Query psy8167
Match_columns 167
No_of_seqs 141 out of 1913
Neff 10.3
Searched_HMMs 46136
Date Fri Aug 16 20:17:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8167.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8167hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 2.2E-24 4.8E-29 151.3 6.6 109 50-161 127-245 (279)
2 KOG2462|consensus 99.9 2.6E-23 5.6E-28 145.9 5.6 102 51-155 159-267 (279)
3 KOG1074|consensus 99.7 5.3E-18 1.2E-22 134.0 5.1 55 105-159 607-661 (958)
4 KOG3576|consensus 99.7 1.9E-17 4.1E-22 111.7 2.9 107 51-160 115-241 (267)
5 KOG1074|consensus 99.7 6.5E-17 1.4E-21 128.0 6.3 57 105-161 881-937 (958)
6 KOG3623|consensus 99.6 1.3E-16 2.9E-21 124.7 1.2 102 51-152 208-330 (1007)
7 KOG3623|consensus 99.6 6E-16 1.3E-20 121.2 4.4 83 48-152 889-971 (1007)
8 KOG3608|consensus 99.4 4.9E-13 1.1E-17 97.4 6.6 97 58-155 184-316 (467)
9 KOG3608|consensus 99.4 4.9E-13 1.1E-17 97.4 5.2 100 54-153 264-374 (467)
10 KOG3576|consensus 99.4 1.3E-13 2.9E-18 93.3 0.7 78 78-155 113-197 (267)
11 PHA00733 hypothetical protein 99.3 9.5E-12 2.1E-16 80.5 4.9 86 51-156 38-124 (128)
12 PHA02768 hypothetical protein; 99.2 3.1E-12 6.7E-17 69.2 1.4 42 104-147 6-47 (55)
13 PLN03086 PRLI-interacting fact 98.9 2.1E-09 4.5E-14 84.5 5.7 97 51-155 451-564 (567)
14 PF13465 zf-H2C2_2: Zinc-finge 98.9 5.3E-10 1.1E-14 51.9 1.1 26 118-143 1-26 (26)
15 PHA02768 hypothetical protein; 98.8 4.4E-09 9.6E-14 57.0 2.3 38 54-94 6-43 (55)
16 KOG3993|consensus 98.8 1.5E-09 3.3E-14 81.1 0.7 83 52-156 266-381 (500)
17 PHA00616 hypothetical protein 98.7 8.1E-09 1.8E-13 53.3 2.4 33 104-136 2-34 (44)
18 PHA00732 hypothetical protein 98.7 7.2E-09 1.6E-13 61.2 2.5 48 103-155 1-48 (79)
19 PHA00616 hypothetical protein 98.7 5.6E-09 1.2E-13 53.9 1.6 34 131-164 1-34 (44)
20 PLN03086 PRLI-interacting fact 98.7 5.5E-08 1.2E-12 76.7 7.9 99 52-161 406-506 (567)
21 PHA00733 hypothetical protein 98.6 8.2E-08 1.8E-12 62.2 5.0 54 51-128 71-124 (128)
22 PF13465 zf-H2C2_2: Zinc-finge 98.5 7.3E-08 1.6E-12 44.6 1.2 25 68-93 1-25 (26)
23 PF05605 zf-Di19: Drought indu 98.4 8.5E-07 1.8E-11 48.7 4.2 51 103-156 2-54 (54)
24 KOG3993|consensus 98.3 3.1E-07 6.8E-12 69.0 2.5 76 52-128 294-381 (500)
25 PF05605 zf-Di19: Drought indu 98.3 1.6E-06 3.5E-11 47.5 4.7 53 53-128 2-54 (54)
26 PHA00732 hypothetical protein 98.3 7.1E-07 1.5E-11 52.7 2.6 46 53-125 1-46 (79)
27 PF00096 zf-C2H2: Zinc finger, 98.2 9.1E-07 2E-11 39.6 2.2 22 104-125 1-22 (23)
28 PF00096 zf-C2H2: Zinc finger, 98.1 8.1E-07 1.8E-11 39.8 0.9 23 132-154 1-23 (23)
29 PF13894 zf-C2H2_4: C2H2-type 98.0 5.4E-06 1.2E-10 37.2 2.4 22 105-126 2-23 (24)
30 PF13894 zf-C2H2_4: C2H2-type 98.0 3.1E-06 6.7E-11 38.1 1.3 24 132-155 1-24 (24)
31 PF12756 zf-C2H2_2: C2H2 type 97.9 5.4E-06 1.2E-10 51.2 1.7 49 106-154 2-73 (100)
32 PF12756 zf-C2H2_2: C2H2 type 97.9 9.8E-06 2.1E-10 50.0 2.7 72 55-126 1-73 (100)
33 PF13912 zf-C2H2_6: C2H2-type 97.9 5.6E-06 1.2E-10 38.5 1.2 23 104-126 2-24 (27)
34 PF09237 GAGA: GAGA factor; I 97.8 6.6E-06 1.4E-10 43.5 1.1 33 128-160 21-53 (54)
35 PF13912 zf-C2H2_6: C2H2-type 97.8 1.6E-05 3.5E-10 37.0 2.0 26 131-156 1-26 (27)
36 COG5189 SFP1 Putative transcri 97.6 6.1E-05 1.3E-09 55.1 3.0 69 51-124 347-419 (423)
37 PF09237 GAGA: GAGA factor; I 97.5 0.0001 2.2E-09 39.0 2.7 31 101-131 22-52 (54)
38 smart00355 ZnF_C2H2 zinc finge 97.5 0.0001 2.2E-09 33.4 2.4 23 132-154 1-23 (26)
39 COG5189 SFP1 Putative transcri 97.4 5E-05 1.1E-09 55.5 0.3 53 101-153 347-420 (423)
40 smart00355 ZnF_C2H2 zinc finge 97.3 0.0002 4.4E-09 32.4 2.1 24 104-127 1-24 (26)
41 PRK04860 hypothetical protein; 97.2 0.00019 4.1E-09 48.3 1.9 38 103-144 119-156 (160)
42 PF13909 zf-H2C2_5: C2H2-type 97.2 0.00036 7.8E-09 31.3 2.1 23 104-127 1-23 (24)
43 PF13909 zf-H2C2_5: C2H2-type 97.2 0.00014 3E-09 32.7 0.5 24 132-156 1-24 (24)
44 PF12874 zf-met: Zinc-finger o 97.1 0.00019 4E-09 32.6 0.8 21 133-153 2-22 (25)
45 PF12874 zf-met: Zinc-finger o 96.9 0.0008 1.7E-08 30.4 1.9 23 104-126 1-23 (25)
46 PF12171 zf-C2H2_jaz: Zinc-fin 96.6 0.00046 1E-08 31.9 -0.0 21 132-152 2-22 (27)
47 KOG1146|consensus 96.5 0.00073 1.6E-08 58.0 0.2 103 50-153 462-611 (1406)
48 PRK04860 hypothetical protein; 96.3 0.0021 4.5E-08 43.3 1.4 38 52-94 118-155 (160)
49 PF12171 zf-C2H2_jaz: Zinc-fin 96.2 0.0023 5E-08 29.5 0.8 22 104-125 2-23 (27)
50 COG4049 Uncharacterized protei 95.9 0.0034 7.4E-08 33.9 0.9 29 127-155 13-41 (65)
51 PF12013 DUF3505: Protein of u 95.8 0.022 4.9E-07 35.8 4.5 27 52-79 10-36 (109)
52 PF13913 zf-C2HC_2: zinc-finge 95.8 0.0083 1.8E-07 27.2 1.7 19 133-152 4-22 (25)
53 KOG1146|consensus 95.6 0.012 2.7E-07 50.9 3.2 52 102-153 464-540 (1406)
54 KOG2231|consensus 95.5 0.021 4.4E-07 46.6 4.3 100 54-157 100-238 (669)
55 smart00451 ZnF_U1 U1-like zinc 95.5 0.01 2.2E-07 29.0 1.5 23 131-153 3-25 (35)
