Q ss_pred eeccccccccc
Q psy4412 7 YACLWCDYHTL 17 (39)
Q Consensus 7 ~~c~~c~~~~~ 17 (39)
..|..|++...
T Consensus 8 v~CP~Cgkpv~ 18 (65)
T COG3024 8 VPCPTCGKPVV 18 (65)
T ss_pred ccCCCCCCccc
Confidence 46888887543
No 266
>KOG1813|consensus
Probab=21.06 E-value=50 Score=14.80 Aligned_cols=14 Identities=14% Similarity=0.455 Sum_probs=9.7
Q ss_pred cceecccccccccc
Q psy4412 5 YLYACLWCDYHTLN 18 (39)
Q Consensus 5 ~~~~c~~c~~~~~~ 18 (39)
.|+.|..|.+.|..
T Consensus 240 ~Pf~c~icr~~f~~ 253 (313)
T KOG1813|consen 240 LPFKCFICRKYFYR 253 (313)
T ss_pred CCcccccccccccc
Confidence 47778888776644
No 267
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=20.98 E-value=23 Score=13.71 Aligned_cols=10 Identities=30% Similarity=0.630 Sum_probs=4.7
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
|.|..|...|
T Consensus 131 ~~c~~c~epf 140 (146)
T TIGR02159 131 YRCRACKEPF 140 (146)
T ss_pred hhhhhhCCcH
Confidence 4455554444
No 268
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=20.97 E-value=49 Score=12.01 Aligned_cols=10 Identities=30% Similarity=0.717 Sum_probs=7.3
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
+.|..|++..
T Consensus 68 ~~C~~C~~~~ 77 (92)
T PRK05767 68 YRCTECGKAH 77 (92)
T ss_pred EEecccChhh
Confidence 6788888654
No 269
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=20.97 E-value=50 Score=10.23 Aligned_cols=9 Identities=22% Similarity=0.549 Sum_probs=4.9
Q ss_pred ceecccccc
Q psy4412 6 LYACLWCDY 14 (39)
Q Consensus 6 ~~~c~~c~~ 14 (39)
...|+.|+.
T Consensus 46 i~~Cp~CgR 54 (56)
T PF02591_consen 46 IVFCPNCGR 54 (56)
T ss_pred eEECcCCCc
Confidence 345666654
No 270
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=20.83 E-value=75 Score=15.04 Aligned_cols=15 Identities=13% Similarity=0.313 Sum_probs=9.5
Q ss_pred Ccceecccccccccc
Q psy4412 4 TYLYACLWCDYHTLN 18 (39)
Q Consensus 4 ~~~~~c~~c~~~~~~ 18 (39)
..-|.|..|+..+..
T Consensus 365 ~~g~rC~kCg~~~~~ 379 (421)
T COG1571 365 RNGFRCKKCGTRARE 379 (421)
T ss_pred CCCcccccccccCCc
Confidence 336778888765543
No 271
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=20.80 E-value=56 Score=10.98 Aligned_cols=15 Identities=13% Similarity=0.208 Sum_probs=9.7
Q ss_pred cceeccccccccccc
Q psy4412 5 YLYACLWCDYHTLNS 19 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~ 19 (39)
.|..|-.||+.....
T Consensus 3 iPiRCFsCGkvi~~~ 17 (63)
T COG1644 3 IPVRCFSCGKVIGHK 17 (63)
T ss_pred CceEeecCCCCHHHH
Confidence 366788888765443
No 272
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=20.78 E-value=26 Score=11.43 Aligned_cols=10 Identities=20% Similarity=0.458 Sum_probs=4.8
Q ss_pred eccccccccc
Q psy4412 8 ACLWCDYHTL 17 (39)
Q Consensus 8 ~c~~c~~~~~ 17 (39)
.|..|.+.+.
T Consensus 18 ~C~~C~k~L~ 27 (58)
T PF04570_consen 18 FCYLCKKKLD 27 (58)
T ss_pred HHHccCCCCC
Confidence 3555555443
No 273
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=20.72 E-value=61 Score=12.96 Aligned_cols=10 Identities=40% Similarity=1.029 Sum_probs=6.8
Q ss_pred ceeccccccc
Q psy4412 6 LYACLWCDYH 15 (39)
Q Consensus 6 ~~~c~~c~~~ 15 (39)
.+.|..|+..
