Query psy9655
Match_columns 96
No_of_seqs 195 out of 1455
Neff 9.4
Searched_HMMs 46136
Date Sat Aug 17 01:13:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9655.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9655hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.5 1.3E-14 2.8E-19 94.3 3.0 62 35-96 188-249 (279)
2 KOG2462|consensus 99.4 2.5E-14 5.5E-19 93.0 0.9 54 41-96 168-221 (279)
3 KOG3623|consensus 99.3 1.7E-13 3.7E-18 98.6 -1.4 60 37-96 897-956 (1007)
4 KOG3623|consensus 99.1 4.3E-11 9.4E-16 86.5 1.1 39 58-96 277-315 (1007)
5 PHA02768 hypothetical protein; 99.0 1.3E-10 2.9E-15 59.0 1.6 32 63-96 6-37 (55)
6 PF13465 zf-H2C2_2: Zinc-finge 98.9 8.2E-10 1.8E-14 48.3 2.0 20 77-96 1-20 (26)
7 PHA00616 hypothetical protein 98.9 5.2E-10 1.1E-14 54.3 1.3 34 62-95 1-34 (44)
8 KOG3576|consensus 98.9 1.8E-10 3.9E-15 72.7 -1.3 40 57-96 140-179 (267)
9 KOG1074|consensus 98.6 1.1E-08 2.5E-13 75.0 1.4 35 62-96 353-387 (958)
10 KOG1074|consensus 98.5 2.4E-08 5.3E-13 73.4 0.9 40 49-88 620-659 (958)
11 PF00096 zf-C2H2: Zinc finger, 98.2 5.9E-07 1.3E-11 37.7 1.3 23 63-85 1-23 (23)
12 PHA00733 hypothetical protein 98.1 2.4E-06 5.1E-11 50.9 2.3 37 58-96 69-105 (128)
13 PHA00732 hypothetical protein 97.9 6.7E-06 1.4E-10 45.0 1.5 32 62-96 1-33 (79)
14 KOG3576|consensus 97.9 6.8E-06 1.5E-10 52.3 1.6 57 40-96 151-218 (267)
15 PF13465 zf-H2C2_2: Zinc-finge 97.7 2.8E-06 6E-11 36.9 -1.2 22 53-74 5-26 (26)
16 PF13894 zf-C2H2_4: C2H2-type 97.7 1.9E-05 4.1E-10 32.9 1.4 23 63-85 1-23 (24)
17 PF13912 zf-C2H2_6: C2H2-type 97.7 2.4E-05 5.1E-10 34.0 1.2 25 62-86 1-25 (27)
18 PRK04860 hypothetical protein; 97.6 4E-05 8.6E-10 47.3 2.4 32 61-96 118-149 (160)
19 smart00355 ZnF_C2H2 zinc finge 97.4 7.5E-05 1.6E-09 31.4 1.2 25 63-87 1-25 (26)
20 PF09237 GAGA: GAGA factor; I 97.4 0.00024 5.2E-09 35.5 2.8 36 55-90 17-52 (54)
21 PF05605 zf-Di19: Drought indu 97.2 0.00027 5.8E-09 35.8 1.9 34 62-96 2-37 (54)
22 KOG3608|consensus 97.1 0.00025 5.5E-09 48.6 1.9 34 63-96 264-298 (467)
23 PF12874 zf-met: Zinc-finger o 96.9 0.00045 9.8E-09 29.2 1.0 23 63-85 1-23 (25)
24 PLN03086 PRLI-interacting fact 96.9 0.00067 1.4E-08 49.2 2.3 47 49-96 491-547 (567)
25 PLN03086 PRLI-interacting fact 96.9 0.00061 1.3E-08 49.4 1.9 34 61-96 477-510 (567)
26 COG5189 SFP1 Putative transcri 96.4 0.0021 4.6E-08 43.6 2.0 37 60-96 347-404 (423)
27 PF12171 zf-C2H2_jaz: Zinc-fin 96.3 0.00075 1.6E-08 29.2 -0.4 22 63-84 2-23 (27)
28 PF13909 zf-H2C2_5: C2H2-type 96.3 0.0027 5.8E-08 26.5 1.3 22 63-85 1-22 (24)
29 PHA02768 hypothetical protein; 95.6 0.0011 2.4E-08 33.8 -1.7 41 37-79 8-48 (55)
30 KOG3608|consensus 95.6 0.0078 1.7E-07 41.6 1.8 40 55-95 285-324 (467)
31 PHA00733 hypothetical protein 95.2 0.0087 1.9E-07 35.6 0.9 47 37-85 76-122 (128)
32 PF13913 zf-C2HC_2: zinc-finge 94.7 0.018 3.9E-07 24.5 1.0 21 63-84 3-23 (25)
33 smart00451 ZnF_U1 U1-like zinc 94.2 0.03 6.6E-07 25.2 1.3 23 62-84 3-25 (35)
34 COG5189 SFP1 Putative transcri 93.8 0.045 9.8E-07 37.4 2.0 28 55-82 391-418 (423)
35 PF12756 zf-C2H2_2: C2H2 type 93.7 0.046 1E-06 30.2 1.6 24 62-85 50-73 (100)
36 cd00350 rubredoxin_like Rubred 93.3 0.061 1.3E-06 24.3 1.4 22 63-96 2-23 (33)
37 KOG3993|consensus 93.0 0.033 7.2E-07 39.3 0.4 25 62-86 356-380 (500)
38 KOG2893|consensus 90.9 0.099 2.1E-06 34.5 0.8 28 65-96 13-40 (341)
39 COG1592 Rubrerythrin [Energy p 90.6 0.17 3.6E-06 31.6 1.5 22 62-96 134-155 (166)
40 KOG3993|consensus 90.4 0.13 2.7E-06 36.5 1.0 25 62-86 295-319 (500)
41 COG5048 FOG: Zn-finger [Genera 89.0 0.38 8.3E-06 32.8 2.5 38 56-93 313-354 (467)
42 cd00729 rubredoxin_SM Rubredox 87.1 0.44 9.6E-06 21.7 1.3 12 62-73 2-13 (34)
43 COG4049 Uncharacterized protei 87.1 0.37 8.1E-06 24.6 1.1 27 57-83 12-38 (65)
44 COG5048 FOG: Zn-finger [Genera 86.8 0.23 4.9E-06 33.9 0.3 34 61-94 288-325 (467)
45 PF02892 zf-BED: BED zinc fing 85.9 0.73 1.6E-05 21.9 1.8 24 60-83 14-41 (45)
46 PF05443 ROS_MUCR: ROS/MUCR tr 85.7 0.49 1.1E-05 28.4 1.3 27 61-90 71-97 (132)
47 smart00614 ZnF_BED BED zinc fi 85.0 0.76 1.7E-05 22.6 1.6 25 62-86 18-48 (50)
48 KOG4167|consensus 80.3 0.5 1.1E-05 35.8 -0.2 25 62-86 792-816 (907)
49 KOG3408|consensus 79.9 1.3 2.8E-05 26.2 1.5 29 56-84 51-79 (129)
50 smart00531 TFIIE Transcription 77.8 2.7 5.9E-05 25.4 2.5 34 59-96 96-129 (147)
51 COG4957 Predicted transcriptio 77.7 1.5 3.3E-05 26.4 1.3 25 63-90 77-101 (148)
52 PF09538 FYDLN_acid: Protein o 77.2 1.5 3.3E-05 25.4 1.3 14 62-75 26-39 (108)
53 TIGR00373 conserved hypothetic 74.7 1.5 3.3E-05 27.0 0.8 29 59-96 106-134 (158)
54 PRK06266 transcription initiat 74.3 1.5 3.2E-05 27.6 0.7 28 60-96 115-142 (178)
55 TIGR02605 CxxC_CxxC_SSSS putat 73.4 1.2 2.6E-05 21.8 0.2 11 63-73 6-16 (52)
56 PF09723 Zn-ribbon_8: Zinc rib 73.1 0.8 1.7E-05 21.7 -0.5 13 63-75 6-18 (42)
57 smart00659 RPOLCX RNA polymera 71.7 3.1 6.7E-05 20.0 1.4 11 63-73 3-13 (44)
58 smart00834 CxxC_CXXC_SSSS Puta 71.3 1.4 3.1E-05 20.3 0.1 12 63-74 6-17 (41)
59 KOG2482|consensus 71.0 3.1 6.7E-05 29.1 1.7 23 62-84 195-217 (423)
60 PF08790 zf-LYAR: LYAR-type C2 69.8 1.7 3.6E-05 19.0 0.2 20 63-83 1-20 (28)
61 PF04959 ARS2: Arsenite-resist 69.5 2.6 5.7E-05 27.3 1.1 24 61-84 76-99 (214)
62 TIGR02300 FYDLN_acid conserved 67.4 3.5 7.7E-05 24.6 1.3 18 61-78 25-42 (129)
63 PRK14890 putative Zn-ribbon RN 66.6 4.5 9.8E-05 20.8 1.4 29 62-96 25-54 (59)
64 PF12013 DUF3505: Protein of u 65.5 4.6 0.0001 23.0 1.5 25 62-86 80-108 (109)
65 PF15269 zf-C2H2_7: Zinc-finge 64.2 7.9 0.00017 18.9 1.9 23 62-84 20-42 (54)
66 PRK00398 rpoP DNA-directed RNA 64.1 2.9 6.3E-05 20.1 0.4 8 63-70 22-29 (46)
67 COG3357 Predicted transcriptio 63.8 2.9 6.2E-05 23.5 0.4 26 61-96 57-82 (97)
68 COG1996 RPC10 DNA-directed RNA 63.4 4.1 9E-05 20.2 0.9 11 62-72 6-16 (49)
69 COG2888 Predicted Zn-ribbon RN 61.3 6.3 0.00014 20.4 1.3 30 62-96 27-56 (61)
70 PRK03824 hypA hydrogenase nick 59.5 4.1 9E-05 24.4 0.6 15 61-75 69-83 (135)
71 PF13719 zinc_ribbon_5: zinc-r 59.4 6.9 0.00015 17.9 1.2 12 64-75 4-15 (37)
72 KOG2593|consensus 57.4 8.2 0.00018 27.7 1.8 36 58-96 124-159 (436)
73 PHA00626 hypothetical protein 57.1 6.1 0.00013 20.2 0.9 15 61-75 22-36 (59)
74 PF10571 UPF0547: Uncharacteri 56.7 4.6 0.0001 17.2 0.3 11 63-73 15-25 (26)
75 COG5112 UFD2 U1-like Zn-finger 55.9 7.8 0.00017 22.5 1.3 29 55-83 48-76 (126)
76 COG1655 Uncharacterized protei 55.9 2.6 5.6E-05 27.8 -0.7 28 61-88 18-45 (267)
77 KOG1146|consensus 55.0 5.5 0.00012 32.5 0.7 27 58-84 461-487 (1406)
78 PF14311 DUF4379: Domain of un 54.1 9.6 0.00021 18.9 1.3 27 63-96 29-55 (55)
79 COG1773 Rubredoxin [Energy pro 54.0 5.8 0.00013 20.2 0.5 16 62-77 3-18 (55)
80 smart00734 ZnF_Rad18 Rad18-lik 53.9 8.3 0.00018 16.3 0.9 20 63-83 2-21 (26)
81 PF05191 ADK_lid: Adenylate ki 51.1 7.5 0.00016 17.8 0.6 11 63-73 2-12 (36)
82 PF13878 zf-C2H2_3: zinc-finge 49.1 11 0.00025 17.7 1.1 24 63-86 14-39 (41)
83 PF07754 DUF1610: Domain of un 49.0 8.2 0.00018 16.2 0.5 9 62-70 16-24 (24)
84 PF13451 zf-trcl: Probable zin 48.1 12 0.00027 18.5 1.1 35 61-96 3-39 (49)
85 TIGR02098 MJ0042_CXXC MJ0042 f 46.9 14 0.0003 16.7 1.2 13 63-75 3-15 (38)
86 TIGR00100 hypA hydrogenase nic 46.7 11 0.00024 21.9 1.0 12 63-74 71-82 (115)
87 PF02176 zf-TRAF: TRAF-type zi 46.2 20 0.00042 17.7 1.8 35 61-95 8-43 (60)
88 PF12760 Zn_Tnp_IS1595: Transp 44.9 5.4 0.00012 19.1 -0.5 9 63-71 19-27 (46)
89 smart00154 ZnF_AN1 AN1-like Zi 44.8 11 0.00024 17.5 0.7 15 62-76 12-26 (39)
90 PF04780 DUF629: Protein of un 44.4 13 0.00028 27.1 1.2 33 56-88 51-84 (466)
91 COG3091 SprT Zn-dependent meta 43.1 12 0.00026 23.1 0.7 32 60-96 115-146 (156)
92 PF09986 DUF2225: Uncharacteri 43.0 10 0.00023 24.4 0.5 23 61-83 4-26 (214)
93 KOG1994|consensus 42.9 12 0.00026 24.7 0.8 21 62-82 239-259 (268)
94 PF09963 DUF2197: Uncharacteri 42.8 14 0.00031 18.8 0.9 8 63-70 32-39 (56)
95 KOG2186|consensus 42.2 19 0.0004 24.2 1.6 30 53-84 21-50 (276)
96 KOG2071|consensus 41.8 18 0.00038 27.1 1.5 27 60-86 416-442 (579)
97 PF10071 DUF2310: Zn-ribbon-co 41.5 13 0.00028 25.0 0.7 28 62-96 220-247 (258)
98 PF10013 DUF2256: Uncharacteri 41.1 8.8 0.00019 18.4 -0.0 15 64-78 10-24 (42)
99 PF00301 Rubredoxin: Rubredoxi 41.1 11 0.00024 18.4 0.3 15 63-77 2-16 (47)
100 PRK12380 hydrogenase nickel in 40.8 17 0.00036 21.1 1.1 12 63-74 71-82 (113)
101 PF01927 Mut7-C: Mut7-C RNAse 39.8 22 0.00049 21.4 1.6 21 61-81 123-143 (147)
102 PRK00564 hypA hydrogenase nick 39.4 17 0.00037 21.2 1.0 12 63-74 72-83 (117)
103 PF12907 zf-met2: Zinc-binding 38.9 13 0.00029 17.5 0.4 31 63-93 2-36 (40)
104 TIGR00622 ssl1 transcription f 38.1 33 0.00071 20.1 2.0 26 61-86 80-105 (112)
105 PF01428 zf-AN1: AN1-like Zinc 38.0 12 0.00026 17.6 0.2 16 61-76 12-27 (43)
106 KOG0717|consensus 37.9 16 0.00034 26.7 0.8 21 63-83 293-313 (508)
107 COG3677 Transposase and inacti 37.5 17 0.00036 21.7 0.8 20 57-76 48-67 (129)
108 PF09845 DUF2072: Zn-ribbon co 37.3 16 0.00034 22.0 0.6 15 62-76 1-15 (131)
109 KOG2636|consensus 36.9 23 0.0005 25.7 1.5 26 57-82 396-422 (497)
110 PF03604 DNA_RNApol_7kD: DNA d 36.0 33 0.00073 15.2 1.5 8 63-70 18-25 (32)
111 cd00730 rubredoxin Rubredoxin; 36.0 13 0.00029 18.4 0.2 13 63-75 2-14 (50)
112 PF14599 zinc_ribbon_6: Zinc-r 34.6 10 0.00022 19.6 -0.4 19 63-81 31-49 (61)
113 PRK03681 hypA hydrogenase nick 34.5 18 0.00038 21.0 0.5 11 63-73 71-81 (114)
114 PF14787 zf-CCHC_5: GAG-polypr 34.1 18 0.00039 16.7 0.4 17 63-79 3-19 (36)
115 PRK00464 nrdR transcriptional 34.0 15 0.00033 22.6 0.2 17 62-78 28-44 (154)