56 COG4049 Uncharacterized protei 95.2 0.011 2.4E-07 31.9 1.3 32 47-78 11-42 (65)
57 KOG2893|consensus 94.8 0.0095 2.1E-07 42.2 0.4 32 55-91 12-43 (341)
58 PF12013 DUF3505: Protein of u 94.3 0.072 1.6E-06 33.5 3.6 25 132-156 81-109 (109)
59 smart00451 ZnF_U1 U1-like zinc 94.0 0.055 1.2E-06 26.3 2.0 21 53-73 3-23 (35)
60 KOG2186|consensus 93.9 0.033 7.1E-07 39.8 1.4 46 104-152 4-49 (276)
61 cd00350 rubredoxin_like Rubred 93.2 0.065 1.4E-06 25.9 1.5 10 130-139 16-25 (33)
62 COG5048 FOG: Zn-finger [Genera 93.1 0.016 3.6E-07 44.6 -1.2 59 102-160 288-352 (467)
63 KOG2482|consensus 93.1 0.14 3.1E-06 38.4 3.7 100 53-153 195-356 (423)
64 KOG4173|consensus 92.9 0.053 1.1E-06 37.7 1.2 75 53-152 79-167 (253)
65 PF09538 FYDLN_acid: Protein o 92.4 0.068 1.5E-06 33.6 1.2 30 83-116 10-39 (108)
66 PF13719 zinc_ribbon_5: zinc-r 92.1 0.087 1.9E-06 26.2 1.1 33 104-141 3-35 (37)
67 PF09986 DUF2225: Uncharacteri 91.7 0.029 6.2E-07 39.8 -1.3 43 102-144 4-61 (214)
68 PF13717 zinc_ribbon_4: zinc-r 91.3 0.13 2.8E-06 25.4 1.3 33 104-141 3-35 (36)
69 COG5048 FOG: Zn-finger [Genera 91.1 0.11 2.3E-06 40.1 1.3 108 52-161 288-448 (467)
70 PRK00398 rpoP DNA-directed RNA 90.8 0.13 2.8E-06 26.9 1.0 9 104-112 22-30 (46)
71 COG2888 Predicted Zn-ribbon RN 90.6 0.15 3.4E-06 28.0 1.2 31 104-139 28-58 (61)
72 COG5236 Uncharacterized conser 90.4 0.38 8.3E-06 36.3 3.4 78 55-155 222-305 (493)
73 TIGR02098 MJ0042_CXXC MJ0042 f 90.1 0.15 3.2E-06 25.4 0.9 33 104-141 3-35 (38)
74 KOG2893|consensus 89.9 0.058 1.2E-06 38.4 -1.0 41 106-150 13-53 (341)
75 PF10571 UPF0547: Uncharacteri 89.9 0.17 3.6E-06 23.1 0.8 9 106-114 17-25 (26)
76 KOG2231|consensus 89.7 0.43 9.2E-06 39.3 3.5 53 55-127 184-236 (669)
77 cd00729 rubredoxin_SM Rubredox 89.4 0.28 6.1E-06 23.9 1.5 9 131-139 18-26 (34)
78 KOG2482|consensus 89.3 0.37 8.1E-06 36.2 2.7 70 54-125 145-217 (423)
79 PHA00626 hypothetical protein 88.8 0.075 1.6E-06 28.8 -0.8 14 131-144 23-36 (59)
80 TIGR00622 ssl1 transcription f 88.4 0.77 1.7E-05 29.0 3.3 22 52-73 14-35 (112)
81 PF04959 ARS2: Arsenite-resist 88.3 0.096 2.1E-06 37.0 -0.8 23 131-153 77-99 (214)
82 PRK06266 transcription initiat 88.1 0.13 2.9E-06 35.3 -0.3 29 82-112 117-145 (178)
83 PF15135 UPF0515: Uncharacteri 87.8 0.48 1E-05 34.0 2.3 12 50-61 109-120 (278)
84 PF06524 NOA36: NOA36 protein; 87.7 0.16 3.5E-06 36.6 -0.1 89 50-154 139-232 (314)
85 TIGR02605 CxxC_CxxC_SSSS putat 87.6 0.17 3.8E-06 27.1 0.0 29 104-139 6-34 (52)
86 TIGR00373 conserved hypothetic 87.3 0.34 7.4E-06 32.6 1.4 29 82-112 109-137 (158)
87 COG1592 Rubrerythrin [Energy p 87.1 0.38 8.3E-06 32.6 1.5 23 103-138 134-156 (166)
88 PF09723 Zn-ribbon_8: Zinc rib 86.1 0.28 6.2E-06 25.1 0.4 13 104-116 6-18 (42)
89 PF02892 zf-BED: BED zinc fing 86.0 0.79 1.7E-05 23.6 2.1 27 51-77 14-44 (45)
90 smart00614 ZnF_BED BED zinc fi 85.9 0.72 1.6E-05 24.5 1.9 21 104-124 19-44 (50)
91 COG5236 Uncharacterized conser 85.8 1.6 3.5E-05 33.1 4.2 92 54-154 152-274 (493)
92 PF05443 ROS_MUCR: ROS/MUCR tr 85.7 0.33 7.2E-06 31.6 0.6 23 104-129 73-95 (132)
93 TIGR02300 FYDLN_acid conserved 85.6 0.42 9.1E-06 30.7 1.0 30 83-116 10-39 (129)
94 smart00531 TFIIE Transcription 85.0 0.29 6.2E-06 32.6 0.1 13 104-116 100-112 (147)
95 COG1592 Rubrerythrin [Energy p 84.9 0.41 8.8E-06 32.5 0.8 23 82-110 134-156 (166)
96 PRK14890 putative Zn-ribbon RN 84.5 0.49 1.1E-05 26.1 0.8 10 130-139 47-56 (59)
97 KOG2785|consensus 83.8 1.2 2.7E-05 34.0 3.0 50 104-153 167-242 (390)
98 PRK00464 nrdR transcriptional 83.8 0.46 9.9E-06 31.9 0.6 12 83-94 29-40 (154)
99 PF05443 ROS_MUCR: ROS/MUCR tr 83.7 0.69 1.5E-05 30.2 1.4 31 127-160 68-98 (132)
100 COG3357 Predicted transcriptio 83.6 0.53 1.1E-05 28.3 0.8 27 81-110 57-83 (97)
101 KOG2785|consensus 83.5 1.5 3.2E-05 33.6 3.3 73 51-125 164-242 (390)
102 KOG2186|consensus 83.1 0.68 1.5E-05 33.4 1.3 38 53-93 3-40 (276)
103 smart00834 CxxC_CXXC_SSSS Puta 83.0 0.53 1.1E-05 23.6 0.6 12 104-115 6-17 (41)
104 PF09986 DUF2225: Uncharacteri 82.8 0.15 3.2E-06 36.2 -2.1 22 52-73 4-25 (214)
105 KOG4167|consensus 82.6 0.34 7.3E-06 40.1 -0.4 27 101-127 790-816 (907)
106 smart00659 RPOLCX RNA polymera 82.5 0.86 1.9E-05 23.6 1.2 11 83-93 3-13 (44)
107 PF14353 CpXC: CpXC protein 82.3 0.63 1.4E-05 30.1 0.8 11 55-65 3-13 (128)
108 smart00734 ZnF_Rad18 Rad18-lik 82.3 1.3 2.8E-05 20.1 1.7 19 105-124 3-21 (26)
109 cd00730 rubredoxin Rubredoxin; 82.2 0.65 1.4E-05 24.8 0.7 9 102-110 33-41 (50)
110 PF04959 ARS2: Arsenite-resist 82.0 0.98 2.1E-05 32.0 1.8 31 50-80 74-104 (214)
111 COG1996 RPC10 DNA-directed RNA 80.6 0.8 1.7E-05 24.3 0.7 7 104-110 25-31 (49)
112 smart00531 TFIIE Transcription 79.2 1.4 3E-05 29.3 1.7 33 82-114 99-134 (147)
113 COG1997 RPL43A Ribosomal prote 78.5 1.2 2.7E-05 26.6 1.1 12 104-115 54-65 (89)
114 TIGR00373 conserved hypothetic 77.9 1.5 3.2E-05 29.6 1.6 33 101-142 107-139 (158)
