Query psy6676
Match_columns 144
No_of_seqs 116 out of 1793
Neff 10.3
Searched_HMMs 46136
Date Sat Aug 17 00:15:12 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6676.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6676hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.8 7.6E-21 1.7E-25 128.4 5.2 86 26-113 159-244 (279)
2 KOG2462|consensus 99.8 1.3E-19 2.9E-24 122.4 5.4 87 24-110 183-269 (279)
3 KOG3576|consensus 99.6 4.6E-16 1E-20 101.2 1.7 87 24-110 113-199 (267)
4 KOG3623|consensus 99.5 5.4E-15 1.2E-19 111.4 2.4 80 26-105 892-971 (1007)
5 KOG1074|consensus 99.4 1.5E-13 3.3E-18 104.9 4.8 60 57-116 880-939 (958)
6 KOG3576|consensus 99.4 1.5E-13 3.2E-18 89.7 1.6 93 21-113 138-241 (267)
7 KOG3623|consensus 99.3 6.6E-13 1.4E-17 100.4 2.8 81 26-106 238-331 (1007)
8 KOG1074|consensus 99.2 3.1E-12 6.6E-17 98.0 1.7 88 25-112 602-696 (958)
9 PHA00733 hypothetical protein 99.2 2.1E-11 4.6E-16 75.8 3.9 84 25-110 37-125 (128)
10 KOG3608|consensus 99.0 1.2E-09 2.5E-14 77.0 6.2 90 21-111 285-379 (467)
11 KOG3608|consensus 98.9 9.2E-10 2E-14 77.6 4.1 90 24-114 259-351 (467)
12 PHA02768 hypothetical protein; 98.9 4.5E-10 9.9E-15 58.7 1.5 42 57-100 6-47 (55)
13 KOG3993|consensus 98.9 2.8E-10 6.1E-15 81.6 0.4 86 29-114 268-386 (500)
14 PF13465 zf-H2C2_2: Zinc-finge 98.7 5.8E-09 1.2E-13 46.8 1.4 25 71-95 1-25 (26)
15 PHA02768 hypothetical protein; 98.7 8.4E-09 1.8E-13 54.0 2.2 43 28-72 5-47 (55)
16 PLN03086 PRLI-interacting fact 98.7 3.3E-08 7.1E-13 74.7 5.8 78 25-107 450-537 (567)
17 PHA00733 hypothetical protein 98.6 1.2E-07 2.6E-12 59.1 4.7 57 23-81 68-124 (128)
18 PLN03086 PRLI-interacting fact 98.4 2.4E-07 5.3E-12 70.2 4.3 78 27-108 477-564 (567)
19 PHA00616 hypothetical protein 98.4 1.6E-07 3.5E-12 46.9 1.9 35 28-62 1-35 (44)
20 PF13465 zf-H2C2_2: Zinc-finge 98.3 4.4E-07 9.5E-12 40.6 2.3 25 43-67 1-25 (26)
21 PHA00732 hypothetical protein 98.3 5.7E-07 1.2E-11 51.2 2.4 47 28-80 1-48 (79)
22 PHA00616 hypothetical protein 98.1 1.9E-06 4.1E-11 43.0 2.3 28 84-111 1-28 (44)
23 PHA00732 hypothetical protein 98.1 2.9E-06 6.3E-11 48.3 3.0 48 56-109 1-49 (79)
24 PF00096 zf-C2H2: Zinc finger, 98.1 1.5E-06 3.2E-11 37.6 1.2 23 85-107 1-23 (23)
25 PF05605 zf-Di19: Drought indu 98.0 1.3E-05 2.8E-10 42.3 4.2 35 29-64 3-39 (54)
26 KOG3993|consensus 98.0 4.4E-06 9.4E-11 60.6 2.8 53 27-79 294-379 (500)
27 PF13894 zf-C2H2_4: C2H2-type 97.9 5.3E-06 1.2E-10 35.9 1.5 24 85-108 1-24 (24)
28 COG5189 SFP1 Putative transcri 97.9 2.3E-06 5E-11 60.0 0.3 71 26-106 347-420 (423)
29 PF05605 zf-Di19: Drought indu 97.9 2.8E-05 6E-10 41.1 3.9 50 56-108 2-53 (54)
30 PF13912 zf-C2H2_6: C2H2-type 97.8 8.2E-06 1.8E-10 36.6 1.2 26 84-109 1-26 (27)
31 PF00096 zf-C2H2: Zinc finger, 97.8 1.8E-05 3.9E-10 34.0 1.9 22 29-50 1-22 (23)
32 PF12756 zf-C2H2_2: C2H2 type 97.6 4.9E-05 1.1E-09 45.0 2.5 74 30-108 1-74 (100)
33 PF13894 zf-C2H2_4: C2H2-type 97.6 7.3E-05 1.6E-09 32.2 2.2 23 29-51 1-23 (24)
34 PF13912 zf-C2H2_6: C2H2-type 97.4 0.0001 2.2E-09 32.9 1.5 24 28-51 1-24 (27)
35 smart00355 ZnF_C2H2 zinc finge 97.4 0.00018 4E-09 31.4 2.3 24 85-108 1-24 (26)
36 PF09237 GAGA: GAGA factor; I 97.0 0.00081 1.7E-08 34.5 2.3 32 80-111 20-51 (54)
37 PF12874 zf-met: Zinc-finger o 96.8 0.00054 1.2E-08 29.9 0.9 22 85-106 1-22 (25)
38 PF09237 GAGA: GAGA factor; I 96.8 0.0017 3.8E-08 33.3 2.8 30 26-55 22-51 (54)
39 smart00355 ZnF_C2H2 zinc finge 96.8 0.0017 3.7E-08 28.1 2.4 23 29-51 1-23 (26)
40 PRK04860 hypothetical protein; 96.7 0.00093 2E-08 43.3 1.7 38 56-97 119-156 (160)
41 PF13909 zf-H2C2_5: C2H2-type 96.7 0.00089 1.9E-08 28.9 1.2 23 85-108 1-23 (24)
42 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.00091 2E-08 29.9 0.5 22 85-106 2-23 (27)
43 PF12874 zf-met: Zinc-finger o 96.4 0.0021 4.5E-08 28.0 1.4 22 29-50 1-22 (25)
44 PF13909 zf-H2C2_5: C2H2-type 96.2 0.0041 8.8E-08 26.8 1.7 23 29-52 1-23 (24)
45 PRK04860 hypothetical protein; 95.9 0.0055 1.2E-07 39.7 2.1 39 27-69 118-156 (160)
46 KOG4173|consensus 95.8 0.0063 1.4E-07 40.6 2.0 80 25-107 76-169 (253)
47 KOG1146|consensus 95.7 0.0056 1.2E-07 50.8 1.5 83 20-106 457-540 (1406)
48 PF12171 zf-C2H2_jaz: Zinc-fin 95.6 0.0031 6.6E-08 28.1 -0.0 20 29-48 2-21 (27)
49 PF13913 zf-C2HC_2: zinc-finge 95.5 0.013 2.7E-07 25.7 1.7 21 85-106 3-23 (25)
50 COG4049 Uncharacterized protei 94.8 0.015 3.3E-07 30.3 1.0 33 21-53 10-42 (65)
51 KOG1146|consensus 93.9 0.026 5.6E-07 47.2 1.1 80 29-113 1261-1358(1406)
52 smart00451 ZnF_U1 U1-like zinc 93.9 0.04 8.7E-07 25.8 1.4 23 84-106 3-25 (35)
53 smart00451 ZnF_U1 U1-like zinc 93.5 0.074 1.6E-06 24.9 2.0 22 28-49 3-24 (35)
54 cd00350 rubredoxin_like Rubred 93.2 0.053 1.2E-06 25.3 1.1 9 83-91 16-24 (33)
55 COG4049 Uncharacterized protei 93.1 0.059 1.3E-06 28.2 1.3 30 79-108 12-41 (65)
56 COG5236 Uncharacterized conser 93.1 0.065 1.4E-06 38.7 1.9 79 28-108 151-244 (493)
57 PF09538 FYDLN_acid: Protein o 92.6 0.089 1.9E-06 31.8 1.8 15 83-97 25-39 (108)
58 PF09538 FYDLN_acid: Protein o 91.7 0.14 3E-06 31.0 1.9 30 29-69 10-39 (108)
59 KOG2482|consensus 91.1 0.26 5.5E-06 35.7 3.0 79 28-106 195-356 (423)
60 COG1592 Rubrerythrin [Energy p 91.0 0.13 2.9E-06 33.5 1.4 24 56-92 134-157 (166)
61 PF12756 zf-C2H2_2: C2H2 type 90.5 0.33 7.2E-06 28.2 2.7 24 56-79 50-73 (100)
62 KOG2231|consensus 90.3 0.42 9.2E-06 37.8 3.8 81 29-112 100-210 (669)
63 KOG2893|consensus 89.8 0.095 2.1E-06 36.0 -0.0 28 33-64 15-42 (341)
64 COG5048 FOG: Zn-finger [Genera 89.7 0.087 1.9E-06 38.8 -0.3 60 28-87 289-354 (467)
65 PF12013 DUF3505: Protein of u 88.9 0.75 1.6E-05 27.7 3.5 26 84-109 80-109 (109)
66 COG1592 Rubrerythrin [Energy p 88.7 0.27 5.8E-06 32.1 1.4 24 28-64 134-157 (166)
67 cd00729 rubredoxin_SM Rubredox 88.6 0.26 5.7E-06 23.2 1.0 10 57-66 3-12 (34)
68 COG5048 FOG: Zn-finger [Genera 88.6 0.12 2.7E-06 38.0 -0.2 59 55-113 288-352 (467)
69 KOG2893|consensus 88.2 0.16 3.6E-06 34.9 0.2 42 59-104 13-54 (341)
70 COG5189 SFP1 Putative transcri 87.5 0.55 1.2E-05 33.8 2.4 28 82-109 347-376 (423)
71 PF09986 DUF2225: Uncharacteri 87.2 0.078 1.7E-06 36.1 -1.8 17 26-42 3-19 (214)
72 KOG2482|consensus 85.9 0.85 1.8E-05 33.2 2.7 54 25-78 141-217 (423)
73 PF02892 zf-BED: BED zinc fing 85.8 0.65 1.4E-05 23.0 1.6 26 81-106 13-42 (45)
74 TIGR00622 ssl1 transcription f 85.6 1.3 2.7E-05 27.0 3.0 82 27-110 14-107 (112)
75 TIGR02300 FYDLN_acid conserved 84.9 0.56 1.2E-05 29.1 1.3 14 55-68 25-38 (129)
76 KOG2186|consensus 84.6 0.63 1.4E-05 32.3 1.6 47 29-78 4-50 (276)
77 PF05443 ROS_MUCR: ROS/MUCR tr 83.0 0.63 1.4E-05 29.2 1.0 25 83-110 71-95 (132)
78 KOG2231|consensus 82.9 1.7 3.8E-05 34.6 3.5 69 29-105 183-260 (669)
79 KOG2186|consensus 82.9 0.94 2E-05 31.5 1.9 46 57-105 4-49 (276)
80 COG5236 Uncharacterized conser 82.8 2.7 5.9E-05 30.7 4.2 79 30-113 222-310 (493)
81 smart00614 ZnF_BED BED zinc fi 82.1 0.99 2.1E-05 23.1 1.4 22 84-105 18-44 (50)
82 TIGR00373 conserved hypothetic 82.1 1.5 3.3E-05 28.4 2.6 34 53-95 106-139 (158)
83 PRK06266 transcription initiat 81.9 0.7 1.5E-05 30.6 0.9 34 54-96 115-148 (178)
84 KOG2785|consensus 81.8 1.5 3.3E-05 32.3 2.7 73 29-106 167-242 (390)
85 KOG3408|consensus 80.9 1.2 2.6E-05 27.3 1.6 27 80-106 53-79 (129)
86 TIGR00373 conserved hypothetic 80.8 1 2.2E-05 29.2 1.4 35 24-67 105-139 (158)
87 COG1997 RPL43A Ribosomal prote 80.0 0.89 1.9E-05 26.2 0.8 33 55-97 34-66 (89)
88 PRK06266 transcription initiat 79.8 1.6 3.4E-05 28.9 2.1 34 25-67 114-147 (178)
89 PRK00464 nrdR transcriptional 79.2 0.41 8.9E-06 30.9 -0.8 13 57-69 29-41 (154)
90 PF13719 zinc_ribbon_5: zinc-r 78.4 1.4 3.1E-05 21.0 1.2 10 31-40 5-14 (37)
91 COG2888 Predicted Zn-ribbon RN 77.9 1.2 2.6E-05 23.7 0.8 33 55-92 26-58 (61)
92 smart00531 TFIIE Transcription 77.8 3.7 8.1E-05 26.2 3.3 39 53-95 96-134 (147)
93 PF07800 DUF1644: Protein of u 77.3 16 0.00035 23.7 5.9 90 24-118 25-142 (162)
94 TIGR02605 CxxC_CxxC_SSSS putat 77.2 0.7 1.5E-05 23.7 -0.1 11 57-67 6-16 (52)
95 TIGR02098 MJ0042_CXXC MJ0042 f 75.1 1.7 3.6E-05 20.7 0.9 10 30-39 4-13 (38)
96 KOG2071|consensus 75.0 2.3 4.9E-05 33.2 2.0 26 26-51 416-441 (579)
97 smart00734 ZnF_Rad18 Rad18-lik 74.5 3.3 7.2E-05 18.1 1.7 18 30-48 3-20 (26)
98 smart00834 CxxC_CXXC_SSSS Puta 73.5 0.95 2.1E-05 21.8 -0.2 11 57-67 6-16 (41)
99 PF04959 ARS2: Arsenite-resist 73.3 1.7 3.7E-05 29.7 0.9 25 57-81 78-102 (214)
100 COG1198 PriA Primosomal protei 72.9 1.2 2.6E-05 35.9 0.2 48 30-93 437-484 (730)
101 smart00659 RPOLCX RNA polymera 71.8 2.5 5.5E-05 21.1 1.1 10 29-38 3-12 (44)
102 KOG1280|consensus 70.5 5.3 0.00011 29.3 2.8 39 25-63 76-116 (381)
103 PRK00398 rpoP DNA-directed RNA 69.6 2.7 5.8E-05 21.0 0.9 10 29-38 4-13 (46)
104 KOG2785|consensus 69.4 8.3 0.00018 28.6 3.7 24 55-78 216-242 (390)
105 PF15135 UPF0515: Uncharacteri 69.0 3.2 7E-05 28.9 1.5 63 22-97 106-168 (278)
106 PF12013 DUF3505: Protein of u 68.0 5.1 0.00011 24.0 2.1 26 28-53 80-109 (109)
107 PF05191 ADK_lid: Adenylate ki 67.8 2.7 5.8E-05 20.0 0.7 9 30-38 3-11 (36)
108 COG4530 Uncharacterized protei 67.6 3.6 7.8E-05 24.9 1.3 13 54-66 24-36 (129)
109 KOG4173|consensus 66.4 3.7 8.1E-05 27.8 1.3 49 55-106 78-128 (253)
110 PF07754 DUF1610: Domain of un 66.3 2.4 5.1E-05 18.3 0.3 10 83-92 15-24 (24)
111 KOG2907|consensus 66.3 2 4.4E-05 26.0 0.1 40 57-96 75-114 (116)
112 PF13878 zf-C2H2_3: zinc-finge 66.1 7.7 0.00017 18.9 2.2 24 29-52 14-39 (41)
113 PRK09678 DNA-binding transcrip 66.0 1.4 2.9E-05 24.6 -0.6 42 57-100 2-45 (72)
114 PF12760 Zn_Tnp_IS1595: Transp 65.5 6 0.00013 19.7 1.8 11 82-92 35-45 (46)
115 COG4957 Predicted transcriptio 64.9 3 6.5E-05 26.2 0.7 24 85-111 77-100 (148)
116 PHA00626 hypothetical protein 64.9 2.5 5.4E-05 22.2 0.3 17 82-98 21-37 (59)
117 COG3357 Predicted transcriptio 64.7 4.8 0.0001 23.4 1.4 28 55-92 57-84 (97)
118 smart00440 ZnF_C2C2 C2C2 Zinc 64.6 0.69 1.5E-05 22.6 -1.8 10 85-94 29-38 (40)
119 KOG0782|consensus 64.5 1.1 2.5E-05 34.9 -1.5 51 42-98 239-290 (1004)
120 KOG4167|consensus 64.2 2.2 4.8E-05 34.3 -0.0 27 83-109 791-817 (907)
121 PRK14890 putative Zn-ribbon RN 63.6 5.4 0.00012 21.3 1.4 51 26-92 5-56 (59)
122 PRK03824 hypA hydrogenase nick 63.3 2.7 5.9E-05 26.5 0.3 10 83-92 106-115 (135)
123 PTZ00255 60S ribosomal protein 63.0 1.9 4.1E-05 25.1 -0.4 33 55-97 35-67 (90)
124 TIGR00280 L37a ribosomal prote 62.7 1.7 3.6E-05 25.4 -0.7 33 55-97 34-66 (91)
125 KOG2593|consensus 62.3 5.6 0.00012 30.0 1.7 38 24-64 124-161 (436)
126 COG5112 UFD2 U1-like Zn-finger 61.5 5.5 0.00012 23.9 1.3 26 81-106 52-77 (126)
127 PF10571 UPF0547: Uncharacteri 60.3 3.7 7.9E-05 18.0 0.3 9 86-94 16-24 (26)
128 PF13717 zinc_ribbon_4: zinc-r 60.1 4.5 9.8E-05 19.1 0.7 32 30-66 4-35 (36)
129 PF00301 Rubredoxin: Rubredoxi 59.5 2.9 6.4E-05 21.2 -0.0 11 29-39 2-12 (47)
130 KOG3408|consensus 58.4 6.6 0.00014 24.2 1.3 26 25-50 54-79 (129)
131 PF08274 PhnA_Zn_Ribbon: PhnA 57.5 3.8 8.2E-05 18.7 0.1 7 57-63 20-26 (30)
132 COG1996 RPC10 DNA-directed RNA 57.1 5.4 0.00012 20.4 0.7 11 28-38 6-16 (49)
133 COG1571 Predicted DNA-binding 56.8 6.5 0.00014 29.7 1.3 14 84-97 367-380 (421)
134 PF06524 NOA36: NOA36 protein; 56.8 5.1 0.00011 28.2 0.7 84 23-107 137-232 (314)
135 TIGR00595 priA primosomal prot 56.8 3.2 6.9E-05 32.2 -0.3 11 82-92 251-261 (505)
136 PRK03976 rpl37ae 50S ribosomal 56.5 2.3 4.9E-05 24.8 -0.8 33 55-97 35-67 (90)
137 PRK14873 primosome assembly pr 56.2 6.5 0.00014 31.7 1.3 44 30-93 385-431 (665)
138 PF08790 zf-LYAR: LYAR-type C2 55.7 1.6 3.5E-05 19.5 -1.2 19 85-104 1-19 (28)
139 PF04959 ARS2: Arsenite-resist 54.5 10 0.00022 26.0 1.8 30 24-53 73-102 (214)
140 COG1655 Uncharacterized protei 54.3 3.1 6.6E-05 28.7 -0.6 8 85-92 63-70 (267)
141 PF09723 Zn-ribbon_8: Zinc rib 53.3 4.2 9E-05 19.9 -0.1 15 85-99 6-20 (42)
142 KOG0717|consensus 52.7 7.2 0.00016 29.8 1.0 21 85-105 293-313 (508)
143 KOG2593|consensus 52.1 7.4 0.00016 29.4 1.0 35 54-91 126-160 (436)
144 KOG2636|consensus 52.0 9.9 0.00021 28.9 1.6 29 77-105 394-423 (497)
145 PF15269 zf-C2H2_7: Zinc-finge 51.7 10 0.00022 19.0 1.1 22 57-78 21-42 (54)
146 COG3091 SprT Zn-dependent meta 51.5 6.3 0.00014 25.4 0.5 32 56-92 117-148 (156)
147 KOG4377|consensus 50.9 9.6 0.00021 28.7 1.4 50 3-52 237-297 (480)
148 cd00924 Cyt_c_Oxidase_Vb Cytoc 49.9 7.4 0.00016 23.1 0.6 16 23-39 75-90 (97)
149 KOG1994|consensus 49.8 7.3 0.00016 26.8 0.6 22 83-104 238-259 (268)
150 KOG0978|consensus 49.6 5.2 0.00011 32.2 -0.1 20 84-103 678-697 (698)
151 PLN03238 probable histone acet 48.9 19 0.0004 25.9 2.5 31 81-111 45-75 (290)
152 PF04780 DUF629: Protein of un 48.3 11 0.00025 28.9 1.5 33 79-111 52-84 (466)
153 PRK04023 DNA polymerase II lar 47.8 14 0.00031 31.2 2.0 12 26-37 624-635 (1121)
154 PF03604 DNA_RNApol_7kD: DNA d 47.6 16 0.00035 16.8 1.4 8 85-92 18-25 (32)
155 PF01096 TFIIS_C: Transcriptio 47.5 0.54 1.2E-05 22.8 -3.8 10 85-94 29-38 (39)
156 KOG4167|consensus 47.4 4.6 0.0001 32.6 -0.7 27 26-52 790-816 (907)
157 PF04216 FdhE: Protein involve 46.7 1.4 3E-05 31.5 -3.4 9 29-37 173-181 (290)
158 COG1773 Rubredoxin [Energy pro 46.3 6.8 0.00015 20.6 0.0 14 84-97 3-16 (55)
159 PF07282 OrfB_Zn_ribbon: Putat 46.0 13 0.00028 20.1 1.2 11 83-93 45-55 (69)
160 KOG0978|consensus 44.8 8.4 0.00018 31.1 0.4 49 26-74 641-696 (698)
161 PF04423 Rad50_zn_hook: Rad50 44.7 22 0.00047 18.3 1.8 10 58-67 22-31 (54)
162 PRK05580 primosome assembly pr 44.2 6.3 0.00014 31.8 -0.4 10 83-92 420-429 (679)
163 PF10083 DUF2321: Uncharacteri 43.8 4.7 0.0001 26.0 -0.9 19 80-98 64-82 (158)
164 TIGR00100 hypA hydrogenase nic 43.8 10 0.00023 23.1 0.6 10 57-66 71-80 (115)
165 PF10276 zf-CHCC: Zinc-finger 43.3 11 0.00024 18.4 0.5 12 27-38 28-39 (40)
166 PRK12380 hydrogenase nickel in 43.2 12 0.00026 22.8 0.8 10 57-66 71-80 (113)
167 KOG4124|consensus 42.9 2.3 5E-05 31.1 -2.7 71 26-105 347-419 (442)
168 PF13824 zf-Mss51: Zinc-finger 42.7 19 0.00041 18.9 1.4 13 54-66 12-24 (55)
169 KOG1842|consensus 42.6 14 0.00029 28.2 1.1 21 57-77 16-36 (505)
170 PRK03564 formate dehydrogenase 42.5 13 0.00029 27.0 1.0 14 25-38 184-197 (309)
171 PF11931 DUF3449: Domain of un 42.3 8.3 0.00018 26.0 0.0 27 78-104 95-122 (196)
172 PF13451 zf-trcl: Probable zin 42.1 10 0.00022 19.5 0.3 20 82-101 2-21 (49)
173 PHA02998 RNA polymerase subuni 42.0 4.2 9E-05 26.9 -1.4 41 57-97 144-184 (195)
174 PF10013 DUF2256: Uncharacteri 42.0 14 0.0003 18.2 0.8 12 86-97 10-21 (42)
175 COG0068 HypF Hydrogenase matur 41.7 4.3 9.2E-05 32.7 -1.6 55 31-92 126-181 (750)
176 PF12907 zf-met2: Zinc-binding 41.7 24 0.00052 17.2 1.6 25 85-109 2-29 (40)
177 TIGR00686 phnA alkylphosphonat 41.0 12 0.00026 22.6 0.5 12 56-67 19-30 (109)
178 COG5027 SAS2 Histone acetyltra 40.5 20 0.00043 26.5 1.6 32 82-113 156-187 (395)
179 PRK00432 30S ribosomal protein 40.1 12 0.00027 19.1 0.4 10 56-65 37-46 (50)
180 TIGR01562 FdhE formate dehydro 40.1 23 0.00049 25.7 1.9 11 27-37 183-193 (305)
181 PLN00104 MYST -like histone ac 40.1 24 0.00053 27.0 2.1 30 82-111 196-225 (450)
182 PF02176 zf-TRAF: TRAF-type zi 39.5 14 0.0003 19.2 0.6 25 71-95 25-53 (60)
183 PTZ00064 histone acetyltransfe 39.4 28 0.0006 27.2 2.3 30 81-110 277-306 (552)
184 COG1327 Predicted transcriptio 39.4 6.9 0.00015 25.2 -0.7 12 57-68 29-40 (156)
185 KOG2747|consensus 39.1 25 0.00054 26.5 2.0 33 82-114 156-188 (396)
186 smart00154 ZnF_AN1 AN1-like Zi 38.3 15 0.00033 17.7 0.6 14 28-41 12-25 (39)
187 cd00730 rubredoxin Rubredoxin; 37.9 11 0.00025 19.3 0.1 13 85-97 2-14 (50)
188 PF01363 FYVE: FYVE zinc finge 37.6 15 0.00032 19.9 0.5 9 30-38 11-19 (69)
189 COG5151 SSL1 RNA polymerase II 36.9 44 0.00096 24.4 2.9 29 82-110 386-414 (421)
190 smart00661 RPOL9 RNA polymeras 36.7 16 0.00035 18.4 0.5 10 84-93 20-29 (52)
191 COG3677 Transposase and inacti 35.9 17 0.00036 22.8 0.6 16 82-97 51-66 (129)
192 PRK05978 hypothetical protein; 35.4 19 0.00042 23.1 0.8 10 86-95 54-63 (148)
193 KOG0717|consensus 35.2 24 0.00051 27.2 1.4 22 29-50 293-314 (508)
194 PF04780 DUF629: Protein of un 35.1 32 0.00069 26.6 2.1 24 27-50 56-79 (466)
195 PLN02294 cytochrome c oxidase 35.0 18 0.00039 23.8 0.7 16 26-41 139-154 (174)
196 PF07975 C1_4: TFIIH C1-like d 34.8 6.4 0.00014 20.4 -1.1 18 27-44 20-37 (51)
197 COG1675 TFA1 Transcription ini 34.7 22 0.00047 23.6 1.0 34 52-94 109-142 (176)
198 KOG2807|consensus 34.5 68 0.0015 23.6 3.5 27 83-109 344-370 (378)
199 KOG0320|consensus 34.5 20 0.00044 23.8 0.8 14 26-39 129-142 (187)
200 smart00064 FYVE Protein presen 34.2 23 0.00049 19.0 0.9 10 30-39 12-21 (68)
201 PF09845 DUF2072: Zn-ribbon co 33.9 21 0.00046 22.4 0.8 14 28-41 1-14 (131)
202 PF01286 XPA_N: XPA protein N- 33.6 12 0.00027 17.5 -0.2 11 58-68 5-15 (34)
203 COG5188 PRP9 Splicing factor 3 33.1 24 0.00053 26.1 1.1 23 83-105 237-259 (470)
204 COG3364 Zn-ribbon containing p 32.8 22 0.00047 21.3 0.7 12 56-67 2-13 (112)
205 PRK10220 hypothetical protein; 32.6 26 0.00056 21.3 1.0 11 56-66 20-30 (111)
206 PRK00564 hypA hydrogenase nick 32.5 20 0.00044 21.9 0.6 9 57-65 72-80 (117)
207 cd00065 FYVE FYVE domain; Zinc 32.5 30 0.00064 17.7 1.2 9 31-39 5-13 (57)
208 PF14803 Nudix_N_2: Nudix N-te 32.2 4.3 9.2E-05 19.1 -1.9 6 86-91 24-29 (34)
209 PRK14714 DNA polymerase II lar 31.6 34 0.00073 29.9 1.8 10 28-37 667-676 (1337)
210 COG1594 RPB9 DNA-directed RNA 31.0 10 0.00022 23.2 -0.9 15 27-41 21-35 (113)
211 COG4391 Uncharacterized protei 30.6 19 0.0004 19.4 0.2 14 26-39 46-59 (62)
212 COG4888 Uncharacterized Zn rib 30.5 6.4 0.00014 23.4 -1.7 13 26-38 20-32 (104)
213 PF14311 DUF4379: Domain of un 30.4 38 0.00082 17.4 1.4 9 29-37 29-37 (55)
214 PTZ00448 hypothetical protein; 30.2 35 0.00076 25.4 1.6 23 84-106 314-336 (373)