116 PF08209 Sgf11: Sgf11 (transcr 33.4 34 0.00073 15.4 1.3 21 62-83 4-24 (33)
117 PRK12860 transcriptional activ 32.2 28 0.00061 22.3 1.2 26 63-96 135-160 (189)
118 KOG2231|consensus 31.5 22 0.00047 27.2 0.7 31 63-96 100-146 (669)
119 PF04423 Rad50_zn_hook: Rad50 31.2 19 0.00042 17.7 0.3 12 64-75 22-33 (54)
120 PRK12722 transcriptional activ 30.3 32 0.00069 22.0 1.2 10 64-73 136-145 (187)
121 PLN02748 tRNA dimethylallyltra 30.1 30 0.00064 25.3 1.2 25 59-83 415-440 (468)
122 cd00924 Cyt_c_Oxidase_Vb Cytoc 29.9 26 0.00057 19.9 0.7 17 57-74 75-91 (97)
123 PRK01343 zinc-binding protein; 29.4 47 0.001 17.0 1.5 12 62-73 9-20 (57)
124 KOG1842|consensus 29.2 28 0.0006 25.4 0.9 28 61-88 14-42 (505)
125 PF01155 HypA: Hydrogenase exp 29.0 18 0.00039 20.9 -0.1 13 62-74 70-82 (113)
126 PF13717 zinc_ribbon_4: zinc-r 28.8 35 0.00075 15.5 0.9 15 59-73 22-36 (36)
127 PTZ00448 hypothetical protein; 28.6 31 0.00066 24.5 1.0 23 62-84 314-336 (373)
128 PLN03238 probable histone acet 28.5 52 0.0011 22.6 2.0 25 60-84 46-70 (290)
129 PF14353 CpXC: CpXC protein 28.3 11 0.00023 22.1 -1.1 20 62-81 38-57 (128)
130 PRK00762 hypA hydrogenase nick 28.3 30 0.00064 20.4 0.8 13 62-75 70-82 (124)
131 KOG1818|consensus 28.2 20 0.00043 27.2 0.1 36 61-96 180-217 (634)
132 PF06220 zf-U1: U1 zinc finger 27.3 42 0.0009 15.5 1.0 15 61-75 2-16 (38)
133 PF02148 zf-UBP: Zn-finger in 27.0 36 0.00078 17.3 0.9 24 60-83 9-35 (63)
134 PRK04351 hypothetical protein; 26.9 35 0.00076 20.8 1.0 27 62-96 112-138 (149)
135 PF10276 zf-CHCC: Zinc-finger 26.6 31 0.00067 16.2 0.5 12 61-72 28-39 (40)
136 PF03811 Zn_Tnp_IS1: InsA N-te 26.4 65 0.0014 14.7 1.6 17 52-68 19-35 (36)
137 PF01096 TFIIS_C: Transcriptio 26.3 28 0.0006 16.1 0.3 11 62-72 28-38 (39)
138 PLN02294 cytochrome c oxidase 26.1 34 0.00073 21.6 0.8 16 60-75 139-154 (174)
139 PRK05452 anaerobic nitric oxid 25.6 34 0.00074 24.9 0.9 19 58-76 421-439 (479)
140 PF11931 DUF3449: Domain of un 25.3 24 0.00051 22.7 0.0 23 60-82 99-122 (196)
141 PF11672 DUF3268: Protein of u 24.5 32 0.0007 19.7 0.4 7 63-69 32-38 (102)
142 COG3364 Zn-ribbon containing p 24.1 41 0.00089 19.4 0.8 15 62-76 2-16 (112)
143 PLN00104 MYST -like histone ac 24.1 55 0.0012 23.9 1.6 23 61-83 197-219 (450)
144 PF06397 Desulfoferrod_N: Desu 23.9 39 0.00086 15.5 0.6 12 61-72 5-16 (36)
145 COG4338 Uncharacterized protei 23.8 17 0.00036 18.0 -0.7 15 63-77 13-27 (54)
146 PF07975 C1_4: TFIIH C1-like d 23.7 15 0.00033 18.3 -0.8 25 61-85 20-44 (51)
147 TIGR00382 clpX endopeptidase C 23.3 40 0.00086 24.2 0.8 10 64-73 9-18 (413)
148 COG1675 TFA1 Transcription ini 23.3 44 0.00095 21.1 0.9 14 60-73 111-124 (176)
149 KOG4727|consensus 23.2 41 0.00088 21.3 0.7 21 62-82 75-95 (193)
150 PF10263 SprT-like: SprT-like 21.9 42 0.00092 20.0 0.7 28 61-96 122-149 (157)
151 PF07282 OrfB_Zn_ribbon: Putat 21.5 50 0.0011 16.8 0.8 15 59-73 43-57 (69)
152 PTZ00064 histone acetyltransfe 21.5 73 0.0016 23.8 1.8 24 61-84 279-302 (552)
153 COG1656 Uncharacterized conser 21.3 66 0.0014 20.2 1.4 23 61-83 129-151 (165)
154 PF02748 PyrI_C: Aspartate car 21.1 51 0.0011 16.4 0.7 16 58-73 31-46 (52)
155 PF08792 A2L_zn_ribbon: A2L zi 21.0 44 0.00095 14.9 0.4 12 62-73 21-32 (33)
156 smart00440 ZnF_C2C2 C2C2 Zinc 20.8 48 0.001 15.3 0.6 12 62-73 28-39 (40)
157 COG5188 PRP9 Splicing factor 3 20.7 54 0.0012 23.3 1.0 23 61-83 237-259 (470)
158 PF12230 PRP21_like_P: Pre-mRN 20.4 34 0.00073 22.2 0.0 31 60-91 166-196 (229)
159 PLN03239 histone acetyltransfe 20.4 62 0.0013 22.8 1.2 23 61-83 105-127 (351)
160 COG4896 Uncharacterized protei 20.3 68 0.0015 16.7 1.1 17 59-75 28-44 (68)
No 1
>KOG2462|consensus
Probab=99.49 E-value=1.3e-14 Score=94.29 Aligned_cols=62 Identities=19% Similarity=0.198 Sum_probs=53.0
Q ss_pred ccCCCCCCCCCCCCCCCcCCCCCCCCCceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 35 ENGQNQIVSEPPTDRTVSYNRPVPPNPSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 35 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
.++....+.+...+.+..|.++|+|+|||.|..|+|+|..+++|+.|+++|.+.|+|+|..|
T Consensus 188 c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C 249 (279)
T KOG2462|consen 188 CECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRC 249 (279)
T ss_pred cccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcch
Confidence 34455677888888888889999999999999999999999999999999999999999877
No 2
>KOG2462|consensus
Probab=99.43 E-value=2.5e-14 Score=92.96 Aligned_cols=54 Identities=28% Similarity=0.316 Sum_probs=43.5
Q ss_pred CCCCCCCCCCCcCCCCCCCCCceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 41 IVSEPPTDRTVSYNRPVPPNPSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 41 ~~~~~~~~~~~~~~~~~~~~~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
.+....-..+..|.++|+ -++.|.+|||.|.+++-|+.|+|+|||||||.|.+|
T Consensus 168 ~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC 221 (279)
T KOG2462|consen 168 GKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHC 221 (279)
T ss_pred CceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcc
Confidence 333444445555666666 358899999999999999999999999999999998
No 3
>KOG3623|consensus
Probab=99.30 E-value=1.7e-13 Score=98.60 Aligned_cols=60 Identities=23% Similarity=0.346 Sum_probs=55.1
Q ss_pred CCCCCCCCCCCCCCCcCCCCCCCCCceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 37 GQNQIVSEPPTDRTVSYNRPVPPNPSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
++.+.+.+..++.+..|+--|+|.+||.|.+|.|+|+.+.+|..|+|.|.|||||.|+.|
T Consensus 897 CDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKC 956 (1007)
T KOG3623|consen 897 CDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKC 956 (1007)
T ss_pred HHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhh
Confidence 344567788888889999999999999999999999999999999999999999999988
No 4
>KOG3623|consensus
Probab=99.05 E-value=4.3e-11 Score=86.50 Aligned_cols=39 Identities=36% Similarity=0.668 Sum_probs=36.3
Q ss_pred CCCCceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 58 PPNPSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 58 ~~~~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
...+.|.|..|+|+|+.+.+|+.|+|+|.|||||.|+-|
T Consensus 277 a~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnC 315 (1007)
T KOG3623|consen 277 ALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNC 315 (1007)
T ss_pred hhhccccccccchhhhhHHHHHhhheeecCCCCcCCccc
Confidence 345779999999999999999999999999999999987
No 5
>PHA02768 hypothetical protein; Provisional
Probab=99.01 E-value=1.3e-10 Score=58.99 Aligned_cols=32 Identities=25% Similarity=0.642 Sum_probs=29.3
Q ss_pred eecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
|.|..||+.|....+|..|+++|+ +||+|..|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C 37 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNC 37 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcc
Confidence 899999999999999999999999 67777665
No 6
>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=98.91 E-value=8.2e-10 Score=48.26 Aligned_cols=20 Identities=50% Similarity=0.853 Sum_probs=18.8
Q ss_pred hHHHHHhhhCCCCCcccccC
Q psy9655 77 DLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 77 ~l~~h~~~htgekp~~C~~C 96 (96)
+|..|+++|+|+|||+|+.|
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C 20 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYC 20 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSS
T ss_pred CHHHHhhhcCCCCCCCCCCC
Confidence 58899999999999999998
No 7
>PHA00616 hypothetical protein
Probab=98.91 E-value=5.2e-10 Score=54.34 Aligned_cols=34 Identities=21% Similarity=0.504 Sum_probs=31.9
Q ss_pred ceecccchhhccCCchHHHHHhhhCCCCCccccc
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRS 95 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~ 95 (96)
+|.|..||+.|..++.|..|++.|+|++||.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 5899999999999999999999999999999863
No 8
>KOG3576|consensus
Probab=98.87 E-value=1.8e-10 Score=72.69 Aligned_cols=40 Identities=33% Similarity=0.630 Sum_probs=34.8
Q ss_pred CCCCCceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 57 VPPNPSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 57 ~~~~~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
|..-+.|.|..|||.|..-.+|++|+|+|||.|||+|..|
T Consensus 140 h~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c 179 (267)
T KOG3576|consen 140 HSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLC 179 (267)
T ss_pred ccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhh
Confidence 4445567788899999999999999999999999999987
No 9
>KOG1074|consensus
Probab=98.62 E-value=1.1e-08 Score=75.03 Aligned_cols=35 Identities=37% Similarity=0.786 Sum_probs=32.8
Q ss_pred ceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
++.|.+|.|.|...+.|+.|+|.|||||||+|.+|
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvC 387 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVC 387 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhccCCCCCeeeccc
Confidence 47799999999999999999999999999999988
No 10
>KOG1074|consensus
Probab=98.53 E-value=2.4e-08 Score=73.38 Aligned_cols=40 Identities=23% Similarity=0.463 Sum_probs=26.0
Q ss_pred CCCcCCCCCCCCCceecccchhhccCCchHHHHHhhhCCC
Q psy9655 49 RTVSYNRPVPPNPSLSCTYCSRAFKKRSDLTRHIRSHTKE 88 (96)
Q Consensus 49 ~~~~~~~~~~~~~~~~C~~C~k~f~~~~~l~~h~~~htge 88 (96)
.+..|-++|+|+++|.|.+||++|.++.+|+.|+.+|.-.