115 PRK06266 transcription initiat 77.2 1.4 3E-05 30.3 1.3 34 101-143 115-148 (178)
116 PRK09678 DNA-binding transcrip 76.7 0.58 1.3E-05 27.1 -0.6 17 129-145 25-43 (72)
117 COG1198 PriA Primosomal protei 76.5 0.63 1.4E-05 39.0 -0.6 15 126-140 470-484 (730)
118 PF00301 Rubredoxin: Rubredoxi 76.3 1.2 2.6E-05 23.5 0.6 10 101-110 32-41 (47)
119 PF13451 zf-trcl: Probable zin 75.8 2.4 5.2E-05 22.5 1.7 39 52-90 3-41 (49)
120 KOG4167|consensus 75.7 1.6 3.4E-05 36.4 1.3 28 51-79 790-817 (907)
121 COG1655 Uncharacterized protei 75.0 0.73 1.6E-05 32.8 -0.5 41 101-141 17-72 (267)
122 PF01363 FYVE: FYVE zinc finge 73.9 1.9 4.1E-05 24.4 1.1 8 56-63 12-19 (69)
123 PF12907 zf-met2: Zinc-binding 73.1 2.9 6.3E-05 21.2 1.5 32 54-85 2-36 (40)
124 PF13240 zinc_ribbon_2: zinc-r 73.1 1.5 3.2E-05 19.3 0.4 6 106-111 16-21 (23)
125 KOG0978|consensus 73.0 1.1 2.3E-05 37.3 -0.1 14 52-65 642-655 (698)
126 PF01780 Ribosomal_L37ae: Ribo 71.7 1.6 3.4E-05 26.4 0.4 32 81-115 34-65 (90)
127 PF12760 Zn_Tnp_IS1595: Transp 71.3 11 0.00025 19.4 3.6 27 83-111 19-45 (46)
128 PF10083 DUF2321: Uncharacteri 68.8 0.76 1.7E-05 30.6 -1.5 12 105-116 70-81 (158)
129 COG4888 Uncharacterized Zn rib 68.7 0.88 1.9E-05 27.9 -1.1 39 100-142 19-57 (104)
130 COG1198 PriA Primosomal protei 68.6 2 4.3E-05 36.2 0.5 46 54-112 436-484 (730)
131 PF13248 zf-ribbon_3: zinc-rib 68.0 2.2 4.8E-05 19.2 0.4 6 106-111 19-24 (26)
132 PRK04023 DNA polymerase II lar 68.0 2.7 6E-05 36.4 1.2 12 131-142 663-674 (1121)
133 PRK14873 primosome assembly pr 67.7 2 4.3E-05 35.9 0.3 26 77-111 405-430 (665)
134 COG4530 Uncharacterized protei 67.6 2.6 5.6E-05 26.4 0.7 10 104-113 27-36 (129)
135 TIGR01206 lysW lysine biosynth 67.3 3.3 7.1E-05 22.5 1.0 7 55-61 4-10 (54)
136 KOG3408|consensus 66.9 4.3 9.3E-05 25.9 1.6 23 131-153 57-79 (129)
137 PF01927 Mut7-C: Mut7-C RNAse 64.6 5.2 0.00011 26.5 1.8 19 103-121 124-142 (147)
138 KOG4602|consensus 64.4 11 0.00024 27.4 3.5 46 51-111 231-276 (318)
139 PF04780 DUF629: Protein of un 63.5 5.8 0.00013 31.6 2.1 30 52-81 56-85 (466)
140 PF07754 DUF1610: Domain of un 63.2 3.9 8.5E-05 18.2 0.7 7 104-110 17-23 (24)
141 PF04438 zf-HIT: HIT zinc fing 63.2 3.1 6.7E-05 19.6 0.4 10 104-113 14-23 (30)
142 PF11931 DUF3449: Domain of un 62.6 2.5 5.4E-05 29.6 0.0 22 101-122 99-121 (196)
143 PTZ00255 60S ribosomal protein 61.6 4.4 9.5E-05 24.5 0.9 31 82-115 36-66 (90)
144 PRK14714 DNA polymerase II lar 61.6 4 8.7E-05 36.4 1.1 11 131-141 709-719 (1337)
145 TIGR00280 L37a ribosomal prote 61.2 4.2 9E-05 24.7 0.8 32 82-116 35-66 (91)
146 COG4957 Predicted transcriptio 61.1 3.2 7E-05 27.0 0.3 22 105-129 78-99 (148)
147 KOG2593|consensus 61.0 7.1 0.00015 30.6 2.2 31 81-111 127-161 (436)
148 PF08271 TF_Zn_Ribbon: TFIIB z 60.9 5.3 0.00012 20.3 1.1 9 104-112 20-28 (43)
149 cd00065 FYVE FYVE domain; Zinc 60.8 5.5 0.00012 21.4 1.2 12 103-114 18-29 (57)
150 TIGR00595 priA primosomal prot 60.4 3.5 7.5E-05 33.3 0.5 47 55-111 215-261 (505)
151 PF09845 DUF2072: Zn-ribbon co 60.0 3.3 7.1E-05 26.9 0.2 13 54-66 2-14 (131)
152 PF15269 zf-C2H2_7: Zinc-finge 60.0 7.3 0.00016 20.2 1.4 22 104-125 21-42 (54)
153 PF03604 DNA_RNApol_7kD: DNA d 59.9 4.6 0.0001 19.3 0.7 6 105-110 19-24 (32)
154 PF10013 DUF2256: Uncharacteri 59.8 5.4 0.00012 20.4 0.9 17 105-121 10-26 (42)
155 COG2879 Uncharacterized small 59.7 11 0.00024 21.1 2.2 18 143-160 24-41 (65)
156 KOG3214|consensus 59.5 3 6.6E-05 25.6 -0.0 41 101-145 21-61 (109)
157 KOG3408|consensus 59.3 6.9 0.00015 25.0 1.5 25 50-74 54-78 (129)
158 KOG2593|consensus 57.7 6.2 0.00013 30.9 1.4 39 52-94 127-165 (436)
159 PF08790 zf-LYAR: LYAR-type C2 57.6 3.4 7.4E-05 19.1 0.0 17 105-122 2-18 (28)
160 PRK04023 DNA polymerase II lar 57.5 6.1 0.00013 34.5 1.4 11 52-62 625-635 (1121)
161 PRK03976 rpl37ae 50S ribosomal 57.2 5.3 0.00011 24.2 0.8 31 82-115 36-66 (90)
162 PF14311 DUF4379: Domain of un 57.0 10 0.00022 20.4 1.8 15 104-118 29-43 (55)
163 KOG1280|consensus 56.9 5 0.00011 30.5 0.7 29 103-131 79-107 (381)
164 PF03833 PolC_DP2: DNA polymer 56.5 3.6 7.9E-05 35.0 0.0 13 82-94 655-667 (900)
165 smart00661 RPOL9 RNA polymeras 56.1 8.1 0.00018 20.3 1.3 10 104-113 21-30 (52)
166 smart00064 FYVE Protein presen 55.9 6.1 0.00013 22.2 0.9 28 83-115 11-38 (68)
167 TIGR00100 hypA hydrogenase nic 55.7 6.1 0.00013 25.1 0.9 12 104-115 71-82 (115)
168 PRK03824 hypA hydrogenase nick 55.5 5.3 0.00012 26.2 0.6 16 101-116 68-83 (135)
169 KOG0782|consensus 55.2 4 8.6E-05 33.3 0.0 49 66-117 238-290 (1004)
170 KOG0717|consensus 54.8 6.4 0.00014 31.2 1.1 22 132-153 293-314 (508)
171 COG5112 UFD2 U1-like Zn-finger 54.4 7.5 0.00016 24.2 1.1 23 131-153 55-77 (126)
172 PF04780 DUF629: Protein of un 53.9 8.3 0.00018 30.8 1.5 22 132-153 58-79 (466)
173 PF02176 zf-TRAF: TRAF-type zi 53.7 3.9 8.5E-05 22.2 -0.2 40 104-144 10-55 (60)