215 PF10537 WAC_Acf1_DNA_bd: ATP- 29.6 80 0.0017 18.9 2.8 38 27-65 2-39 (102)
216 KOG2636|consensus 29.5 41 0.00088 25.8 1.8 27 51-77 396-423 (497)
217 PF01428 zf-AN1: AN1-like Zinc 29.2 17 0.00038 17.7 -0.1 16 27-42 12-27 (43)
218 PRK00420 hypothetical protein; 27.9 33 0.00071 21.0 0.9 10 85-94 41-50 (112)
219 COG4338 Uncharacterized protei 27.7 21 0.00045 18.2 0.1 12 86-97 14-25 (54)
220 PRK05452 anaerobic nitric oxid 27.6 18 0.00039 27.9 -0.2 14 55-68 424-437 (479)
221 PRK03681 hypA hydrogenase nick 27.6 20 0.00043 21.8 -0.0 10 57-66 71-80 (114)
222 PRK14138 NAD-dependent deacety 26.7 75 0.0016 22.2 2.7 40 21-64 112-151 (244)
223 KOG2071|consensus 26.7 40 0.00086 26.8 1.4 26 83-108 417-442 (579)
224 PF08792 A2L_zn_ribbon: A2L zi 26.7 23 0.00051 16.4 0.1 11 85-95 22-32 (33)
225 KOG4118|consensus 26.6 45 0.00097 18.2 1.2 27 85-111 39-65 (74)
226 PRK00762 hypA hydrogenase nick 26.5 27 0.00058 21.7 0.4 10 57-67 71-80 (124)
227 PF06397 Desulfoferrod_N: Desu 26.4 25 0.00055 16.7 0.2 11 83-93 5-15 (36)
228 PLN03239 histone acetyltransfe 26.1 66 0.0014 23.9 2.3 25 82-106 104-128 (351)
229 PF11672 DUF3268: Protein of u 26.1 32 0.00069 20.6 0.7 11 27-37 1-11 (102)
230 TIGR01384 TFS_arch transcripti 26.1 9.2 0.0002 22.7 -1.7 14 27-40 15-28 (104)
231 PF01155 HypA: Hydrogenase exp 25.7 20 0.00042 21.8 -0.3 10 57-66 71-80 (113)
232 PF09416 UPF1_Zn_bind: RNA hel 25.5 79 0.0017 20.5 2.4 11 82-92 58-68 (152)
233 KOG2932|consensus 25.4 86 0.0019 23.0 2.7 29 80-108 140-171 (389)
234 PF07295 DUF1451: Protein of u 25.4 28 0.00061 22.3 0.4 28 55-92 111-138 (146)
235 KOG4727|consensus 25.4 33 0.00072 22.6 0.7 23 83-105 74-96 (193)
236 PF14353 CpXC: CpXC protein 24.9 26 0.00057 21.6 0.2 25 83-107 37-61 (128)
237 COG5216 Uncharacterized conser 24.5 45 0.00098 17.8 1.0 9 54-62 42-50 (67)
238 KOG2857|consensus 24.2 92 0.002 20.0 2.4 21 57-77 18-38 (157)
239 COG4306 Uncharacterized protei 24.2 24 0.00052 22.0 -0.1 14 55-68 67-80 (160)
240 KOG3214|consensus 24.0 24 0.00053 21.0 -0.1 13 84-96 47-59 (109)
241 TIGR00627 tfb4 transcription f 23.4 48 0.001 23.8 1.2 10 85-94 256-265 (279)
242 PF03966 Trm112p: Trm112p-like 23.2 32 0.00068 18.7 0.3 19 22-40 47-65 (68)
243 KOG0696|consensus 22.8 27 0.00058 26.9 -0.1 46 46-92 83-129 (683)
244 KOG1409|consensus 22.1 28 0.0006 25.8 -0.1 8 59-66 285-292 (404)
245 PF14787 zf-CCHC_5: GAG-polypr 22.0 29 0.00063 16.5 -0.0 15 86-100 4-18 (36)
246 cd01410 SIRT7 SIRT7: Eukaryoti 22.0 1.4E+02 0.003 20.2 3.2 41 21-64 88-128 (206)
247 PF13821 DUF4187: Domain of un 22.0 46 0.001 17.4 0.7 19 84-102 27-45 (55)
248 COG4640 Predicted membrane pro 21.6 58 0.0013 24.7 1.4 14 87-100 18-31 (465)
249 PF08209 Sgf11: Sgf11 (transcr 21.5 51 0.0011 15.3 0.7 22 85-107 5-26 (33)
250 TIGR00515 accD acetyl-CoA carb 21.5 47 0.001 23.9 0.9 32 29-69 27-58 (285)
251 PF10263 SprT-like: SprT-like 21.3 21 0.00045 22.7 -0.8 10 85-94 144-153 (157)
252 COG1779 C4-type Zn-finger prot 21.0 13 0.00028 25.1 -1.8 7 30-36 16-22 (201)
253 PF05495 zf-CHY: CHY zinc fing 20.5 12 0.00027 20.6 -1.7 57 29-93 11-70 (71)
254 PF04988 AKAP95: A-kinase anch 20.4 70 0.0015 21.0 1.4 21 29-49 1-21 (165)
255 KOG4696|consensus 20.4 65 0.0014 23.5 1.4 29 86-115 4-32 (393)
256 KOG4602|consensus 20.1 39 0.00085 23.9 0.3 11 83-93 267-277 (318)
No 1
>KOG2462|consensus
Probab=99.83 E-value=7.6e-21 Score=128.41 Aligned_cols=86 Identities=35% Similarity=0.692 Sum_probs=76.9
Q ss_pred CCcccccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcChHHHHHhHh
Q psy6676 26 EKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRNCDLRRHSL 105 (144)
Q Consensus 26 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 105 (144)
++-+.|++|++.|.....|..|+++|. .++.|.+||+.|...+.|+.|+|.|+||+||.|..|+|+|...++|+.|++
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQ 236 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQ 236 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHH
Confidence 566889999999999999999999986 578999999999999999999999999999999999999999999999999
Q ss_pred hccCCCCC
Q psy6676 106 THNLGSAT 113 (144)
Q Consensus 106 ~h~~~~~~ 113 (144)
+|......
T Consensus 237 THS~~K~~ 244 (279)
T KOG2462|consen 237 THSDVKKH 244 (279)
T ss_pred hhcCCccc
Confidence 99876543
No 2
>KOG2462|consensus
Probab=99.79 E-value=1.3e-19 Score=122.42 Aligned_cols=87 Identities=38% Similarity=0.735 Sum_probs=80.6
Q ss_pred CCCCcccccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcChHHHHHh
Q psy6676 24 SKEKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRNCDLRRH 103 (144)
Q Consensus 24 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H 103 (144)
...-+++|.+||+.|-..=-|+.|+++|+|++||.|+.|++.|...++|+-||++|.+.++|.|..|+|.|...+.|.+|
T Consensus 183 TH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH 262 (279)
T KOG2462|consen 183 THTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKH 262 (279)
T ss_pred ccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHh
Confidence 34478999999999999888999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhccCC
Q psy6676 104 SLTHNLG 110 (144)
Q Consensus 104 ~~~h~~~ 110 (144)
....-..
T Consensus 263 ~ES~C~~ 269 (279)
T KOG2462|consen 263 SESACLK 269 (279)
T ss_pred hhhcccc
Confidence 9764433
No 3
>KOG3576|consensus
Probab=99.58 E-value=4.6e-16 Score=101.22 Aligned_cols=87 Identities=36% Similarity=0.702 Sum_probs=79.6
Q ss_pred CCCCcccccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcChHHHHHh
Q psy6676 24 SKEKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRNCDLRRH 103 (144)
Q Consensus 24 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H 103 (144)
.+.-.|.|.+|++.|....-|.+|++.|...+.+.|..||+.|...-.|.+|++.|+|.+||+|..|+|+|+..-.|..|
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcslesh 192 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESH 192 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHH
Confidence 34556899999999999999999999999889999999999999999999999999999999999999999999999999
Q ss_pred HhhccCC
Q psy6676 104 SLTHNLG 110 (144)
Q Consensus 104 ~~~h~~~ 110 (144)
++.-|..
T Consensus 193 l~kvhgv 199 (267)
T KOG3576|consen 193 LKKVHGV 199 (267)
T ss_pred HHHHcCc
Confidence 9765533
No 4
>KOG3623|consensus
Probab=99.51 E-value=5.4e-15 Score=111.37 Aligned_cols=80 Identities=29% Similarity=0.652 Sum_probs=76.6
Q ss_pred CCcccccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcChHHHHHhHh
Q psy6676 26 EKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRNCDLRRHSL 105 (144)
Q Consensus 26 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 105 (144)
...|.|..|++.|--...|.+|.-.|.|.+||.|.+|.+.|..+-.|..|+|.|.|++||.|.+|+|.|+....+.+|+.
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 46799999999999999999999999999999999999999999999999999999999999999999999999999984
No 5
>KOG1074|consensus
Probab=99.43 E-value=1.5e-13 Score=104.89 Aligned_cols=60 Identities=33% Similarity=0.619 Sum_probs=56.4
Q ss_pred cccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcChHHHHHhHhhccCCCCCCCC
Q psy6676 57 HKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRNCDLRRHSLTHNLGSATSTS 116 (144)
Q Consensus 57 ~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~ 116 (144)
..|.+|++.|.....|..|+++|+++++|.|.+|++.|....+|+.|+.+|++......-
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~srr 939 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSRR 939 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCccC
Confidence 679999999999999999999999999999999999999999999999999998776655
No 6
>KOG3576|consensus
Probab=99.37 E-value=1.5e-13 Score=89.65 Aligned_cols=93 Identities=34% Similarity=0.523 Sum_probs=83.5
Q ss_pred cccCCCCcccccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCC-----------CCCcccCc
Q psy6676 21 YIHSKEKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTD-----------IKPYNCAA 89 (144)
Q Consensus 21 ~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~-----------~~~~~C~~ 89 (144)
+.|+..+.|.|..||+.|.+.-+|.+|+++|+|.+||+|..|++.|...-.|..|.+.-++ .+.|+|..
T Consensus 138 kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vced 217 (267)
T KOG3576|consen 138 KCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCED 217 (267)
T ss_pred hhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecc
Confidence 6788899999999999999999999999999999999999999999999999999864333 35689999
Q ss_pred chhhhcChHHHHHhHhhccCCCCC
Q psy6676 90 CGKVFRRNCDLRRHSLTHNLGSAT 113 (144)
Q Consensus 90 C~~~f~~~~~l~~H~~~h~~~~~~ 113 (144)
||.+-.....+..|++.||..++.
T Consensus 218 cg~t~~~~e~~~~h~~~~hp~Spa 241 (267)
T KOG3576|consen 218 CGYTSERPEVYYLHLKLHHPFSPA 241 (267)
T ss_pred cCCCCCChhHHHHHHHhcCCCCHH
Confidence 999999999999999999977654
No 7
>KOG3623|consensus
Probab=99.33 E-value=6.6e-13 Score=100.37 Aligned_cols=81 Identities=31% Similarity=0.613 Sum_probs=71.4
Q ss_pred CCcccccccccccCChHHHHHHHHHhCCC-------------CCcccccccccccCchHHHHHHhhcCCCCCcccCcchh
Q psy6676 26 EKPFKCTECGKGFCQSRTLAVHKILHLEE-------------SPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGK 92 (144)
Q Consensus 26 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~-------------~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 92 (144)
+..|.|..|..+|.+...|.+|+..|... +.|+|..|++.|..+-.|+.|+|+|.|++||.|..|+|
T Consensus 238 e~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkK 317 (1007)
T KOG3623|consen 238 EPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKK 317 (1007)
T ss_pred CCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCccccc
Confidence 45588999999999999999998877432 44999999999999999999999999999999999999
Q ss_pred hhcChHHHHHhHhh
Q psy6676 93 VFRRNCDLRRHSLT 106 (144)
Q Consensus 93 ~f~~~~~l~~H~~~ 106 (144)
.|+....+..|+..
T Consensus 318 RFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 318 RFSHSGSYSSHMSS 331 (1007)
T ss_pred ccccCCcccccccc
Confidence 99999999999853
No 8
>KOG1074|consensus
Probab=99.22 E-value=3.1e-12 Score=97.97 Aligned_cols=88 Identities=30% Similarity=0.594 Sum_probs=79.3
Q ss_pred CCCcccccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCCC----CCcccC---cchhhhcCh
Q psy6676 25 KEKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDI----KPYNCA---ACGKVFRRN 97 (144)
Q Consensus 25 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~----~~~~C~---~C~~~f~~~ 97 (144)
...|..|-+|.+..-....|+.|+++|+|++||+|.+|++.|..+.+|+.|+..|... ..+.|+ +|-+.|...
T Consensus 602 ~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~ 681 (958)
T KOG1074|consen 602 RTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNA 681 (958)
T ss_pred cCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccc
Confidence 3466889999999999999999999999999999999999999999999999888654 447899 999999999
Q ss_pred HHHHHhHhhccCCCC
Q psy6676 98 CDLRRHSLTHNLGSA 112 (144)
Q Consensus 98 ~~l~~H~~~h~~~~~ 112 (144)
-.|..|.++|..+..
T Consensus 682 V~lpQhIriH~~~~~ 696 (958)
T KOG1074|consen 682 VTLPQHIRIHLGGQI 696 (958)
T ss_pred ccccceEEeecCCCC
Confidence 999999999985433
No 9
>PHA00733 hypothetical protein
Probab=99.19 E-value=2.1e-11 Score=75.82 Aligned_cols=84 Identities=21% Similarity=0.312 Sum_probs=70.1
Q ss_pred CCCcccccccccccCChHHHHHH--H---HHhCCCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcChHH
Q psy6676 25 KEKPFKCTECGKGFCQSRTLAVH--K---ILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRNCD 99 (144)
Q Consensus 25 ~~~~~~C~~C~~~f~~~~~l~~h--~---~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~ 99 (144)
.++++.|..|...|.....|..+ . ..+.+.++|.|..|++.|.....|..|++.+ ..+|.|..|++.|.....
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~s 114 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDS 114 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHH
Confidence 36779999999999887777665 1 1234467899999999999999999999876 357999999999999999
Q ss_pred HHHhHhhccCC
Q psy6676 100 LRRHSLTHNLG 110 (144)
Q Consensus 100 l~~H~~~h~~~ 110 (144)
|..|+...|..
T Consensus 115 L~~H~~~~h~~ 125 (128)
T PHA00733 115 TLDHVCKKHNI 125 (128)
T ss_pred HHHHHHHhcCc
Confidence 99999887643
No 10
>KOG3608|consensus
Probab=98.99 E-value=1.2e-09 Score=77.05 Aligned_cols=90 Identities=29% Similarity=0.554 Sum_probs=55.5
Q ss_pred cccCCCCcccccccccccCChHHHHHHHHHhCCCCCccccc--ccccccCchHHHHHHhhcC-C--CCCcccCcchhhhc
Q psy6676 21 YIHSKEKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPV--CSRSFNQRSNLKTHLLTHT-D--IKPYNCAACGKVFR 95 (144)
Q Consensus 21 ~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~--C~~~~~~~~~l~~h~~~h~-~--~~~~~C~~C~~~f~ 95 (144)
..|+..+||+|..|+..+.++.+|..|+.+|. ...|.|.. |...+.+...+..|++.+. + ..+|.|-.|.+.|+
T Consensus 285 ~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft 363 (467)
T KOG3608|consen 285 YRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFT 363 (467)
T ss_pred hhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhc
Confidence 44566666666666666666666666666555 44566655 6666666666666665432 2 33466777777777
Q ss_pred ChHHHHHhHhhccCCC
Q psy6676 96 RNCDLRRHSLTHNLGS 111 (144)
Q Consensus 96 ~~~~l~~H~~~h~~~~ 111 (144)
+..+|..|+...|...
T Consensus 364 ~G~~L~~HL~kkH~f~ 379 (467)
T KOG3608|consen 364 SGKSLSAHLMKKHGFR 379 (467)
T ss_pred cchhHHHHHHHhhccc
Confidence 7777777766555443
No 11
>KOG3608|consensus
Probab=98.94 E-value=9.2e-10 Score=77.56 Aligned_cols=90 Identities=26% Similarity=0.510 Sum_probs=80.2
Q ss_pred CCCCcccccccccccCChHHHHHHHHH-hCCCCCcccccccccccCchHHHHHHhhcCCCCCcccCc--chhhhcChHHH
Q psy6676 24 SKEKPFKCTECGKGFCQSRTLAVHKIL-HLEESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAA--CGKVFRRNCDL 100 (144)
Q Consensus 24 ~~~~~~~C~~C~~~f~~~~~l~~h~~~-~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~--C~~~f~~~~~l 100 (144)
.....|+|+.|+........|..|++. |...+||+|..|...|.....|..|...|. +..|.|.. |...|.+...+
T Consensus 259 rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~ 337 (467)
T KOG3608|consen 259 RHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQM 337 (467)
T ss_pred HhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHH
Confidence 345679999999999999999999875 777899999999999999999999999888 68899987 99999999999
Q ss_pred HHhHhhccCCCCCC
Q psy6676 101 RRHSLTHNLGSATS 114 (144)
Q Consensus 101 ~~H~~~h~~~~~~~ 114 (144)
.+|.+-++.+..+.
T Consensus 338 ~~H~~evhEg~np~ 351 (467)
T KOG3608|consen 338 RRHFLEVHEGNNPI 351 (467)
T ss_pred HHHHHHhccCCCCC
Confidence 99999888665543
No 12
>PHA02768 hypothetical protein; Provisional
Probab=98.92 E-value=4.5e-10 Score=58.69 Aligned_cols=42 Identities=24% Similarity=0.597 Sum_probs=31.3
Q ss_pred cccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcChHHH
Q psy6676 57 HKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRNCDL 100 (144)
Q Consensus 57 ~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l 100 (144)
|.|+.||+.|.....|..|++.|+ ++|+|..|++.|...+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 677777777777777777777776 577777788777766554
No 13
>KOG3993|consensus
Probab=98.90 E-value=2.8e-10 Score=81.64 Aligned_cols=86 Identities=30% Similarity=0.617 Sum_probs=72.5
Q ss_pred ccccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCC---------------------------
Q psy6676 29 FKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTD--------------------------- 81 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~--------------------------- 81 (144)
|+|+.|...|.+--.|.+|.-.-....-|+|+.|++.|....+|..|+|+|--
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~r 347 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAER 347 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccc
Confidence 99999999999999999996544444569999999999999999999998831
Q ss_pred ------CCCcccCcchhhhcChHHHHHhHhhccCCCCCC
Q psy6676 82 ------IKPYNCAACGKVFRRNCDLRRHSLTHNLGSATS 114 (144)
Q Consensus 82 ------~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~ 114 (144)
+..|.|..|+|.|.+...|+.|+.+|+......
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k 386 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAK 386 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccch
Confidence 124899999999999999999999888654433
No 14
>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=98.72 E-value=5.8e-09 Score=46.77 Aligned_cols=25 Identities=56% Similarity=1.084 Sum_probs=19.3
Q ss_pred HHHHHHhhcCCCCCcccCcchhhhc
Q psy6676 71 NLKTHLLTHTDIKPYNCAACGKVFR 95 (144)
Q Consensus 71 ~l~~h~~~h~~~~~~~C~~C~~~f~ 95 (144)
+|..|++.|+++++|.|..|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 3677888888888888888887775
No 15
>PHA02768 hypothetical protein; Provisional
Probab=98.72 E-value=8.4e-09 Score=53.95 Aligned_cols=43 Identities=19% Similarity=0.406 Sum_probs=38.2
Q ss_pred cccccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHH
Q psy6676 28 PFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNL 72 (144)
Q Consensus 28 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l 72 (144)
.|.|+.||+.|.....|..|++.|. +++.|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 4799999999999999999999998 689999999998765544
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.70 E-value=3.3e-08 Score=74.73 Aligned_cols=78 Identities=18% Similarity=0.517 Sum_probs=64.5
Q ss_pred CCCcccccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcC--------
Q psy6676 25 KEKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRR-------- 96 (144)
Q Consensus 25 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~-------- 96 (144)
..+++.|+.|+..|. ...|..|+..++ .++.|+ |+..+ ....|..|+..|...+++.|..|++.|..