T Consensus 620 aLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~ 659 (958)
T KOG1074|consen 620 ALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAK 659 (958)
T ss_pred hhhhhhhcccCcCccccccccchhccccchhhcccccccC
Confidence 3445556667777777777777777777777776666543
No 11
>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=98.23 E-value=5.9e-07 Score=37.74 Aligned_cols=23 Identities=39% Similarity=0.996 Sum_probs=21.6
Q ss_pred eecccchhhccCCchHHHHHhhh
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIRSH 85 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~~h 85 (96)
|.|..|++.|..+..|..|++.|
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 78999999999999999999876
No 12
>PHA00733 hypothetical protein
Probab=98.08 E-value=2.4e-06 Score=50.88 Aligned_cols=37 Identities=22% Similarity=0.341 Sum_probs=32.6
Q ss_pred CCCCceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 58 PPNPSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 58 ~~~~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
.+.++|.|..|++.|.....|..|++.| +.+|.|..|
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~C 105 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVC 105 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCC
Confidence 3477899999999999999999999987 468999987
No 13
>PHA00732 hypothetical protein
Probab=97.88 E-value=6.7e-06 Score=45.03 Aligned_cols=32 Identities=25% Similarity=0.337 Sum_probs=26.9
Q ss_pred ceecccchhhccCCchHHHHHh-hhCCCCCcccccC
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIR-SHTKEKPFKVRSL 96 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~-~htgekp~~C~~C 96 (96)
+|.|..|++.|....+|+.|++ .|++ +.|+.|
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~C 33 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVC 33 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCC
Confidence 4789999999999999999998 4764 578877
No 14
>KOG3576|consensus
Probab=97.87 E-value=6.8e-06 Score=52.29 Aligned_cols=57 Identities=19% Similarity=0.283 Sum_probs=47.0
Q ss_pred CCCCCCCCCCCCcCCCCCCCCCceecccchhhccCCchHHHHHhh-hC----------CCCCcccccC
Q psy9655 40 QIVSEPPTDRTVSYNRPVPPNPSLSCTYCSRAFKKRSDLTRHIRS-HT----------KEKPFKVRSL 96 (96)
Q Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~k~f~~~~~l~~h~~~-ht----------gekp~~C~~C 96 (96)
+.+.+...-..+.+.++|+|-+||.|..|+|+|.+.-.|..|.+. |. .+|-|.|..|
T Consensus 151 cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedc 218 (267)
T KOG3576|consen 151 CGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDC 218 (267)
T ss_pred ccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeeccc
Confidence 456666777888999999999999999999999999999999863 53 2566788776
No 15
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=97.74 E-value=2.8e-06 Score=36.90 Aligned_cols=22 Identities=23% Similarity=0.617 Sum_probs=18.9
Q ss_pred CCCCCCCCCceecccchhhccC
Q psy9655 53 YNRPVPPNPSLSCTYCSRAFKK 74 (96)
Q Consensus 53 ~~~~~~~~~~~~C~~C~k~f~~ 74 (96)
+.+.|+++++|.|..|++.|..
T Consensus 5 H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 5 HMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHSSSSSEEESSSSEEESS
T ss_pred HhhhcCCCCCCCCCCCcCeeCc
Confidence 4567899999999999999963
No 16
>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=97.72 E-value=1.9e-05 Score=32.92 Aligned_cols=23 Identities=35% Similarity=1.045 Sum_probs=19.5
Q ss_pred eecccchhhccCCchHHHHHhhh
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIRSH 85 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~~h 85 (96)
|.|..|++.|.....|..|++.|
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 78999999999999999999875
No 17
>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=97.66 E-value=2.4e-05 Score=33.97 Aligned_cols=25 Identities=36% Similarity=0.720 Sum_probs=23.0
Q ss_pred ceecccchhhccCCchHHHHHhhhC
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRSHT 86 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~ht 86 (96)
+|.|..|++.|.....|..|++.|-
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 5899999999999999999998874
No 18
>PRK04860 hypothetical protein; Provisional
Probab=97.64 E-value=4e-05 Score=47.26 Aligned_cols=32 Identities=22% Similarity=0.441 Sum_probs=28.9
Q ss_pred CceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
-+|.|. |+. ....+..|.++|+|+++|.|..|
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C 149 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRC 149 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCC
Confidence 469998 998 67889999999999999999988
No 19
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.43 E-value=7.5e-05 Score=31.43 Aligned_cols=25 Identities=36% Similarity=0.789 Sum_probs=22.3
Q ss_pred eecccchhhccCCchHHHHHhhhCC
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIRSHTK 87 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~~htg 87 (96)
|.|..|++.|.....|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 5799999999999999999998753
No 20
>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=97.38 E-value=0.00024 Score=35.48 Aligned_cols=36 Identities=19% Similarity=0.501 Sum_probs=25.4
Q ss_pred CCCCCCCceecccchhhccCCchHHHHHhhhCCCCC
Q psy9655 55 RPVPPNPSLSCTYCSRAFKKRSDLTRHIRSHTKEKP 90 (96)
Q Consensus 55 ~~~~~~~~~~C~~C~k~f~~~~~l~~h~~~htgekp 90 (96)
..+....+-.|+.|+..+.+..+|++|+.++-+.||
T Consensus 17 ~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 17 SKSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CCCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred HhhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 344567789999999999999999999988777776
No 21
>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=97.20 E-value=0.00027 Score=35.80 Aligned_cols=34 Identities=29% Similarity=0.497 Sum_probs=26.5
Q ss_pred ceecccchhhccCCchHHHHHhh-hCCC-CCcccccC
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRS-HTKE-KPFKVRSL 96 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~-htge-kp~~C~~C 96 (96)
.|.|++|++ ......|..|... |.++ +.+.|++|
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC 37 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPIC 37 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCc
Confidence 389999999 4556789999754 7765 57899988
No 22
>KOG3608|consensus
Probab=97.15 E-value=0.00025 Score=48.60 Aligned_cols=34 Identities=41% Similarity=0.745 Sum_probs=17.8
Q ss_pred eecccchhhccCCchHHHHHhh-hCCCCCcccccC
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIRS-HTKEKPFKVRSL 96 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~~-htgekp~~C~~C 96 (96)
|.|+.|.-.....+.|..|++. |...|||+|+.|
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~C 298 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDEC 298 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCCccccch
Confidence 3344444444444455555543 555677777665
No 23
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.92 E-value=0.00045 Score=29.21 Aligned_cols=23 Identities=30% Similarity=0.836 Sum_probs=21.0
Q ss_pred eecccchhhccCCchHHHHHhhh
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIRSH 85 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~~h 85 (96)
|.|..|++.|.....+..|++.+
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 68999999999999999999764
No 24
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.90 E-value=0.00067 Score=49.23 Aligned_cols=47 Identities=13% Similarity=0.256 Sum_probs=26.7
Q ss_pred CCCcCCCCCCCCCceecccchhhccC----------CchHHHHHhhhCCCCCcccccC
Q psy9655 49 RTVSYNRPVPPNPSLSCTYCSRAFKK----------RSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 49 ~~~~~~~~~~~~~~~~C~~C~k~f~~----------~~~l~~h~~~htgekp~~C~~C 96 (96)
....|...|.+.+++.|.+|++.|.. .+.|..|..++ |.+++.|..|
T Consensus 491 ~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~C 547 (567)
T PLN03086 491 QMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSC 547 (567)
T ss_pred HHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEcccc
Confidence 33444455556666666666666631 23566666553 6666666655
No 25
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.87 E-value=0.00061 Score=49.43 Aligned_cols=34 Identities=18% Similarity=0.397 Sum_probs=27.5
Q ss_pred CceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
+++.|. |++.+ .+..|..|+++|.+++|+.|..|
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC 510 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFC 510 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCC
Confidence 567788 88654 56788888888999999999887
No 26
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.41 E-value=0.0021 Score=43.64 Aligned_cols=37 Identities=24% Similarity=0.671 Sum_probs=30.9
Q ss_pred CCceeccc--chhhccCCchHHHHHhh-h------------------CCCCCcccccC
Q psy9655 60 NPSLSCTY--CSRAFKKRSDLTRHIRS-H------------------TKEKPFKVRSL 96 (96)
Q Consensus 60 ~~~~~C~~--C~k~f~~~~~l~~h~~~-h------------------tgekp~~C~~C 96 (96)
+|+|.|++ |.|.|+....|+-|+.. | ...|||.|+.|
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC 404 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVC 404 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceecccc
Confidence 48999998 99999999999999753 3 12489999988
No 27
>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=96.31 E-value=0.00075 Score=29.21 Aligned_cols=22 Identities=27% Similarity=0.762 Sum_probs=20.2
Q ss_pred eecccchhhccCCchHHHHHhh
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIRS 84 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~~ 84 (96)
|.|..|++.|.....+..|++.
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 7899999999999999999864
No 28
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.27 E-value=0.0027 Score=26.54 Aligned_cols=22 Identities=36% Similarity=0.812 Sum_probs=17.6
Q ss_pred eecccchhhccCCchHHHHHhhh
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIRSH 85 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~~h 85 (96)
|.|..|++... +..|..|++.|
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 78999999888 88999999874
No 29
>PHA02768 hypothetical protein; Provisional
Probab=95.61 E-value=0.0011 Score=33.76 Aligned_cols=41 Identities=10% Similarity=-0.014 Sum_probs=33.2
Q ss_pred CCCCCCCCCCCCCCCcCCCCCCCCCceecccchhhccCCchHH
Q psy9655 37 GQNQIVSEPPTDRTVSYNRPVPPNPSLSCTYCSRAFKKRSDLT 79 (96)
Q Consensus 37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~k~f~~~~~l~ 79 (96)
++.....+........|.++|+ ++|.|..|++.|.+.+.|.
T Consensus 8 C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 8 CPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 4456667777788888899998 6799999999999887764
No 30
>KOG3608|consensus
Probab=95.59 E-value=0.0078 Score=41.56 Aligned_cols=40 Identities=18% Similarity=0.479 Sum_probs=28.8
Q ss_pred CCCCCCCceecccchhhccCCchHHHHHhhhCCCCCccccc
Q psy9655 55 RPVPPNPSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRS 95 (96)
Q Consensus 55 ~~~~~~~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~ 95 (96)
-.|...++|.|..|.+.|.+.+.|..|..+|. +--|.|..
T Consensus 285 ~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h 324 (467)
T KOG3608|consen 285 YRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEH 324 (467)
T ss_pred hhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCC
Confidence 34556677888888888888888888877776 55566654
No 31
>PHA00733 hypothetical protein
Probab=95.18 E-value=0.0087 Score=35.63 Aligned_cols=47 Identities=13% Similarity=0.188 Sum_probs=33.3
Q ss_pred CCCCCCCCCCCCCCCcCCCCCCCCCceecccchhhccCCchHHHHHhhh
Q psy9655 37 GQNQIVSEPPTDRTVSYNRPVPPNPSLSCTYCSRAFKKRSDLTRHIRSH 85 (96)
Q Consensus 37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~k~f~~~~~l~~h~~~h 85 (96)
+......+........+.+.+ ..+|.|..|++.|.....|..|++..
T Consensus 76 C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~ 122 (128)
T PHA00733 76 CPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKK 122 (128)
T ss_pred CCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHh
Confidence 344555555555555555544 34699999999999999999998753
No 32
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.68 E-value=0.018 Score=24.48 Aligned_cols=21 Identities=29% Similarity=0.749 Sum_probs=17.2
Q ss_pred eecccchhhccCCchHHHHHhh
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIRS 84 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~~ 84 (96)
..|..||+.| ....|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 5799999999 67888888753
No 33
>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=94.20 E-value=0.03 Score=25.24 Aligned_cols=23 Identities=17% Similarity=0.621 Sum_probs=20.1
Q ss_pred ceecccchhhccCCchHHHHHhh
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRS 84 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~ 84 (96)
+|.|..|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 48999999999998899998753
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=93.81 E-value=0.045 Score=37.42 Aligned_cols=28 Identities=18% Similarity=0.388 Sum_probs=23.4
Q ss_pred CCCCCCCceecccchhhccCCchHHHHH
Q psy9655 55 RPVPPNPSLSCTYCSRAFKKRSDLTRHI 82 (96)
Q Consensus 55 ~~~~~~~~~~C~~C~k~f~~~~~l~~h~ 82 (96)
......|||.|.+|+|.|+.--.|+-|.