174 TIGR00595 priA primosomal prot 52.4 4.4 9.5E-05 32.8 -0.2 14 127-140 249-262 (505)
175 PRK14873 primosome assembly pr 52.3 4.5 9.8E-05 33.9 -0.1 11 130-140 421-431 (665)
176 KOG2636|consensus 52.1 9.2 0.0002 30.2 1.5 23 101-123 399-422 (497)
177 PF13878 zf-C2H2_3: zinc-finge 51.7 16 0.00035 18.4 2.0 23 54-77 14-38 (41)
178 PF01155 HypA: Hydrogenase exp 51.5 6 0.00013 25.0 0.4 13 104-116 71-83 (113)
179 PF15135 UPF0515: Uncharacteri 51.4 7.8 0.00017 28.1 1.0 28 82-111 155-182 (278)
180 PF07649 C1_3: C1-like domain; 51.3 8.1 0.00018 17.9 0.8 7 104-110 16-22 (30)
181 PF05191 ADK_lid: Adenylate ki 50.6 6.3 0.00014 19.4 0.3 8 106-113 4-11 (36)
182 COG1773 Rubredoxin [Energy pro 50.5 8 0.00017 21.1 0.7 15 103-117 3-17 (55)
183 COG3091 SprT Zn-dependent meta 50.3 6.4 0.00014 26.3 0.4 35 101-140 115-149 (156)
184 KOG2636|consensus 50.0 11 0.00024 29.8 1.7 29 124-152 394-423 (497)
185 KOG0978|consensus 49.9 4 8.7E-05 34.1 -0.7 22 129-150 676-697 (698)
186 PF08274 PhnA_Zn_Ribbon: PhnA 49.7 4.6 9.9E-05 19.0 -0.3 8 131-138 19-26 (30)
187 PRK00564 hypA hydrogenase nick 49.4 8.4 0.00018 24.6 0.8 12 104-115 72-83 (117)
188 COG5151 SSL1 RNA polymerase II 49.0 12 0.00026 28.1 1.7 48 105-154 364-411 (421)
189 PHA02998 RNA polymerase subuni 49.0 2.4 5.2E-05 29.0 -1.8 38 103-144 143-184 (195)
190 PF07800 DUF1644: Protein of u 48.7 31 0.00067 23.3 3.4 61 103-164 80-142 (162)
191 PF02150 RNA_POL_M_15KD: RNA p 48.6 10 0.00022 18.5 0.9 9 105-113 22-30 (35)
192 PF09332 Mcm10: Mcm10 replicat 48.3 5 0.00011 30.7 -0.4 39 54-94 253-297 (344)
193 COG4338 Uncharacterized protei 48.1 6.9 0.00015 20.6 0.2 19 105-123 14-32 (54)
194 PF01286 XPA_N: XPA protein N- 48.1 6.9 0.00015 19.0 0.2 9 85-93 6-14 (34)
195 KOG4173|consensus 48.1 15 0.00032 26.0 1.9 47 103-152 79-127 (253)
196 COG1675 TFA1 Transcription ini 48.0 12 0.00025 25.8 1.4 30 81-112 112-141 (176)
197 COG1656 Uncharacterized conser 47.8 12 0.00026 25.4 1.4 17 104-120 131-147 (165)
198 PF12773 DZR: Double zinc ribb 47.8 13 0.00028 19.4 1.3 9 131-139 29-37 (50)
199 PRK14559 putative protein seri 47.6 16 0.00035 30.6 2.4 7 106-112 44-50 (645)
200 COG5152 Uncharacterized conser 47.2 8 0.00017 27.1 0.5 48 81-143 195-242 (259)
201 KOG4118|consensus 46.8 14 0.00031 20.8 1.4 30 131-160 38-67 (74)
202 KOG1842|consensus 46.6 13 0.00029 29.3 1.7 29 53-81 15-43 (505)
203 PF04810 zf-Sec23_Sec24: Sec23 46.5 11 0.00024 18.9 0.8 10 102-111 23-32 (40)
204 PF07975 C1_4: TFIIH C1-like d 45.8 5.1 0.00011 21.5 -0.5 24 103-126 21-44 (51)
205 smart00154 ZnF_AN1 AN1-like Zi 45.5 9.7 0.00021 19.0 0.5 15 53-67 12-26 (39)
206 PF11789 zf-Nse: Zinc-finger o 44.8 11 0.00024 20.6 0.8 44 81-136 10-53 (57)
207 KOG2807|consensus 43.8 36 0.00077 25.9 3.4 21 53-73 290-310 (378)
208 KOG1701|consensus 43.7 18 0.00038 28.5 1.9 45 54-100 275-320 (468)
209 KOG1280|consensus 43.0 27 0.00058 26.8 2.7 39 51-89 77-116 (381)
210 PF04641 Rtf2: Rtf2 RING-finge 42.9 2.9 6.3E-05 30.6 -2.3 17 50-66 110-126 (260)
211 COG3364 Zn-ribbon containing p 42.6 11 0.00024 23.3 0.5 11 104-114 3-13 (112)
212 PTZ00448 hypothetical protein; 42.4 24 0.00052 27.3 2.4 22 104-125 315-336 (373)
213 PF04423 Rad50_zn_hook: Rad50 41.6 11 0.00024 20.2 0.4 12 105-116 22-33 (54)
214 TIGR01562 FdhE formate dehydro 41.5 15 0.00032 27.7 1.2 77 53-144 184-265 (305)
215 PRK05452 anaerobic nitric oxid 41.3 13 0.00027 30.0 0.9 7 104-110 459-465 (479)
216 KOG2071|consensus 41.1 13 0.00029 30.4 0.9 28 128-155 415-442 (579)
217 COG4640 Predicted membrane pro 40.7 16 0.00035 28.5 1.3 16 104-119 16-31 (465)
218 PF01096 TFIIS_C: Transcriptio 40.5 8.5 0.00018 19.2 -0.1 9 104-112 29-37 (39)
219 smart00504 Ubox Modified RING 40.4 30 0.00065 18.7 2.1 29 108-142 18-46 (63)
220 PRK12496 hypothetical protein; 40.0 11 0.00025 25.5 0.4 11 83-93 128-138 (164)
221 PF14446 Prok-RING_1: Prokaryo 39.9 17 0.00038 19.7 1.0 25 83-112 6-30 (54)
222 PRK05580 primosome assembly pr 39.8 7.8 0.00017 32.6 -0.5 13 128-140 418-430 (679)
223 COG1594 RPB9 DNA-directed RNA 39.7 4.5 9.7E-05 25.7 -1.5 16 52-67 21-36 (113)
224 PRK00420 hypothetical protein; 39.4 18 0.0004 22.9 1.2 29 83-115 24-52 (112)
225 PF06044 DRP: Dam-replacing fa 38.9 3.8 8.3E-05 29.5 -2.1 37 81-117 30-67 (254)
226 PRK03564 formate dehydrogenase 38.7 17 0.00036 27.5 1.1 78 52-144 186-265 (309)
227 cd00924 Cyt_c_Oxidase_Vb Cytoc 38.6 13 0.00029 22.8 0.5 20 123-143 72-91 (97)
228 PF10122 Mu-like_Com: Mu-like 38.1 22 0.00049 19.0 1.2 9 104-112 25-33 (51)
229 COG1571 Predicted DNA-binding 38.1 17 0.00036 28.7 1.0 14 131-144 367-380 (421)
230 PTZ00303 phosphatidylinositol 37.9 16 0.00034 31.3 0.9 33 84-116 462-494 (1374)
231 PLN03238 probable histone acet 37.9 31 0.00068 25.7 2.3 22 131-152 48-69 (290)
232 PF04606 Ogr_Delta: Ogr/Delta- 37.7 3.5 7.6E-05 21.6 -1.9 12 131-142 25-38 (47)