T Consensus 450 l~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~ 524 (567)
T PLN03086 450 AKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVR 524 (567)
T ss_pred cccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchh
Confidence 346678999999985 677999998875 779999 99755 56889999999999999999999998852
Q ss_pred --hHHHHHhHhhc
Q psy6676 97 --NCDLRRHSLTH 107 (144)
Q Consensus 97 --~~~l~~H~~~h 107 (144)
...|..|...+
T Consensus 525 d~~s~Lt~HE~~C 537 (567)
T PLN03086 525 DRLRGMSEHESIC 537 (567)
T ss_pred hhhhhHHHHHHhc
Confidence 35788998875
No 17
>PHA00733 hypothetical protein
Probab=98.57 E-value=1.2e-07 Score=59.05 Aligned_cols=57 Identities=25% Similarity=0.519 Sum_probs=50.0
Q ss_pred cCCCCcccccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCC
Q psy6676 23 HSKEKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTD 81 (144)
Q Consensus 23 h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~ 81 (144)
+.+.+||.|+.|++.|.+...|..|+..+ ..++.|..|++.|.....|..|+...++
T Consensus 68 ~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 68 SKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred cCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 34588999999999999999999998876 3469999999999999999999986554
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.44 E-value=2.4e-07 Score=70.15 Aligned_cols=78 Identities=15% Similarity=0.419 Sum_probs=64.9
Q ss_pred CcccccccccccCChHHHHHHHHHhCCCCCcccccccccccC----------chHHHHHHhhcCCCCCcccCcchhhhcC
Q psy6676 27 KPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQ----------RSNLKTHLLTHTDIKPYNCAACGKVFRR 96 (144)
Q Consensus 27 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~----------~~~l~~h~~~h~~~~~~~C~~C~~~f~~ 96 (144)
+++.|+ |+..+ ....|..|...|-..+++.|..|+..+.. ...|..|+... +.+++.|..||+.+..
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrl 553 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVML 553 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeee
Confidence 789999 99755 66889999999999999999999998842 35788998875 8899999999987766
Q ss_pred hHHHHHhHhhcc
Q psy6676 97 NCDLRRHSLTHN 108 (144)
Q Consensus 97 ~~~l~~H~~~h~ 108 (144)
. .+..|+-..|
T Consensus 554 r-dm~~H~~~~h 564 (567)
T PLN03086 554 K-EMDIHQIAVH 564 (567)
T ss_pred h-hHHHHHHHhh
Confidence 5 6788886654
No 19
>PHA00616 hypothetical protein
Probab=98.41 E-value=1.6e-07 Score=46.85 Aligned_cols=35 Identities=14% Similarity=0.321 Sum_probs=29.9
Q ss_pred cccccccccccCChHHHHHHHHHhCCCCCcccccc
Q psy6676 28 PFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVC 62 (144)
Q Consensus 28 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C 62 (144)
||.|+.||+.|.....|..|++.+++.+++.|..-
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~ 35 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEYF 35 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeEE
Confidence 57899999999999999999999998888887653
No 20
>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=98.34 E-value=4.4e-07 Score=40.56 Aligned_cols=25 Identities=44% Similarity=0.822 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCCCCccccccccccc
Q psy6676 43 TLAVHKILHLEESPHKCPVCSRSFN 67 (144)
Q Consensus 43 ~l~~h~~~~~~~~~~~C~~C~~~~~ 67 (144)
+|..|++.|.+.++|.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4778888898888999999988875
No 21
>PHA00732 hypothetical protein
Probab=98.28 E-value=5.7e-07 Score=51.18 Aligned_cols=47 Identities=34% Similarity=0.646 Sum_probs=34.7
Q ss_pred cccccccccccCChHHHHHHHHH-hCCCCCcccccccccccCchHHHHHHhhcC
Q psy6676 28 PFKCTECGKGFCQSRTLAVHKIL-HLEESPHKCPVCSRSFNQRSNLKTHLLTHT 80 (144)
Q Consensus 28 ~~~C~~C~~~f~~~~~l~~h~~~-~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~ 80 (144)
||.|..|++.|.....|..|++. |. ++.|..|++.|. .+..|.+...
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccC
Confidence 57788888888888888888874 43 357888888886 3667775443
No 22
>PHA00616 hypothetical protein
Probab=98.15 E-value=1.9e-06 Score=43.00 Aligned_cols=28 Identities=29% Similarity=0.681 Sum_probs=16.5
Q ss_pred CcccCcchhhhcChHHHHHhHhhccCCC
Q psy6676 84 PYNCAACGKVFRRNCDLRRHSLTHNLGS 111 (144)
Q Consensus 84 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~ 111 (144)
+|+|..||+.|...+.|..|++.||...
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~ 28 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQN 28 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCC
Confidence 3556666666666666666666655543
No 23
>PHA00732 hypothetical protein
Probab=98.12 E-value=2.9e-06 Score=48.31 Aligned_cols=48 Identities=31% Similarity=0.555 Sum_probs=39.6
Q ss_pred CcccccccccccCchHHHHHHhh-cCCCCCcccCcchhhhcChHHHHHhHhhccC
Q psy6676 56 PHKCPVCSRSFNQRSNLKTHLLT-HTDIKPYNCAACGKVFRRNCDLRRHSLTHNL 109 (144)
Q Consensus 56 ~~~C~~C~~~~~~~~~l~~h~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 109 (144)
+|.|..|++.|.....|..|++. |. ++.|..|++.|. .+..|.++..+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccCC
Confidence 47899999999999999999984 54 368999999998 47778766543
No 24
>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=98.09 E-value=1.5e-06 Score=37.59 Aligned_cols=23 Identities=43% Similarity=1.002 Sum_probs=18.8
Q ss_pred cccCcchhhhcChHHHHHhHhhc
Q psy6676 85 YNCAACGKVFRRNCDLRRHSLTH 107 (144)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~h 107 (144)
|.|..|++.|.+...|..|++.|
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 57888888888888888888763
No 25
>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=98.03 E-value=1.3e-05 Score=42.34 Aligned_cols=35 Identities=31% Similarity=0.591 Sum_probs=17.3
Q ss_pred ccccccccccCChHHHHHHHHHhCC--CCCcccccccc
Q psy6676 29 FKCTECGKGFCQSRTLAVHKILHLE--ESPHKCPVCSR 64 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~~~~~~--~~~~~C~~C~~ 64 (144)
|.||+|++ ..+...|..|+...+. .+.+.|++|..
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~ 39 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSS 39 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchh
Confidence 55666666 4445556666443222 12345555544
No 26
>KOG3993|consensus
Probab=98.00 E-value=4.4e-06 Score=60.63 Aligned_cols=53 Identities=32% Similarity=0.683 Sum_probs=43.8
Q ss_pred CcccccccccccCChHHHHHHHHHhCC---------------------------------CCCcccccccccccCchHHH
Q psy6676 27 KPFKCTECGKGFCQSRTLAVHKILHLE---------------------------------ESPHKCPVCSRSFNQRSNLK 73 (144)
Q Consensus 27 ~~~~C~~C~~~f~~~~~l~~h~~~~~~---------------------------------~~~~~C~~C~~~~~~~~~l~ 73 (144)
.-|.|+.|++.|....+|..|.+.|.- ..-|.|..|++.|.....|.
T Consensus 294 vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLr 373 (500)
T KOG3993|consen 294 VEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLR 373 (500)
T ss_pred eeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHH
Confidence 458999999999999999999887731 12388999999999999999
Q ss_pred HHHhhc
Q psy6676 74 THLLTH 79 (144)
Q Consensus 74 ~h~~~h 79 (144)
.|+-.|
T Consensus 374 KHqlth 379 (500)
T KOG3993|consen 374 KHQLTH 379 (500)
T ss_pred HhHHhh
Confidence 996554
No 27
>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=97.94 E-value=5.3e-06 Score=35.95 Aligned_cols=24 Identities=46% Similarity=1.034 Sum_probs=18.5
Q ss_pred cccCcchhhhcChHHHHHhHhhcc
Q psy6676 85 YNCAACGKVFRRNCDLRRHSLTHN 108 (144)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~h~ 108 (144)
|.|..|++.|.+...|..|++++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 578889999999999999888765
No 28
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.93 E-value=2.3e-06 Score=59.97 Aligned_cols=71 Identities=27% Similarity=0.527 Sum_probs=41.4
Q ss_pred CCcccccc--cccccCChHHHHHHHHHhC-CCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcChHHHHH
Q psy6676 26 EKPFKCTE--CGKGFCQSRTLAVHKILHL-EESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRNCDLRR 102 (144)
Q Consensus 26 ~~~~~C~~--C~~~f~~~~~l~~h~~~~~-~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~ 102 (144)
.|||+|++ |.+.|+....|+-|+.--+ ..+...-+ . -..+.-.-...+||+|++|+|.|+....|+-
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p---------~-p~~~~~F~~~~KPYrCevC~KRYKNlNGLKY 416 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP---------S-PEKMNIFSAKDKPYRCEVCDKRYKNLNGLKY 416 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCC---------C-ccccccccccCCceeccccchhhccCcccee
Confidence 36777765 7777777777776643221 11110000 0 0001111234589999999999999999998
Q ss_pred hHhh
Q psy6676 103 HSLT 106 (144)
Q Consensus 103 H~~~ 106 (144)
|+.-
T Consensus 417 Hr~H 420 (423)
T COG5189 417 HRKH 420 (423)
T ss_pred cccc
Confidence 8753
No 29
>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=97.88 E-value=2.8e-05 Score=41.06 Aligned_cols=50 Identities=26% Similarity=0.440 Sum_probs=39.3
Q ss_pred CcccccccccccCchHHHHHHh-hcCCC-CCcccCcchhhhcChHHHHHhHhhcc
Q psy6676 56 PHKCPVCSRSFNQRSNLKTHLL-THTDI-KPYNCAACGKVFRRNCDLRRHSLTHN 108 (144)
Q Consensus 56 ~~~C~~C~~~~~~~~~l~~h~~-~h~~~-~~~~C~~C~~~f~~~~~l~~H~~~h~ 108 (144)
.|.|+.|++ ......|..|.. .|..+ +.+.|++|...+. .+|..|+..+|
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 489999999 556688999976 45543 5699999998655 48999998776
No 30
>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=97.84 E-value=8.2e-06 Score=36.65 Aligned_cols=26 Identities=38% Similarity=0.847 Sum_probs=20.4
Q ss_pred CcccCcchhhhcChHHHHHhHhhccC
Q psy6676 84 PYNCAACGKVFRRNCDLRRHSLTHNL 109 (144)
Q Consensus 84 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 109 (144)
+|.|..|++.|.+...|..|++.|+.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 47788888888888888888877653
No 31
>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=97.79 E-value=1.8e-05 Score=34.05 Aligned_cols=22 Identities=36% Similarity=0.730 Sum_probs=15.3
Q ss_pred ccccccccccCChHHHHHHHHH
Q psy6676 29 FKCTECGKGFCQSRTLAVHKIL 50 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~~~ 50 (144)
|.|+.|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4677777777777777777654
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.61 E-value=4.9e-05 Score=44.96 Aligned_cols=74 Identities=20% Similarity=0.347 Sum_probs=22.4
Q ss_pred cccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcChHHHHHhHhhcc
Q psy6676 30 KCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRNCDLRRHSLTHN 108 (144)
Q Consensus 30 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 108 (144)
+|..|+..|.....+..|+...++-.. .. ...+.....+..+.+.. ....+.|..|++.|.+...|..|++.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~---~~-~~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDI---PD-QKYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred Ccccccccccccccccccccccccccc---cc-ccccccccccccccccc-cCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 489999999999999999876554321 11 11111223333333322 2236999999999999999999998754
No 33
>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=97.57 E-value=7.3e-05 Score=32.17 Aligned_cols=23 Identities=39% Similarity=0.764 Sum_probs=15.6
Q ss_pred ccccccccccCChHHHHHHHHHh
Q psy6676 29 FKCTECGKGFCQSRTLAVHKILH 51 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~~~~ 51 (144)
|.|++|++.|.+...|..|+..+
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 56777888887777777777655
No 34
>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=97.39 E-value=0.0001 Score=32.94 Aligned_cols=24 Identities=50% Similarity=0.956 Sum_probs=15.1
Q ss_pred cccccccccccCChHHHHHHHHHh
Q psy6676 28 PFKCTECGKGFCQSRTLAVHKILH 51 (144)
Q Consensus 28 ~~~C~~C~~~f~~~~~l~~h~~~~ 51 (144)
+|.|..|++.|.+...|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 456666666666666666666554
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.39 E-value=0.00018 Score=31.36 Aligned_cols=24 Identities=46% Similarity=1.005 Sum_probs=18.9
Q ss_pred cccCcchhhhcChHHHHHhHhhcc
Q psy6676 85 YNCAACGKVFRRNCDLRRHSLTHN 108 (144)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~h~ 108 (144)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 568888888888888888887554
No 36
>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=96.96 E-value=0.00081 Score=34.47 Aligned_cols=32 Identities=31% Similarity=0.647 Sum_probs=19.6
Q ss_pred CCCCCcccCcchhhhcChHHHHHhHhhccCCC
Q psy6676 80 TDIKPYNCAACGKVFRRNCDLRRHSLTHNLGS 111 (144)
Q Consensus 80 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~ 111 (144)
..+.|..|++|+..+....+|++|+.+.|...
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 34567788888888888888888887766543
No 37
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.82 E-value=0.00054 Score=29.89 Aligned_cols=22 Identities=32% Similarity=0.724 Sum_probs=17.0
Q ss_pred cccCcchhhhcChHHHHHhHhh
Q psy6676 85 YNCAACGKVFRRNCDLRRHSLT 106 (144)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~ 106 (144)
|.|.+|++.|.+...+..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 5678888888888888888764
No 38
>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=96.82 E-value=0.0017 Score=33.27 Aligned_cols=30 Identities=33% Similarity=0.492 Sum_probs=14.3
Q ss_pred CCcccccccccccCChHHHHHHHHHhCCCC
Q psy6676 26 EKPFKCTECGKGFCQSRTLAVHKILHLEES 55 (144)
Q Consensus 26 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~ 55 (144)
..|..|++|+..+.+..+|.+|+...++.+
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 455566666666666666666655554443
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.78 E-value=0.0017 Score=28.09 Aligned_cols=23 Identities=39% Similarity=0.790 Sum_probs=15.2
Q ss_pred ccccccccccCChHHHHHHHHHh
Q psy6676 29 FKCTECGKGFCQSRTLAVHKILH 51 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~~~~ 51 (144)
|.|..|++.|.....+..|+..|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 45667777777777777776644
No 40
>PRK04860 hypothetical protein; Provisional
Probab=96.72 E-value=0.00093 Score=43.25 Aligned_cols=38 Identities=21% Similarity=0.576 Sum_probs=31.3
Q ss_pred CcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcCh
Q psy6676 56 PHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRN 97 (144)
Q Consensus 56 ~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~ 97 (144)
+|.|. |+. ....+..|.+.++++++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 48887 876 566788999999999999999999887654
No 41
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.71 E-value=0.00089 Score=28.93 Aligned_cols=23 Identities=30% Similarity=0.715 Sum_probs=16.6
Q ss_pred cccCcchhhhcChHHHHHhHhhcc
Q psy6676 85 YNCAACGKVFRRNCDLRRHSLTHN 108 (144)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~h~ 108 (144)
|+|..|..... ...|..|++.+|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 57888887777 778888888765
No 42
>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=96.50 E-value=0.00091 Score=29.85 Aligned_cols=22 Identities=32% Similarity=0.755 Sum_probs=18.1
Q ss_pred cccCcchhhhcChHHHHHhHhh
Q psy6676 85 YNCAACGKVFRRNCDLRRHSLT 106 (144)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~ 106 (144)
|.|..|++.|.+...+..|++.
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 6788888888888888888764
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.42 E-value=0.0021 Score=27.98 Aligned_cols=22 Identities=32% Similarity=0.603 Sum_probs=13.9
Q ss_pred ccccccccccCChHHHHHHHHH
Q psy6676 29 FKCTECGKGFCQSRTLAVHKIL 50 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~~~ 50 (144)
|.|.+|+..|.+...|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4566666666666666666543
No 44
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.20 E-value=0.0041 Score=26.78 Aligned_cols=23 Identities=26% Similarity=0.495 Sum_probs=15.2
Q ss_pred ccccccccccCChHHHHHHHHHhC
Q psy6676 29 FKCTECGKGFCQSRTLAVHKILHL 52 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~~~~~ 52 (144)
|.|+.|..... ...|..|+..++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 56788887776 777888876653
No 45
>PRK04860 hypothetical protein; Provisional
Probab=95.94 E-value=0.0055 Score=39.72 Aligned_cols=39 Identities=21% Similarity=0.541 Sum_probs=33.0
Q ss_pred CcccccccccccCChHHHHHHHHHhCCCCCcccccccccccCc
Q psy6676 27 KPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQR 69 (144)
Q Consensus 27 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~ 69 (144)
-+|.|. |+. ....+..|.+.+.+.++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 368998 987 566789999999999999999999887543
No 46
>KOG4173|consensus
Probab=95.83 E-value=0.0063 Score=40.57 Aligned_cols=80 Identities=24% Similarity=0.501 Sum_probs=63.0
Q ss_pred CCCcccccc--cccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhh-c---------CCCCCcccC--cc
Q psy6676 25 KEKPFKCTE--CGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLT-H---------TDIKPYNCA--AC 90 (144)
Q Consensus 25 ~~~~~~C~~--C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~-h---------~~~~~~~C~--~C 90 (144)
+...+.|++ |-+.|...-++..|..+.++ ..|.+|.+.|...-.|..|+-. | .|.-.|.|. .|
T Consensus 76 ~~~~~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgC 152 (253)
T KOG4173|consen 76 RVPAFACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGC 152 (253)
T ss_pred ccccccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhh
Confidence 445578887 77888888888998766655 4899999999999888888753 3 345568995 59
Q ss_pred hhhhcChHHHHHhHhhc
Q psy6676 91 GKVFRRNCDLRRHSLTH 107 (144)
Q Consensus 91 ~~~f~~~~~l~~H~~~h 107 (144)
+..|.+....+.|+-.-
T Consensus 153 t~KFkT~r~RkdH~I~~ 169 (253)
T KOG4173|consen 153 TEKFKTSRDRKDHMIRM 169 (253)
T ss_pred hhhhhhhhhhhhHHHHh
Confidence 99999999999998543
No 47
>KOG1146|consensus
Probab=95.66 E-value=0.0056 Score=50.84 Aligned_cols=83 Identities=27% Similarity=0.378 Sum_probs=52.9
Q ss_pred ccccCCCCcccccccccccCChHHHHHHHHHhCCC-CCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcChH
Q psy6676 20 GYIHSKEKPFKCTECGKGFCQSRTLAVHKILHLEE-SPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRNC 98 (144)
Q Consensus 20 ~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~-~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~ 98 (144)
..+++..+.++|++|++.|+....|..|++..+.+ .. .+|. .+...-.+..-...-.+.++|.|..|...++...
T Consensus 457 ~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~---~~c~-~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng 532 (1406)
T KOG1146|consen 457 VVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS---AYCK-AGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNG 532 (1406)
T ss_pred eeeecccccccCCccchhhhhHHHhhhcccccccccch---hHhH-hccccccccccccccCCCCcccceeeeeeeecch
Confidence 35567778899999999999999999998874322 21 2221 1111000000011223457899999999999999
Q ss_pred HHHHhHhh
Q psy6676 99 DLRRHSLT 106 (144)
Q Consensus 99 ~l~~H~~~ 106 (144)
.|.+|+..
T Consensus 533 ~LsihlqS 540 (1406)
T KOG1146|consen 533 NLSIHLQS 540 (1406)
T ss_pred HHHHHHHH
Confidence 99999864
No 48
>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=95.61 E-value=0.0031 Score=28.09 Aligned_cols=20 Identities=35% Similarity=0.695 Sum_probs=11.2
Q ss_pred ccccccccccCChHHHHHHH
Q psy6676 29 FKCTECGKGFCQSRTLAVHK 48 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~ 48 (144)
|.|..|++.|.+...+..|+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHM 21 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCT
T ss_pred CCcccCCCCcCCHHHHHHHH
Confidence 45555665665555555554
No 49
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.46 E-value=0.013 Score=25.66 Aligned_cols=21 Identities=29% Similarity=0.660 Sum_probs=13.3
Q ss_pred cccCcchhhhcChHHHHHhHhh
Q psy6676 85 YNCAACGKVFRRNCDLRRHSLT 106 (144)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~ 106 (144)
..|+.||+.| ....|.+|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3567777777 45566666654
No 50
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.77 E-value=0.015 Score=30.33 Aligned_cols=33 Identities=18% Similarity=0.278 Sum_probs=27.8
Q ss_pred cccCCCCcccccccccccCChHHHHHHHHHhCC
Q psy6676 21 YIHSKEKPFKCTECGKGFCQSRTLAVHKILHLE 53 (144)
Q Consensus 21 ~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~ 53 (144)
....|+.-+.|+.|+..|....++.+|++.-++
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 446788889999999999999999999876554
No 51
>KOG1146|consensus
Probab=93.90 E-value=0.026 Score=47.17 Aligned_cols=80 Identities=16% Similarity=0.225 Sum_probs=55.2
Q ss_pred ccccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhc-----------------CCCCCcccCcch
Q psy6676 29 FKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTH-----------------TDIKPYNCAACG 91 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h-----------------~~~~~~~C~~C~ 91 (144)
+.|..|.+.+...-.+. ++ ....+|.|..|...|.....+..|.+.- ....+| |..|.
T Consensus 1261 ~~c~~~~~~~~~~~~~~-~l---~~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~ 1335 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGIS-TL---DVTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACE 1335 (1406)
T ss_pred chhhhccccccCcccee-ec---ccchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHH
Confidence 66878887776655555 32 2234578888888888888887777422 122335 99999
Q ss_pred hhhcChHHHHHhHhh-ccCCCCC
Q psy6676 92 KVFRRNCDLRRHSLT-HNLGSAT 113 (144)
Q Consensus 92 ~~f~~~~~l~~H~~~-h~~~~~~ 113 (144)
..|+....|++|+++ ++.....
T Consensus 1336 ~~~~~~~alqihm~~~~~~~kt~ 1358 (1406)
T KOG1146|consen 1336 VLLSGREALQIHMRSSAHRRKTA 1358 (1406)
T ss_pred hhcchhHHHHHHHHHhhhcccCC
Confidence 999999999999986 4433333
No 52
>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=93.90 E-value=0.04 Score=25.82 Aligned_cols=23 Identities=17% Similarity=0.455 Sum_probs=18.7
Q ss_pred CcccCcchhhhcChHHHHHhHhh
Q psy6676 84 PYNCAACGKVFRRNCDLRRHSLT 106 (144)
Q Consensus 84 ~~~C~~C~~~f~~~~~l~~H~~~ 106 (144)
+|.|..|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57888899988888888888753
No 53
>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=93.55 E-value=0.074 Score=24.85 Aligned_cols=22 Identities=23% Similarity=0.480 Sum_probs=14.2
Q ss_pred cccccccccccCChHHHHHHHH
Q psy6676 28 PFKCTECGKGFCQSRTLAVHKI 49 (144)
Q Consensus 28 ~~~C~~C~~~f~~~~~l~~h~~ 49 (144)
+|.|.+|+..|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4667777777766666666643
No 54
>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=93.22 E-value=0.053 Score=25.33 Aligned_cols=9 Identities=44% Similarity=1.446 Sum_probs=4.3
Q ss_pred CCcccCcch
Q psy6676 83 KPYNCAACG 91 (144)
Q Consensus 83 ~~~~C~~C~ 91 (144)
.++.|+.|+
T Consensus 16 ~~~~CP~Cg 24 (33)
T cd00350 16 APWVCPVCG 24 (33)
T ss_pred CCCcCcCCC
Confidence 344555554
No 55
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.08 E-value=0.059 Score=28.18 Aligned_cols=30 Identities=33% Similarity=0.561 Sum_probs=23.4
Q ss_pred cCCCCCcccCcchhhhcChHHHHHhHhhcc
Q psy6676 79 HTDIKPYNCAACGKVFRRNCDLRRHSLTHN 108 (144)
Q Consensus 79 h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 108 (144)
-.|+.-+.|+-|+..|.+...+.+|...-|
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 356677889999999999888888885433
No 56
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.07 E-value=0.065 Score=38.75 Aligned_cols=79 Identities=24% Similarity=0.383 Sum_probs=49.2
Q ss_pred cccccc--cccccCChHHHHHHHHHhCCCCCcccccccc---cc------cCchHHHHHHhhcCCCCC----cccCcchh
Q psy6676 28 PFKCTE--CGKGFCQSRTLAVHKILHLEESPHKCPVCSR---SF------NQRSNLKTHLLTHTDIKP----YNCAACGK 92 (144)
Q Consensus 28 ~~~C~~--C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~---~~------~~~~~l~~h~~~h~~~~~----~~C~~C~~ 92 (144)
.|.|+. |.........|..|.++.++. +.|..|-. .| .....|..|......+.. -.|..|..
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~--~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~ 228 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGF--VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKI 228 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCc--EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccc
Confidence 377875 666666677888888776643 56666652 22 233556666543332222 25788888
Q ss_pred hhcChHHHHHhHhhcc
Q psy6676 93 VFRRNCDLRRHSLTHN 108 (144)
Q Consensus 93 ~f~~~~~l~~H~~~h~ 108 (144)
-|.....|.+|.+..|
T Consensus 229 ~FYdDDEL~~HcR~~H 244 (493)
T COG5236 229 YFYDDDELRRHCRLRH 244 (493)
T ss_pred eecChHHHHHHHHhhh
Confidence 8888888888877543
No 57
>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=92.63 E-value=0.089 Score=31.82 Aligned_cols=15 Identities=33% Similarity=0.866 Sum_probs=8.0
Q ss_pred CCcccCcchhhhcCh
Q psy6676 83 KPYNCAACGKVFRRN 97 (144)
Q Consensus 83 ~~~~C~~C~~~f~~~ 97 (144)
.|..|+.||..|.-.