T Consensus 391 ~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 391 IFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cccccCCceeccccchhhccCccceecc
Confidence 3344569999999999999999999884
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=93.68 E-value=0.046 Score=30.18 Aligned_cols=24 Identities=42% Similarity=1.025 Sum_probs=21.2
Q ss_pred ceecccchhhccCCchHHHHHhhh
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRSH 85 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~h 85 (96)
.+.|..|++.|.....|..|++.+
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 599999999999999999999864
No 36
>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=93.32 E-value=0.061 Score=24.32 Aligned_cols=22 Identities=14% Similarity=0.449 Sum_probs=14.1
Q ss_pred eecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
|.|..||..+.... .|+.|+.|
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~C 23 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVC 23 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCC
Confidence 67788887664322 56677766
No 37
>KOG3993|consensus
Probab=93.01 E-value=0.033 Score=39.30 Aligned_cols=25 Identities=28% Similarity=0.720 Sum_probs=22.7
Q ss_pred ceecccchhhccCCchHHHHHhhhC
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRSHT 86 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~ht 86 (96)
-|.|.+|+|.|.+...|+.|+.+|-
T Consensus 356 i~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 356 IFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred eeecHHhhhhhHHHHHHHHhHHhhh
Confidence 5999999999999999999987763
No 38
>KOG2893|consensus
Probab=90.93 E-value=0.099 Score=34.49 Aligned_cols=28 Identities=36% Similarity=0.714 Sum_probs=18.6
Q ss_pred cccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 65 CTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 65 C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
|-+|++-|....-|.+|++. |-|+|.+|
T Consensus 13 cwycnrefddekiliqhqka----khfkchic 40 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KHFKCHIC 40 (341)
T ss_pred eeecccccchhhhhhhhhhh----ccceeeee
Confidence 66677777777777776643 44677666
No 39
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=90.63 E-value=0.17 Score=31.56 Aligned_cols=22 Identities=23% Similarity=0.369 Sum_probs=18.7
Q ss_pred ceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
.|.|.+||+. |-|+-|-.|++|
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiC 155 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPIC 155 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCC
Confidence 5999999874 567889999998
No 40
>KOG3993|consensus
Probab=90.43 E-value=0.13 Score=36.51 Aligned_cols=25 Identities=28% Similarity=0.612 Sum_probs=22.6
Q ss_pred ceecccchhhccCCchHHHHHhhhC
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRSHT 86 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~ht 86 (96)
-|.|..|+|.|.-..+|.-|.|-|.
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred eecCCcccccccCchhhhhhhcccC
Confidence 3889999999999999999998774
No 41
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.02 E-value=0.38 Score=32.78 Aligned_cols=38 Identities=32% Similarity=0.555 Sum_probs=19.0
Q ss_pred CCCCC--Cceecc--cchhhccCCchHHHHHhhhCCCCCccc
Q psy9655 56 PVPPN--PSLSCT--YCSRAFKKRSDLTRHIRSHTKEKPFKV 93 (96)
Q Consensus 56 ~~~~~--~~~~C~--~C~k~f~~~~~l~~h~~~htgekp~~C 93 (96)
.|.++ +++.|. .|++.|.+...+..|..+|++.++++|
T Consensus 313 ~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (467)
T COG5048 313 NHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354 (467)
T ss_pred ccccccCCceeeeccCCCccccccccccCCcccccCCCcccc
Confidence 34444 455555 455555555555555555555444443
No 42
>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=87.08 E-value=0.44 Score=21.66 Aligned_cols=12 Identities=17% Similarity=0.506 Sum_probs=8.6
Q ss_pred ceecccchhhcc
Q psy9655 62 SLSCTYCSRAFK 73 (96)
Q Consensus 62 ~~~C~~C~k~f~ 73 (96)
.|.|..||..+.
T Consensus 2 ~~~C~~CG~i~~ 13 (34)
T cd00729 2 VWVCPVCGYIHE 13 (34)
T ss_pred eEECCCCCCEeE
Confidence 378888887654
No 43
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=87.06 E-value=0.37 Score=24.58 Aligned_cols=27 Identities=30% Similarity=0.650 Sum_probs=23.1
Q ss_pred CCCCCceecccchhhccCCchHHHHHh
Q psy9655 57 VPPNPSLSCTYCSRAFKKRSDLTRHIR 83 (96)
Q Consensus 57 ~~~~~~~~C~~C~k~f~~~~~l~~h~~ 83 (96)
..|+.-+.|+.|+..|....+..+|.-
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhh
Confidence 356777899999999999999999974
No 44
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=86.75 E-value=0.23 Score=33.88 Aligned_cols=34 Identities=38% Similarity=0.728 Sum_probs=31.7
Q ss_pred CceecccchhhccCCchHHHHHh--hhCCC--CCcccc
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIR--SHTKE--KPFKVR 94 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~--~htge--kp~~C~ 94 (96)
..+.|..|...|.....|..|.+ .|+++ +|+.|.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p 325 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCP 325 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeee
Confidence 36889999999999999999999 89999 999998
No 45
>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=85.87 E-value=0.73 Score=21.86 Aligned_cols=24 Identities=33% Similarity=0.832 Sum_probs=15.3
Q ss_pred CCceecccchhhccCC----chHHHHHh
Q psy9655 60 NPSLSCTYCSRAFKKR----SDLTRHIR 83 (96)
Q Consensus 60 ~~~~~C~~C~k~f~~~----~~l~~h~~ 83 (96)
.....|..|++.+... ++|..|++
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 4457999999988875 57888883
No 46
>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=85.68 E-value=0.49 Score=28.39 Aligned_cols=27 Identities=37% Similarity=0.786 Sum_probs=16.6
Q ss_pred CceecccchhhccCCchHHHHHhhhCCCCC
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIRSHTKEKP 90 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~~htgekp 90 (96)
....|-.||+.|+. |++|++.|-|-.|
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred CeeEEccCCcccch---HHHHHHHccCCCH
Confidence 34789999999964 6999999866443
No 47
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=84.99 E-value=0.76 Score=22.55 Aligned_cols=25 Identities=36% Similarity=0.926 Sum_probs=19.6
Q ss_pred ceecccchhhccCC-----chHHHHHh-hhC
Q psy9655 62 SLSCTYCSRAFKKR-----SDLTRHIR-SHT 86 (96)
Q Consensus 62 ~~~C~~C~k~f~~~-----~~l~~h~~-~ht 86 (96)
.-.|..|++.+... ++|.+|+. .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 36899999988776 48889987 554
No 48
>KOG4167|consensus
Probab=80.28 E-value=0.5 Score=35.84 Aligned_cols=25 Identities=24% Similarity=0.603 Sum_probs=22.6
Q ss_pred ceecccchhhccCCchHHHHHhhhC
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRSHT 86 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~ht 86 (96)
.|.|..|+|.|..-..+..||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4899999999999889999999885
No 49
>KOG3408|consensus
Probab=79.93 E-value=1.3 Score=26.24 Aligned_cols=29 Identities=24% Similarity=0.566 Sum_probs=24.9
Q ss_pred CCCCCCceecccchhhccCCchHHHHHhh
Q psy9655 56 PVPPNPSLSCTYCSRAFKKRSDLTRHIRS 84 (96)
Q Consensus 56 ~~~~~~~~~C~~C~k~f~~~~~l~~h~~~ 84 (96)
..+|.-.|.|..|.+-|.....|..|.++
T Consensus 51 dlPG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 51 DLPGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCCCceeehhhhhhhhcchHHHHHHHhc
Confidence 34566779999999999999999999864
No 50
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=77.83 E-value=2.7 Score=25.44 Aligned_cols=34 Identities=12% Similarity=0.208 Sum_probs=21.3
Q ss_pred CCCceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 59 PNPSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 59 ~~~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
....|.|+.|+..|..-..+.. .+. ..-|.|+.|
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~C 129 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRC 129 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCC
Confidence 3446999999998874332221 122 334999988
No 51
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=77.69 E-value=1.5 Score=26.44 Aligned_cols=25 Identities=32% Similarity=0.607 Sum_probs=21.0
Q ss_pred eecccchhhccCCchHHHHHhhhCCCCC
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIRSHTKEKP 90 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~~htgekp 90 (96)
..|..+|+.|+ .|++|+.+|-|--|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 57999999995 69999999887654
No 52
>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=77.24 E-value=1.5 Score=25.37 Aligned_cols=14 Identities=21% Similarity=0.705 Sum_probs=6.6
Q ss_pred ceecccchhhccCC
Q psy9655 62 SLSCTYCSRAFKKR 75 (96)
Q Consensus 62 ~~~C~~C~k~f~~~ 75 (96)
|-.|+.||..|...
T Consensus 26 PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 26 PIVCPKCGTEFPPE 39 (108)
T ss_pred CccCCCCCCccCcc
Confidence 34455555554433
No 53
>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=74.71 E-value=1.5 Score=26.97 Aligned_cols=29 Identities=14% Similarity=0.150 Sum_probs=21.0
Q ss_pred CCCceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 59 PNPSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 59 ~~~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
...-|.|+.|+..|+.-..+. --|.|+.|
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~C 134 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRC 134 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCC
Confidence 345689999998887655553 26899887
No 54
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=74.32 E-value=1.5 Score=27.60 Aligned_cols=28 Identities=18% Similarity=0.313 Sum_probs=20.2
Q ss_pred CCceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 60 NPSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 60 ~~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
...|.|+.|+..|+.-..+. --|.|+.|
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~C 142 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------YGFRCPQC 142 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------cCCcCCCC
Confidence 45589999998887554432 36999888
No 55
>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=73.38 E-value=1.2 Score=21.84 Aligned_cols=11 Identities=36% Similarity=0.960 Sum_probs=6.7
Q ss_pred eecccchhhcc
Q psy9655 63 LSCTYCSRAFK 73 (96)
Q Consensus 63 ~~C~~C~k~f~ 73 (96)
|.|..|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 56666666554
No 56
>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=73.13 E-value=0.8 Score=21.74 Aligned_cols=13 Identities=23% Similarity=0.649 Sum_probs=9.6
Q ss_pred eecccchhhccCC
Q psy9655 63 LSCTYCSRAFKKR 75 (96)
Q Consensus 63 ~~C~~C~k~f~~~ 75 (96)
|.|..||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 6 YRCEECGHEFEVL 18 (42)
T ss_pred EEeCCCCCEEEEE
Confidence 7888888777543
No 57
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=71.72 E-value=3.1 Score=20.04 Aligned_cols=11 Identities=27% Similarity=0.625 Sum_probs=6.0
Q ss_pred eecccchhhcc
Q psy9655 63 LSCTYCSRAFK 73 (96)
Q Consensus 63 ~~C~~C~k~f~ 73 (96)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 55555555544
No 58
>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=71.29 E-value=1.4 Score=20.30 Aligned_cols=12 Identities=25% Similarity=0.778 Sum_probs=8.8
Q ss_pred eecccchhhccC
Q psy9655 63 LSCTYCSRAFKK 74 (96)
Q Consensus 63 ~~C~~C~k~f~~ 74 (96)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (41)
T smart00834 6 YRCEDCGHTFEV 17 (41)
T ss_pred EEcCCCCCEEEE
Confidence 678888887753
No 59
>KOG2482|consensus
Probab=70.99 E-value=3.1 Score=29.07 Aligned_cols=23 Identities=35% Similarity=0.967 Sum_probs=21.1
Q ss_pred ceecccchhhccCCchHHHHHhh
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRS 84 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~ 84 (96)
.+.|-.|.+.|..+..|+.|||.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 47899999999999999999985
No 60
>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=69.81 E-value=1.7 Score=19.00 Aligned_cols=20 Identities=30% Similarity=0.683 Sum_probs=12.7
Q ss_pred eecccchhhccCCchHHHHHh
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIR 83 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~ 83 (96)
|.|..|++.| .....+.|..
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEE-EGGGTTT---
T ss_pred CeeecCCCCc-CcCCcCCCCc
Confidence 5799999999 4455566654
No 61
>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=69.54 E-value=2.6 Score=27.35 Aligned_cols=24 Identities=25% Similarity=0.548 Sum_probs=19.2
Q ss_pred CceecccchhhccCCchHHHHHhh
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIRS 84 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~~ 84 (96)
..|.|..|+|.|....-+..|+..