233 PF01428 zf-AN1: AN1-like Zinc 37.7 15 0.00033 18.7 0.5 15 102-116 12-26 (43)
234 KOG0402|consensus 37.4 16 0.00035 21.7 0.7 30 82-114 36-65 (92)
235 COG3809 Uncharacterized protei 37.4 27 0.00058 20.5 1.6 40 85-125 4-43 (88)
236 TIGR00416 sms DNA repair prote 37.3 16 0.00034 29.2 0.8 7 104-110 22-28 (454)
237 PRK00762 hypA hydrogenase nick 37.2 15 0.00032 23.7 0.6 11 53-64 70-80 (124)
238 KOG2071|consensus 37.2 20 0.00042 29.5 1.3 28 51-79 416-443 (579)
239 PF10276 zf-CHCC: Zinc-finger 37.1 15 0.00032 18.6 0.4 10 104-113 30-39 (40)
240 COG0068 HypF Hydrogenase matur 37.1 9.3 0.0002 32.1 -0.5 72 53-139 101-181 (750)
241 PF13824 zf-Mss51: Zinc-finger 37.1 17 0.00038 19.8 0.7 7 104-110 15-21 (55)
242 PRK04351 hypothetical protein; 36.4 17 0.00036 24.3 0.7 33 103-143 112-144 (149)
243 PLN02294 cytochrome c oxidase 36.4 14 0.00029 25.3 0.3 21 123-144 134-154 (174)
244 COG0846 SIR2 NAD-dependent pro 36.4 22 0.00048 26.0 1.4 34 102-139 121-154 (250)
245 PF07282 OrfB_Zn_ribbon: Putat 36.0 24 0.00053 19.7 1.3 9 132-140 47-55 (69)
246 PRK00432 30S ribosomal protein 35.9 25 0.00054 18.7 1.2 7 132-138 38-44 (50)
247 COG1327 Predicted transcriptio 35.8 16 0.00035 24.4 0.6 12 83-94 29-40 (156)
248 PTZ00303 phosphatidylinositol 35.6 19 0.00041 30.9 1.1 33 105-144 462-494 (1374)
249 TIGR00244 transcriptional regu 35.5 18 0.0004 24.1 0.8 11 105-115 30-40 (147)
250 smart00440 ZnF_C2C2 C2C2 Zinc 35.3 17 0.00037 18.2 0.5 8 132-139 29-36 (40)
251 KOG1729|consensus 35.3 5.6 0.00012 29.6 -1.8 6 133-138 216-221 (288)
252 PRK11823 DNA repair protein Ra 35.1 18 0.00039 28.8 0.8 7 104-110 22-28 (446)
253 KOG2907|consensus 35.0 29 0.00064 21.9 1.6 8 54-61 75-82 (116)
254 smart00731 SprT SprT homologue 34.9 23 0.00049 23.4 1.2 33 103-142 112-144 (146)
255 PF05290 Baculo_IE-1: Baculovi 34.8 25 0.00054 23.0 1.3 57 78-145 76-135 (140)
256 PF10071 DUF2310: Zn-ribbon-co 34.7 17 0.00038 26.6 0.7 27 105-138 222-248 (258)
257 PRK14892 putative transcriptio 34.3 10 0.00023 23.4 -0.4 12 132-143 43-54 (99)
258 PF11672 DUF3268: Protein of u 34.2 14 0.0003 23.0 0.1 8 132-139 32-39 (102)
259 COG5188 PRP9 Splicing factor 3 33.7 88 0.0019 24.2 4.1 22 52-73 373-395 (470)
260 PRK05978 hypothetical protein; 33.7 21 0.00046 23.8 0.9 8 54-61 34-41 (148)
261 PF10263 SprT-like: SprT-like 33.7 16 0.00035 24.2 0.3 31 103-141 123-153 (157)
262 COG4306 Uncharacterized protei 33.6 19 0.00041 23.2 0.6 13 105-117 70-82 (160)
263 KOG1994|consensus 33.5 23 0.0005 25.4 1.1 21 52-72 238-258 (268)
264 COG1779 C4-type Zn-finger prot 33.2 17 0.00038 25.4 0.4 9 54-62 15-23 (201)
265 PF15616 TerY-C: TerY-C metal 32.5 26 0.00057 22.9 1.1 9 131-139 105-113 (131)
266 cd01121 Sms Sms (bacterial rad 31.6 24 0.00052 27.4 1.0 21 83-110 1-21 (372)
267 KOG3990|consensus 31.4 29 0.00062 25.3 1.3 15 53-67 6-20 (305)
268 COG4391 Uncharacterized protei 31.4 19 0.00042 20.0 0.3 12 104-115 49-60 (62)
269 COG3677 Transposase and inacti 31.4 24 0.00052 22.9 0.8 16 51-66 51-66 (129)
270 PTZ00448 hypothetical protein; 30.8 36 0.00078 26.4 1.8 23 131-153 314-336 (373)
271 cd02335 ZZ_ADA2 Zinc finger, Z 30.7 31 0.00068 18.0 1.1 6 104-109 16-21 (49)
272 PTZ00064 histone acetyltransfe 30.6 45 0.00097 27.1 2.3 31 130-160 279-309 (552)
273 PLN00104 MYST -like histone ac 30.5 43 0.00093 26.8 2.2 31 131-161 198-228 (450)
274 TIGR00310 ZPR1_znf ZPR1 zinc f 30.3 26 0.00055 24.5 0.9 8 55-62 2-9 (192)
275 PLN02748 tRNA dimethylallyltra 30.1 36 0.00077 27.4 1.7 24 130-153 417-441 (468)
276 PF09082 DUF1922: Domain of un 30.1 8.7 0.00019 21.9 -1.2 26 83-113 4-29 (68)
277 cd02341 ZZ_ZZZ3 Zinc finger, Z 29.5 34 0.00074 18.0 1.1 6 104-109 16-21 (48)
278 COG5574 PEX10 RING-finger-cont 29.4 22 0.00048 26.1 0.4 33 104-140 228-260 (271)
279 COG5188 PRP9 Splicing factor 3 29.3 35 0.00075 26.3 1.5 30 123-152 366-396 (470)
280 PF06220 zf-U1: U1 zinc finger 29.2 45 0.00098 16.5 1.4 10 132-141 4-13 (38)
281 PF06397 Desulfoferrod_N: Desu 28.6 28 0.0006 17.2 0.6 11 103-113 6-16 (36)
282 KOG3362|consensus 28.6 16 0.00034 24.2 -0.4 22 131-152 129-150 (156)
283 smart00290 ZnF_UBP Ubiquitin C 28.5 28 0.00061 18.0 0.7 13 104-116 12-24 (50)
284 KOG1842|consensus 28.5 34 0.00073 27.2 1.3 29 101-129 13-41 (505)
285 COG1545 Predicted nucleic-acid 28.3 24 0.00053 23.2 0.5 12 83-94 30-41 (140)
286 PF04216 FdhE: Protein involve 28.2 26 0.00056 26.1 0.7 78 54-143 173-250 (290)
287 PF05129 Elf1: Transcription e 27.8 23 0.00051 20.9 0.3 11 105-115 48-58 (81)
288 KOG4317|consensus 27.6 15 0.00032 27.7 -0.7 12 83-94 20-31 (383)
289 PF14803 Nudix_N_2: Nudix N-te 27.5 35 0.00075 16.5 0.8 6 133-138 24-29 (34)
290 smart00709 Zpr1 Duplicated dom 27.3 26 0.00057 23.7 0.5 6 56-61 3-8 (160)
291 KOG0782|consensus 26.5 21 0.00045 29.4 -0.1 30 118-147 240-269 (1004)