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 445555565555444
No 58
>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=91.72 E-value=0.14 Score=31.01 Aligned_cols=30 Identities=30% Similarity=0.805 Sum_probs=23.8
Q ss_pred ccccccccccCChHHHHHHHHHhCCCCCcccccccccccCc
Q psy6676 29 FKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQR 69 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~ 69 (144)
..|+.||..|-.. +..|.+|+.||..|...
T Consensus 10 R~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 4799999998543 24688999999988665
No 59
>KOG2482|consensus
Probab=91.11 E-value=0.26 Score=35.72 Aligned_cols=79 Identities=24% Similarity=0.380 Sum_probs=57.9
Q ss_pred cccccccccccCChHHHHHHHHHhCCC-----------------------------------------------------
Q psy6676 28 PFKCTECGKGFCQSRTLAVHKILHLEE----------------------------------------------------- 54 (144)
Q Consensus 28 ~~~C~~C~~~f~~~~~l~~h~~~~~~~----------------------------------------------------- 54 (144)
.+.|-.|.+.|+.+..|..||+.....
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~ 274 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDD 274 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCC
Confidence 478999999999999999998743210
Q ss_pred -CC--cccccccccccCchHHHHHHhh-cCC--------------------------CCCcccCcchhhhcChHHHHHhH
Q psy6676 55 -SP--HKCPVCSRSFNQRSNLKTHLLT-HTD--------------------------IKPYNCAACGKVFRRNCDLRRHS 104 (144)
Q Consensus 55 -~~--~~C~~C~~~~~~~~~l~~h~~~-h~~--------------------------~~~~~C~~C~~~f~~~~~l~~H~ 104 (144)
.+ .+|..|...+.+...|..||+. |.- .....|-.|.-.|.....|..|+
T Consensus 275 a~a~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm 354 (423)
T KOG2482|consen 275 AEALSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHM 354 (423)
T ss_pred CCccceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhc
Confidence 01 3688888888888888888874 321 11246778888899999999888
Q ss_pred hh
Q psy6676 105 LT 106 (144)
Q Consensus 105 ~~ 106 (144)
.-
T Consensus 355 ~e 356 (423)
T KOG2482|consen 355 VE 356 (423)
T ss_pred cc
Confidence 53
No 60
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=91.03 E-value=0.13 Score=33.47 Aligned_cols=24 Identities=33% Similarity=0.805 Sum_probs=18.9
Q ss_pred CcccccccccccCchHHHHHHhhcCCCCCcccCcchh
Q psy6676 56 PHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGK 92 (144)
Q Consensus 56 ~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 92 (144)
.|+|.+||..+ .++.|.+|++||.
T Consensus 134 ~~vC~vCGy~~-------------~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTH-------------EGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcc-------------cCCCCCcCCCCCC
Confidence 69999998663 4478889999983
No 61
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=90.51 E-value=0.33 Score=28.23 Aligned_cols=24 Identities=29% Similarity=0.886 Sum_probs=17.1
Q ss_pred CcccccccccccCchHHHHHHhhc
Q psy6676 56 PHKCPVCSRSFNQRSNLKTHLLTH 79 (144)
Q Consensus 56 ~~~C~~C~~~~~~~~~l~~h~~~h 79 (144)
.+.|..|++.|.+...|..|++.+
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 577777777777777777777653
No 62
>KOG2231|consensus
Probab=90.33 E-value=0.42 Score=37.81 Aligned_cols=81 Identities=23% Similarity=0.399 Sum_probs=49.1
Q ss_pred cccccccccc---------------CChHHHHHHHHHhCCCCCccccccc----------ccccCchHHHHHHhhc-CCC
Q psy6676 29 FKCTECGKGF---------------CQSRTLAVHKILHLEESPHKCPVCS----------RSFNQRSNLKTHLLTH-TDI 82 (144)
Q Consensus 29 ~~C~~C~~~f---------------~~~~~l~~h~~~~~~~~~~~C~~C~----------~~~~~~~~l~~h~~~h-~~~ 82 (144)
+.|.+|.+.| .....|+.|+...++ .+.|..|. +.|. ...|..|++.. .++
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~--~~~c~lC~~~~kif~~e~k~Yt-~~el~~h~~~gd~d~ 176 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHK--LHLCSLCLQNLKIFINERKLYT-RAELNLHLMFGDPDD 176 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhh--hhccccccccceeeeeeeeheh-HHHHHHHHhcCCCcc
Confidence 4566666666 367788999865443 23444433 2332 34566666532 222
Q ss_pred CC----cccCcchhhhcChHHHHHhHhhccCCCC
Q psy6676 83 KP----YNCAACGKVFRRNCDLRRHSLTHNLGSA 112 (144)
Q Consensus 83 ~~----~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 112 (144)
+. -.|+.|...|.....|.+|++..|..--
T Consensus 177 ~s~rGhp~C~~C~~~fld~~el~rH~~~~h~~ch 210 (669)
T KOG2231|consen 177 ESCRGHPLCKFCHERFLDDDELYRHLRFDHEFCH 210 (669)
T ss_pred ccccCCccchhhhhhhccHHHHHHhhccceehee
Confidence 22 3678888888888888888887654433
No 63
>KOG2893|consensus
Probab=89.77 E-value=0.095 Score=35.97 Aligned_cols=28 Identities=25% Similarity=0.644 Sum_probs=13.5
Q ss_pred ccccccCChHHHHHHHHHhCCCCCcccccccc
Q psy6676 33 ECGKGFCQSRTLAVHKILHLEESPHKCPVCSR 64 (144)
Q Consensus 33 ~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~ 64 (144)
+|++.|..+.-|-+|++.. .|+|.+|.+
T Consensus 15 ycnrefddekiliqhqkak----hfkchichk 42 (341)
T KOG2893|consen 15 YCNREFDDEKILIQHQKAK----HFKCHICHK 42 (341)
T ss_pred ecccccchhhhhhhhhhhc----cceeeeehh
Confidence 4555555555444443332 245555543
No 64
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.70 E-value=0.087 Score=38.80 Aligned_cols=60 Identities=37% Similarity=0.712 Sum_probs=30.4
Q ss_pred cccccccccccCChHHHHHHHH--HhCCC--CCcccc--cccccccCchHHHHHHhhcCCCCCccc
Q psy6676 28 PFKCTECGKGFCQSRTLAVHKI--LHLEE--SPHKCP--VCSRSFNQRSNLKTHLLTHTDIKPYNC 87 (144)
Q Consensus 28 ~~~C~~C~~~f~~~~~l~~h~~--~~~~~--~~~~C~--~C~~~~~~~~~l~~h~~~h~~~~~~~C 87 (144)
++.|..|...|.....+..|.. .|.+. +++.|. .|++.|.....+..|...|.+..++.+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccc
Confidence 4455555555555555555555 44444 455555 455555555555555555544444433
No 65
>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=88.93 E-value=0.75 Score=27.70 Aligned_cols=26 Identities=27% Similarity=0.576 Sum_probs=23.1
Q ss_pred Cccc----CcchhhhcChHHHHHhHhhccC
Q psy6676 84 PYNC----AACGKVFRRNCDLRRHSLTHNL 109 (144)
Q Consensus 84 ~~~C----~~C~~~f~~~~~l~~H~~~h~~ 109 (144)
.|.| ..|++...+...++.|.+.+|.
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3899 9999999999999999988763
No 66
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=88.66 E-value=0.27 Score=32.08 Aligned_cols=24 Identities=38% Similarity=0.994 Sum_probs=19.7
Q ss_pred cccccccccccCChHHHHHHHHHhCCCCCcccccccc
Q psy6676 28 PFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSR 64 (144)
Q Consensus 28 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~ 64 (144)
-|.|++||.. +.+..|.+|++|+-
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCCC
Confidence 6999999976 45567899999984
No 67
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=88.60 E-value=0.26 Score=23.16 Aligned_cols=10 Identities=40% Similarity=0.939 Sum_probs=5.1
Q ss_pred cccccccccc
Q psy6676 57 HKCPVCSRSF 66 (144)
Q Consensus 57 ~~C~~C~~~~ 66 (144)
|+|.+||..+
T Consensus 3 ~~C~~CG~i~ 12 (34)
T cd00729 3 WVCPVCGYIH 12 (34)
T ss_pred EECCCCCCEe
Confidence 4555555443
No 68
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=88.59 E-value=0.12 Score=38.01 Aligned_cols=59 Identities=42% Similarity=0.723 Sum_probs=52.3
Q ss_pred CCcccccccccccCchHHHHHHh--hcCCC--CCcccC--cchhhhcChHHHHHhHhhccCCCCC
Q psy6676 55 SPHKCPVCSRSFNQRSNLKTHLL--THTDI--KPYNCA--ACGKVFRRNCDLRRHSLTHNLGSAT 113 (144)
Q Consensus 55 ~~~~C~~C~~~~~~~~~l~~h~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~ 113 (144)
.++.|..|...|.....+..|.+ .|.++ +++.|. .|++.|.+...+..|..+|......
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPA 352 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcc
Confidence 35788889999999999999999 89999 999999 7999999999999999888766533
No 69
>KOG2893|consensus
Probab=88.18 E-value=0.16 Score=34.85 Aligned_cols=42 Identities=29% Similarity=0.543 Sum_probs=32.5
Q ss_pred cccccccccCchHHHHHHhhcCCCCCcccCcchhhhcChHHHHHhH
Q psy6676 59 CPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRNCDLRRHS 104 (144)
Q Consensus 59 C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 104 (144)
|=.|++.|.....|.+|++. +.|+|-+|-|.+-+.-.|..|-
T Consensus 13 cwycnrefddekiliqhqka----khfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred eeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeeh
Confidence 55688999998888888874 5589999988777766666664
No 70
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=87.48 E-value=0.55 Score=33.80 Aligned_cols=28 Identities=32% Similarity=0.699 Sum_probs=24.2
Q ss_pred CCCcccCc--chhhhcChHHHHHhHhhccC
Q psy6676 82 IKPYNCAA--CGKVFRRNCDLRRHSLTHNL 109 (144)
Q Consensus 82 ~~~~~C~~--C~~~f~~~~~l~~H~~~h~~ 109 (144)
++||+|++ |.|.|+....|+-|+.-.|.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~ 376 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQ 376 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhcccc
Confidence 58999976 99999999999999876553
No 71
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=87.23 E-value=0.078 Score=36.10 Aligned_cols=17 Identities=35% Similarity=0.854 Sum_probs=12.3
Q ss_pred CCcccccccccccCChH
Q psy6676 26 EKPFKCTECGKGFCQSR 42 (144)
Q Consensus 26 ~~~~~C~~C~~~f~~~~ 42 (144)
.+...||+|+..|....
T Consensus 3 ~k~~~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKK 19 (214)
T ss_pred CCceECCCCCCeeeeeE
Confidence 35667888888887664
No 72
>KOG2482|consensus
Probab=85.92 E-value=0.85 Score=33.17 Aligned_cols=54 Identities=19% Similarity=0.351 Sum_probs=36.1
Q ss_pred CCCcccccccccccCCh-HHHHHHHHH-hC---C------------------CCCcccccccccccCchHHHHHHhh
Q psy6676 25 KEKPFKCTECGKGFCQS-RTLAVHKIL-HL---E------------------ESPHKCPVCSRSFNQRSNLKTHLLT 78 (144)
Q Consensus 25 ~~~~~~C~~C~~~f~~~-~~l~~h~~~-~~---~------------------~~~~~C~~C~~~~~~~~~l~~h~~~ 78 (144)
......|-.|...+.-. +.+-.|+-. |. | -..+.|..|.+.|.....|..||+.
T Consensus 141 t~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 141 TIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred CeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHh
Confidence 34556788888776543 334455422 21 1 1237899999999999999999974
No 73
>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=85.78 E-value=0.65 Score=23.00 Aligned_cols=26 Identities=38% Similarity=0.715 Sum_probs=14.7
Q ss_pred CCCCcccCcchhhhcCh----HHHHHhHhh
Q psy6676 81 DIKPYNCAACGKVFRRN----CDLRRHSLT 106 (144)
Q Consensus 81 ~~~~~~C~~C~~~f~~~----~~l~~H~~~ 106 (144)
+....+|..|++.+... ..|..|++.
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 34556788888776653 678888744
No 74
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=85.59 E-value=1.3 Score=27.01 Aligned_cols=82 Identities=26% Similarity=0.394 Sum_probs=49.1
Q ss_pred CcccccccccccCChHHHHHHHHHhCCCCC------------cccccccccccCchHHHHHHhhcCCCCCcccCcchhhh
Q psy6676 27 KPFKCTECGKGFCQSRTLAVHKILHLEESP------------HKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVF 94 (144)
Q Consensus 27 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~------------~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f 94 (144)
-|-.|+.|+-.......|.+...-.-.-++ ..|-.|...|........- .-.....|.|..|...|
T Consensus 14 LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~--~~~~~~~y~C~~C~~~F 91 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFD--ELKDSHRYVCAVCKNVF 91 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCccccccc--ccccccceeCCCCCCcc
Confidence 567899999887777777654211000111 1377777777553211100 01223468999999999
Q ss_pred cChHHHHHhHhhccCC
Q psy6676 95 RRNCDLRRHSLTHNLG 110 (144)
Q Consensus 95 ~~~~~l~~H~~~h~~~ 110 (144)
=..=..-.|...|.-.
T Consensus 92 C~dCD~fiHe~Lh~CP 107 (112)
T TIGR00622 92 CVDCDVFVHESLHCCP 107 (112)
T ss_pred ccccchhhhhhccCCc
Confidence 8777777787777643
No 75
>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=84.90 E-value=0.56 Score=29.07 Aligned_cols=14 Identities=21% Similarity=0.427 Sum_probs=6.6
Q ss_pred CCcccccccccccC
Q psy6676 55 SPHKCPVCSRSFNQ 68 (144)
Q Consensus 55 ~~~~C~~C~~~~~~ 68 (144)
.|.+|+.||..|..
T Consensus 25 ~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 25 RPAVSPYTGEQFPP 38 (129)
T ss_pred CCccCCCcCCccCc
Confidence 34455555544433
No 76
>KOG2186|consensus
Probab=84.62 E-value=0.63 Score=32.32 Aligned_cols=47 Identities=21% Similarity=0.493 Sum_probs=33.4
Q ss_pred ccccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhh
Q psy6676 29 FKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLT 78 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~ 78 (144)
|.|..||....-. .+..|+..-++ .-|.|..|+..|.. ..+..|..-
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 6788888776554 46668777766 55888888888877 556666653
No 77
>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=83.01 E-value=0.63 Score=29.22 Aligned_cols=25 Identities=36% Similarity=0.538 Sum_probs=16.0
Q ss_pred CCcccCcchhhhcChHHHHHhHhhccCC
Q psy6676 83 KPYNCAACGKVFRRNCDLRRHSLTHNLG 110 (144)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~ 110 (144)
....|..||+.|... ++|++.||+-
T Consensus 71 d~i~clecGk~~k~L---krHL~~~~gl 95 (132)
T PF05443_consen 71 DYIICLECGKKFKTL---KRHLRTHHGL 95 (132)
T ss_dssp S-EE-TBT--EESBH---HHHHHHTT-S
T ss_pred CeeEEccCCcccchH---HHHHHHccCC
Confidence 346899999988765 8999998654
No 78
>KOG2231|consensus
Probab=82.92 E-value=1.7 Score=34.55 Aligned_cols=69 Identities=22% Similarity=0.411 Sum_probs=44.5
Q ss_pred ccccccccccCChHHHHHHHHHhCCCCCccccccc------ccccCchHHHHHHhhcCCCCCcccC--cch-hhhcChHH
Q psy6676 29 FKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCS------RSFNQRSNLKTHLLTHTDIKPYNCA--ACG-KVFRRNCD 99 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~------~~~~~~~~l~~h~~~h~~~~~~~C~--~C~-~~f~~~~~ 99 (144)
-.|..|...|.....+..|++.++ |.|..|. ..|.....|..|.+.++ |.|. .|. +.|.....
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H----flCE~~~C~~~~f~~~~~ 254 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH----FLCEEEFCRTKKFYVAFE 254 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC----ccccccccccceeeehhH
Confidence 358899999999999998877655 4566653 45666778888887544 5665 453 33444433
Q ss_pred HHHhHh
Q psy6676 100 LRRHSL 105 (144)
Q Consensus 100 l~~H~~ 105 (144)
+..+++
T Consensus 255 ~ei~lk 260 (669)
T KOG2231|consen 255 LEIELK 260 (669)
T ss_pred HHHHHH
Confidence 444444
No 79
>KOG2186|consensus
Probab=82.90 E-value=0.94 Score=31.50 Aligned_cols=46 Identities=26% Similarity=0.697 Sum_probs=31.3
Q ss_pred cccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcChHHHHHhHh
Q psy6676 57 HKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRNCDLRRHSL 105 (144)
Q Consensus 57 ~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 105 (144)
|.|.+||....-. .+..|+...++ ..|.|..|++.|.. ..+..|..
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 6778887665443 35557766666 56788888888877 45666655
No 80
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=82.84 E-value=2.7 Score=30.75 Aligned_cols=79 Identities=27% Similarity=0.442 Sum_probs=52.7
Q ss_pred cccccccccCChHHHHHHHHHhCCCCCccccccc----ccccCchHHHHHHhhcCCCCCcccCc--c--h--hhhcChHH
Q psy6676 30 KCTECGKGFCQSRTLAVHKILHLEESPHKCPVCS----RSFNQRSNLKTHLLTHTDIKPYNCAA--C--G--KVFRRNCD 99 (144)
Q Consensus 30 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~----~~~~~~~~l~~h~~~h~~~~~~~C~~--C--~--~~f~~~~~ 99 (144)
.|..|...|-+.-.|..|++..+. +-+.|+.-+ ..|.+...|..|.+.. .|.|.+ | + ..|.+...
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE-~ChICD~v~p~~~QYFK~Y~~Le~HF~~~----hy~ct~qtc~~~k~~vf~~~~e 296 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHE-ACHICDMVGPIRYQYFKSYEDLEAHFRNA----HYCCTFQTCRVGKCYVFPYHTE 296 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhh-hhhhhhccCccchhhhhCHHHHHHHhhcC----ceEEEEEEEecCcEEEeccHHH
Confidence 589999999888889999887663 334444322 2456667777777643 255533 3 2 47899999
Q ss_pred HHHhHhhccCCCCC
Q psy6676 100 LRRHSLTHNLGSAT 113 (144)
Q Consensus 100 l~~H~~~h~~~~~~ 113 (144)
|..|+-.-|.....
T Consensus 297 l~~h~~~~h~~~~~ 310 (493)
T COG5236 297 LLEHLTRFHKVNAR 310 (493)
T ss_pred HHHHHHHHhhcccc
Confidence 99998765554433
No 81
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=82.11 E-value=0.99 Score=23.07 Aligned_cols=22 Identities=41% Similarity=0.773 Sum_probs=15.1
Q ss_pred CcccCcchhhhcCh-----HHHHHhHh
Q psy6676 84 PYNCAACGKVFRRN-----CDLRRHSL 105 (144)
Q Consensus 84 ~~~C~~C~~~f~~~-----~~l~~H~~ 105 (144)
.-.|..|++.+... +.|.+|++
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 35677777777554 57777877
No 82
>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=82.08 E-value=1.5 Score=28.38 Aligned_cols=34 Identities=18% Similarity=0.512 Sum_probs=23.6
Q ss_pred CCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhc
Q psy6676 53 EESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFR 95 (144)
Q Consensus 53 ~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~ 95 (144)
...-|.|+.|+..|.....+. ..|.|+.||....
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEee
Confidence 345688888888776665553 3588988886543
No 83
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=81.86 E-value=0.7 Score=30.59 Aligned_cols=34 Identities=21% Similarity=0.622 Sum_probs=22.4
Q ss_pred CCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcC
Q psy6676 54 ESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRR 96 (144)
Q Consensus 54 ~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~ 96 (144)
..-|.|+.|+..|.....+. ..|.|+.||.....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 45678888887776654431 35888888865543
No 84
>KOG2785|consensus
Probab=81.76 E-value=1.5 Score=32.27 Aligned_cols=73 Identities=15% Similarity=0.118 Sum_probs=39.0
Q ss_pred ccccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCCCCCcccCcch---hhhcChHHHHHhHh
Q psy6676 29 FKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACG---KVFRRNCDLRRHSL 105 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~---~~f~~~~~l~~H~~ 105 (144)
-.|-.|+..+.+...-..||..++|- |.... ........|...+...-+ ..+.|..|. +.|.+..+.+.|+.
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~Hgf--fIPdr--eYL~D~~GLl~YLgeKV~-~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGF--FIPDR--EYLTDEKGLLKYLGEKVG-IGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCC--cCCch--HhhhchhHHHHHHHHHhc-cCceEEEeccccCcccccHHHHHHHh
Confidence 44555555555555555555554431 11111 111122233333322222 348899998 99999999999985
Q ss_pred h
Q psy6676 106 T 106 (144)
Q Consensus 106 ~ 106 (144)
.
T Consensus 242 ~ 242 (390)
T KOG2785|consen 242 D 242 (390)
T ss_pred h
Confidence 3
No 85
>KOG3408|consensus
Probab=80.88 E-value=1.2 Score=27.35 Aligned_cols=27 Identities=22% Similarity=0.413 Sum_probs=22.8
Q ss_pred CCCCCcccCcchhhhcChHHHHHhHhh
Q psy6676 80 TDIKPYNCAACGKVFRRNCDLRRHSLT 106 (144)
Q Consensus 80 ~~~~~~~C~~C~~~f~~~~~l~~H~~~ 106 (144)
.|-..|.|..|.+-|.+...|..|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 455669999999999999999999865
No 86
>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=80.85 E-value=1 Score=29.24 Aligned_cols=35 Identities=17% Similarity=0.445 Sum_probs=27.0
Q ss_pred CCCCcccccccccccCChHHHHHHHHHhCCCCCccccccccccc
Q psy6676 24 SKEKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFN 67 (144)
Q Consensus 24 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~ 67 (144)
.+..-|.|+.|+..|.....+. ..|.|+.||....
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEee
Confidence 3456799999999998777664 2499999997543
No 87
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=79.97 E-value=0.89 Score=26.22 Aligned_cols=33 Identities=27% Similarity=0.658 Sum_probs=21.4
Q ss_pred CCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcCh
Q psy6676 55 SPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRN 97 (144)
Q Consensus 55 ~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~ 97 (144)
..+.|+.|++.- +.+.. ...|.|..||..|.-.
T Consensus 34 ~~~~Cp~C~~~~--------VkR~a--~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRTT--------VKRIA--TGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCcc--------eeeec--cCeEEcCCCCCeeccc
Confidence 347888888651 22332 3568899998887543
No 88
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=79.75 E-value=1.6 Score=28.94 Aligned_cols=34 Identities=21% Similarity=0.573 Sum_probs=23.6
Q ss_pred CCCcccccccccccCChHHHHHHHHHhCCCCCccccccccccc
Q psy6676 25 KEKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFN 67 (144)
Q Consensus 25 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~ 67 (144)
...-|.|+.|+..|.....+. ..|.|+.||....
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 345688988888887665543 2488999886543
No 89
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=79.18 E-value=0.41 Score=30.89 Aligned_cols=13 Identities=23% Similarity=0.764 Sum_probs=8.3
Q ss_pred cccccccccccCc
Q psy6676 57 HKCPVCSRSFNQR 69 (144)
Q Consensus 57 ~~C~~C~~~~~~~ 69 (144)
+.|+.||+.|...
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 5677777666543
No 90
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=78.43 E-value=1.4 Score=21.00 Aligned_cols=10 Identities=30% Similarity=0.846 Sum_probs=4.8
Q ss_pred ccccccccCC
Q psy6676 31 CTECGKGFCQ 40 (144)
Q Consensus 31 C~~C~~~f~~ 40 (144)
|+.|+..|..
T Consensus 5 CP~C~~~f~v 14 (37)
T PF13719_consen 5 CPNCQTRFRV 14 (37)
T ss_pred CCCCCceEEc
Confidence 4555544433
No 91
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=77.85 E-value=1.2 Score=23.73 Aligned_cols=33 Identities=27% Similarity=0.526 Sum_probs=16.8
Q ss_pred CCcccccccccccCchHHHHHHhhcCCCCCcccCcchh
Q psy6676 55 SPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGK 92 (144)
Q Consensus 55 ~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 92 (144)
..|.|+.||..--.. -.+--....+|+|+.||.