T Consensus 28 sf~C~~CGyr 37 (163)
T TIGR00340 28 TYICEKCGYR 37 (163)
T ss_pred EEECCCCCCc
Confidence 3678888754
No 274
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 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. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=20.66 E-value=53 Score=10.85 Aligned_cols=14 Identities=14% Similarity=0.294 Sum_probs=8.6
Q ss_pred ceeccccccccccc
Q psy4412 6 LYACLWCDYHTLNS 19 (39)
Q Consensus 6 ~~~c~~c~~~~~~~ 19 (39)
+..|..||......
T Consensus 4 ~lvCSTCGrDlSee 17 (63)
T PF05864_consen 4 QLVCSTCGRDLSEE 17 (63)
T ss_pred eeeecccCCcchHH
Confidence 34677888765443
No 275
>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=20.66 E-value=33 Score=9.93 Aligned_cols=8 Identities=25% Similarity=0.493 Sum_probs=4.4
Q ss_pred eccccccc
Q psy4412 8 ACLWCDYH 15 (39)
Q Consensus 8 ~c~~c~~~ 15 (39)
.|..|+..
T Consensus 3 ~CP~Cg~~ 10 (39)
T PF01396_consen 3 KCPKCGGP 10 (39)
T ss_pred CCCCCCce
Confidence 36666643
No 276
>KOG3497|consensus
Probab=20.39 E-value=60 Score=10.85 Aligned_cols=15 Identities=13% Similarity=0.235 Sum_probs=10.0
Q ss_pred cceeccccccccccc
Q psy4412 5 YLYACLWCDYHTLNS 19 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~ 19 (39)
.|..|-.|++....+
T Consensus 3 iPiRCFtCGKvig~K 17 (69)
T KOG3497|consen 3 IPIRCFTCGKVIGDK 17 (69)
T ss_pred eeeEeeecccccccc
Confidence 466788888765544
No 277
>PRK12722 transcriptional activator FlhC; Provisional
Probab=20.36 E-value=91 Score=12.94 Aligned_cols=8 Identities=38% Similarity=0.787 Sum_probs=3.8
Q ss_pred cccccccc
Q psy4412 9 CLWCDYHT 16 (39)
Q Consensus 9 c~~c~~~~ 16 (39)
|..|+..|
T Consensus 137 C~~Cgg~f 144 (187)
T PRK12722 137 CNCCGGHF 144 (187)
T ss_pred CCCCCCCe
Confidence 44455444
No 278
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=20.30 E-value=36 Score=14.00 Aligned_cols=15 Identities=13% Similarity=0.184 Sum_probs=9.6
Q ss_pred cceeccccccccccc
Q psy4412 5 YLYACLWCDYHTLNS 19 (39)
Q Consensus 5 ~~~~c~~c~~~~~~~ 19 (39)
++-.|..|+..|...
T Consensus 5 k~rKCKvCg~~F~P~ 19 (189)
T PF05766_consen 5 KRRKCKVCGEWFVPA 19 (189)
T ss_pred CCCcCcccCCccccC
Confidence 345677888777543
No 279
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.13 E-value=62 Score=13.46 Aligned_cols=10 Identities=50% Similarity=1.232 Sum_probs=7.2
Q ss_pred eecccccccc
Q psy4412 7 YACLWCDYHT 16 (39)
Q Consensus 7 ~~c~~c~~~~ 16 (39)
|.|..|.++.
T Consensus 50 YkC~~Cd~tW 59 (203)
T COG4332 50 YKCTHCDYTW 59 (203)
T ss_pred EEeeccCCcc
Confidence 7788887654
No 280
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=20.00 E-value=61 Score=11.43 Aligned_cols=9 Identities=44% Similarity=1.165 Sum_probs=4.5
Q ss_pred eeccccccc
Q psy4412 7 YACLWCDYH 15 (39)
Q Consensus 7 ~~c~~c~~~ 15 (39)
|.|..|+..
T Consensus 91 y~C~~C~~~ 99 (104)
T TIGR01384 91 YKCTKCGYV 99 (104)
T ss_pred EEeCCCCCe
Confidence 455555543
Done!