292 PF03107 C1_2: C1 domain; Int 26.4 41 0.00088 15.5 0.9 7 104-110 16-22 (30)
293 PLN03208 E3 ubiquitin-protein 26.4 70 0.0015 22.4 2.4 12 52-63 17-28 (193)
294 KOG1819|consensus 26.0 37 0.0008 27.5 1.1 8 85-92 920-927 (990)
295 KOG1044|consensus 25.5 30 0.00066 28.4 0.6 36 105-147 194-234 (670)
296 PF03145 Sina: Seven in absent 25.5 40 0.00086 23.5 1.2 51 104-157 15-73 (198)
297 PRK06450 threonine synthase; V 25.3 31 0.00068 26.3 0.7 10 54-63 4-13 (338)
298 PTZ00409 Sir2 (Silent Informat 25.3 68 0.0015 23.7 2.4 34 104-138 138-171 (271)
299 PF07503 zf-HYPF: HypF finger; 25.2 45 0.00098 16.2 1.0 9 105-113 23-31 (35)
300 PF12230 PRP21_like_P: Pre-mRN 24.8 24 0.00053 25.2 0.0 28 104-132 169-196 (229)
301 PF02748 PyrI_C: Aspartate car 24.6 38 0.00083 18.2 0.7 16 101-116 33-48 (52)
302 PLN03239 histone acetyltransfe 24.5 67 0.0015 24.8 2.2 23 130-152 105-127 (351)
303 KOG0320|consensus 24.3 29 0.00062 24.0 0.3 10 131-140 167-176 (187)
304 cd01396 MeCP2_MBD MeCP2, MBD1, 24.3 64 0.0014 18.8 1.7 18 137-154 34-51 (77)
305 COG1379 PHP family phosphoeste 24.3 74 0.0016 24.4 2.4 53 105-166 248-301 (403)
306 TIGR00515 accD acetyl-CoA carb 23.9 25 0.00055 26.2 -0.0 11 53-63 26-36 (285)
307 PLN02748 tRNA dimethylallyltra 23.5 55 0.0012 26.4 1.7 25 101-125 416-441 (468)
308 CHL00174 accD acetyl-CoA carbo 23.2 27 0.0006 26.2 0.0 11 53-63 38-48 (296)
309 PRK14138 NAD-dependent deacety 23.0 76 0.0016 23.0 2.3 32 104-139 120-151 (244)
310 PF10537 WAC_Acf1_DNA_bd: ATP- 22.9 77 0.0017 19.7 2.0 37 52-90 2-38 (102)
311 PF03884 DUF329: Domain of unk 22.8 38 0.00081 18.6 0.5 12 104-115 3-14 (57)
312 COG1326 Uncharacterized archae 22.8 59 0.0013 22.8 1.5 10 132-141 31-40 (201)
313 COG1066 Sms Predicted ATP-depe 22.7 35 0.00077 27.0 0.5 6 105-110 23-28 (456)
314 COG1645 Uncharacterized Zn-fin 22.4 50 0.0011 21.6 1.1 27 82-113 28-54 (131)
315 PRK07218 replication factor A; 22.4 37 0.00081 26.9 0.6 7 55-61 299-305 (423)
316 TIGR00627 tfb4 transcription f 22.3 43 0.00093 25.0 0.9 27 101-141 253-279 (279)
317 COG2331 Uncharacterized protei 22.3 22 0.00048 20.8 -0.5 9 54-62 13-21 (82)
318 PRK07591 threonine synthase; V 21.9 40 0.00087 26.6 0.7 28 53-94 18-45 (421)
319 TIGR00340 zpr1_rel ZPR1-relate 21.8 37 0.00081 23.1 0.4 6 56-61 1-6 (163)
320 PF07295 DUF1451: Protein of u 21.8 26 0.00057 23.3 -0.3 6 105-110 132-137 (146)
321 cd01413 SIR2_Af2 SIR2_Af2: Arc 21.7 78 0.0017 22.5 2.1 31 104-139 114-144 (222)
322 PRK05654 acetyl-CoA carboxylas 21.7 30 0.00065 26.0 -0.1 11 52-62 26-36 (292)
323 KOG3352|consensus 21.7 38 0.00082 22.7 0.4 17 127-143 129-145 (153)
324 PF14787 zf-CCHC_5: GAG-polypr 21.7 41 0.00089 16.5 0.4 16 105-120 4-19 (36)
325 PRK01343 zinc-binding protein; 21.5 47 0.001 18.3 0.7 11 104-114 10-20 (57)
326 PF03367 zf-ZPR1: ZPR1 zinc-fi 21.4 30 0.00065 23.4 -0.1 8 104-111 31-38 (161)
327 PF08209 Sgf11: Sgf11 (transcr 21.4 47 0.001 16.0 0.6 20 104-124 5-24 (33)
328 PF06467 zf-FCS: MYM-type Zinc 20.8 61 0.0013 16.0 1.0 15 104-118 7-21 (43)
329 PF14634 zf-RING_5: zinc-RING 20.6 89 0.0019 15.7 1.6 10 129-138 34-43 (44)
330 COG0068 HypF Hydrogenase matur 20.5 22 0.00047 30.0 -1.0 68 83-151 102-171 (750)
331 PF05495 zf-CHY: CHY zinc fing 20.3 27 0.00058 20.0 -0.4 13 54-66 11-23 (71)
332 COG3880 Modulator of heat shoc 20.3 30 0.00066 23.6 -0.2 31 104-144 75-105 (176)
333 PTZ00043 cytochrome c oxidase 20.1 49 0.0011 23.8 0.7 17 127-143 177-193 (268)
334 PRK12722 transcriptional activ 20.0 61 0.0013 22.6 1.2 28 104-139 135-162 (187)
335 PF04328 DUF466: Protein of un 20.0 1E+02 0.0022 17.4 1.9 18 143-160 24-41 (65)
No 1
>KOG2462|consensus
Probab=99.90 E-value=2.2e-24 Score=151.28 Aligned_cols=109 Identities=17% Similarity=0.231 Sum_probs=83.8
Q ss_pred CCCcccccccccccCCHHHHHHHHHHhcCC---CCcccccchhhhhhccccccc-------cCceecccccccccChhHH
Q psy8167 50 PIDRIPCTLCDKTFTRKDSLKKHIRIFHTQ---NQPQHTNVIEVALGARANAAF-------IDRIRCELCDKSFTRKDSL 119 (167)
Q Consensus 50 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~---~~~~~c~~c~~~~~~~~~~~l-------~k~~~C~~C~k~f~~~~~l 119 (167)
....|.|..||+.+....+|.+|. +.|.. .+.+.|+.|++.+.. ...| .-++.|.+|||.|.+...|
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHk-Q~H~~~~s~ka~~C~~C~K~YvS--mpALkMHirTH~l~c~C~iCGKaFSRPWLL 203 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHK-QTHRSLDSKKAFSCKYCGKVYVS--MPALKMHIRTHTLPCECGICGKAFSRPWLL 203 (279)
T ss_pred cCCceeccccccccccccccchhh-cccccccccccccCCCCCceeee--hHHHhhHhhccCCCcccccccccccchHHh
Confidence 345688888888888888888887 65643 456888888888776 5444 3356788888888888888
Q ss_pred HHHHHhhcCCCCCCCCchhhhcCCHHHHHHHHhhcCCCCCcc
Q psy8167 120 KKHNRIFHGGADPKLMDEQMARGSADFLEVVLNEDGEGEPVS 161 (167)
Q Consensus 120 ~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~ 161 (167)
+-|+|+|+|||||.|..|+|+|..+++|+-|+++|.+.++..