T Consensus 26 v~F~CPnCGe~~I~R-----c~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYR-----CAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeeh-----hhhHHHcCCceECCCcCc
Confidence 347788887432111 111111236788888874
No 92
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=77.79 E-value=3.7 Score=26.18 Aligned_cols=39 Identities=18% Similarity=0.492 Sum_probs=24.4
Q ss_pred CCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhc
Q psy6676 53 EESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFR 95 (144)
Q Consensus 53 ~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~ 95 (144)
....|.|+.|+..|.....+.. ... ...|.|+.||....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEELE 134 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEEE
Confidence 3456899999988875432221 012 34499999987553
No 93
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=77.31 E-value=16 Score=23.72 Aligned_cols=90 Identities=17% Similarity=0.331 Sum_probs=50.0
Q ss_pred CCCCcccccccccccCChHHHHHHHHHhCCC--------------------------CCcccccccccccCchHHHHHHh
Q psy6676 24 SKEKPFKCTECGKGFCQSRTLAVHKILHLEE--------------------------SPHKCPVCSRSFNQRSNLKTHLL 77 (144)
Q Consensus 24 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~--------------------------~~~~C~~C~~~~~~~~~l~~h~~ 77 (144)
.|-+||.|.. .+....-|.+-.+.+... ....|+.|............ -+
T Consensus 25 kgcRpymc~T---s~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~CPLCRG~V~GWtvve~-AR 100 (162)
T PF07800_consen 25 KGCRPYMCDT---SYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPELACPLCRGEVKGWTVVEP-AR 100 (162)
T ss_pred CCccccccCC---ccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccccccCccccCceeceEEchH-HH
Confidence 4557777655 555555566554443221 23678888753333322222 23
Q ss_pred hcCCCCCcccCc--chhhhcChHHHHHhHhhccCCCCCCCCCC
Q psy6676 78 THTDIKPYNCAA--CGKVFRRNCDLRRHSLTHNLGSATSTSSG 118 (144)
Q Consensus 78 ~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~~~~~ 118 (144)
.+-..++-.|.. |.. -.+...|++|.+.-|....+...++
T Consensus 101 ~~LN~K~RsC~~e~C~F-~GtY~eLrKHar~~HP~~rP~~vDP 142 (162)
T PF07800_consen 101 RFLNAKKRSCSQESCSF-SGTYSELRKHARSEHPSARPSEVDP 142 (162)
T ss_pred HHhccCCccCccccccc-ccCHHHHHHHHHhhCCCCCCccCCH
Confidence 333345555643 543 3467789999999887666555443
No 94
>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=77.17 E-value=0.7 Score=23.74 Aligned_cols=11 Identities=27% Similarity=0.981 Sum_probs=4.8
Q ss_pred ccccccccccc
Q psy6676 57 HKCPVCSRSFN 67 (144)
Q Consensus 57 ~~C~~C~~~~~ 67 (144)
|.|..|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 34444444443
No 95
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=75.10 E-value=1.7 Score=20.68 Aligned_cols=10 Identities=30% Similarity=0.989 Sum_probs=4.5
Q ss_pred cccccccccC
Q psy6676 30 KCTECGKGFC 39 (144)
Q Consensus 30 ~C~~C~~~f~ 39 (144)
.|+.|+..|.
T Consensus 4 ~CP~C~~~~~ 13 (38)
T TIGR02098 4 QCPNCKTSFR 13 (38)
T ss_pred ECCCCCCEEE
Confidence 3444444443
No 96
>KOG2071|consensus
Probab=75.03 E-value=2.3 Score=33.24 Aligned_cols=26 Identities=31% Similarity=0.636 Sum_probs=20.5
Q ss_pred CCcccccccccccCChHHHHHHHHHh
Q psy6676 26 EKPFKCTECGKGFCQSRTLAVHKILH 51 (144)
Q Consensus 26 ~~~~~C~~C~~~f~~~~~l~~h~~~~ 51 (144)
..+..|..||.+|........|+-.|
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhh
Confidence 46689999999999887776666555
No 97
>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=74.53 E-value=3.3 Score=18.05 Aligned_cols=18 Identities=17% Similarity=0.444 Sum_probs=11.3
Q ss_pred cccccccccCChHHHHHHH
Q psy6676 30 KCTECGKGFCQSRTLAVHK 48 (144)
Q Consensus 30 ~C~~C~~~f~~~~~l~~h~ 48 (144)
.||+|++.+ ....+..|.
T Consensus 3 ~CPiC~~~v-~~~~in~HL 20 (26)
T smart00734 3 QCPVCFREV-PENLINSHL 20 (26)
T ss_pred cCCCCcCcc-cHHHHHHHH
Confidence 577887776 444555554
No 98
>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=73.51 E-value=0.95 Score=21.80 Aligned_cols=11 Identities=27% Similarity=0.923 Sum_probs=5.3
Q ss_pred ccccccccccc
Q psy6676 57 HKCPVCSRSFN 67 (144)
Q Consensus 57 ~~C~~C~~~~~ 67 (144)
|.|..|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 44555555443
No 99
>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=73.30 E-value=1.7 Score=29.66 Aligned_cols=25 Identities=20% Similarity=0.717 Sum_probs=10.4
Q ss_pred cccccccccccCchHHHHHHhhcCC
Q psy6676 57 HKCPVCSRSFNQRSNLKTHLLTHTD 81 (144)
Q Consensus 57 ~~C~~C~~~~~~~~~l~~h~~~h~~ 81 (144)
|.|..|++.|.-...+..|+...+.
T Consensus 78 ~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred ECCCCCCcccCChHHHHHHHhhcCH
Confidence 4444444444444444444444443
No 100
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=72.93 E-value=1.2 Score=35.93 Aligned_cols=48 Identities=23% Similarity=0.500 Sum_probs=27.0
Q ss_pred cccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhh
Q psy6676 30 KCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKV 93 (144)
Q Consensus 30 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 93 (144)
.|..||..+..... ...+..|.......|..||+ ....|..|+.||..
T Consensus 437 ~C~~Cg~v~~Cp~C-d~~lt~H~~~~~L~CH~Cg~---------------~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 437 LCRDCGYIAECPNC-DSPLTLHKATGQLRCHYCGY---------------QEPIPQSCPECGSE 484 (730)
T ss_pred ecccCCCcccCCCC-CcceEEecCCCeeEeCCCCC---------------CCCCCCCCCCCCCC
Confidence 47777766654421 01122344444567777753 23577899999864
No 101
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=71.81 E-value=2.5 Score=21.08 Aligned_cols=10 Identities=40% Similarity=1.129 Sum_probs=4.9
Q ss_pred cccccccccc
Q psy6676 29 FKCTECGKGF 38 (144)
Q Consensus 29 ~~C~~C~~~f 38 (144)
|.|..|+..|
T Consensus 3 Y~C~~Cg~~~ 12 (44)
T smart00659 3 YICGECGREN 12 (44)
T ss_pred EECCCCCCEe
Confidence 4455555444
No 102
>KOG1280|consensus
Probab=70.49 E-value=5.3 Score=29.26 Aligned_cols=39 Identities=26% Similarity=0.600 Sum_probs=28.6
Q ss_pred CCCcccccccccccCChHHHHHHHHHhCCCC--Cccccccc
Q psy6676 25 KEKPFKCTECGKGFCQSRTLAVHKILHLEES--PHKCPVCS 63 (144)
Q Consensus 25 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~--~~~C~~C~ 63 (144)
....|.|++|+..-.+...|..|+...+..- ...|++|+
T Consensus 76 ~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 76 DPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 3456999999999999999999987654332 24566665
No 103
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=69.57 E-value=2.7 Score=21.01 Aligned_cols=10 Identities=40% Similarity=1.361 Sum_probs=5.2
Q ss_pred cccccccccc
Q psy6676 29 FKCTECGKGF 38 (144)
Q Consensus 29 ~~C~~C~~~f 38 (144)
|.|+.|+..|
T Consensus 4 y~C~~CG~~~ 13 (46)
T PRK00398 4 YKCARCGREV 13 (46)
T ss_pred EECCCCCCEE
Confidence 4555555544
No 104
>KOG2785|consensus
Probab=69.42 E-value=8.3 Score=28.64 Aligned_cols=24 Identities=21% Similarity=0.538 Sum_probs=20.2
Q ss_pred CCccccccc---ccccCchHHHHHHhh
Q psy6676 55 SPHKCPVCS---RSFNQRSNLKTHLLT 78 (144)
Q Consensus 55 ~~~~C~~C~---~~~~~~~~l~~h~~~ 78 (144)
..+.|..|. +.|........||..
T Consensus 216 ~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 216 IGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cCceEEEeccccCcccccHHHHHHHhh
Confidence 347888888 899999999999974
No 105
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=69.01 E-value=3.2 Score=28.90 Aligned_cols=63 Identities=19% Similarity=0.554 Sum_probs=29.4
Q ss_pred ccCCCCcccccccccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcCh
Q psy6676 22 IHSKEKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRN 97 (144)
Q Consensus 22 ~h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~ 97 (144)
+-+...+|.|..|+... +.+.-.....-.|..|.+.|.-.- .-.. =|..-|.|+.|+..|.-.
T Consensus 106 ip~~drqFaC~~Cd~~W--------wRrvp~rKeVSRCr~C~~rYDPVP---~dkm--wG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 106 IPSVDRQFACSSCDHMW--------WRRVPQRKEVSRCRKCRKRYDPVP---CDKM--WGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred ccccceeeeccccchHH--------HhccCcccccccccccccccCCCc---cccc--cceeeeecccccccchhh
Confidence 34445778888886432 112222223345666655542211 0000 112236677777666554
No 106
>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=67.98 E-value=5.1 Score=24.03 Aligned_cols=26 Identities=19% Similarity=0.347 Sum_probs=21.1
Q ss_pred cccc----cccccccCChHHHHHHHHHhCC
Q psy6676 28 PFKC----TECGKGFCQSRTLAVHKILHLE 53 (144)
Q Consensus 28 ~~~C----~~C~~~f~~~~~l~~h~~~~~~ 53 (144)
.|.| ..|+..+.+...|..|.+.++|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3778 8899998899999999877653
No 107
>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=67.77 E-value=2.7 Score=20.00 Aligned_cols=9 Identities=33% Similarity=1.187 Sum_probs=4.3
Q ss_pred ccccccccc
Q psy6676 30 KCTECGKGF 38 (144)
Q Consensus 30 ~C~~C~~~f 38 (144)
.|+.|+..|
T Consensus 3 ~C~~Cg~~Y 11 (36)
T PF05191_consen 3 ICPKCGRIY 11 (36)
T ss_dssp EETTTTEEE
T ss_pred CcCCCCCcc
Confidence 344555444
No 108
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.65 E-value=3.6 Score=24.85 Aligned_cols=13 Identities=23% Similarity=0.542 Sum_probs=7.0
Q ss_pred CCCcccccccccc
Q psy6676 54 ESPHKCPVCSRSF 66 (144)
Q Consensus 54 ~~~~~C~~C~~~~ 66 (144)
+.|.+|+.||+.|
T Consensus 24 rdPiVsPytG~s~ 36 (129)
T COG4530 24 RDPIVSPYTGKSY 36 (129)
T ss_pred CCccccCcccccc
Confidence 3455555555555
No 109
>KOG4173|consensus
Probab=66.44 E-value=3.7 Score=27.80 Aligned_cols=49 Identities=24% Similarity=0.525 Sum_probs=34.8
Q ss_pred CCccccc--ccccccCchHHHHHHhhcCCCCCcccCcchhhhcChHHHHHhHhh
Q psy6676 55 SPHKCPV--CSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRNCDLRRHSLT 106 (144)
Q Consensus 55 ~~~~C~~--C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 106 (144)
..+.|++ |.+.|........|.-.-++ -.|.+|.+.|.+...|..|+.-
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E 128 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILE 128 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHH
Confidence 3477887 66777666655555433222 4899999999999999988753
No 110
>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=66.34 E-value=2.4 Score=18.27 Aligned_cols=10 Identities=40% Similarity=1.212 Sum_probs=6.0
Q ss_pred CCcccCcchh
Q psy6676 83 KPYNCAACGK 92 (144)
Q Consensus 83 ~~~~C~~C~~ 92 (144)
..|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4566666663
No 111
>KOG2907|consensus
Probab=66.28 E-value=2 Score=26.00 Aligned_cols=40 Identities=25% Similarity=0.509 Sum_probs=20.7
Q ss_pred cccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcC
Q psy6676 57 HKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRR 96 (144)
Q Consensus 57 ~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~ 96 (144)
.+|+.||..-.....++..-.--....-|.|..|++.|+.
T Consensus 75 ~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCchhhhhhhhcccccCCceEEEEcCccceeeec
Confidence 5788887543332222221111112234789899887764
No 112
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=66.06 E-value=7.7 Score=18.93 Aligned_cols=24 Identities=25% Similarity=0.495 Sum_probs=17.6
Q ss_pred ccccccccccC--ChHHHHHHHHHhC
Q psy6676 29 FKCTECGKGFC--QSRTLAVHKILHL 52 (144)
Q Consensus 29 ~~C~~C~~~f~--~~~~l~~h~~~~~ 52 (144)
-.|+.|+..|. ...+...|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 57999999986 4466777766653
No 113
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=66.04 E-value=1.4 Score=24.64 Aligned_cols=42 Identities=19% Similarity=0.464 Sum_probs=22.4
Q ss_pred cccccccccccCchHHHHHHhhcCCCCCcccC--cchhhhcChHHH
Q psy6676 57 HKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCA--ACGKVFRRNCDL 100 (144)
Q Consensus 57 ~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~--~C~~~f~~~~~l 100 (144)
+.|+.|+..-......... ....+..+.|. .||..|.....+
T Consensus 2 m~CP~Cg~~a~irtSr~~s--~~~~~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYIT--DTTKERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred ccCCCCCCccEEEEChhcC--hhhheeeeecCCCCCCCEEEEEEEE
Confidence 3566676543222211111 11345667887 788888876543
No 114
>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=65.49 E-value=6 Score=19.74 Aligned_cols=11 Identities=45% Similarity=0.936 Sum_probs=7.7
Q ss_pred CCCcccCcchh
Q psy6676 82 IKPYNCAACGK 92 (144)
Q Consensus 82 ~~~~~C~~C~~ 92 (144)
...|+|..|++
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 46678887765
No 115
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=64.94 E-value=3 Score=26.18 Aligned_cols=24 Identities=38% Similarity=0.497 Sum_probs=18.5
Q ss_pred cccCcchhhhcChHHHHHhHhhccCCC
Q psy6676 85 YNCAACGKVFRRNCDLRRHSLTHNLGS 111 (144)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~h~~~~ 111 (144)
..|..+|+.|+ .|++|+.+|+.-.
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmT 100 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLT 100 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCC
Confidence 57888998776 4789999887543
No 116
>PHA00626 hypothetical protein
Probab=64.87 E-value=2.5 Score=22.24 Aligned_cols=17 Identities=24% Similarity=0.585 Sum_probs=13.0
Q ss_pred CCCcccCcchhhhcChH
Q psy6676 82 IKPYNCAACGKVFRRNC 98 (144)
Q Consensus 82 ~~~~~C~~C~~~f~~~~ 98 (144)
...|+|+.||..|+..+
T Consensus 21 snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 21 SDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CcceEcCCCCCeechhh
Confidence 35689999998887653
No 117
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=64.69 E-value=4.8 Score=23.45 Aligned_cols=28 Identities=29% Similarity=0.721 Sum_probs=18.7
Q ss_pred CCcccccccccccCchHHHHHHhhcCCCCCcccCcchh
Q psy6676 55 SPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGK 92 (144)
Q Consensus 55 ~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 92 (144)
+|..|..||+.|... .-.+|-+|+.|..
T Consensus 57 ~Pa~CkkCGfef~~~----------~ik~pSRCP~CKS 84 (97)
T COG3357 57 RPARCKKCGFEFRDD----------KIKKPSRCPKCKS 84 (97)
T ss_pred cChhhcccCcccccc----------ccCCcccCCcchh
Confidence 567888888887541 1235678888864
No 118
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=64.56 E-value=0.69 Score=22.57 Aligned_cols=10 Identities=40% Similarity=1.251 Sum_probs=6.4
Q ss_pred cccCcchhhh
Q psy6676 85 YNCAACGKVF 94 (144)
Q Consensus 85 ~~C~~C~~~f 94 (144)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 6676676554
No 119
>KOG0782|consensus
Probab=64.50 E-value=1.1 Score=34.93 Aligned_cols=51 Identities=20% Similarity=0.496 Sum_probs=35.7
Q ss_pred HHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCCC-CCcccCcchhhhcChH
Q psy6676 42 RTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDI-KPYNCAACGKVFRRNC 98 (144)
Q Consensus 42 ~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~-~~~~C~~C~~~f~~~~ 98 (144)
..+.+|-.+|.....-+|..|++.|..+..+ |..+ ....|.+|..+|-...
T Consensus 239 ~~fvrHHWVHrrRqeGkC~~CgKgFQQKf~F------hsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 239 SGFVRHHWVHRRRQEGKCNTCGKGFQQKFFF------HSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred ccchHHhHhhHhhhccccchhhhhhhhheee------ccccEEEEEehHHHHHhhcch
Confidence 4677776677666667899999999776443 3332 3468999998887654
No 120
>KOG4167|consensus
Probab=64.20 E-value=2.2 Score=34.26 Aligned_cols=27 Identities=33% Similarity=0.552 Sum_probs=23.2
Q ss_pred CCcccCcchhhhcChHHHHHhHhhccC
Q psy6676 83 KPYNCAACGKVFRRNCDLRRHSLTHNL 109 (144)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~~~h~~ 109 (144)
..|-|..|+|.|.....+..|+++|..
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 459999999999998899999988753
No 121
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=63.59 E-value=5.4 Score=21.28 Aligned_cols=51 Identities=27% Similarity=0.645 Sum_probs=26.5
Q ss_pred CCcccccccccccCChHHHHHHHHHhCCCCCccccccccc-ccCchHHHHHHhhcCCCCCcccCcchh
Q psy6676 26 EKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRS-FNQRSNLKTHLLTHTDIKPYNCAACGK 92 (144)
Q Consensus 26 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~-~~~~~~l~~h~~~h~~~~~~~C~~C~~ 92 (144)
..+..|..|+....-. .....|.|+.||.. ...-. +--....+|.|+.||.
T Consensus 5 ~~~~~CtSCg~~i~~~----------~~~~~F~CPnCG~~~I~RC~------~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 5 MEPPKCTSCGIEIAPR----------EKAVKFLCPNCGEVIIYRCE------KCRKQSNPYTCPKCGF 56 (59)
T ss_pred ccCccccCCCCcccCC----------CccCEeeCCCCCCeeEeech------hHHhcCCceECCCCCC
Confidence 3445677777553211 11234788888764 21111 1111236788888884
No 122
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=63.27 E-value=2.7 Score=26.47 Aligned_cols=10 Identities=30% Similarity=0.873 Sum_probs=6.0
Q ss_pred CCcccCcchh
Q psy6676 83 KPYNCAACGK 92 (144)
Q Consensus 83 ~~~~C~~C~~ 92 (144)
..+.|+.||.
T Consensus 106 ~~~~CP~Cgs 115 (135)
T PRK03824 106 AFLKCPKCGS 115 (135)
T ss_pred cCcCCcCCCC
Confidence 3356777764
No 123
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=63.00 E-value=1.9 Score=25.14 Aligned_cols=33 Identities=18% Similarity=0.516 Sum_probs=21.4
Q ss_pred CCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcCh
Q psy6676 55 SPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRN 97 (144)
Q Consensus 55 ~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~ 97 (144)
..|.|+.|++.-.. + .+...|.|..|++.|.-.
T Consensus 35 a~y~CpfCgk~~vk--------R--~a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 35 AKYFCPFCGKHAVK--------R--QAVGIWRCKGCKKTVAGG 67 (90)
T ss_pred CCccCCCCCCCcee--------e--eeeEEEEcCCCCCEEeCC
Confidence 45889999754211 1 223668999999888654
No 124
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=62.74 E-value=1.7 Score=25.41 Aligned_cols=33 Identities=21% Similarity=0.580 Sum_probs=21.3
Q ss_pred CCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcCh
Q psy6676 55 SPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRN 97 (144)
Q Consensus 55 ~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~ 97 (144)
..|.|+.|++.-.. + .+...|.|..|++.|.-.
T Consensus 34 a~y~CpfCgk~~vk--------R--~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 34 AKYVCPFCGKKTVK--------R--GSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred cCccCCCCCCCceE--------E--EeeEEEEcCCCCCEEeCC
Confidence 35889999754211 1 223568999999888654
No 125
>KOG2593|consensus
Probab=62.35 E-value=5.6 Score=30.01 Aligned_cols=38 Identities=18% Similarity=0.486 Sum_probs=22.1
Q ss_pred CCCCcccccccccccCChHHHHHHHHHhCCCCCcccccccc
Q psy6676 24 SKEKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSR 64 (144)
Q Consensus 24 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~ 64 (144)
.....|.|+.|.+.|.....++.- .-....|.|..|+.
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~L~---~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQLL---DNETGEFHCENCGG 161 (436)
T ss_pred cccccccCCccccchhhhHHHHhh---cccCceEEEecCCC
Confidence 345667788888777655444321 22233477777764
No 126
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=61.46 E-value=5.5 Score=23.92 Aligned_cols=26 Identities=19% Similarity=0.387 Sum_probs=21.7
Q ss_pred CCCCcccCcchhhhcChHHHHHhHhh
Q psy6676 81 DIKPYNCAACGKVFRRNCDLRRHSLT 106 (144)
Q Consensus 81 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 106 (144)
|-..+.|..|.+-|.+...|..|.+.
T Consensus 52 GlGqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 52 GLGQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred CCceeeeehhHHHHHHHHHHHHHhcc
Confidence 44558999999999999999999763
No 127
>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=60.33 E-value=3.7 Score=17.98 Aligned_cols=9 Identities=44% Similarity=1.036 Sum_probs=5.0
Q ss_pred ccCcchhhh
Q psy6676 86 NCAACGKVF 94 (144)
Q Consensus 86 ~C~~C~~~f 94 (144)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 455555555
No 128
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=60.07 E-value=4.5 Score=19.15 Aligned_cols=32 Identities=16% Similarity=0.503 Sum_probs=18.2
Q ss_pred cccccccccCChHHHHHHHHHhCCCCCcccccccccc
Q psy6676 30 KCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSF 66 (144)
Q Consensus 30 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~ 66 (144)
.|+.|+..|...... .-.......|..|+..|
T Consensus 4 ~Cp~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHH-----CCCCCcEEECCCCCCEe
Confidence 577777777665431 11223345777777655
No 129
>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=59.54 E-value=2.9 Score=21.20 Aligned_cols=11 Identities=27% Similarity=0.935 Sum_probs=5.7
Q ss_pred ccccccccccC
Q psy6676 29 FKCTECGKGFC 39 (144)
Q Consensus 29 ~~C~~C~~~f~ 39 (144)
|.|..|+..|.
T Consensus 2 y~C~~CgyvYd 12 (47)
T PF00301_consen 2 YQCPVCGYVYD 12 (47)
T ss_dssp EEETTTSBEEE
T ss_pred cCCCCCCEEEc
Confidence 45555555543
No 130
>KOG3408|consensus
Probab=58.44 E-value=6.6 Score=24.24 Aligned_cols=26 Identities=27% Similarity=0.526 Sum_probs=20.3
Q ss_pred CCCcccccccccccCChHHHHHHHHH
Q psy6676 25 KEKPFKCTECGKGFCQSRTLAVHKIL 50 (144)
Q Consensus 25 ~~~~~~C~~C~~~f~~~~~l~~h~~~ 50 (144)
|-.+|-|-.|.+-|.+...|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 56668888888888888888888654
No 131
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=57.51 E-value=3.8 Score=18.66 Aligned_cols=7 Identities=43% Similarity=1.213 Sum_probs=3.3
Q ss_pred ccccccc
Q psy6676 57 HKCPVCS 63 (144)
Q Consensus 57 ~~C~~C~ 63 (144)
+.|+.|+
T Consensus 20 ~vCp~C~ 26 (30)
T PF08274_consen 20 LVCPECG 26 (30)
T ss_dssp EEETTTT
T ss_pred EeCCccc
Confidence 4444444
No 132
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=57.11 E-value=5.4 Score=20.45 Aligned_cols=11 Identities=36% Similarity=1.223 Sum_probs=6.3
Q ss_pred ccccccccccc
Q psy6676 28 PFKCTECGKGF 38 (144)
Q Consensus 28 ~~~C~~C~~~f 38 (144)
.|.|..|++.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 35566666555
No 133
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=56.85 E-value=6.5 Score=29.70 Aligned_cols=14 Identities=29% Similarity=0.809 Sum_probs=7.7
Q ss_pred CcccCcchhhhcCh
Q psy6676 84 PYNCAACGKVFRRN 97 (144)
Q Consensus 84 ~~~C~~C~~~f~~~ 97 (144)
-|+|+.||..+...