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHH
T ss_pred CEECCCCCCcccCChHHHHHHHhh
Confidence 349999999999999999999865
No 62
>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=67.35 E-value=3.5 Score=24.59 Aligned_cols=18 Identities=17% Similarity=0.289 Sum_probs=10.7
Q ss_pred CceecccchhhccCCchH
Q psy9655 61 PSLSCTYCSRAFKKRSDL 78 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l 78 (96)
.|..|+.||..|.....+
T Consensus 25 ~p~vcP~cg~~~~~~~~~ 42 (129)
T TIGR02300 25 RPAVSPYTGEQFPPEEAL 42 (129)
T ss_pred CCccCCCcCCccCcchhh
Confidence 456677777776554333
No 63
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=66.63 E-value=4.5 Score=20.84 Aligned_cols=29 Identities=10% Similarity=0.423 Sum_probs=18.3
Q ss_pred ceecccchhh-ccCCchHHHHHhhhCCCCCcccccC
Q psy9655 62 SLSCTYCSRA-FKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 62 ~~~C~~C~k~-f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
.|.|+.||.. ..+-...+. -..+|.|+.|
T Consensus 25 ~F~CPnCG~~~I~RC~~CRk------~~~~Y~CP~C 54 (59)
T PRK14890 25 KFLCPNCGEVIIYRCEKCRK------QSNPYTCPKC 54 (59)
T ss_pred EeeCCCCCCeeEeechhHHh------cCCceECCCC
Confidence 4999999987 333222222 2368999876
No 64
>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=65.47 E-value=4.6 Score=22.99 Aligned_cols=25 Identities=16% Similarity=0.490 Sum_probs=21.8
Q ss_pred ceec----ccchhhccCCchHHHHHhhhC
Q psy9655 62 SLSC----TYCSRAFKKRSDLTRHIRSHT 86 (96)
Q Consensus 62 ~~~C----~~C~k~f~~~~~l~~h~~~ht 86 (96)
.|.| ..|++.......+..|.+.+-
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 4899 999999999999999998653
No 65
>PF15269 zf-C2H2_7: Zinc-finger
Probab=64.16 E-value=7.9 Score=18.87 Aligned_cols=23 Identities=22% Similarity=0.508 Sum_probs=19.5
Q ss_pred ceecccchhhccCCchHHHHHhh
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRS 84 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~ 84 (96)
.|.|-+|......+++|-.||.-
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred cceeecCCcccchHHHHHHHHHH
Confidence 47899999998889999999863
No 66
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=64.06 E-value=2.9 Score=20.06 Aligned_cols=8 Identities=38% Similarity=1.294 Sum_probs=4.2
Q ss_pred eecccchh
Q psy9655 63 LSCTYCSR 70 (96)
Q Consensus 63 ~~C~~C~k 70 (96)
+.|+.||.
T Consensus 22 ~~Cp~CG~ 29 (46)
T PRK00398 22 VRCPYCGY 29 (46)
T ss_pred eECCCCCC
Confidence 45555554
No 67
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=63.77 E-value=2.9 Score=23.52 Aligned_cols=26 Identities=19% Similarity=0.445 Sum_probs=17.3
Q ss_pred CceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
+|-.|..||+.|.. . .-.+|-.|+.|
T Consensus 57 ~Pa~CkkCGfef~~-~---------~ik~pSRCP~C 82 (97)
T COG3357 57 RPARCKKCGFEFRD-D---------KIKKPSRCPKC 82 (97)
T ss_pred cChhhcccCccccc-c---------ccCCcccCCcc
Confidence 45679999999975 1 11346677766
No 68
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=63.35 E-value=4.1 Score=20.18 Aligned_cols=11 Identities=27% Similarity=0.827 Sum_probs=7.8
Q ss_pred ceecccchhhc
Q psy9655 62 SLSCTYCSRAF 72 (96)
Q Consensus 62 ~~~C~~C~k~f 72 (96)
-|.|..||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 37777777776
No 69
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=61.30 E-value=6.3 Score=20.38 Aligned_cols=30 Identities=13% Similarity=0.401 Sum_probs=18.3
Q ss_pred ceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
.|.|+.||..--..-. +-..-..+|.|+.|
T Consensus 27 ~F~CPnCGe~~I~Rc~-----~CRk~g~~Y~Cp~C 56 (61)
T COG2888 27 KFPCPNCGEVEIYRCA-----KCRKLGNPYRCPKC 56 (61)
T ss_pred EeeCCCCCceeeehhh-----hHHHcCCceECCCc
Confidence 4899999965443222 11222468999876
No 70
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=59.51 E-value=4.1 Score=24.40 Aligned_cols=15 Identities=20% Similarity=0.663 Sum_probs=11.3
Q ss_pred CceecccchhhccCC
Q psy9655 61 PSLSCTYCSRAFKKR 75 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~ 75 (96)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 348999999887654
No 71
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=59.37 E-value=6.9 Score=17.92 Aligned_cols=12 Identities=25% Similarity=0.825 Sum_probs=6.0
Q ss_pred ecccchhhccCC
Q psy9655 64 SCTYCSRAFKKR 75 (96)
Q Consensus 64 ~C~~C~k~f~~~ 75 (96)
.|+.|+..|.-.
T Consensus 4 ~CP~C~~~f~v~ 15 (37)
T PF13719_consen 4 TCPNCQTRFRVP 15 (37)
T ss_pred ECCCCCceEEcC
Confidence 455555555443
No 72
>KOG2593|consensus
Probab=57.40 E-value=8.2 Score=27.72 Aligned_cols=36 Identities=11% Similarity=0.292 Sum_probs=23.6
Q ss_pred CCCCceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 58 PPNPSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 58 ~~~~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
+....|.|+.|.+.|..-..++ ..-.-.--|.|..|
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C 159 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENC 159 (436)
T ss_pred cccccccCCccccchhhhHHHH---hhcccCceEEEecC
Confidence 3445699999999997655444 23333345888877
No 73
>PHA00626 hypothetical protein
Probab=57.14 E-value=6.1 Score=20.19 Aligned_cols=15 Identities=20% Similarity=0.341 Sum_probs=12.3
Q ss_pred CceecccchhhccCC
Q psy9655 61 PSLSCTYCSRAFKKR 75 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~ 75 (96)
..|.|..||+.|+.-
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 459999999998753
No 74
>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=56.71 E-value=4.6 Score=17.16 Aligned_cols=11 Identities=27% Similarity=0.682 Sum_probs=8.7
Q ss_pred eecccchhhcc
Q psy9655 63 LSCTYCSRAFK 73 (96)
Q Consensus 63 ~~C~~C~k~f~ 73 (96)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 46889998885
No 75
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=55.93 E-value=7.8 Score=22.48 Aligned_cols=29 Identities=24% Similarity=0.427 Sum_probs=23.7
Q ss_pred CCCCCCCceecccchhhccCCchHHHHHh
Q psy9655 55 RPVPPNPSLSCTYCSRAFKKRSDLTRHIR 83 (96)
Q Consensus 55 ~~~~~~~~~~C~~C~k~f~~~~~l~~h~~ 83 (96)
...+|--.|.|..|.+-|.+...|..|.+
T Consensus 48 p~lPGlGqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 48 PELPGLGQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred CCCCCCceeeeehhHHHHHHHHHHHHHhc
Confidence 34455566999999999999999999875
No 76
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.92 E-value=2.6 Score=27.83 Aligned_cols=28 Identities=29% Similarity=0.517 Sum_probs=21.6
Q ss_pred CceecccchhhccCCchHHHHHhhhCCC
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIRSHTKE 88 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~~htge 88 (96)
+.+.|++|+..|....-+....|+-.|+
T Consensus 18 k~ieCPvC~tkFkkeev~tgsiRiiagD 45 (267)
T COG1655 18 KTIECPVCNTKFKKEEVKTGSIRIIAGD 45 (267)
T ss_pred ceeccCcccchhhhhheeccceeEeccc
Confidence 4589999999999887776666665554
No 77
>KOG1146|consensus
Probab=55.04 E-value=5.5 Score=32.47 Aligned_cols=27 Identities=30% Similarity=0.496 Sum_probs=24.1
Q ss_pred CCCCceecccchhhccCCchHHHHHhh
Q psy9655 58 PPNPSLSCTYCSRAFKKRSDLTRHIRS 84 (96)
Q Consensus 58 ~~~~~~~C~~C~k~f~~~~~l~~h~~~ 84 (96)
.-.+.|.|..|+..|+....|-.|+|.
T Consensus 461 S~~kt~~cpkc~~~yk~a~~L~vhmRs 487 (1406)
T KOG1146|consen 461 SFFKTLKCPKCNWHYKLAQTLGVHMRS 487 (1406)
T ss_pred cccccccCCccchhhhhHHHhhhcccc
Confidence 335789999999999999999999997
No 78
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=54.11 E-value=9.6 Score=18.89 Aligned_cols=27 Identities=11% Similarity=0.235 Sum_probs=17.3
Q ss_pred eecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
+.|..||..|...-..+ + .+...|+.|
T Consensus 29 W~C~~Cgh~w~~~v~~R----~---~~~~~CP~C 55 (55)
T PF14311_consen 29 WKCPKCGHEWKASVNDR----T---RRGKGCPYC 55 (55)
T ss_pred EECCCCCCeeEccHhhh----c---cCCCCCCCC
Confidence 78999988776544332 2 344567776
No 79
>COG1773 Rubredoxin [Energy production and conversion]
Probab=54.00 E-value=5.8 Score=20.16 Aligned_cols=16 Identities=13% Similarity=0.555 Sum_probs=12.5
Q ss_pred ceecccchhhccCCch
Q psy9655 62 SLSCTYCSRAFKKRSD 77 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~ 77 (96)
.|+|..||..|.-...
T Consensus 3 ~~~C~~CG~vYd~e~G 18 (55)
T COG1773 3 RWRCSVCGYVYDPEKG 18 (55)
T ss_pred ceEecCCceEeccccC
Confidence 5899999998875443
No 80
>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=53.92 E-value=8.3 Score=16.26 Aligned_cols=20 Identities=20% Similarity=0.572 Sum_probs=14.2
Q ss_pred eecccchhhccCCchHHHHHh
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIR 83 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~ 83 (96)
..|+.|++.+ ....+..|..
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 4689999988 4456667754
No 81
>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=51.06 E-value=7.5 Score=17.83 Aligned_cols=11 Identities=27% Similarity=0.818 Sum_probs=6.8
Q ss_pred eecccchhhcc
Q psy9655 63 LSCTYCSRAFK 73 (96)
Q Consensus 63 ~~C~~C~k~f~ 73 (96)
..|..||+.|.
T Consensus 2 r~C~~Cg~~Yh 12 (36)
T PF05191_consen 2 RICPKCGRIYH 12 (36)
T ss_dssp EEETTTTEEEE
T ss_pred cCcCCCCCccc
Confidence 45666666664
No 82
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=49.11 E-value=11 Score=17.67 Aligned_cols=24 Identities=21% Similarity=0.463 Sum_probs=17.6
Q ss_pred eecccchhhccC--CchHHHHHhhhC
Q psy9655 63 LSCTYCSRAFKK--RSDLTRHIRSHT 86 (96)
Q Consensus 63 ~~C~~C~k~f~~--~~~l~~h~~~ht 86 (96)
-.|..||-.|.. ...-..|.+-|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 589999976655 456778877774
No 83
>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=48.99 E-value=8.2 Score=16.15 Aligned_cols=9 Identities=22% Similarity=0.803 Sum_probs=7.3
Q ss_pred ceecccchh
Q psy9655 62 SLSCTYCSR 70 (96)
Q Consensus 62 ~~~C~~C~k 70 (96)
.|.|+.||+
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 599999984
No 84
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=48.08 E-value=12 Score=18.49 Aligned_cols=35 Identities=17% Similarity=0.345 Sum_probs=19.8
Q ss_pred CceecccchhhccCCchHHHHHhhhCC--CCCcccccC
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIRSHTK--EKPFKVRSL 96 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~~htg--ekp~~C~~C 96 (96)
+.+.|..||..|..-..=+....- .| ..|-.|..|
T Consensus 3 k~l~C~dCg~~FvfTa~EQ~fy~e-Kgf~n~p~RC~~C 39 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAGEQKFYAE-KGFDNEPKRCPSC 39 (49)
T ss_pred eeEEcccCCCeEEEehhHHHHHHh-cCCcCCCccCHHH
Confidence 458899999888765544433222 22 235556544
No 85
>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=46.85 E-value=14 Score=16.68 Aligned_cols=13 Identities=23% Similarity=0.812 Sum_probs=6.2
Q ss_pred eecccchhhccCC
Q psy9655 63 LSCTYCSRAFKKR 75 (96)
Q Consensus 63 ~~C~~C~k~f~~~ 75 (96)
+.|+.|+..|...
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 3455555554433
No 86
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=46.66 E-value=11 Score=21.85 Aligned_cols=12 Identities=25% Similarity=0.584 Sum_probs=8.7
Q ss_pred eecccchhhccC
Q psy9655 63 LSCTYCSRAFKK 74 (96)
Q Consensus 63 ~~C~~C~k~f~~ 74 (96)
+.|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (115)
T TIGR00100 71 CECEDCSEEVSP 82 (115)
T ss_pred EEcccCCCEEec
Confidence 778888876654
No 87
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=46.20 E-value=20 Score=17.74 Aligned_cols=35 Identities=17% Similarity=0.491 Sum_probs=20.4
Q ss_pred Cceeccc-chhhccCCchHHHHHhhhCCCCCccccc
Q psy9655 61 PSLSCTY-CSRAFKKRSDLTRHIRSHTKEKPFKVRS 95 (96)
Q Consensus 61 ~~~~C~~-C~k~f~~~~~l~~h~~~htgekp~~C~~ 95 (96)
.+..|+. |+..-..+..|..|....-..++..|.+
T Consensus 8 ~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp SEEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS
T ss_pred CEeeCCCCCcccceeHHHHHHHHHccCCCCcEECCC
Confidence 3467877 4433233667888988666667777766
No 88
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=44.88 E-value=5.4 Score=19.14 Aligned_cols=9 Identities=22% Similarity=0.840 Sum_probs=6.6
Q ss_pred eecccchhh
Q psy9655 63 LSCTYCSRA 71 (96)
Q Consensus 63 ~~C~~C~k~ 71 (96)
+.|+.||..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 668888864
No 89
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=44.85 E-value=11 Score=17.49 Aligned_cols=15 Identities=20% Similarity=0.576 Sum_probs=12.2
Q ss_pred ceecccchhhccCCc
Q psy9655 62 SLSCTYCSRAFKKRS 76 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~ 76 (96)
+|.|..|++.|-..-
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 689999999987544
No 90
>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=44.39 E-value=13 Score=27.08 Aligned_cols=33 Identities=18% Similarity=0.323 Sum_probs=26.6
Q ss_pred CCCCCCceecccchhhccCCchHHHHHh-hhCCC
Q psy9655 56 PVPPNPSLSCTYCSRAFKKRSDLTRHIR-SHTKE 88 (96)
Q Consensus 56 ~~~~~~~~~C~~C~k~f~~~~~l~~h~~-~htge 88 (96)
.+...+.+.|..|.+.|.....+..|+. .|.+.