T Consensus 204 QGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~q 245 (279)
T KOG2462|consen 204 QGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQ 245 (279)
T ss_pred hcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCcccc
Confidence 888888888888888888888888888888888887766544
No 2
>KOG2462|consensus
Probab=99.88 E-value=2.6e-23 Score=145.92 Aligned_cols=102 Identities=18% Similarity=0.245 Sum_probs=91.1
Q ss_pred CCcccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccc-------cCceecccccccccChhHHHHHH
Q psy8167 51 IDRIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAF-------IDRIRCELCDKSFTRKDSLKKHN 123 (167)
Q Consensus 51 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l-------~k~~~C~~C~k~f~~~~~l~~H~ 123 (167)
.+.+.|+.|++.|..-..|.+|+ ++|+ .+++|.+||+.|...=.+.- +|+|.|+.|+|+|..+++|+.||
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHi-rTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHm 235 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHI-RTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHM 235 (279)
T ss_pred cccccCCCCCceeeehHHHhhHh-hccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHH
Confidence 56799999999999999999999 6685 78999999999985111111 99999999999999999999999
Q ss_pred HhhcCCCCCCCCchhhhcCCHHHHHHHHhhcC
Q psy8167 124 RIFHGGADPKLMDEQMARGSADFLEVVLNEDG 155 (167)
Q Consensus 124 ~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 155 (167)
++|.+.|+|+|..|+|+|...+.|.+|...-.
T Consensus 236 QTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~C 267 (279)
T KOG2462|consen 236 QTHSDVKKHQCPRCGKSFALKSYLNKHSESAC 267 (279)
T ss_pred HhhcCCccccCcchhhHHHHHHHHHHhhhhcc
Confidence 99999999999999999999999999998544
No 3
>KOG1074|consensus
Probab=99.72 E-value=5.3e-18 Score=134.05 Aligned_cols=55 Identities=18% Similarity=0.214 Sum_probs=51.7
Q ss_pred ecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCCHHHHHHHHhhcCCCCC
Q psy8167 105 RCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSADFLEVVLNEDGEGEP 159 (167)
Q Consensus 105 ~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~ 159 (167)
.|-+|.++..-++.|+.|.|+|+|++||+|.+||+.|..+-+|+.|+-+|....|
T Consensus 607 qCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~ 661 (958)
T KOG1074|consen 607 QCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPP 661 (958)
T ss_pred ceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCcc
Confidence 6999999999999999999999999999999999999999999999998876444
No 4
>KOG3576|consensus
Probab=99.68 E-value=1.9e-17 Score=111.70 Aligned_cols=107 Identities=21% Similarity=0.366 Sum_probs=90.2
Q ss_pred CCcccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccc---------cCceecccccccccChhHHHH
Q psy8167 51 IDRIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAF---------IDRIRCELCDKSFTRKDSLKK 121 (167)
Q Consensus 51 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l---------~k~~~C~~C~k~f~~~~~l~~ 121 (167)
...|.|.+|++.|....-|.+|+ ..|...+-+-|..||+.|.+ .+.| .++|+|..|+|+|.++-.|..
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~-kch~~vkr~lct~cgkgfnd--tfdlkrh~rthtgvrpykc~~c~kaftqrcsles 191 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHL-KCHSDVKRHLCTFCGKGFND--TFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLES 191 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHh-hhccHHHHHHHhhccCcccc--hhhhhhhhccccCccccchhhhhHHHHhhccHHH
Confidence 46799999999999999999999 88998888899999988877 5555 678889999999999988888
Q ss_pred HHHhhcC-----------CCCCCCCchhhhcCCHHHHHHHHhhcCCCCCc
Q psy8167 122 HNRIFHG-----------GADPKLMDEQMARGSADFLEVVLNEDGEGEPV 160 (167)
Q Consensus 122 H~~~h~~-----------~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 160 (167)
|++.-|+ .+.|.|..||..-.....+-.|++.||+..|.
T Consensus 192 hl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Spa 241 (267)
T KOG3576|consen 192 HLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSPA 241 (267)
T ss_pred HHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCHH
Confidence 8876665 35688999998888888888888888876553
No 5
>KOG1074|consensus
Probab=99.68 E-value=6.5e-17 Score=128.02 Aligned_cols=57 Identities=23% Similarity=0.223 Sum_probs=53.5
Q ss_pred ecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCCHHHHHHHHhhcCCCCCcc
Q psy8167 105 RCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSADFLEVVLNEDGEGEPVS 161 (167)
Q Consensus 105 ~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~ 161 (167)
-|.+||+.|...+.|+.|+++|.++|||.|.+|++.|..+-+|+.||.+|....|.+
T Consensus 881 ~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~s 937 (958)
T KOG1074|consen 881 VCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPS 937 (958)
T ss_pred hhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCc
Confidence 499999999999999999999999999999999999999999999999998766543
No 6
>KOG3623|consensus
Probab=99.61 E-value=1.3e-16 Score=124.72 Aligned_cols=102 Identities=22% Similarity=0.374 Sum_probs=88.4
Q ss_pred CCcccccccccccCCHHHHHHHHHHhcCC-CCcccccchhhhhhccccccc--------------------cCceecccc
Q psy8167 51 IDRIPCTLCDKTFTRKDSLKKHIRIFHTQ-NQPQHTNVIEVALGARANAAF--------------------IDRIRCELC 109 (167)
Q Consensus 51 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~-~~~~~c~~c~~~~~~~~~~~l--------------------~k~~~C~~C 109 (167)
.....|++|.+.+.+...|..|++..|.. +..|.|..|..+|..++.+-- .++|+|..|
T Consensus 208 sqlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtEC 287 (1007)
T KOG3623|consen 208 SQLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTEC 287 (1007)
T ss_pred hhhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhcccccccc
Confidence 34578999999999999999999766644 346999999999987432211 688999999
Q ss_pred cccccChhHHHHHHHhhcCCCCCCCCchhhhcCCHHHHHHHHh
Q psy8167 110 DKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSADFLEVVLN 152 (167)
Q Consensus 110 ~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 152 (167)
||+|..+-+|+.|+|+|.|+|||.|+.|+|.|...-.+..|+-
T Consensus 288 gKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 288 GKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred chhhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 9999999999999999999999999999999999999999985
No 7
>KOG3623|consensus
Probab=99.60 E-value=6e-16 Score=121.15 Aligned_cols=83 Identities=24% Similarity=0.432 Sum_probs=76.1
Q ss_pred cCCCCcccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccccCceecccccccccChhHHHHHHHhhc
Q psy8167 48 VVPIDRIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRIFH 127 (167)
Q Consensus 48 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~h~ 127 (167)
..++..|.|..|+++|...+.|.+|. -.|+|.+| |.|.+|.|+|.++-+|..|+|.|.
T Consensus 889 kte~gmyaCDqCDK~FqKqSSLaRHK-YEHsGqRP---------------------yqC~iCkKAFKHKHHLtEHkRLHS 946 (1007)
T KOG3623|consen 889 KTEDGMYACDQCDKAFQKQSSLARHK-YEHSGQRP---------------------YQCIICKKAFKHKHHLTEHKRLHS 946 (1007)
T ss_pred cCccccchHHHHHHHHHhhHHHHHhh-hhhcCCCC---------------------cccchhhHhhhhhhhhhhhhhhcc
Confidence 34567899999999999999999998 66999988 577778889999999999999999
Q ss_pred CCCCCCCCchhhhcCCHHHHHHHHh
Q psy8167 128 GGADPKLMDEQMARGSADFLEVVLN 152 (167)
Q Consensus 128 ~~~~~~C~~C~~~f~~~~~l~~H~~ 152 (167)
|+|||+|+.|+|.|...-.+..||.
T Consensus 947 GEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 947 GEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred CCCcchhhhhhhhcccccchHhhhc
Confidence 9999999999999999999999996
No 8
>KOG3608|consensus
Probab=99.41 E-value=4.9e-13 Score=97.38 Aligned_cols=97 Identities=18% Similarity=0.240 Sum_probs=54.3
Q ss_pred ccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccc----------------------------cc-------cC
Q psy8167 58 LCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANA----------------------------AF-------ID 102 (167)
Q Consensus 58 ~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~----------------------------~l-------~k 102 (167)
.|-+.|.++..|++|+ +.|+++|...|+.||..|..++.+ .| ..