T Consensus 367 g~rC~kCg~~~~~~ 380 (421)
T COG1571 367 GFRCKKCGTRARET 380 (421)
T ss_pred CcccccccccCCcc
Confidence 56666666555443
No 134
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=56.78 E-value=5.1 Score=28.19 Aligned_cols=84 Identities=24% Similarity=0.366 Sum_probs=47.1
Q ss_pred cCCCCcccccccccccCChHHHHHHHHH--hCCCCCcccccccccccCc------hHHHHHHhh----cCCCCCcccCcc
Q psy6676 23 HSKEKPFKCTECGKGFCQSRTLAVHKIL--HLEESPHKCPVCSRSFNQR------SNLKTHLLT----HTDIKPYNCAAC 90 (144)
Q Consensus 23 h~~~~~~~C~~C~~~f~~~~~l~~h~~~--~~~~~~~~C~~C~~~~~~~------~~l~~h~~~----h~~~~~~~C~~C 90 (144)
..|.+-|.|..|.... .+-+-=.|+.. ......|+|.-|.+.-..+ -....|.+. ....+++.|+.|
T Consensus 137 ~hGGrif~CsfC~~fl-CEDDQFEHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKC 215 (314)
T PF06524_consen 137 DHGGRIFKCSFCDNFL-CEDDQFEHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKC 215 (314)
T ss_pred cCCCeEEEeecCCCee-eccchhhhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccccCCCCCCCCC
Confidence 3466778999998544 33333334332 2334567887777643321 112234432 123367899999
Q ss_pred hhhhcChHHHHHhHhhc
Q psy6676 91 GKVFRRNCDLRRHSLTH 107 (144)
Q Consensus 91 ~~~f~~~~~l~~H~~~h 107 (144)
+.-......|.--.|+|
T Consensus 216 g~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 216 GYETQETKDLSMSTRSH 232 (314)
T ss_pred CCcccccccceeeeecc
Confidence 98776666665444444
No 135
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=56.76 E-value=3.2 Score=32.17 Aligned_cols=11 Identities=36% Similarity=0.942 Sum_probs=7.2
Q ss_pred CCCcccCcchh
Q psy6676 82 IKPYNCAACGK 92 (144)
Q Consensus 82 ~~~~~C~~C~~ 92 (144)
..+..|+.|+.
T Consensus 251 ~~~~~Cp~C~s 261 (505)
T TIGR00595 251 PIPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCCC
Confidence 34567878865
No 136
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=56.53 E-value=2.3 Score=24.83 Aligned_cols=33 Identities=30% Similarity=0.719 Sum_probs=21.1
Q ss_pred CCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcCh
Q psy6676 55 SPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRN 97 (144)
Q Consensus 55 ~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~ 97 (144)
..|.|+.|++.-.. + .+...|.|..|++.|.-.
T Consensus 35 a~y~CpfCgk~~vk--------R--~a~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 35 AKHVCPVCGRPKVK--------R--VGTGIWECRKCGAKFAGG 67 (90)
T ss_pred cCccCCCCCCCceE--------E--EEEEEEEcCCCCCEEeCC
Confidence 35889998754211 1 223568999999888654
No 137
>PRK14873 primosome assembly protein PriA; Provisional
Probab=56.18 E-value=6.5 Score=31.68 Aligned_cols=44 Identities=20% Similarity=0.558 Sum_probs=26.0
Q ss_pred cccccccccCChH---HHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhh
Q psy6676 30 KCTECGKGFCQSR---TLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKV 93 (144)
Q Consensus 30 ~C~~C~~~f~~~~---~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 93 (144)
.|..|+..+.... .|.. |.......|..||.. ..++.|+.||..
T Consensus 385 ~C~~Cg~~~~C~~C~~~L~~----h~~~~~l~Ch~CG~~----------------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 385 ACARCRTPARCRHCTGPLGL----PSAGGTPRCRWCGRA----------------APDWRCPRCGSD 431 (665)
T ss_pred EhhhCcCeeECCCCCCceeE----ecCCCeeECCCCcCC----------------CcCccCCCCcCC
Confidence 5777777665442 2332 333445678888632 146788888754
No 138
>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=55.65 E-value=1.6 Score=19.53 Aligned_cols=19 Identities=26% Similarity=0.754 Sum_probs=10.3
Q ss_pred cccCcchhhhcChHHHHHhH
Q psy6676 85 YNCAACGKVFRRNCDLRRHS 104 (144)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~ 104 (144)
|.|..|++.| .....+.|.
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHT 19 (28)
T ss_dssp EEETTTTEEE-EGGGTTT--
T ss_pred CeeecCCCCc-CcCCcCCCC
Confidence 4577788877 333444443
No 139
>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=54.46 E-value=10 Score=26.01 Aligned_cols=30 Identities=23% Similarity=0.419 Sum_probs=22.5
Q ss_pred CCCCcccccccccccCChHHHHHHHHHhCC
Q psy6676 24 SKEKPFKCTECGKGFCQSRTLAVHKILHLE 53 (144)
Q Consensus 24 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~ 53 (144)
.++..|.|+.|++.|.-..-+..|+...+.
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 355679999999999999999999876554
No 140
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.27 E-value=3.1 Score=28.72 Aligned_cols=8 Identities=25% Similarity=0.546 Sum_probs=6.3
Q ss_pred cccCcchh
Q psy6676 85 YNCAACGK 92 (144)
Q Consensus 85 ~~C~~C~~ 92 (144)
..|+.|+.
T Consensus 63 vvCP~C~y 70 (267)
T COG1655 63 VVCPICYY 70 (267)
T ss_pred EEcchhhH
Confidence 57899975
No 141
>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=53.29 E-value=4.2 Score=19.95 Aligned_cols=15 Identities=33% Similarity=0.820 Sum_probs=11.8
Q ss_pred cccCcchhhhcChHH
Q psy6676 85 YNCAACGKVFRRNCD 99 (144)
Q Consensus 85 ~~C~~C~~~f~~~~~ 99 (144)
|+|..||..|.....
T Consensus 6 y~C~~Cg~~fe~~~~ 20 (42)
T PF09723_consen 6 YRCEECGHEFEVLQS 20 (42)
T ss_pred EEeCCCCCEEEEEEE
Confidence 789999988876644
No 142
>KOG0717|consensus
Probab=52.68 E-value=7.2 Score=29.82 Aligned_cols=21 Identities=29% Similarity=0.684 Sum_probs=18.9
Q ss_pred cccCcchhhhcChHHHHHhHh
Q psy6676 85 YNCAACGKVFRRNCDLRRHSL 105 (144)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~ 105 (144)
+.|.+|.|.|.+...+..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 789999999999999988864
No 143
>KOG2593|consensus
Probab=52.12 E-value=7.4 Score=29.40 Aligned_cols=35 Identities=20% Similarity=0.653 Sum_probs=21.9
Q ss_pred CCCcccccccccccCchHHHHHHhhcCCCCCcccCcch
Q psy6676 54 ESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACG 91 (144)
Q Consensus 54 ~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~ 91 (144)
...|.|+.|.+.|...-.++- .......|.|..|+
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQL---LDNETGEFHCENCG 160 (436)
T ss_pred cccccCCccccchhhhHHHHh---hcccCceEEEecCC
Confidence 455889999888866543322 22223458888885
No 144
>KOG2636|consensus
Probab=52.03 E-value=9.9 Score=28.92 Aligned_cols=29 Identities=31% Similarity=0.500 Sum_probs=23.4
Q ss_pred hhcCCCCCcccCcch-hhhcChHHHHHhHh
Q psy6676 77 LTHTDIKPYNCAACG-KVFRRNCDLRRHSL 105 (144)
Q Consensus 77 ~~h~~~~~~~C~~C~-~~f~~~~~l~~H~~ 105 (144)
+.|.....|.|.+|| +++.-...+.+|-.
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 566667789999999 78888888888853
No 145
>PF15269 zf-C2H2_7: Zinc-finger
Probab=51.65 E-value=10 Score=19.01 Aligned_cols=22 Identities=32% Similarity=0.519 Sum_probs=15.3
Q ss_pred cccccccccccCchHHHHHHhh
Q psy6676 57 HKCPVCSRSFNQRSNLKTHLLT 78 (144)
Q Consensus 57 ~~C~~C~~~~~~~~~l~~h~~~ 78 (144)
|.|-.|...+...+.|..||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 5666677777777777777763
No 146
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=51.49 E-value=6.3 Score=25.37 Aligned_cols=32 Identities=25% Similarity=0.788 Sum_probs=17.4
Q ss_pred CcccccccccccCchHHHHHHhhcCCCCCcccCcchh
Q psy6676 56 PHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGK 92 (144)
Q Consensus 56 ~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 92 (144)
+|.|. |+..|.. ...|-..-.|+ .|.|..|+-
T Consensus 117 ~Y~C~-C~q~~l~---~RRhn~~~~g~-~YrC~~C~g 148 (156)
T COG3091 117 PYRCQ-CQQHYLR---IRRHNTVRRGE-VYRCGKCGG 148 (156)
T ss_pred eEEee-cCCccch---hhhcccccccc-eEEeccCCc
Confidence 46676 7665433 23333344454 677777764
No 147
>KOG4377|consensus
Probab=50.92 E-value=9.6 Score=28.69 Aligned_cols=50 Identities=16% Similarity=0.187 Sum_probs=33.3
Q ss_pred cccccccccccccccccc---------cccCCCCcccc--cccccccCChHHHHHHHHHhC
Q psy6676 3 RAQHRDDMALETINLAQG---------YIHSKEKPFKC--TECGKGFCQSRTLAVHKILHL 52 (144)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~---------~~h~~~~~~~C--~~C~~~f~~~~~l~~h~~~~~ 52 (144)
|+-+++.+.|....+... .+..+.+.|.| +.|+..+..+.++-.|+..|.
T Consensus 237 ~a~le~~~~lqg~arfsss~~c~~~~c~~e~~rEhyhcl~e~C~ykr~~k~DvirH~~~hk 297 (480)
T KOG4377|consen 237 RARLEGTGQLQGYARFSSSVKCSFFGCHVEAGREHYHCLNEYCFYKRGQKNDVIRHVEIHK 297 (480)
T ss_pred hhhccchhhhhhhhhhhhhhhhccccceeeccchhhcccCccccccccchhhhHHHHHHHh
Confidence 455666666666544433 23345667888 459888888888888887664
No 148
>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=49.89 E-value=7.4 Score=23.08 Aligned_cols=16 Identities=44% Similarity=0.924 Sum_probs=11.3
Q ss_pred cCCCCcccccccccccC
Q psy6676 23 HSKEKPFKCTECGKGFC 39 (144)
Q Consensus 23 h~~~~~~~C~~C~~~f~ 39 (144)
+.| +++.|+.|+..|.
T Consensus 75 ~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 75 EKG-KPKRCPECGHVFK 90 (97)
T ss_pred eCC-CceeCCCCCcEEE
Confidence 444 6778888887775
No 149
>KOG1994|consensus
Probab=49.76 E-value=7.3 Score=26.83 Aligned_cols=22 Identities=32% Similarity=0.705 Sum_probs=18.9
Q ss_pred CCcccCcchhhhcChHHHHHhH
Q psy6676 83 KPYNCAACGKVFRRNCDLRRHS 104 (144)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~ 104 (144)
..|.|-+||..|.+...|..|-
T Consensus 238 eh~YC~fCG~~y~~~edl~ehC 259 (268)
T KOG1994|consen 238 EHYYCFFCGIKYKDEEDLYEHC 259 (268)
T ss_pred cceEEEEeccccCCHHHHHHhC
Confidence 3489999999999999998774
No 150
>KOG0978|consensus
Probab=49.61 E-value=5.2 Score=32.20 Aligned_cols=20 Identities=30% Similarity=0.522 Sum_probs=14.6
Q ss_pred CcccCcchhhhcChHHHHHh
Q psy6676 84 PYNCAACGKVFRRNCDLRRH 103 (144)
Q Consensus 84 ~~~C~~C~~~f~~~~~l~~H 103 (144)
.-+||.|+.+|....-+..|
T Consensus 678 qRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 678 QRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred cCCCCCCCCCCCcccccccC
Confidence 34899999999877665544
No 151
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=48.94 E-value=19 Score=25.89 Aligned_cols=31 Identities=29% Similarity=0.434 Sum_probs=25.3
Q ss_pred CCCCcccCcchhhhcChHHHHHhHhhccCCC
Q psy6676 81 DIKPYNCAACGKVFRRNCDLRRHSLTHNLGS 111 (144)
Q Consensus 81 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~ 111 (144)
....|.|..|-+-|.+...|.+|+..+....
T Consensus 45 ~~~lyiCe~Clky~~~~~~l~~H~~~C~~r~ 75 (290)
T PLN03238 45 CTKLYICEYCLKYMRKKKSLLRHLAKCDIRQ 75 (290)
T ss_pred CCeEEEcCCCcchhCCHHHHHHHHHhCCCCC
Confidence 3567999999999999999999998765443
No 152
>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=48.33 E-value=11 Score=28.89 Aligned_cols=33 Identities=15% Similarity=0.270 Sum_probs=25.8
Q ss_pred cCCCCCcccCcchhhhcChHHHHHhHhhccCCC
Q psy6676 79 HTDIKPYNCAACGKVFRRNCDLRRHSLTHNLGS 111 (144)
Q Consensus 79 h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~ 111 (144)
+...+-+.|+.|.+.|.....+..|+...|.+.
T Consensus 52 n~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 52 NKSWRFWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred cCceeEeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 444566889999999999999999998766554
No 153
>PRK04023 DNA polymerase II large subunit; Validated
Probab=47.80 E-value=14 Score=31.20 Aligned_cols=12 Identities=42% Similarity=0.767 Sum_probs=8.1
Q ss_pred CCcccccccccc
Q psy6676 26 EKPFKCTECGKG 37 (144)
Q Consensus 26 ~~~~~C~~C~~~ 37 (144)
.....|+.||..
T Consensus 624 Vg~RfCpsCG~~ 635 (1121)
T PRK04023 624 IGRRKCPSCGKE 635 (1121)
T ss_pred ccCccCCCCCCc
Confidence 344578888866
No 154
>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=47.59 E-value=16 Score=16.83 Aligned_cols=8 Identities=38% Similarity=1.252 Sum_probs=3.5
Q ss_pred cccCcchh
Q psy6676 85 YNCAACGK 92 (144)
Q Consensus 85 ~~C~~C~~ 92 (144)
.+|+.||.
T Consensus 18 irC~~CG~ 25 (32)
T PF03604_consen 18 IRCPECGH 25 (32)
T ss_dssp SSBSSSS-
T ss_pred EECCcCCC
Confidence 35555543
No 155
>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=47.51 E-value=0.54 Score=22.81 Aligned_cols=10 Identities=40% Similarity=1.251 Sum_probs=6.7
Q ss_pred cccCcchhhh
Q psy6676 85 YNCAACGKVF 94 (144)
Q Consensus 85 ~~C~~C~~~f 94 (144)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 6777777654
No 156
>KOG4167|consensus
Probab=47.36 E-value=4.6 Score=32.59 Aligned_cols=27 Identities=33% Similarity=0.595 Sum_probs=22.5
Q ss_pred CCcccccccccccCChHHHHHHHHHhC
Q psy6676 26 EKPFKCTECGKGFCQSRTLAVHKILHL 52 (144)
Q Consensus 26 ~~~~~C~~C~~~f~~~~~l~~h~~~~~ 52 (144)
..-|.|..|++.|.-...+..|++.|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 344889999999988888888888885
No 157
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=46.71 E-value=1.4 Score=31.47 Aligned_cols=9 Identities=33% Similarity=0.704 Sum_probs=3.5
Q ss_pred ccccccccc
Q psy6676 29 FKCTECGKG 37 (144)
Q Consensus 29 ~~C~~C~~~ 37 (144)
-.||+||..
T Consensus 173 g~CPvCGs~ 181 (290)
T PF04216_consen 173 GYCPVCGSP 181 (290)
T ss_dssp SS-TTT---
T ss_pred CcCCCCCCc
Confidence 368888854
No 158
>COG1773 Rubredoxin [Energy production and conversion]
Probab=46.28 E-value=6.8 Score=20.61 Aligned_cols=14 Identities=29% Similarity=0.961 Sum_probs=10.2
Q ss_pred CcccCcchhhhcCh
Q psy6676 84 PYNCAACGKVFRRN 97 (144)
Q Consensus 84 ~~~C~~C~~~f~~~ 97 (144)
.|+|.+||..|.-.
T Consensus 3 ~~~C~~CG~vYd~e 16 (55)
T COG1773 3 RWRCSVCGYVYDPE 16 (55)
T ss_pred ceEecCCceEeccc
Confidence 57888888777544
No 159
>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=45.99 E-value=13 Score=20.10 Aligned_cols=11 Identities=27% Similarity=0.936 Sum_probs=5.5
Q ss_pred CCcccCcchhh
Q psy6676 83 KPYNCAACGKV 93 (144)
Q Consensus 83 ~~~~C~~C~~~ 93 (144)
+.|.|+.||..
T Consensus 45 r~~~C~~Cg~~ 55 (69)
T PF07282_consen 45 RVFTCPNCGFE 55 (69)
T ss_pred ceEEcCCCCCE
Confidence 44555555543
No 160
>KOG0978|consensus
Probab=44.82 E-value=8.4 Score=31.07 Aligned_cols=49 Identities=20% Similarity=0.461 Sum_probs=29.2
Q ss_pred CCcccccccccccCChHH-HHHH------HHHhCCCCCcccccccccccCchHHHH
Q psy6676 26 EKPFKCTECGKGFCQSRT-LAVH------KILHLEESPHKCPVCSRSFNQRSNLKT 74 (144)
Q Consensus 26 ~~~~~C~~C~~~f~~~~~-l~~h------~~~~~~~~~~~C~~C~~~~~~~~~l~~ 74 (144)
+....|+.|+..++..-- -..| +..-.+.+.-+||.|+..|.....+..
T Consensus 641 K~~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 641 KELLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRI 696 (698)
T ss_pred HhceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccccccc
Confidence 345689999877654421 1333 222233344699999999977654443
No 161
>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=44.67 E-value=22 Score=18.32 Aligned_cols=10 Identities=40% Similarity=1.308 Sum_probs=3.6
Q ss_pred cccccccccc
Q psy6676 58 KCPVCSRSFN 67 (144)
Q Consensus 58 ~C~~C~~~~~ 67 (144)
.|++|++.|.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 5666665553
No 162
>PRK05580 primosome assembly protein PriA; Validated
Probab=44.15 E-value=6.3 Score=31.80 Aligned_cols=10 Identities=40% Similarity=1.102 Sum_probs=6.3
Q ss_pred CCcccCcchh
Q psy6676 83 KPYNCAACGK 92 (144)
Q Consensus 83 ~~~~C~~C~~ 92 (144)
.+..|+.||.
T Consensus 420 ~~~~Cp~Cg~ 429 (679)
T PRK05580 420 IPKACPECGS 429 (679)
T ss_pred CCCCCCCCcC
Confidence 4556777754
No 163
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=43.80 E-value=4.7 Score=26.02 Aligned_cols=19 Identities=26% Similarity=0.494 Sum_probs=14.2
Q ss_pred CCCCCcccCcchhhhcChH
Q psy6676 80 TDIKPYNCAACGKVFRRNC 98 (144)
Q Consensus 80 ~~~~~~~C~~C~~~f~~~~ 98 (144)
+.+.|..|..||+.|++-.
T Consensus 64 ~~~~PsYC~~CGkpyPWt~ 82 (158)
T PF10083_consen 64 HYEAPSYCHNCGKPYPWTE 82 (158)
T ss_pred CCCCChhHHhCCCCCchHH
Confidence 3457788888998888853
No 164
>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=43.76 E-value=10 Score=23.10 Aligned_cols=10 Identities=30% Similarity=0.747 Sum_probs=5.2
Q ss_pred cccccccccc
Q psy6676 57 HKCPVCSRSF 66 (144)
Q Consensus 57 ~~C~~C~~~~ 66 (144)
+.|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (115)
T TIGR00100 71 CECEDCSEEV 80 (115)
T ss_pred EEcccCCCEE
Confidence 4555555444
No 165
>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=43.31 E-value=11 Score=18.42 Aligned_cols=12 Identities=33% Similarity=1.002 Sum_probs=9.4
Q ss_pred Cccccccccccc
Q psy6676 27 KPFKCTECGKGF 38 (144)
Q Consensus 27 ~~~~C~~C~~~f 38 (144)
++-.|++|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 467899998876
No 166
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=43.19 E-value=12 Score=22.75 Aligned_cols=10 Identities=30% Similarity=0.454 Sum_probs=5.3
Q ss_pred cccccccccc
Q psy6676 57 HKCPVCSRSF 66 (144)
Q Consensus 57 ~~C~~C~~~~ 66 (144)
+.|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 4555565444
No 167
>KOG4124|consensus
Probab=42.86 E-value=2.3 Score=31.12 Aligned_cols=71 Identities=25% Similarity=0.460 Sum_probs=38.5
Q ss_pred CCcccccc--cccccCChHHHHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcChHHHHHh
Q psy6676 26 EKPFKCTE--CGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRNCDLRRH 103 (144)
Q Consensus 26 ~~~~~C~~--C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H 103 (144)
.++|.|++ |++.+.....|..|....+-. -- ..... .-..|+..-...++|+|++|.+.++....|.-|
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s------~i--~~~s~-~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCS------PI--TTPTP-APIPHQGFVVENKPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCC------CC--CCCCC-CCCCcceeeeccCcccChhhhhhhccCCCCCce
Confidence 46677755 777777666666553221110 00 00000 111233333345789999999988887776655
Q ss_pred Hh
Q psy6676 104 SL 105 (144)
Q Consensus 104 ~~ 105 (144)
+-
T Consensus 418 ~~ 419 (442)
T KOG4124|consen 418 RT 419 (442)
T ss_pred ee
Confidence 43
No 168
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=42.67 E-value=19 Score=18.94 Aligned_cols=13 Identities=23% Similarity=0.603 Sum_probs=6.5
Q ss_pred CCCcccccccccc
Q psy6676 54 ESPHKCPVCSRSF 66 (144)
Q Consensus 54 ~~~~~C~~C~~~~ 66 (144)
...|.|+.||..+
T Consensus 12 ~v~~~Cp~cGipt 24 (55)
T PF13824_consen 12 HVNFECPDCGIPT 24 (55)
T ss_pred ccCCcCCCCCCcC
Confidence 3445555555433
No 169
>KOG1842|consensus
Probab=42.56 E-value=14 Score=28.23 Aligned_cols=21 Identities=33% Similarity=0.635 Sum_probs=12.7
Q ss_pred cccccccccccCchHHHHHHh
Q psy6676 57 HKCPVCSRSFNQRSNLKTHLL 77 (144)
Q Consensus 57 ~~C~~C~~~~~~~~~l~~h~~ 77 (144)
|.|++|...|.+...|..|..
T Consensus 16 flCPiC~~dl~~~~~L~~H~d 36 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLD 36 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHh
Confidence 566666666666666666654
No 170
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=42.48 E-value=13 Score=26.96 Aligned_cols=14 Identities=29% Similarity=0.425 Sum_probs=9.7
Q ss_pred CCCccccccccccc
Q psy6676 25 KEKPFKCTECGKGF 38 (144)
Q Consensus 25 ~~~~~~C~~C~~~f 38 (144)
+.....||+||...
T Consensus 184 ~~~~~~CPvCGs~P 197 (309)
T PRK03564 184 GEQRQFCPVCGSMP 197 (309)
T ss_pred ccCCCCCCCCCCcc
Confidence 44556799999653
No 171
>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=42.29 E-value=8.3 Score=25.99 Aligned_cols=27 Identities=22% Similarity=0.533 Sum_probs=0.0
Q ss_pred hcCCCCCcccCcch-hhhcChHHHHHhH
Q psy6676 78 THTDIKPYNCAACG-KVFRRNCDLRRHS 104 (144)
Q Consensus 78 ~h~~~~~~~C~~C~-~~f~~~~~l~~H~ 104 (144)
.|...+.|.|.+|| .+|.-...+.+|-
T Consensus 95 LhGL~~ey~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 95 LHGLGVEYKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp ----------------------------
T ss_pred HhCCCCeeeeEeCCCcceecHHHHHHhc
Confidence 44455668888887 3555566666664
No 172
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=42.06 E-value=10 Score=19.47 Aligned_cols=20 Identities=25% Similarity=0.471 Sum_probs=13.2
Q ss_pred CCCcccCcchhhhcChHHHH
Q psy6676 82 IKPYNCAACGKVFRRNCDLR 101 (144)
Q Consensus 82 ~~~~~C~~C~~~f~~~~~l~ 101 (144)
++.+.|..||..|.....-+
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ 21 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQ 21 (49)
T ss_pred CeeEEcccCCCeEEEehhHH
Confidence 35677888888776655443
No 173
>PHA02998 RNA polymerase subunit; Provisional
Probab=42.05 E-value=4.2 Score=26.88 Aligned_cols=41 Identities=20% Similarity=0.432 Sum_probs=20.1
Q ss_pred cccccccccccCchHHHHHHhhcCCCCCcccCcchhhhcCh
Q psy6676 57 HKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVFRRN 97 (144)
Q Consensus 57 ~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~ 97 (144)
..|+.|+..-.....++..-.--.--.-|.|..||+.|.-.