T Consensus 51 ~n~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 51 ENKSWRFWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred hcCceeEeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 3455667899999999999999999986 47653
No 91
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=43.06 E-value=12 Score=23.13 Aligned_cols=32 Identities=16% Similarity=0.449 Sum_probs=23.2
Q ss_pred CCceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 60 NPSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 60 ~~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
.-.|.|. |+..|.+ .++|-.+-.|+ -|.|..|
T Consensus 115 ~~~Y~C~-C~q~~l~---~RRhn~~~~g~-~YrC~~C 146 (156)
T COG3091 115 TYPYRCQ-CQQHYLR---IRRHNTVRRGE-VYRCGKC 146 (156)
T ss_pred ceeEEee-cCCccch---hhhcccccccc-eEEeccC
Confidence 4469999 9988654 34555666677 8999887
No 92
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=42.98 E-value=10 Score=24.44 Aligned_cols=23 Identities=26% Similarity=0.677 Sum_probs=17.3
Q ss_pred CceecccchhhccCCchHHHHHh
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIR 83 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~ 83 (96)
+...|++|++.|..+.-.....+
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r 26 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIR 26 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCce
Confidence 45899999999998765554443
No 93
>KOG1994|consensus
Probab=42.94 E-value=12 Score=24.73 Aligned_cols=21 Identities=29% Similarity=0.681 Sum_probs=18.9
Q ss_pred ceecccchhhccCCchHHHHH
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHI 82 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~ 82 (96)
.|.|-+||..|.....|..|-
T Consensus 239 h~YC~fCG~~y~~~edl~ehC 259 (268)
T KOG1994|consen 239 HYYCFFCGIKYKDEEDLYEHC 259 (268)
T ss_pred ceEEEEeccccCCHHHHHHhC
Confidence 399999999999999998874
No 94
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=42.84 E-value=14 Score=18.83 Aligned_cols=8 Identities=25% Similarity=0.808 Sum_probs=4.0
Q ss_pred eecccchh
Q psy9655 63 LSCTYCSR 70 (96)
Q Consensus 63 ~~C~~C~k 70 (96)
|.|..|.-
T Consensus 32 YmC~eC~~ 39 (56)
T PF09963_consen 32 YMCDECKE 39 (56)
T ss_pred eeChhHHH
Confidence 55555543
No 95
>KOG2186|consensus
Probab=42.21 E-value=19 Score=24.24 Aligned_cols=30 Identities=17% Similarity=0.419 Sum_probs=20.9
Q ss_pred CCCCCCCCCceecccchhhccCCchHHHHHhh
Q psy9655 53 YNRPVPPNPSLSCTYCSRAFKKRSDLTRHIRS 84 (96)
Q Consensus 53 ~~~~~~~~~~~~C~~C~k~f~~~~~l~~h~~~ 84 (96)
|....++ ..|.|..|++.|.. ...+.|..-
T Consensus 21 H~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 21 HMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred HHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 4444444 56899999999987 666777653
No 96
>KOG2071|consensus
Probab=41.78 E-value=18 Score=27.11 Aligned_cols=27 Identities=19% Similarity=0.545 Sum_probs=21.9
Q ss_pred CCceecccchhhccCCchHHHHHhhhC
Q psy9655 60 NPSLSCTYCSRAFKKRSDLTRHIRSHT 86 (96)
Q Consensus 60 ~~~~~C~~C~k~f~~~~~l~~h~~~ht 86 (96)
..+..|..||..|........||-.|.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 456889999999999888777776664
No 97
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=41.49 E-value=13 Score=24.98 Aligned_cols=28 Identities=21% Similarity=0.406 Sum_probs=19.5
Q ss_pred ceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
.-.|+.||....-...| |- -=.|+|+.|
T Consensus 220 ~r~CP~Cg~~W~L~~pl--h~-----iFdFKCD~C 247 (258)
T PF10071_consen 220 ARKCPSCGGDWRLKEPL--HD-----IFDFKCDPC 247 (258)
T ss_pred CCCCCCCCCccccCCch--hh-----ceeccCCcc
Confidence 35699999987776665 22 234889887
No 98
>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=41.11 E-value=8.8 Score=18.37 Aligned_cols=15 Identities=33% Similarity=0.751 Sum_probs=11.8
Q ss_pred ecccchhhccCCchH
Q psy9655 64 SCTYCSRAFKKRSDL 78 (96)
Q Consensus 64 ~C~~C~k~f~~~~~l 78 (96)
.|..|++.|....-.
T Consensus 10 ~C~~C~rpf~WRKKW 24 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKW 24 (42)
T ss_pred cCcccCCcchHHHHH
Confidence 699999999875543
No 99
>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=41.09 E-value=11 Score=18.40 Aligned_cols=15 Identities=13% Similarity=0.589 Sum_probs=12.0
Q ss_pred eecccchhhccCCch
Q psy9655 63 LSCTYCSRAFKKRSD 77 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~ 77 (96)
|+|..|+..|.-...
T Consensus 2 y~C~~CgyvYd~~~G 16 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKG 16 (47)
T ss_dssp EEETTTSBEEETTTB
T ss_pred cCCCCCCEEEcCCcC
Confidence 899999998876554
No 100
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=40.78 E-value=17 Score=21.07 Aligned_cols=12 Identities=25% Similarity=0.423 Sum_probs=8.1
Q ss_pred eecccchhhccC
Q psy9655 63 LSCTYCSRAFKK 74 (96)
Q Consensus 63 ~~C~~C~k~f~~ 74 (96)
+.|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PRK12380 71 AWCWDCSQVVEI 82 (113)
T ss_pred EEcccCCCEEec
Confidence 677778766643
No 101
>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=39.82 E-value=22 Score=21.40 Aligned_cols=21 Identities=19% Similarity=0.384 Sum_probs=17.2
Q ss_pred CceecccchhhccCCchHHHH
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRH 81 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h 81 (96)
.-+.|..|++.|-.-+++..-
T Consensus 123 ~f~~C~~C~kiyW~GsH~~~~ 143 (147)
T PF01927_consen 123 EFWRCPGCGKIYWEGSHWRRM 143 (147)
T ss_pred eEEECCCCCCEecccccHHHH
Confidence 468999999999888877654
No 102
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.42 E-value=17 Score=21.19 Aligned_cols=12 Identities=50% Similarity=1.027 Sum_probs=8.4
Q ss_pred eecccchhhccC
Q psy9655 63 LSCTYCSRAFKK 74 (96)
Q Consensus 63 ~~C~~C~k~f~~ 74 (96)
+.|..|+..|..
T Consensus 72 ~~C~~Cg~~~~~ 83 (117)
T PRK00564 72 LECKDCSHVFKP 83 (117)
T ss_pred EEhhhCCCcccc
Confidence 678888866653
No 103
>PF12907 zf-met2: Zinc-binding
Probab=38.90 E-value=13 Score=17.53 Aligned_cols=31 Identities=23% Similarity=0.511 Sum_probs=20.7
Q ss_pred eecccchhhccCC---chHHHHHh-hhCCCCCccc
Q psy9655 63 LSCTYCSRAFKKR---SDLTRHIR-SHTKEKPFKV 93 (96)
Q Consensus 63 ~~C~~C~k~f~~~---~~l~~h~~-~htgekp~~C 93 (96)
+.|.+|--.|..- ..|..|-. .|....+-.|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~~C 36 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTFEEC 36 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHHHc
Confidence 5788998666554 45888875 4776544444
No 104
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.15 E-value=33 Score=20.08 Aligned_cols=26 Identities=23% Similarity=0.409 Sum_probs=22.0
Q ss_pred CceecccchhhccCCchHHHHHhhhC
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIRSHT 86 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~~ht 86 (96)
..|.|..|...|-..-+.-.|...|.
T Consensus 80 ~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 80 HRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cceeCCCCCCccccccchhhhhhccC
Confidence 35999999999998888888877774
No 105
>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=38.02 E-value=12 Score=17.62 Aligned_cols=16 Identities=19% Similarity=0.623 Sum_probs=10.0
Q ss_pred CceecccchhhccCCc
Q psy9655 61 PSLSCTYCSRAFKKRS 76 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~ 76 (96)
-+|.|..|++.|-..-
T Consensus 12 ~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKH 27 (43)
T ss_dssp SHEE-TTTS-EE-TTT
T ss_pred CCeECCCCCcccCccc
Confidence 3699999999987543
No 106
>KOG0717|consensus
Probab=37.87 E-value=16 Score=26.72 Aligned_cols=21 Identities=33% Similarity=0.768 Sum_probs=19.2
Q ss_pred eecccchhhccCCchHHHHHh
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIR 83 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~ 83 (96)
+.|..|.|.|.+.-.++.|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 899999999999999998864
No 107
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=37.51 E-value=17 Score=21.69 Aligned_cols=20 Identities=15% Similarity=0.429 Sum_probs=15.3
Q ss_pred CCCCCceecccchhhccCCc
Q psy9655 57 VPPNPSLSCTYCSRAFKKRS 76 (96)
Q Consensus 57 ~~~~~~~~C~~C~k~f~~~~ 76 (96)
..+...|.|..|++.|....
T Consensus 48 ~~~~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 48 RRGHQRYKCKSCGSTFTVET 67 (129)
T ss_pred cccccccccCCcCcceeeec
Confidence 34466799999999987654
No 108
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=37.29 E-value=16 Score=22.00 Aligned_cols=15 Identities=40% Similarity=0.826 Sum_probs=11.5
Q ss_pred ceecccchhhccCCc
Q psy9655 62 SLSCTYCSRAFKKRS 76 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~ 76 (96)
|+.|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 467888888887655
No 109
>KOG2636|consensus
Probab=36.92 E-value=23 Score=25.75 Aligned_cols=26 Identities=23% Similarity=0.528 Sum_probs=20.6
Q ss_pred CCCCCceecccch-hhccCCchHHHHH
Q psy9655 57 VPPNPSLSCTYCS-RAFKKRSDLTRHI 82 (96)
Q Consensus 57 ~~~~~~~~C~~C~-k~f~~~~~l~~h~ 82 (96)
|.=.+-|.|.+|| +++.-+..+.+|-
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHh
Confidence 4445679999999 7888888888875
No 110
>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=36.04 E-value=33 Score=15.24 Aligned_cols=8 Identities=25% Similarity=0.999 Sum_probs=3.6
Q ss_pred eecccchh
Q psy9655 63 LSCTYCSR 70 (96)
Q Consensus 63 ~~C~~C~k 70 (96)
..|..||.
T Consensus 18 irC~~CG~ 25 (32)
T PF03604_consen 18 IRCPECGH 25 (32)
T ss_dssp SSBSSSS-
T ss_pred EECCcCCC
Confidence 34555553
No 111
>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=36.02 E-value=13 Score=18.36 Aligned_cols=13 Identities=15% Similarity=0.628 Sum_probs=10.9
Q ss_pred eecccchhhccCC
Q psy9655 63 LSCTYCSRAFKKR 75 (96)
Q Consensus 63 ~~C~~C~k~f~~~ 75 (96)
|+|..||+.|.-.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 7899999988754
No 112
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=34.55 E-value=10 Score=19.62 Aligned_cols=19 Identities=16% Similarity=0.359 Sum_probs=9.5
Q ss_pred eecccchhhccCCchHHHH
Q psy9655 63 LSCTYCSRAFKKRSDLTRH 81 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h 81 (96)
..|..|++....+.++..|
T Consensus 31 IlCNDC~~~s~v~fH~lg~ 49 (61)
T PF14599_consen 31 ILCNDCNAKSEVPFHFLGH 49 (61)
T ss_dssp EEESSS--EEEEE--TT--
T ss_pred EECCCCCCccceeeeHhhh
Confidence 5699999877666665554
No 113
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=34.49 E-value=18 Score=21.03 Aligned_cols=11 Identities=18% Similarity=0.482 Sum_probs=7.6
Q ss_pred eecccchhhcc
Q psy9655 63 LSCTYCSRAFK 73 (96)
Q Consensus 63 ~~C~~C~k~f~ 73 (96)
+.|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (114)
T PRK03681 71 CWCETCQQYVT 81 (114)
T ss_pred EEcccCCCeee
Confidence 67777876554
No 114
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=34.08 E-value=18 Score=16.71 Aligned_cols=17 Identities=24% Similarity=0.493 Sum_probs=10.3
Q ss_pred eecccchhhccCCchHH
Q psy9655 63 LSCTYCSRAFKKRSDLT 79 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~ 79 (96)
-.|..|++.|.+.+...