T Consensus 144 v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 144 TPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCCc
Confidence 57888875433322222111000111237899999877543
No 174
>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=42.00 E-value=14 Score=18.23 Aligned_cols=12 Identities=33% Similarity=0.933 Sum_probs=6.6
Q ss_pred ccCcchhhhcCh
Q psy6676 86 NCAACGKVFRRN 97 (144)
Q Consensus 86 ~C~~C~~~f~~~ 97 (144)
.|.+|++.|+..
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 455566555544
No 175
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=41.69 E-value=4.3 Score=32.68 Aligned_cols=55 Identities=27% Similarity=0.652 Sum_probs=26.6
Q ss_pred ccccccccCChHHHHHHHHHhCCCCC-cccccccccccCchHHHHHHhhcCCCCCcccCcchh
Q psy6676 31 CTECGKGFCQSRTLAVHKILHLEESP-HKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGK 92 (144)
Q Consensus 31 C~~C~~~f~~~~~l~~h~~~~~~~~~-~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 92 (144)
|..||.+|.....|--- +.++.-.. -.|+.|.+-|....+. |.|. .+.-|+.||-
T Consensus 126 CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~nR----RfHA--Qp~aCp~CGP 181 (750)
T COG0068 126 CTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLNR----RFHA--QPIACPKCGP 181 (750)
T ss_pred cCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCcccc----cccc--ccccCcccCC
Confidence 66666666554433110 11111111 2466676666555433 2332 4567777874
No 176
>PF12907 zf-met2: Zinc-binding
Probab=41.68 E-value=24 Score=17.23 Aligned_cols=25 Identities=20% Similarity=0.481 Sum_probs=16.8
Q ss_pred cccCcchhhh---cChHHHHHhHhhccC
Q psy6676 85 YNCAACGKVF---RRNCDLRRHSLTHNL 109 (144)
Q Consensus 85 ~~C~~C~~~f---~~~~~l~~H~~~h~~ 109 (144)
++|.+|...| .....|..|-..-|.
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHp 29 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHP 29 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCC
Confidence 5788888555 455678888765443
No 177
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=40.98 E-value=12 Score=22.61 Aligned_cols=12 Identities=33% Similarity=0.808 Sum_probs=6.5
Q ss_pred Cccccccccccc
Q psy6676 56 PHKCPVCSRSFN 67 (144)
Q Consensus 56 ~~~C~~C~~~~~ 67 (144)
.|.|+.|+.-|.
T Consensus 19 ~~iCpeC~~EW~ 30 (109)
T TIGR00686 19 QLICPSCLYEWN 30 (109)
T ss_pred eeECcccccccc
Confidence 356666655443
No 178
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=40.54 E-value=20 Score=26.51 Aligned_cols=32 Identities=25% Similarity=0.351 Sum_probs=27.2
Q ss_pred CCCcccCcchhhhcChHHHHHhHhhccCCCCC
Q psy6676 82 IKPYNCAACGKVFRRNCDLRRHSLTHNLGSAT 113 (144)
Q Consensus 82 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~ 113 (144)
...|.|..|-+.|.+...|.+|++.+....++
T Consensus 156 d~vyICefClkY~~s~~~~~rH~~kC~~~~pP 187 (395)
T COG5027 156 DIVYICEFCLKYYGSQTSLVRHRKKCSLQHPP 187 (395)
T ss_pred ceEEEhhhhHHHhcchhHHHHHHhcCcCcCCC
Confidence 45699999999999999999999988776533
No 179
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=40.15 E-value=12 Score=19.14 Aligned_cols=10 Identities=20% Similarity=0.624 Sum_probs=5.9
Q ss_pred Cccccccccc
Q psy6676 56 PHKCPVCSRS 65 (144)
Q Consensus 56 ~~~C~~C~~~ 65 (144)
.+.|..|+..
T Consensus 37 r~~C~~Cgyt 46 (50)
T PRK00432 37 RWHCGKCGYT 46 (50)
T ss_pred cEECCCcCCE
Confidence 4566666644
No 180
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=40.11 E-value=23 Score=25.74 Aligned_cols=11 Identities=27% Similarity=0.700 Sum_probs=7.8
Q ss_pred Ccccccccccc
Q psy6676 27 KPFKCTECGKG 37 (144)
Q Consensus 27 ~~~~C~~C~~~ 37 (144)
....||+||..
T Consensus 183 ~~~~CPvCGs~ 193 (305)
T TIGR01562 183 SRTLCPACGSP 193 (305)
T ss_pred CCCcCCCCCCh
Confidence 34479999955
No 181
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=40.07 E-value=24 Score=27.05 Aligned_cols=30 Identities=33% Similarity=0.529 Sum_probs=25.2
Q ss_pred CCCcccCcchhhhcChHHHHHhHhhccCCC
Q psy6676 82 IKPYNCAACGKVFRRNCDLRRHSLTHNLGS 111 (144)
Q Consensus 82 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~ 111 (144)
...|.|..|-+-|.....|.+|+..+....
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~~C~~~~ 225 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMKKCDLKH 225 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHhcCCCCC
Confidence 355999999999999999999998765543
No 182
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=39.55 E-value=14 Score=19.22 Aligned_cols=25 Identities=24% Similarity=0.493 Sum_probs=10.6
Q ss_pred HHHHHHhhcCCCCCcccCc----chhhhc
Q psy6676 71 NLKTHLLTHTDIKPYNCAA----CGKVFR 95 (144)
Q Consensus 71 ~l~~h~~~h~~~~~~~C~~----C~~~f~ 95 (144)
.|..|....-..++..|.. |+..+.
T Consensus 25 ~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 25 ELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp CHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred HHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 4555555433444455555 554443
No 183
>PTZ00064 histone acetyltransferase; Provisional
Probab=39.42 E-value=28 Score=27.17 Aligned_cols=30 Identities=23% Similarity=0.170 Sum_probs=25.4
Q ss_pred CCCCcccCcchhhhcChHHHHHhHhhccCC
Q psy6676 81 DIKPYNCAACGKVFRRNCDLRRHSLTHNLG 110 (144)
Q Consensus 81 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~ 110 (144)
....|.|..|-+-|.....|.+|+..+...
T Consensus 277 ~d~LYICEfCLkY~~s~~~l~rH~~~C~~r 306 (552)
T PTZ00064 277 VDTLHFCEYCLDFFCFEDELIRHLSRCQLR 306 (552)
T ss_pred CCeEEEccchhhhhCCHHHHHHHHhcCCCC
Confidence 345699999999999999999999876554
No 184
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=39.37 E-value=6.9 Score=25.15 Aligned_cols=12 Identities=25% Similarity=0.797 Sum_probs=7.2
Q ss_pred cccccccccccC
Q psy6676 57 HKCPVCSRSFNQ 68 (144)
Q Consensus 57 ~~C~~C~~~~~~ 68 (144)
-.|..|+..|+.
T Consensus 29 ReC~~C~~RFTT 40 (156)
T COG1327 29 RECLECGERFTT 40 (156)
T ss_pred hcccccccccch
Confidence 356666666654
No 185
>KOG2747|consensus
Probab=39.07 E-value=25 Score=26.46 Aligned_cols=33 Identities=27% Similarity=0.406 Sum_probs=27.7
Q ss_pred CCCcccCcchhhhcChHHHHHhHhhccCCCCCC
Q psy6676 82 IKPYNCAACGKVFRRNCDLRRHSLTHNLGSATS 114 (144)
Q Consensus 82 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~ 114 (144)
...|.|..|-+-+.....|++|+..+....++.
T Consensus 156 ~~lYiCEfCLkY~~s~~~l~rH~~kC~~rhPPG 188 (396)
T KOG2747|consen 156 DKLYICEFCLKYMKSRTSLQRHLKKCKLRHPPG 188 (396)
T ss_pred CeEEEehHHHhHhchHHHHHHHHHhcCCCCCCc
Confidence 456899999999999999999999887764443
No 186
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=38.30 E-value=15 Score=17.66 Aligned_cols=14 Identities=50% Similarity=1.248 Sum_probs=11.7
Q ss_pred cccccccccccCCh
Q psy6676 28 PFKCTECGKGFCQS 41 (144)
Q Consensus 28 ~~~C~~C~~~f~~~ 41 (144)
|+.|..|+..|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78899999988765
No 187
>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=37.92 E-value=11 Score=19.31 Aligned_cols=13 Identities=31% Similarity=1.063 Sum_probs=9.7
Q ss_pred cccCcchhhhcCh
Q psy6676 85 YNCAACGKVFRRN 97 (144)
Q Consensus 85 ~~C~~C~~~f~~~ 97 (144)
|+|..||..|.-.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 7888998777543
No 188
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=37.55 E-value=15 Score=19.86 Aligned_cols=9 Identities=56% Similarity=1.339 Sum_probs=2.8
Q ss_pred ccccccccc
Q psy6676 30 KCTECGKGF 38 (144)
Q Consensus 30 ~C~~C~~~f 38 (144)
.|..|++.|
T Consensus 11 ~C~~C~~~F 19 (69)
T PF01363_consen 11 NCMICGKKF 19 (69)
T ss_dssp B-TTT--B-
T ss_pred cCcCcCCcC
Confidence 355566665
No 189
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=36.95 E-value=44 Score=24.39 Aligned_cols=29 Identities=28% Similarity=0.520 Sum_probs=22.3
Q ss_pred CCCcccCcchhhhcChHHHHHhHhhccCC
Q psy6676 82 IKPYNCAACGKVFRRNCDLRRHSLTHNLG 110 (144)
Q Consensus 82 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~ 110 (144)
...|.|+.|...|-..-..-.|...|...
T Consensus 386 s~rY~Ce~CK~~FC~dCdvfiHe~Lh~C~ 414 (421)
T COG5151 386 SGRYQCELCKSTFCSDCDVFIHETLHFCI 414 (421)
T ss_pred ccceechhhhhhhhhhhHHHHHHHHhhCC
Confidence 45699999999998877777777766543
No 190
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=36.73 E-value=16 Score=18.40 Aligned_cols=10 Identities=30% Similarity=0.886 Sum_probs=4.8
Q ss_pred CcccCcchhh
Q psy6676 84 PYNCAACGKV 93 (144)
Q Consensus 84 ~~~C~~C~~~ 93 (144)
.+.|+.||..
T Consensus 20 ~~vC~~Cg~~ 29 (52)
T smart00661 20 RFVCRKCGYE 29 (52)
T ss_pred EEECCcCCCe
Confidence 3455555543
No 191
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=35.90 E-value=17 Score=22.76 Aligned_cols=16 Identities=31% Similarity=0.897 Sum_probs=12.9
Q ss_pred CCCcccCcchhhhcCh
Q psy6676 82 IKPYNCAACGKVFRRN 97 (144)
Q Consensus 82 ~~~~~C~~C~~~f~~~ 97 (144)
...|+|..|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 5669999999988654
No 192
>PRK05978 hypothetical protein; Provisional
Probab=35.37 E-value=19 Score=23.14 Aligned_cols=10 Identities=60% Similarity=1.354 Sum_probs=5.5
Q ss_pred ccCcchhhhc
Q psy6676 86 NCAACGKVFR 95 (144)
Q Consensus 86 ~C~~C~~~f~ 95 (144)
.|+.||..|.
T Consensus 54 ~C~~CG~~~~ 63 (148)
T PRK05978 54 HCAACGEDFT 63 (148)
T ss_pred CccccCCccc
Confidence 5666665443
No 193
>KOG0717|consensus
Probab=35.23 E-value=24 Score=27.18 Aligned_cols=22 Identities=27% Similarity=0.546 Sum_probs=19.6
Q ss_pred ccccccccccCChHHHHHHHHH
Q psy6676 29 FKCTECGKGFCQSRTLAVHKIL 50 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~~~ 50 (144)
+-|.+|+++|.+...+..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999999643
No 194
>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=35.13 E-value=32 Score=26.59 Aligned_cols=24 Identities=21% Similarity=0.473 Sum_probs=20.9
Q ss_pred CcccccccccccCChHHHHHHHHH
Q psy6676 27 KPFKCTECGKGFCQSRTLAVHKIL 50 (144)
Q Consensus 27 ~~~~C~~C~~~f~~~~~l~~h~~~ 50 (144)
+-+.|+.|.+.|.....+..|+..
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHH
Confidence 347899999999999999999764
No 195
>PLN02294 cytochrome c oxidase subunit Vb
Probab=34.99 E-value=18 Score=23.80 Aligned_cols=16 Identities=31% Similarity=0.650 Sum_probs=11.3
Q ss_pred CCcccccccccccCCh
Q psy6676 26 EKPFKCTECGKGFCQS 41 (144)
Q Consensus 26 ~~~~~C~~C~~~f~~~ 41 (144)
.+++.|+.|+..|+-+
T Consensus 139 Gkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 139 GKSFECPVCTQYFELE 154 (174)
T ss_pred CCceeCCCCCCEEEEE
Confidence 3577788888887543
No 196
>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=34.81 E-value=6.4 Score=20.36 Aligned_cols=18 Identities=22% Similarity=0.857 Sum_probs=6.5
Q ss_pred CcccccccccccCChHHH
Q psy6676 27 KPFKCTECGKGFCQSRTL 44 (144)
Q Consensus 27 ~~~~C~~C~~~f~~~~~l 44 (144)
..|.|+.|+..|-..-++
T Consensus 20 ~~y~C~~C~~~FC~dCD~ 37 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDV 37 (51)
T ss_dssp EEE--TTTT--B-HHHHH
T ss_pred CeEECCCCCCccccCcCh
Confidence 345566665555444443
No 197
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=34.75 E-value=22 Score=23.61 Aligned_cols=34 Identities=21% Similarity=0.601 Sum_probs=16.9
Q ss_pred CCCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhhh
Q psy6676 52 LEESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVF 94 (144)
Q Consensus 52 ~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f 94 (144)
....-|.|+.|...|...... . ..|.|+.||...
T Consensus 109 ~~~~~y~C~~~~~r~sfdeA~------~---~~F~Cp~Cg~~L 142 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDEAM------E---LGFTCPKCGEDL 142 (176)
T ss_pred ccCCceeCCCCCCcccHHHHH------H---hCCCCCCCCchh
Confidence 334557776665554332111 1 117777777543
No 198
>KOG2807|consensus
Probab=34.52 E-value=68 Score=23.65 Aligned_cols=27 Identities=37% Similarity=0.760 Sum_probs=19.2
Q ss_pred CCcccCcchhhhcChHHHHHhHhhccC
Q psy6676 83 KPYNCAACGKVFRRNCDLRRHSLTHNL 109 (144)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~~~h~~ 109 (144)
..|.|..|...|=..-..-.|...|..
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh~C 370 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLHNC 370 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhhcC
Confidence 448888888888766666667666654
No 199
>KOG0320|consensus
Probab=34.50 E-value=20 Score=23.80 Aligned_cols=14 Identities=29% Similarity=0.667 Sum_probs=8.8
Q ss_pred CCcccccccccccC
Q psy6676 26 EKPFKCTECGKGFC 39 (144)
Q Consensus 26 ~~~~~C~~C~~~f~ 39 (144)
+..|.|+.|--.+.
T Consensus 129 ~~~~~CPiCl~~~s 142 (187)
T KOG0320|consen 129 EGTYKCPICLDSVS 142 (187)
T ss_pred ccccCCCceecchh
Confidence 44478888765553
No 200
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=33.86 E-value=21 Score=22.39 Aligned_cols=14 Identities=43% Similarity=1.118 Sum_probs=7.5
Q ss_pred cccccccccccCCh
Q psy6676 28 PFKCTECGKGFCQS 41 (144)
Q Consensus 28 ~~~C~~C~~~f~~~ 41 (144)
|+.|..|++.|...
T Consensus 1 PH~Ct~Cg~~f~dg 14 (131)
T PF09845_consen 1 PHQCTKCGRVFEDG 14 (131)
T ss_pred CcccCcCCCCcCCC
Confidence 34555666555543
No 202
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=33.57 E-value=12 Score=17.53 Aligned_cols=11 Identities=36% Similarity=0.993 Sum_probs=3.0
Q ss_pred ccccccccccC
Q psy6676 58 KCPVCSRSFNQ 68 (144)
Q Consensus 58 ~C~~C~~~~~~ 68 (144)
.|..|++.|..
T Consensus 5 ~C~eC~~~f~d 15 (34)
T PF01286_consen 5 KCDECGKPFMD 15 (34)
T ss_dssp E-TTT--EES-
T ss_pred hHhHhCCHHHH
Confidence 34444444433
No 203
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=33.10 E-value=24 Score=26.13 Aligned_cols=23 Identities=26% Similarity=0.505 Sum_probs=20.1
Q ss_pred CCcccCcchhhhcChHHHHHhHh
Q psy6676 83 KPYNCAACGKVFRRNCDLRRHSL 105 (144)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~~ 105 (144)
..+.|.+|++-|.....+..|+.
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~Hl~ 259 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYHLE 259 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHHHh
Confidence 34789999999999999999984
No 204
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=32.82 E-value=22 Score=21.31 Aligned_cols=12 Identities=42% Similarity=1.254 Sum_probs=6.8
Q ss_pred Cccccccccccc
Q psy6676 56 PHKCPVCSRSFN 67 (144)
Q Consensus 56 ~~~C~~C~~~~~ 67 (144)
++.|..||..|.
T Consensus 2 pH~CtrCG~vf~ 13 (112)
T COG3364 2 PHQCTRCGEVFD 13 (112)
T ss_pred Cceecccccccc
Confidence 455666666553
No 205
>PRK10220 hypothetical protein; Provisional
Probab=32.59 E-value=26 Score=21.27 Aligned_cols=11 Identities=27% Similarity=0.833 Sum_probs=6.3
Q ss_pred Ccccccccccc
Q psy6676 56 PHKCPVCSRSF 66 (144)
Q Consensus 56 ~~~C~~C~~~~ 66 (144)
.|.|+.|+.-|
T Consensus 20 ~~vCpeC~hEW 30 (111)
T PRK10220 20 MYICPECAHEW 30 (111)
T ss_pred eEECCcccCcC
Confidence 36666666544
No 206
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.54 E-value=20 Score=21.93 Aligned_cols=9 Identities=33% Similarity=0.763 Sum_probs=3.9
Q ss_pred ccccccccc
Q psy6676 57 HKCPVCSRS 65 (144)
Q Consensus 57 ~~C~~C~~~ 65 (144)
+.|..|+..
T Consensus 72 ~~C~~Cg~~ 80 (117)
T PRK00564 72 LECKDCSHV 80 (117)
T ss_pred EEhhhCCCc
Confidence 344444433
No 207
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=32.47 E-value=30 Score=17.72 Aligned_cols=9 Identities=56% Similarity=1.342 Sum_probs=4.6
Q ss_pred ccccccccC
Q psy6676 31 CTECGKGFC 39 (144)
Q Consensus 31 C~~C~~~f~ 39 (144)
|..|++.|.
T Consensus 5 C~~C~~~F~ 13 (57)
T cd00065 5 CMGCGKPFT 13 (57)
T ss_pred CcccCcccc
Confidence 455555553
No 208
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=32.16 E-value=4.3 Score=19.06 Aligned_cols=6 Identities=67% Similarity=1.669 Sum_probs=2.3
Q ss_pred ccCcch
Q psy6676 86 NCAACG 91 (144)
Q Consensus 86 ~C~~C~ 91 (144)
.|..||
T Consensus 24 vC~~Cg 29 (34)
T PF14803_consen 24 VCPACG 29 (34)
T ss_dssp EETTTT
T ss_pred ECCCCC
Confidence 343333
No 209
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=31.61 E-value=34 Score=29.89 Aligned_cols=10 Identities=30% Similarity=0.926 Sum_probs=6.6
Q ss_pred cccccccccc
Q psy6676 28 PFKCTECGKG 37 (144)
Q Consensus 28 ~~~C~~C~~~ 37 (144)
.+.|+.|+..
T Consensus 667 ~rkCPkCG~~ 676 (1337)
T PRK14714 667 RRRCPSCGTE 676 (1337)
T ss_pred EEECCCCCCc
Confidence 3667777754
No 210
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=30.98 E-value=10 Score=23.17 Aligned_cols=15 Identities=27% Similarity=0.476 Sum_probs=10.7
Q ss_pred CcccccccccccCCh
Q psy6676 27 KPFKCTECGKGFCQS 41 (144)
Q Consensus 27 ~~~~C~~C~~~f~~~ 41 (144)
.-+.|..|+..+...
T Consensus 21 ~~l~C~kCgye~~~~ 35 (113)
T COG1594 21 GKLVCRKCGYEEEAS 35 (113)
T ss_pred cEEECCCCCcchhcc
Confidence 367888888776544
No 211
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.60 E-value=19 Score=19.40 Aligned_cols=14 Identities=21% Similarity=0.553 Sum_probs=10.2
Q ss_pred CCcccccccccccC
Q psy6676 26 EKPFKCTECGKGFC 39 (144)
Q Consensus 26 ~~~~~C~~C~~~f~ 39 (144)
..--.|++|+..|.
T Consensus 46 ~gev~CPYC~t~y~ 59 (62)
T COG4391 46 EGEVVCPYCSTRYR 59 (62)
T ss_pred CCcEecCccccEEE
Confidence 34457999998875
No 212
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=30.47 E-value=6.4 Score=23.43 Aligned_cols=13 Identities=38% Similarity=0.935 Sum_probs=8.1
Q ss_pred CCccccccccccc
Q psy6676 26 EKPFKCTECGKGF 38 (144)
Q Consensus 26 ~~~~~C~~C~~~f 38 (144)
.+.|.|+.|+..-
T Consensus 20 ~k~FtCp~Cghe~ 32 (104)
T COG4888 20 PKTFTCPRCGHEK 32 (104)
T ss_pred CceEecCccCCee
Confidence 4457777777553
No 213
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=30.37 E-value=38 Score=17.43 Aligned_cols=9 Identities=44% Similarity=1.387 Sum_probs=3.6
Q ss_pred ccccccccc
Q psy6676 29 FKCTECGKG 37 (144)
Q Consensus 29 ~~C~~C~~~ 37 (144)
+.|+.|+..
T Consensus 29 W~C~~Cgh~ 37 (55)
T PF14311_consen 29 WKCPKCGHE 37 (55)
T ss_pred EECCCCCCe
Confidence 334444333
No 214
>PTZ00448 hypothetical protein; Provisional
Probab=30.20 E-value=35 Score=25.44 Aligned_cols=23 Identities=13% Similarity=0.322 Sum_probs=20.6
Q ss_pred CcccCcchhhhcChHHHHHhHhh
Q psy6676 84 PYNCAACGKVFRRNCDLRRHSLT 106 (144)
Q Consensus 84 ~~~C~~C~~~f~~~~~l~~H~~~ 106 (144)
.|.|..|+-.|.+....+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999988899999886
No 215
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=29.61 E-value=80 Score=18.90 Aligned_cols=38 Identities=18% Similarity=0.206 Sum_probs=27.4
Q ss_pred CcccccccccccCChHHHHHHHHHhCCCCCccccccccc
Q psy6676 27 KPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRS 65 (144)
Q Consensus 27 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 65 (144)
+-|.|+.-+..|.+...+-..+.... .+.|.|.+.|+.
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~~y~-~~vwtC~~TGk~ 39 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMILYN-QRVWTCEITGKS 39 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHHHHh-CCeeEEecCCCC
Confidence 34678888888888888766655544 466889888763
No 216
>KOG2636|consensus
Probab=29.55 E-value=41 Score=25.83 Aligned_cols=27 Identities=19% Similarity=0.466 Sum_probs=16.6
Q ss_pred hCCCCCccccccc-ccccCchHHHHHHh
Q psy6676 51 HLEESPHKCPVCS-RSFNQRSNLKTHLL 77 (144)
Q Consensus 51 ~~~~~~~~C~~C~-~~~~~~~~l~~h~~ 77 (144)
|--...|.|.+|| ..|.....+.+|..
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHhH
Confidence 3334556777777 56666666666654
No 217
>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=29.16 E-value=17 Score=17.75 Aligned_cols=16 Identities=56% Similarity=1.394 Sum_probs=10.1
Q ss_pred CcccccccccccCChH
Q psy6676 27 KPFKCTECGKGFCQSR 42 (144)
Q Consensus 27 ~~~~C~~C~~~f~~~~ 42 (144)
-|+.|..|+..|-...
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 5788999999987653
No 218
>PRK00420 hypothetical protein; Validated
Probab=27.88 E-value=33 Score=20.98 Aligned_cols=10 Identities=40% Similarity=0.853 Sum_probs=5.1
Q ss_pred cccCcchhhh
Q psy6676 85 YNCAACGKVF 94 (144)
Q Consensus 85 ~~C~~C~~~f 94 (144)
..|+.||...
T Consensus 41 ~~Cp~Cg~~~ 50 (112)
T PRK00420 41 VVCPVHGKVY 50 (112)
T ss_pred eECCCCCCee
Confidence 4555555533
No 219
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.66 E-value=21 Score=18.17 Aligned_cols=12 Identities=25% Similarity=0.722 Sum_probs=6.1
Q ss_pred ccCcchhhhcCh
Q psy6676 86 NCAACGKVFRRN 97 (144)
Q Consensus 86 ~C~~C~~~f~~~ 97 (144)
.|++|+.-|+..
T Consensus 14 ICpvCqRPFsWR 25 (54)
T COG4338 14 ICPVCQRPFSWR 25 (54)
T ss_pred hhhhhcCchHHH
Confidence 455555555443
No 220
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=27.63 E-value=18 Score=27.93 Aligned_cols=14 Identities=21% Similarity=0.724 Sum_probs=8.4
Q ss_pred CCcccccccccccC
Q psy6676 55 SPHKCPVCSRSFNQ 68 (144)
Q Consensus 55 ~~~~C~~C~~~~~~ 68 (144)
..|.|..|+..|.-
T Consensus 424 ~~~~c~~c~~~yd~ 437 (479)
T PRK05452 424 PRMQCSVCQWIYDP 437 (479)
T ss_pred CeEEECCCCeEECC
Confidence 34667777766543
No 221
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=27.62 E-value=20 Score=21.84 Aligned_cols=10 Identities=20% Similarity=0.587 Sum_probs=5.1
Q ss_pred cccccccccc
Q psy6676 57 HKCPVCSRSF 66 (144)
Q Consensus 57 ~~C~~C~~~~ 66 (144)
+.|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 4555555433
No 222
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=26.73 E-value=75 Score=22.16 Aligned_cols=40 Identities=23% Similarity=0.571 Sum_probs=24.0
Q ss_pred cccCCCCcccccccccccCChHHHHHHHHHhCCCCCcccccccc
Q psy6676 21 YIHSKEKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSR 64 (144)
Q Consensus 21 ~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~ 64 (144)
++|..-....|..|+..|.....+. ..... ..-.|+.|+.
T Consensus 112 elHG~~~~~~C~~C~~~~~~~~~~~---~~~~~-~~p~Cp~Cgg 151 (244)
T PRK14138 112 ELHGNVEEYYCVRCGKRYTVEDVIE---KLEKS-DVPRCDDCSG 151 (244)
T ss_pred EccCCcCeeEECCCCCcccHHHHHH---HHhcC-CCCCCCCCCC
Confidence 5677777788999998876543322 11111 2237888874
No 223
>KOG2071|consensus
Probab=26.69 E-value=40 Score=26.76 Aligned_cols=26 Identities=27% Similarity=0.625 Sum_probs=20.5
Q ss_pred CCcccCcchhhhcChHHHHHhHhhcc
Q psy6676 83 KPYNCAACGKVFRRNCDLRRHSLTHN 108 (144)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~~~h~ 108 (144)
.+-.|..||..|........|+-+|-
T Consensus 417 ~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 417 SPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CcchhcccccccccchhhhhHhhhhh
Confidence 45789999999998887777776653
No 224
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=26.67 E-value=23 Score=16.37 Aligned_cols=11 Identities=36% Similarity=0.812 Sum_probs=6.4
Q ss_pred cccCcchhhhc
Q psy6676 85 YNCAACGKVFR 95 (144)
Q Consensus 85 ~~C~~C~~~f~ 95 (144)
+.|..|+..|.
T Consensus 22 ~~C~~Cg~~~~ 32 (33)
T PF08792_consen 22 EVCIFCGSSFP 32 (33)
T ss_pred EEcccCCcEee
Confidence 46666666553
No 225
>KOG4118|consensus
Probab=26.60 E-value=45 Score=18.22 Aligned_cols=27 Identities=11% Similarity=0.224 Sum_probs=18.9
Q ss_pred cccCcchhhhcChHHHHHhHhhccCCC
Q psy6676 85 YNCAACGKVFRRNCDLRRHSLTHNLGS 111 (144)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~h~~~~ 111 (144)
|+|.+|.-.......+..|...-|...
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHpk~ 65 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHPKE 65 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCCCC
Confidence 677788777777777777776655443
No 226
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.49 E-value=27 Score=21.66 Aligned_cols=10 Identities=20% Similarity=0.384 Sum_probs=5.4
Q ss_pred ccccccccccc
Q psy6676 57 HKCPVCSRSFN 67 (144)
Q Consensus 57 ~~C~~C~~~~~ 67 (144)
+.| .|+..|.
T Consensus 71 ~~C-~Cg~~~~ 80 (124)
T PRK00762 71 IEC-ECGYEGV 80 (124)
T ss_pred EEe-eCcCccc
Confidence 556 6665543
No 227
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=26.43 E-value=25 Score=16.70 Aligned_cols=11 Identities=36% Similarity=1.171 Sum_probs=5.7
Q ss_pred CCcccCcchhh
Q psy6676 83 KPYNCAACGKV 93 (144)
Q Consensus 83 ~~~~C~~C~~~ 93 (144)
+.|+|..||..
T Consensus 5 ~~YkC~~CGni 15 (36)
T PF06397_consen 5 EFYKCEHCGNI 15 (36)
T ss_dssp EEEE-TTT--E
T ss_pred cEEEccCCCCE
Confidence 45888888854
No 228
>PLN03239 histone acetyltransferase; Provisional
Probab=26.11 E-value=66 Score=23.92 Aligned_cols=25 Identities=24% Similarity=0.283 Sum_probs=22.1
Q ss_pred CCCcccCcchhhhcChHHHHHhHhh
Q psy6676 82 IKPYNCAACGKVFRRNCDLRRHSLT 106 (144)
Q Consensus 82 ~~~~~C~~C~~~f~~~~~l~~H~~~ 106 (144)
...|.|..|-+-|.+...|.+|+..
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~~ 128 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQAK 128 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHHh
Confidence 4679999999999999999999864
No 229
>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=26.07 E-value=32 Score=20.64 Aligned_cols=11 Identities=45% Similarity=1.029 Sum_probs=6.5
Q ss_pred Ccccccccccc
Q psy6676 27 KPFKCTECGKG 37 (144)
Q Consensus 27 ~~~~C~~C~~~ 37 (144)
||-.|+.|+..
T Consensus 1 ~p~~CpYCg~~ 11 (102)
T PF11672_consen 1 KPIICPYCGGP 11 (102)
T ss_pred CCcccCCCCCe
Confidence 34566666654
No 230
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=26.06 E-value=9.2 Score=22.69 Aligned_cols=14 Identities=21% Similarity=0.541 Sum_probs=10.3
Q ss_pred CcccccccccccCC
Q psy6676 27 KPFKCTECGKGFCQ 40 (144)
Q Consensus 27 ~~~~C~~C~~~f~~ 40 (144)
..+.|+.|+..+..
T Consensus 15 ~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 15 GVYVCPSCGYEKEK 28 (104)
T ss_pred CeEECcCCCCcccc
Confidence 36889999977654
No 231
>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=25.71 E-value=20 Score=21.80 Aligned_cols=10 Identities=30% Similarity=0.976 Sum_probs=4.9
Q ss_pred cccccccccc
Q psy6676 57 HKCPVCSRSF 66 (144)
Q Consensus 57 ~~C~~C~~~~ 66 (144)
+.|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PF01155_consen 71 ARCRDCGHEF 80 (113)
T ss_dssp EEETTTS-EE
T ss_pred EECCCCCCEE
Confidence 4555555554
No 232
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=25.51 E-value=79 Score=20.48 Aligned_cols=11 Identities=27% Similarity=0.685 Sum_probs=3.0
Q ss_pred CCCcccCcchh
Q psy6676 82 IKPYNCAACGK 92 (144)
Q Consensus 82 ~~~~~C~~C~~ 92 (144)
+..++|-.||-
T Consensus 58 dt~leCy~Cg~ 68 (152)
T PF09416_consen 58 DTVLECYNCGS 68 (152)
T ss_dssp S-B---TTT--
T ss_pred CcEEEEEecCC
Confidence 34567777764
No 233
>KOG2932|consensus
Probab=25.44 E-value=86 Score=23.00 Aligned_cols=29 Identities=24% Similarity=0.354 Sum_probs=22.6
Q ss_pred CCCCCcccCc---chhhhcChHHHHHhHhhcc
Q psy6676 80 TDIKPYNCAA---CGKVFRRNCDLRRHSLTHN 108 (144)
Q Consensus 80 ~~~~~~~C~~---C~~~f~~~~~l~~H~~~h~ 108 (144)
.-...|.|.. |.++|.+...|+.|+.--|
T Consensus 140 ~~g~iFmC~~~~GC~RTyLsqrDlqAHInhrH 171 (389)
T KOG2932|consen 140 MMGGIFMCAAPHGCLRTYLSQRDLQAHINHRH 171 (389)
T ss_pred cccceEEeecchhHHHHHhhHHHHHHHhhhhh
Confidence 3446789954 9999999999999986443
No 234
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=25.39 E-value=28 Score=22.31 Aligned_cols=28 Identities=25% Similarity=0.662 Sum_probs=15.5
Q ss_pred CCcccccccccccCchHHHHHHhhcCCCCCcccCcchh
Q psy6676 55 SPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGK 92 (144)
Q Consensus 55 ~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 92 (144)
..++|..||..... .+++ ..-.|+.|+.
T Consensus 111 G~l~C~~Cg~~~~~---------~~~~-~l~~Cp~C~~ 138 (146)
T PF07295_consen 111 GTLVCENCGHEVEL---------THPE-RLPPCPKCGH 138 (146)
T ss_pred ceEecccCCCEEEe---------cCCC-cCCCCCCCCC
Confidence 44777777754311 1232 3447777764
No 235
>KOG4727|consensus
Probab=25.37 E-value=33 Score=22.65 Aligned_cols=23 Identities=22% Similarity=0.470 Sum_probs=19.5
Q ss_pred CCcccCcchhhhcChHHHHHhHh
Q psy6676 83 KPYNCAACGKVFRRNCDLRRHSL 105 (144)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~~ 105 (144)
..|.|.+|.-.+....++..|+.
T Consensus 74 ~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 74 GGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred CceeeeecceeehhhHHHHHHhc
Confidence 34999999999999988888873
No 236
>PF14353 CpXC: CpXC protein
Probab=24.88 E-value=26 Score=21.55 Aligned_cols=25 Identities=28% Similarity=0.620 Sum_probs=18.2
Q ss_pred CCcccCcchhhhcChHHHHHhHhhc
Q psy6676 83 KPYNCAACGKVFRRNCDLRRHSLTH 107 (144)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~~~h 107 (144)
..|.|+.||..|.-...+.-|...+
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~D~~~ 61 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYHDPEK 61 (128)
T ss_pred CEEECCCCCCceecCCCEEEEcCCC
Confidence 4589999999887776666555443
No 237
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=24.53 E-value=45 Score=17.77 Aligned_cols=9 Identities=44% Similarity=1.195 Sum_probs=4.0
Q ss_pred CCCcccccc
Q psy6676 54 ESPHKCPVC 62 (144)
Q Consensus 54 ~~~~~C~~C 62 (144)
....+|+-|
T Consensus 42 E~VArCPSC 50 (67)
T COG5216 42 EVVARCPSC 50 (67)
T ss_pred ceEEEcCCc
Confidence 334445444
No 238
>KOG2857|consensus
Probab=24.18 E-value=92 Score=19.96 Aligned_cols=21 Identities=33% Similarity=0.585 Sum_probs=13.8
Q ss_pred cccccccccccCchHHHHHHh
Q psy6676 57 HKCPVCSRSFNQRSNLKTHLL 77 (144)
Q Consensus 57 ~~C~~C~~~~~~~~~l~~h~~ 77 (144)
|+|+.|...|-+...+..|..
T Consensus 18 YKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 18 YKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred ccCCCCCCccccchhhhhccC
Confidence 667777766666666666654
No 239
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.16 E-value=24 Score=21.98 Aligned_cols=14 Identities=29% Similarity=0.657 Sum_probs=8.1
Q ss_pred CCcccccccccccC
Q psy6676 55 SPHKCPVCSRSFNQ 68 (144)
Q Consensus 55 ~~~~C~~C~~~~~~ 68 (144)
.|-.|..||..|.+
T Consensus 67 ~psfchncgs~fpw 80 (160)
T COG4306 67 PPSFCHNCGSRFPW 80 (160)
T ss_pred CcchhhcCCCCCCc
Confidence 44556666666654
No 240
>KOG3214|consensus
Probab=24.02 E-value=24 Score=20.99 Aligned_cols=13 Identities=23% Similarity=0.703 Sum_probs=7.3
Q ss_pred CcccCcchhhhcC
Q psy6676 84 PYNCAACGKVFRR 96 (144)
Q Consensus 84 ~~~C~~C~~~f~~ 96 (144)
...|.+|+..|..
T Consensus 47 ~~sC~iC~esFqt 59 (109)
T KOG3214|consen 47 KASCRICEESFQT 59 (109)
T ss_pred eeeeeehhhhhcc
Confidence 3456666666644
No 241
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.38 E-value=48 Score=23.78 Aligned_cols=10 Identities=30% Similarity=0.939 Sum_probs=4.7
Q ss_pred cccCcchhhh
Q psy6676 85 YNCAACGKVF 94 (144)
Q Consensus 85 ~~C~~C~~~f 94 (144)
|.|++|.-.|
T Consensus 256 yvCs~Clsi~ 265 (279)
T TIGR00627 256 FVCSVCLSVL 265 (279)
T ss_pred EECCCccCCc
Confidence 5555554433
No 242
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=23.22 E-value=32 Score=18.68 Aligned_cols=19 Identities=26% Similarity=0.653 Sum_probs=14.2
Q ss_pred ccCCCCcccccccccccCC
Q psy6676 22 IHSKEKPFKCTECGKGFCQ 40 (144)
Q Consensus 22 ~h~~~~~~~C~~C~~~f~~ 40 (144)
++..+....|+.|++.|..
T Consensus 47 ~~i~eg~L~Cp~c~r~YPI 65 (68)
T PF03966_consen 47 VEIVEGELICPECGREYPI 65 (68)
T ss_dssp EETTTTEEEETTTTEEEEE
T ss_pred ccccCCEEEcCCCCCEEeC
Confidence 4556677889999988864
No 243
>KOG0696|consensus
Probab=22.81 E-value=27 Score=26.91 Aligned_cols=46 Identities=28% Similarity=0.429 Sum_probs=18.3
Q ss_pred HHHHHhCCCCCcccccccccccCchHHHHHH-hhcCCCCCcccCcchh
Q psy6676 46 VHKILHLEESPHKCPVCSRSFNQRSNLKTHL-LTHTDIKPYNCAACGK 92 (144)
Q Consensus 46 ~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~-~~h~~~~~~~C~~C~~ 92 (144)
.|.+.|.- ..|.|+.-++.+........|. +.|+-.-|--|..||.
T Consensus 83 vHkrChef-VtF~CPGadkg~dtDdpr~kHkf~~~tYssPTFCDhCGs 129 (683)
T KOG0696|consen 83 VHKRCHEF-VTFSCPGADKGPDTDDPRSKHKFKIHTYSSPTFCDHCGS 129 (683)
T ss_pred hhhhhcce-EEEECCCCCCCCCCCCcccccceeeeecCCCchhhhHHH
Confidence 34444432 2345554444444433333333 2233333333444443
No 244
>KOG1409|consensus
Probab=22.10 E-value=28 Score=25.84 Aligned_cols=8 Identities=38% Similarity=1.286 Sum_probs=3.5
Q ss_pred cccccccc
Q psy6676 59 CPVCSRSF 66 (144)
Q Consensus 59 C~~C~~~~ 66 (144)
|+.|...|
T Consensus 285 cQ~c~qpf 292 (404)
T KOG1409|consen 285 CQKCNQPF 292 (404)
T ss_pred hhhhCchH
Confidence 44444443
No 245
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=22.02 E-value=29 Score=16.49 Aligned_cols=15 Identities=33% Similarity=0.738 Sum_probs=7.7
Q ss_pred ccCcchhhhcChHHH
Q psy6676 86 NCAACGKVFRRNCDL 100 (144)
Q Consensus 86 ~C~~C~~~f~~~~~l 100 (144)
.|..|++.|-+.+..
T Consensus 4 ~CprC~kg~Hwa~~C 18 (36)
T PF14787_consen 4 LCPRCGKGFHWASEC 18 (36)
T ss_dssp C-TTTSSSCS-TTT-
T ss_pred cCcccCCCcchhhhh
Confidence 466777777665543
No 246
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=22.02 E-value=1.4e+02 Score=20.24 Aligned_cols=41 Identities=17% Similarity=0.430 Sum_probs=23.0
Q ss_pred cccCCCCcccccccccccCChHHHHHHHHHhCCCCCcccccccc
Q psy6676 21 YIHSKEKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSR 64 (144)
Q Consensus 21 ~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~ 64 (144)
++|..-....|..|+..+.....+.. .......-.|+.|+.
T Consensus 88 elHG~~~~~~C~~C~~~~~~~~~~~~---~~~~~~~p~C~~Cgg 128 (206)
T cd01410 88 ELHGNMFIEVCKSCGPEYVRDDVVET---RGDKETGRRCHACGG 128 (206)
T ss_pred EecCCcCcccCCCCCCccchHHHHHH---hhcCCCCCcCCCCcC
Confidence 56666677788888877654332211 111222346888874
No 247
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=21.96 E-value=46 Score=17.42 Aligned_cols=19 Identities=32% Similarity=0.604 Sum_probs=13.0
Q ss_pred CcccCcchhhhcChHHHHH
Q psy6676 84 PYNCAACGKVFRRNCDLRR 102 (144)
Q Consensus 84 ~~~C~~C~~~f~~~~~l~~ 102 (144)
-+.|-.||..|.+...|..
T Consensus 27 ~~YC~~Cg~~Y~d~~dL~~ 45 (55)
T PF13821_consen 27 HNYCFWCGTKYDDEEDLER 45 (55)
T ss_pred CceeeeeCCccCCHHHHHh
Confidence 3567777777777766653
No 248
>COG4640 Predicted membrane protein [Function unknown]
Probab=21.56 E-value=58 Score=24.68 Aligned_cols=14 Identities=29% Similarity=0.769 Sum_probs=7.5
Q ss_pred cCcchhhhcChHHH
Q psy6676 87 CAACGKVFRRNCDL 100 (144)
Q Consensus 87 C~~C~~~f~~~~~l 100 (144)
|..||..|.....+
T Consensus 18 C~qCG~~~t~~~sq 31 (465)
T COG4640 18 CTQCGHKFTSRQSQ 31 (465)
T ss_pred ccccCCcCCchhhh
Confidence 55565555554443
No 249
>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=21.54 E-value=51 Score=15.30 Aligned_cols=22 Identities=18% Similarity=0.459 Sum_probs=10.8
Q ss_pred cccCcchhhhcChHHHHHhHhhc
Q psy6676 85 YNCAACGKVFRRNCDLRRHSLTH 107 (144)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~h 107 (144)
+.|+.|++..... -+..|+..+
T Consensus 5 ~~C~nC~R~v~a~-RfA~HLekC 26 (33)
T PF08209_consen 5 VECPNCGRPVAAS-RFAPHLEKC 26 (33)
T ss_dssp EE-TTTSSEEEGG-GHHHHHHHH
T ss_pred EECCCCcCCcchh-hhHHHHHHH
Confidence 5666676644332 345555443
No 250
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=21.45 E-value=47 Score=23.90 Aligned_cols=32 Identities=25% Similarity=0.639 Sum_probs=19.2
Q ss_pred ccccccccccCChHHHHHHHHHhCCCCCcccccccccccCc
Q psy6676 29 FKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQR 69 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~ 69 (144)
.+|+.|+.....+ .|.. ..++|+.|+..|...
T Consensus 27 ~~c~~c~~~~~~~-~l~~--------~~~vc~~c~~h~rl~ 58 (285)
T TIGR00515 27 TKCPKCGQVLYTK-ELER--------NLEVCPKCDHHMRMD 58 (285)
T ss_pred eECCCCcchhhHH-HHHh--------hCCCCCCCCCcCcCC
Confidence 4588888665332 2221 226899998876543
No 251
>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=21.31 E-value=21 Score=22.68 Aligned_cols=10 Identities=40% Similarity=1.222 Sum_probs=5.8
Q ss_pred cccCcchhhh
Q psy6676 85 YNCAACGKVF 94 (144)
Q Consensus 85 ~~C~~C~~~f 94 (144)
|.|..|+-.|
T Consensus 144 ~~C~~C~~~l 153 (157)
T PF10263_consen 144 YRCGRCGGPL 153 (157)
T ss_pred EECCCCCCEE
Confidence 6666666433
No 252
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=21.03 E-value=13 Score=25.08 Aligned_cols=7 Identities=43% Similarity=1.293 Sum_probs=3.9
Q ss_pred ccccccc
Q psy6676 30 KCTECGK 36 (144)
Q Consensus 30 ~C~~C~~ 36 (144)
.||.|+.
T Consensus 16 ~CPvCg~ 22 (201)
T COG1779 16 DCPVCGG 22 (201)
T ss_pred cCCcccc
Confidence 4566654
No 253
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=20.53 E-value=12 Score=20.63 Aligned_cols=57 Identities=19% Similarity=0.297 Sum_probs=22.2
Q ss_pred ccccccccccCChHH---HHHHHHHhCCCCCcccccccccccCchHHHHHHhhcCCCCCcccCcchhh
Q psy6676 29 FKCTECGKGFCQSRT---LAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKV 93 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~---l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 93 (144)
+.++-|++.|.-..- +..|...........|..|...+..... ..+ ..+.|+.|+..
T Consensus 11 ~~~~cC~~~y~C~~CHde~~~H~~~~~~~~~v~Cg~C~~~~~~~~~-------~c~-~~~~C~~C~~~ 70 (71)
T PF05495_consen 11 IRFPCCGKYYPCRFCHDELEDHPFDRWPVKRVICGKCRTEQPIDEY-------SCG-ADYFCPICGLY 70 (71)
T ss_dssp EEETTTTEEESSHHHHHHCSSS---TTT--EEEETTT--EEES-SB-------TT---SEEETTTTEE
T ss_pred EECCcccCeecHHHHHHHhccCccccccccCeECCCCCCccChhhh-------hcC-CCccCcCcCCC
Confidence 445566666654311 1122111122224566666654433221 111 45677777654
No 254
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=20.43 E-value=70 Score=20.97 Aligned_cols=21 Identities=19% Similarity=0.415 Sum_probs=18.3
Q ss_pred ccccccccccCChHHHHHHHH
Q psy6676 29 FKCTECGKGFCQSRTLAVHKI 49 (144)
Q Consensus 29 ~~C~~C~~~f~~~~~l~~h~~ 49 (144)
|.|..|.........+..|..
T Consensus 1 F~Cs~CKfrtf~~~ei~~Hle 21 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLE 21 (165)
T ss_pred CccceeeeecccHHHHHHHHc
Confidence 679999999999999999964
No 255
>KOG4696|consensus
Probab=20.42 E-value=65 Score=23.45 Aligned_cols=29 Identities=14% Similarity=0.138 Sum_probs=15.8
Q ss_pred ccCcchhhhcChHHHHHhHhhccCCCCCCC
Q psy6676 86 NCAACGKVFRRNCDLRRHSLTHNLGSATST 115 (144)
Q Consensus 86 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~ 115 (144)
.|++|..+ .....+.-|...|.......+
T Consensus 4 iCP~CkLs-v~~~~m~~HieaHFEqDEvN~ 32 (393)
T KOG4696|consen 4 ICPFCKLS-VNYDEMCFHIEAHFEQDEVNS 32 (393)
T ss_pred cccceecc-cCHHHHHHHHHhhccccccch
Confidence 46666655 445555666666555544433
No 256
>KOG4602|consensus
Probab=20.08 E-value=39 Score=23.89 Aligned_cols=11 Identities=36% Similarity=1.132 Sum_probs=7.1
Q ss_pred CCcccCcchhh
Q psy6676 83 KPYNCAACGKV 93 (144)
Q Consensus 83 ~~~~C~~C~~~ 93 (144)
+.|.|++||.+
T Consensus 267 R~YVCPiCGAT 277 (318)
T KOG4602|consen 267 RSYVCPICGAT 277 (318)
T ss_pred hhhcCcccccc
Confidence 34777777753
Done!