T Consensus 3 ~~CprC~kg~Hwa~~C~ 19 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECR 19 (36)
T ss_dssp -C-TTTSSSCS-TTT--
T ss_pred ccCcccCCCcchhhhhh
Confidence 46899999998877655
No 115
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=33.96 E-value=15 Score=22.63 Aligned_cols=17 Identities=18% Similarity=0.501 Sum_probs=13.6
Q ss_pred ceecccchhhccCCchH
Q psy9655 62 SLSCTYCSRAFKKRSDL 78 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l 78 (96)
.+.|..||+.|..-..+
T Consensus 28 ~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 28 RRECLACGKRFTTFERV 44 (154)
T ss_pred eeeccccCCcceEeEec
Confidence 38999999999875543
No 116
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=33.45 E-value=34 Score=15.40 Aligned_cols=21 Identities=24% Similarity=0.621 Sum_probs=14.2
Q ss_pred ceecccchhhccCCchHHHHHh
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIR 83 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~ 83 (96)
.|.|..|++.+. .+.+..|+-
T Consensus 4 ~~~C~nC~R~v~-a~RfA~HLe 24 (33)
T PF08209_consen 4 YVECPNCGRPVA-ASRFAPHLE 24 (33)
T ss_dssp EEE-TTTSSEEE-GGGHHHHHH
T ss_pred eEECCCCcCCcc-hhhhHHHHH
Confidence 488999999775 455666764
No 117
>PRK12860 transcriptional activator FlhC; Provisional
Probab=32.20 E-value=28 Score=22.27 Aligned_cols=26 Identities=19% Similarity=0.387 Sum_probs=14.2
Q ss_pred eecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 63 LSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
..|..|+-.|-... |.....|.|+.|
T Consensus 135 ~~C~~Cgg~fv~~~--------~e~~~~f~CplC 160 (189)
T PRK12860 135 ARCCRCGGKFVTHA--------HDLRHNFVCGLC 160 (189)
T ss_pred ccCCCCCCCeeccc--------cccCCCCcCCCC
Confidence 45777777665321 122236777776
No 118
>KOG2231|consensus
Probab=31.48 E-value=22 Score=27.16 Aligned_cols=31 Identities=29% Similarity=0.567 Sum_probs=20.1
Q ss_pred eecccchhhcc---------------CCchHHHHHh-hhCCCCCcccccC
Q psy9655 63 LSCTYCSRAFK---------------KRSDLTRHIR-SHTKEKPFKVRSL 96 (96)
Q Consensus 63 ~~C~~C~k~f~---------------~~~~l~~h~~-~htgekp~~C~~C 96 (96)
+.|..|++.|. ....|+.|++ .|- -+.|.+|
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~---~~~c~lC 146 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHK---LHLCSLC 146 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhh---hhccccc
Confidence 55777777663 5678999984 463 3455554
No 119
>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=31.16 E-value=19 Score=17.72 Aligned_cols=12 Identities=25% Similarity=0.908 Sum_probs=6.5
Q ss_pred ecccchhhccCC
Q psy9655 64 SCTYCSRAFKKR 75 (96)
Q Consensus 64 ~C~~C~k~f~~~ 75 (96)
.|+.|++.|...
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 899999998753
No 120
>PRK12722 transcriptional activator FlhC; Provisional
Probab=30.33 E-value=32 Score=21.98 Aligned_cols=10 Identities=40% Similarity=0.969 Sum_probs=6.1
Q ss_pred ecccchhhcc
Q psy9655 64 SCTYCSRAFK 73 (96)
Q Consensus 64 ~C~~C~k~f~ 73 (96)
.|..|+-.|-
T Consensus 136 ~C~~Cgg~fv 145 (187)
T PRK12722 136 SCNCCGGHFV 145 (187)
T ss_pred cCCCCCCCee
Confidence 4666666664
No 121
>PLN02748 tRNA dimethylallyltransferase
Probab=30.07 E-value=30 Score=25.28 Aligned_cols=25 Identities=12% Similarity=0.355 Sum_probs=20.0
Q ss_pred CCCceecccchh-hccCCchHHHHHh
Q psy9655 59 PNPSLSCTYCSR-AFKKRSDLTRHIR 83 (96)
Q Consensus 59 ~~~~~~C~~C~k-~f~~~~~l~~h~~ 83 (96)
..+.|.|..|++ .+........|+.
T Consensus 415 ~~~~~~Ce~C~~~~~~G~~eW~~Hlk 440 (468)
T PLN02748 415 LWTQYVCEACGNKVLRGAHEWEQHKQ 440 (468)
T ss_pred ccccccccCCCCcccCCHHHHHHHhc
Confidence 356789999997 7888887888874
No 122
>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=29.87 E-value=26 Score=19.87 Aligned_cols=17 Identities=24% Similarity=0.452 Sum_probs=13.1
Q ss_pred CCCCCceecccchhhccC
Q psy9655 57 VPPNPSLSCTYCSRAFKK 74 (96)
Q Consensus 57 ~~~~~~~~C~~C~k~f~~ 74 (96)
+.+ +++.|..||..|..
T Consensus 75 ~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 75 EKG-KPKRCPECGHVFKL 91 (97)
T ss_pred eCC-CceeCCCCCcEEEE
Confidence 344 68999999998864
No 123
>PRK01343 zinc-binding protein; Provisional
Probab=29.37 E-value=47 Score=16.98 Aligned_cols=12 Identities=17% Similarity=0.578 Sum_probs=9.5
Q ss_pred ceecccchhhcc
Q psy9655 62 SLSCTYCSRAFK 73 (96)
Q Consensus 62 ~~~C~~C~k~f~ 73 (96)
...|.+|++.+.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 467999999875
No 124
>KOG1842|consensus
Probab=29.16 E-value=28 Score=25.38 Aligned_cols=28 Identities=25% Similarity=0.475 Sum_probs=23.9
Q ss_pred CceecccchhhccCCchHHHHHhh-hCCC
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIRS-HTKE 88 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~~-htge 88 (96)
..|.|+.|..-|..-..|..|.-. |.++
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 459999999999999999999854 7655
No 125
>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=28.97 E-value=18 Score=20.89 Aligned_cols=13 Identities=23% Similarity=0.692 Sum_probs=9.1
Q ss_pred ceecccchhhccC
Q psy9655 62 SLSCTYCSRAFKK 74 (96)
Q Consensus 62 ~~~C~~C~k~f~~ 74 (96)
.+.|..|++.|..
T Consensus 70 ~~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 70 RARCRDCGHEFEP 82 (113)
T ss_dssp EEEETTTS-EEEC
T ss_pred cEECCCCCCEEec
Confidence 3789999988864
No 126
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=28.80 E-value=35 Score=15.46 Aligned_cols=15 Identities=20% Similarity=0.618 Sum_probs=10.7
Q ss_pred CCCceecccchhhcc
Q psy9655 59 PNPSLSCTYCSRAFK 73 (96)
Q Consensus 59 ~~~~~~C~~C~k~f~ 73 (96)
......|..|+..|.
T Consensus 22 ~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 22 KGRKVRCSKCGHVFF 36 (36)
T ss_pred CCcEEECCCCCCEeC
Confidence 334588999988763
No 127
>PTZ00448 hypothetical protein; Provisional
Probab=28.61 E-value=31 Score=24.45 Aligned_cols=23 Identities=26% Similarity=0.546 Sum_probs=19.5
Q ss_pred ceecccchhhccCCchHHHHHhh
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRS 84 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~ 84 (96)
.|.|..|+-.|......+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 48899999999877778888875
No 128
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=28.53 E-value=52 Score=22.55 Aligned_cols=25 Identities=28% Similarity=0.688 Sum_probs=21.7
Q ss_pred CCceecccchhhccCCchHHHHHhh
Q psy9655 60 NPSLSCTYCSRAFKKRSDLTRHIRS 84 (96)
Q Consensus 60 ~~~~~C~~C~k~f~~~~~l~~h~~~ 84 (96)
..-|.|..|-+-|.....+.+|+..
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHh
Confidence 3459999999999999999999863
No 129
>PF14353 CpXC: CpXC protein
Probab=28.35 E-value=11 Score=22.07 Aligned_cols=20 Identities=30% Similarity=0.663 Sum_probs=15.0
Q ss_pred ceecccchhhccCCchHHHH
Q psy9655 62 SLSCTYCSRAFKKRSDLTRH 81 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h 81 (96)
.|.|+.||..|.-...+.-|
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred EEECCCCCCceecCCCEEEE
Confidence 48999999988766655443
No 130
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.27 E-value=30 Score=20.40 Aligned_cols=13 Identities=15% Similarity=0.340 Sum_probs=8.7
Q ss_pred ceecccchhhccCC
Q psy9655 62 SLSCTYCSRAFKKR 75 (96)
Q Consensus 62 ~~~C~~C~k~f~~~ 75 (96)
.+.| .|+..|...
T Consensus 70 ~~~C-~Cg~~~~~~ 82 (124)
T PRK00762 70 EIEC-ECGYEGVVD 82 (124)
T ss_pred eEEe-eCcCccccc
Confidence 3778 888776543
No 131
>KOG1818|consensus
Probab=28.19 E-value=20 Score=27.15 Aligned_cols=36 Identities=17% Similarity=0.267 Sum_probs=23.5
Q ss_pred CceecccchhhccCCchHHHHHhhhCCC-CCcc-cccC
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIRSHTKE-KPFK-VRSL 96 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~~htge-kp~~-C~~C 96 (96)
+.+.|..||..|...-..+.-...+.|. +|.+ |..|
T Consensus 180 rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C 217 (634)
T KOG1818|consen 180 RKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSC 217 (634)
T ss_pred ccccccccchhhccCccccccCcccccccccceehhhh
Confidence 4578889999998877666555556664 5543 5444
No 132
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=27.26 E-value=42 Score=15.46 Aligned_cols=15 Identities=27% Similarity=0.873 Sum_probs=5.7
Q ss_pred CceecccchhhccCC
Q psy9655 61 PSLSCTYCSRAFKKR 75 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~ 75 (96)
+.|-|..|..-|..-
T Consensus 2 ~ryyCdyC~~~~~~d 16 (38)
T PF06220_consen 2 PRYYCDYCKKYLTHD 16 (38)
T ss_dssp -S-B-TTT--B-S--
T ss_pred cCeecccccceecCC
Confidence 358999999988443
No 133
>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=27.04 E-value=36 Score=17.29 Aligned_cols=24 Identities=17% Similarity=0.254 Sum_probs=15.4
Q ss_pred CCceecccchhhccCC---chHHHHHh
Q psy9655 60 NPSLSCTYCSRAFKKR---SDLTRHIR 83 (96)
Q Consensus 60 ~~~~~C~~C~k~f~~~---~~l~~h~~ 83 (96)
...|.|..|++.+-.. .+...|.+
T Consensus 9 ~~lw~CL~Cg~~~C~~~~~~Ha~~H~~ 35 (63)
T PF02148_consen 9 SNLWLCLTCGYVGCGRYSNGHALKHYK 35 (63)
T ss_dssp SSEEEETTTS-EEETTTSTSHHHHHHH
T ss_pred CceEEeCCCCcccccCCcCcHHHHhhc
Confidence 3469999999877764 44455543
No 134
>PRK04351 hypothetical protein; Provisional
Probab=26.91 E-value=35 Score=20.84 Aligned_cols=27 Identities=15% Similarity=0.468 Sum_probs=17.6
Q ss_pred ceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
.|.|..|+..+.+. .+ | +..-|.|..|
T Consensus 112 ~Y~C~~Cg~~~~r~------Rr-~-n~~~yrCg~C 138 (149)
T PRK04351 112 LYECQSCGQQYLRK------RR-I-NTKRYRCGKC 138 (149)
T ss_pred EEECCCCCCEeeee------ee-c-CCCcEEeCCC
Confidence 48998899766432 12 2 2467888777
No 135
>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=26.57 E-value=31 Score=16.24 Aligned_cols=12 Identities=25% Similarity=0.977 Sum_probs=9.6
Q ss_pred Cceecccchhhc
Q psy9655 61 PSLSCTYCSRAF 72 (96)
Q Consensus 61 ~~~~C~~C~k~f 72 (96)
....|..|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 357899999876
No 136
>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=26.37 E-value=65 Score=14.69 Aligned_cols=17 Identities=12% Similarity=0.395 Sum_probs=10.2
Q ss_pred cCCCCCCCCCceecccc
Q psy9655 52 SYNRPVPPNPSLSCTYC 68 (96)
Q Consensus 52 ~~~~~~~~~~~~~C~~C 68 (96)
.+-....|...|.|..|
T Consensus 19 k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 19 KNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eCCCCCCCCEeEecCcC
Confidence 33444455566888776
No 137
>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=26.29 E-value=28 Score=16.07 Aligned_cols=11 Identities=18% Similarity=0.646 Sum_probs=8.7
Q ss_pred ceecccchhhc
Q psy9655 62 SLSCTYCSRAF 72 (96)
Q Consensus 62 ~~~C~~C~k~f 72 (96)
-|.|..|+..|
T Consensus 28 fy~C~~C~~~w 38 (39)
T PF01096_consen 28 FYVCCNCGHRW 38 (39)
T ss_dssp EEEESSSTEEE
T ss_pred EEEeCCCCCee
Confidence 38899998766
No 138
>PLN02294 cytochrome c oxidase subunit Vb
Probab=26.08 E-value=34 Score=21.60 Aligned_cols=16 Identities=25% Similarity=0.698 Sum_probs=12.5
Q ss_pred CCceecccchhhccCC
Q psy9655 60 NPSLSCTYCSRAFKKR 75 (96)
Q Consensus 60 ~~~~~C~~C~k~f~~~ 75 (96)
.+++.|..||..|...
T Consensus 139 Gkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 139 GKSFECPVCTQYFELE 154 (174)
T ss_pred CCceeCCCCCCEEEEE
Confidence 3678899999988654
No 139
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=25.62 E-value=34 Score=24.88 Aligned_cols=19 Identities=16% Similarity=0.588 Sum_probs=14.6
Q ss_pred CCCCceecccchhhccCCc
Q psy9655 58 PPNPSLSCTYCSRAFKKRS 76 (96)
Q Consensus 58 ~~~~~~~C~~C~k~f~~~~ 76 (96)
.....|.|..|++.|.-..
T Consensus 421 ~~~~~~~c~~c~~~yd~~~ 439 (479)
T PRK05452 421 DLGPRMQCSVCQWIYDPAK 439 (479)
T ss_pred CCCCeEEECCCCeEECCCC
Confidence 3456799999999887543
No 140
>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=25.27 E-value=24 Score=22.73 Aligned_cols=23 Identities=22% Similarity=0.670 Sum_probs=0.0
Q ss_pred CCceecccchh-hccCCchHHHHH
Q psy9655 60 NPSLSCTYCSR-AFKKRSDLTRHI 82 (96)
Q Consensus 60 ~~~~~C~~C~k-~f~~~~~l~~h~ 82 (96)
...|.|.+||. +|.-+..+..|-
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp ------------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHhc
Confidence 45699999995 454555566553
No 141
>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=24.46 E-value=32 Score=19.73 Aligned_cols=7 Identities=43% Similarity=1.042 Sum_probs=3.1
Q ss_pred eecccch
Q psy9655 63 LSCTYCS 69 (96)
Q Consensus 63 ~~C~~C~ 69 (96)
|.|..|+
T Consensus 32 y~C~~C~ 38 (102)
T PF11672_consen 32 YVCTPCD 38 (102)
T ss_pred EECCCCC
Confidence 4444443
No 142
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=24.11 E-value=41 Score=19.42 Aligned_cols=15 Identities=33% Similarity=0.722 Sum_probs=11.7
Q ss_pred ceecccchhhccCCc
Q psy9655 62 SLSCTYCSRAFKKRS 76 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~ 76 (96)
+++|..||..|..-+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 578889999888743
No 143
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=24.10 E-value=55 Score=23.89 Aligned_cols=23 Identities=26% Similarity=0.754 Sum_probs=20.8
Q ss_pred CceecccchhhccCCchHHHHHh
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIR 83 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~ 83 (96)
.-|.|..|-+-|.....|.+|+.
T Consensus 197 ~lyiCe~Cl~y~~~~~~~~~H~~ 219 (450)
T PLN00104 197 KLYFCEFCLKFMKRKEQLQRHMK 219 (450)
T ss_pred eEEEchhhhhhhcCHHHHHHHHh
Confidence 45889999999999999999986
No 144
>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=23.94 E-value=39 Score=15.52 Aligned_cols=12 Identities=17% Similarity=0.487 Sum_probs=6.8
Q ss_pred Cceecccchhhc
Q psy9655 61 PSLSCTYCSRAF 72 (96)
Q Consensus 61 ~~~~C~~C~k~f 72 (96)
+.|.|..||...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 459999999865
No 145
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.80 E-value=17 Score=18.00 Aligned_cols=15 Identities=33% Similarity=0.716 Sum_probs=11.6
Q ss_pred eecccchhhccCCch
Q psy9655 63 LSCTYCSRAFKKRSD 77 (96)
Q Consensus 63 ~~C~~C~k~f~~~~~ 77 (96)
-.|+.|++.|.+..-
T Consensus 13 KICpvCqRPFsWRkK 27 (54)
T COG4338 13 KICPVCQRPFSWRKK 27 (54)
T ss_pred hhhhhhcCchHHHHH
Confidence 469999999987543
No 146
>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=23.72 E-value=15 Score=18.28 Aligned_cols=25 Identities=24% Similarity=0.420 Sum_probs=13.2
Q ss_pred CceecccchhhccCCchHHHHHhhh
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIRSH 85 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~~h 85 (96)
..|.|..|...|-.-=++-.|...|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CeEECCCCCCccccCcChhhhcccc
Confidence 4599999999987666666665444
No 147
>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
Probab=23.35 E-value=40 Score=24.20 Aligned_cols=10 Identities=20% Similarity=0.992 Sum_probs=5.9
Q ss_pred ecccchhhcc
Q psy9655 64 SCTYCSRAFK 73 (96)
Q Consensus 64 ~C~~C~k~f~ 73 (96)
.|+.||+.-.
T Consensus 9 ~c~fc~~~~~ 18 (413)
T TIGR00382 9 YCSFCGKSQD 18 (413)
T ss_pred ecCCCCCChh
Confidence 5666666533
No 148
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=23.33 E-value=44 Score=21.14 Aligned_cols=14 Identities=21% Similarity=0.579 Sum_probs=8.0
Q ss_pred CCceecccchhhcc
Q psy9655 60 NPSLSCTYCSRAFK 73 (96)
Q Consensus 60 ~~~~~C~~C~k~f~ 73 (96)
...|.|+.|.-.|+
T Consensus 111 ~~~y~C~~~~~r~s 124 (176)
T COG1675 111 NNYYVCPNCHVKYS 124 (176)
T ss_pred CCceeCCCCCCccc
Confidence 34477766665443
No 149
>KOG4727|consensus
Probab=23.23 E-value=41 Score=21.32 Aligned_cols=21 Identities=24% Similarity=0.528 Sum_probs=18.6
Q ss_pred ceecccchhhccCCchHHHHH
Q psy9655 62 SLSCTYCSRAFKKRSDLTRHI 82 (96)
Q Consensus 62 ~~~C~~C~k~f~~~~~l~~h~ 82 (96)
.|.|.+|.-.|...-++..|+
T Consensus 75 GyyCdVCdcvvKDSinflDHi 95 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHI 95 (193)
T ss_pred ceeeeecceeehhhHHHHHHh
Confidence 499999999999988888886
No 150
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=21.87 E-value=42 Score=20.01 Aligned_cols=28 Identities=21% Similarity=0.501 Sum_probs=16.9
Q ss_pred CceecccchhhccCCchHHHHHhhhCCCCCcccccC
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVRSL 96 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~~htgekp~~C~~C 96 (96)
-.|.|..|+..+.....+ ...-|.|..|
T Consensus 122 ~~~~C~~C~~~~~r~~~~--------~~~~~~C~~C 149 (157)
T PF10263_consen 122 YVYRCPSCGREYKRHRRS--------KRKRYRCGRC 149 (157)
T ss_pred eEEEcCCCCCEeeeeccc--------chhhEECCCC
Confidence 358899999877443332 1123777766
No 151
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.54 E-value=50 Score=16.84 Aligned_cols=15 Identities=13% Similarity=0.521 Sum_probs=10.2
Q ss_pred CCCceecccchhhcc
Q psy9655 59 PNPSLSCTYCSRAFK 73 (96)
Q Consensus 59 ~~~~~~C~~C~k~f~ 73 (96)
..+.|.|..||..+.
T Consensus 43 ~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 43 SGRVFTCPNCGFEMD 57 (69)
T ss_pred ccceEEcCCCCCEEC
Confidence 445688888887643
No 152
>PTZ00064 histone acetyltransferase; Provisional
Probab=21.50 E-value=73 Score=23.77 Aligned_cols=24 Identities=29% Similarity=0.560 Sum_probs=21.0
Q ss_pred CceecccchhhccCCchHHHHHhh
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIRS 84 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~~ 84 (96)
.-|.|..|-+-|.....|.+|+..
T Consensus 279 ~LYICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 279 TLHFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred eEEEccchhhhhCCHHHHHHHHhc
Confidence 458899999999999999999863
No 153
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=21.28 E-value=66 Score=20.18 Aligned_cols=23 Identities=22% Similarity=0.468 Sum_probs=17.9
Q ss_pred CceecccchhhccCCchHHHHHh
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIR 83 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~ 83 (96)
.-+.|..||+.|-.-+++..-.+
T Consensus 129 ~f~~C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 129 EFYRCPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred ceeECCCCcccccCchHHHHHHH
Confidence 34779999999988888775444
No 154
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=21.09 E-value=51 Score=16.38 Aligned_cols=16 Identities=31% Similarity=0.729 Sum_probs=10.4
Q ss_pred CCCCceecccchhhcc
Q psy9655 58 PPNPSLSCTYCSRAFK 73 (96)
Q Consensus 58 ~~~~~~~C~~C~k~f~ 73 (96)
.....|.|.+|++.+.
T Consensus 31 ~~~~~~rC~YCe~~~~ 46 (52)
T PF02748_consen 31 KEPIKLRCHYCERIIT 46 (52)
T ss_dssp TTTCEEEETTT--EEE
T ss_pred CCCCEEEeeCCCCEec
Confidence 3455699999998775
No 155
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=21.01 E-value=44 Score=14.93 Aligned_cols=12 Identities=25% Similarity=0.819 Sum_probs=9.1
Q ss_pred ceecccchhhcc
Q psy9655 62 SLSCTYCSRAFK 73 (96)
Q Consensus 62 ~~~C~~C~k~f~ 73 (96)
.+.|..|+..|.
T Consensus 21 ~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 21 YEVCIFCGSSFP 32 (33)
T ss_pred eEEcccCCcEee
Confidence 368888988764
No 156
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=20.77 E-value=48 Score=15.34 Aligned_cols=12 Identities=25% Similarity=0.731 Sum_probs=9.4
Q ss_pred ceecccchhhcc
Q psy9655 62 SLSCTYCSRAFK 73 (96)
Q Consensus 62 ~~~C~~C~k~f~ 73 (96)
-|.|..|+..|.
T Consensus 28 fy~C~~C~~~w~ 39 (40)
T smart00440 28 FYVCTKCGHRWR 39 (40)
T ss_pred EEEeCCCCCEeC
Confidence 488999998764
No 157
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=20.70 E-value=54 Score=23.31 Aligned_cols=23 Identities=26% Similarity=0.720 Sum_probs=19.6
Q ss_pred CceecccchhhccCCchHHHHHh
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIR 83 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~ 83 (96)
+.+.|..|++-|....-+..|..
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~Hl~ 259 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYHLE 259 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHHHh
Confidence 34899999999999888888873
No 158
>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=20.44 E-value=34 Score=22.18 Aligned_cols=31 Identities=10% Similarity=0.322 Sum_probs=0.0
Q ss_pred CCceecccchhhccCCchHHHHHhhhCCCCCc
Q psy9655 60 NPSLSCTYCSRAFKKRSDLTRHIRSHTKEKPF 91 (96)
Q Consensus 60 ~~~~~C~~C~k~f~~~~~l~~h~~~htgekp~ 91 (96)
.....|+.||.... ...+..|+|+....-.|
T Consensus 166 ~~~~~cPitGe~IP-~~e~~eHmRi~LlDP~w 196 (229)
T PF12230_consen 166 EKMIICPITGEMIP-ADEMDEHMRIELLDPRW 196 (229)
T ss_dssp --------------------------------
T ss_pred cccccccccccccc-ccccccccccccccccc
Confidence 34478999999775 45688999987654433
No 159
>PLN03239 histone acetyltransferase; Provisional
Probab=20.40 E-value=62 Score=22.82 Aligned_cols=23 Identities=22% Similarity=0.397 Sum_probs=20.2
Q ss_pred CceecccchhhccCCchHHHHHh
Q psy9655 61 PSLSCTYCSRAFKKRSDLTRHIR 83 (96)
Q Consensus 61 ~~~~C~~C~k~f~~~~~l~~h~~ 83 (96)
.-|.|..|-+-|.....|.+|+.
T Consensus 105 ~lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 105 VLYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred eEEEeccchhhhcCHHHHHHHHH
Confidence 45999999999999999999875
No 160
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.25 E-value=68 Score=16.73 Aligned_cols=17 Identities=18% Similarity=0.489 Sum_probs=11.6
Q ss_pred CCCceecccchhhccCC
Q psy9655 59 PNPSLSCTYCSRAFKKR 75 (96)
Q Consensus 59 ~~~~~~C~~C~k~f~~~ 75 (96)
+-+.|.|+.|.-....+
T Consensus 28 PIrtymC~eC~~Rva~k 44 (68)
T COG4896 28 PIRTYMCPECEHRVAIK 44 (68)
T ss_pred CceeEechhhHhhhchh
Confidence 34569999998765543
Done!