T Consensus 184 ~Ct~~~~~k~~LreH~-r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn 262 (467)
T KOG3608|consen 184 MCTKHMGNKYRLREHI-RTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN 262 (467)
T ss_pred hhhhhhccHHHHHHHH-HhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh
Confidence 4556666666666666 556666666666666655552211 11 22
Q ss_pred ceecccccccccChhHHHHHHHh-hcCCCCCCCCchhhhcCCHHHHHHHHhhcC
Q psy8167 103 RIRCELCDKSFTRKDSLKKHNRI-FHGGADPKLMDEQMARGSADFLEVVLNEDG 155 (167)
Q Consensus 103 ~~~C~~C~k~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 155 (167)
-|+|+.|.-.....+.|..||+. |..++|++|+.|++.|.+.+.|.+|+..|.
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 34566666666666666666553 334566666666666666666666665553
No 9
>KOG3608|consensus
Probab=99.39 E-value=4.9e-13 Score=97.36 Aligned_cols=100 Identities=22% Similarity=0.253 Sum_probs=53.1
Q ss_pred ccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccc------cCceeccc--ccccccChhHHHHHHHh
Q psy8167 54 IPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAF------IDRIRCEL--CDKSFTRKDSLKKHNRI 125 (167)
Q Consensus 54 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l------~k~~~C~~--C~k~f~~~~~l~~H~~~ 125 (167)
|+|+.|++.....++|..|++..|..++||+|..|.+.+...+.++- +-.|.|.. |-..|.+...|++|++.
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~e 343 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLE 343 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHHH
Confidence 45555555555555555555555555555555555555554211111 23345544 55555555555555555
Q ss_pred hcC---CCCCCCCchhhhcCCHHHHHHHHhh
Q psy8167 126 FHG---GADPKLMDEQMARGSADFLEVVLNE 153 (167)
Q Consensus 126 h~~---~~~~~C~~C~~~f~~~~~l~~H~~~ 153 (167)
++. ..+|.|..|++.|.+..+|..|+..
T Consensus 344 vhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~k 374 (467)
T KOG3608|consen 344 VHEGNNPILYACHCCDRFFTSGKSLSAHLMK 374 (467)
T ss_pred hccCCCCCceeeecchhhhccchhHHHHHHH
Confidence 542 2345666666666666666666554
No 10
>KOG3576|consensus
Probab=99.36 E-value=1.3e-13 Score=93.26 Aligned_cols=78 Identities=22% Similarity=0.209 Sum_probs=67.0
Q ss_pred CCCCcccccchhhhhhccccccc-------cCceecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCCHHHHHHH
Q psy8167 78 TQNQPQHTNVIEVALGARANAAF-------IDRIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSADFLEVV 150 (167)
Q Consensus 78 ~~~~~~~c~~c~~~~~~~~~~~l-------~k~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H 150 (167)
.+...|.|.+|++.|.....++- .+++-|..|||.|..--.|.+|+|+|+|.+||+|..|+|+|.....|..|
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 34457999999999987332222 56778999999999999999999999999999999999999999999999
Q ss_pred HhhcC
Q psy8167 151 LNEDG 155 (167)
Q Consensus 151 ~~~~~ 155 (167)
++.-|
T Consensus 193 l~kvh 197 (267)
T KOG3576|consen 193 LKKVH 197 (267)
T ss_pred HHHHc
Confidence 98544
No 11
>PHA00733 hypothetical protein
Probab=99.25 E-value=9.5e-12 Score=80.48 Aligned_cols=86 Identities=14% Similarity=0.050 Sum_probs=65.9
Q ss_pred CCcccccccccccCCHHHHHHHHH-HhcCCCCcccccchhhhhhccccccccCceecccccccccChhHHHHHHHhhcCC
Q psy8167 51 IDRIPCTLCDKTFTRKDSLKKHIR-IFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRIFHGG 129 (167)
Q Consensus 51 ~~~~~C~~C~~~f~~~~~l~~H~~-~~h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~h~~~ 129 (167)
.+++.|.+|.+.|.....|..+.. ..|.. ..-.++|.|..||+.|.....|..|++.| .
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~------------------~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~ 97 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLT------------------SKAVSPYVCPLCLMPFSSSVSLKQHIRYT--E 97 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcc------------------cCCCCCccCCCCCCcCCCHHHHHHHHhcC--C
Confidence 466788888888887776666521 11111 00145689999999999999999999975 4
Q ss_pred CCCCCCchhhhcCCHHHHHHHHhhcCC
Q psy8167 130 ADPKLMDEQMARGSADFLEVVLNEDGE 156 (167)
Q Consensus 130 ~~~~C~~C~~~f~~~~~l~~H~~~~~~ 156 (167)
.++.|..|++.|.....|..|+..+|+
T Consensus 98 ~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 98 HSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred cCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 579999999999999999999987664
No 12
>PHA02768 hypothetical protein; Provisional
Probab=99.23 E-value=3.1e-12 Score=69.19 Aligned_cols=42 Identities=17% Similarity=0.328 Sum_probs=39.1
Q ss_pred eecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCCHHHH
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSADFL 147 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l 147 (167)
|.|+.||+.|.+.+.|..|+++|+ ++++|..|++.|...+.|
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 789999999999999999999988 799999999999987665
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.92 E-value=2.1e-09 Score=84.53 Aligned_cols=97 Identities=14% Similarity=0.274 Sum_probs=71.8
Q ss_pred CCcccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhcccccc-------ccCceecccccccccC--------
Q psy8167 51 IDRIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAA-------FIDRIRCELCDKSFTR-------- 115 (167)
Q Consensus 51 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~-------l~k~~~C~~C~k~f~~-------- 115 (167)
+..+.|+.|++.|. ...|..|+ ..|. +++.|+ |++.+.. ..+. ..+++.|..|++.|..
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~-~~~H--kpv~Cp-Cg~~~~R-~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~ 524 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHM-KVFH--EPLQCP-CGVVLEK-EQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVR 524 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHH-HhcC--CCccCC-CCCCcch-hHHHhhhhccCCCCceeCCCCCCccccCccccchh
Confidence 34578999999996 67799999 4452 789998 9865432 1111 1678899999998852
Q ss_pred --hhHHHHHHHhhcCCCCCCCCchhhhcCCHHHHHHHHhhcC
Q psy8167 116 --KDSLKKHNRIFHGGADPKLMDEQMARGSADFLEVVLNEDG 155 (167)
Q Consensus 116 --~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 155 (167)
.+.|..|... .+.+++.|..||+.|..+ .|..|+-.-|
T Consensus 525 d~~s~Lt~HE~~-CG~rt~~C~~Cgk~Vrlr-dm~~H~~~~h 564 (567)
T PLN03086 525 DRLRGMSEHESI-CGSRTAPCDSCGRSVMLK-EMDIHQIAVH 564 (567)
T ss_pred hhhhhHHHHHHh-cCCcceEccccCCeeeeh-hHHHHHHHhh
Confidence 4578889888 688999999999988776 4667776544
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=98.89 E-value=5.3e-10 Score=51.94 Aligned_cols=26 Identities=19% Similarity=0.126 Sum_probs=24.0
Q ss_pred HHHHHHHhhcCCCCCCCCchhhhcCC
Q psy8167 118 SLKKHNRIFHGGADPKLMDEQMARGS 143 (167)
Q Consensus 118 ~l~~H~~~h~~~~~~~C~~C~~~f~~ 143 (167)
+|.+|+++|.+++||.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 58899999999999999999999964
No 15
>PHA02768 hypothetical protein; Provisional
Probab=98.78 E-value=4.4e-09 Score=56.95 Aligned_cols=38 Identities=13% Similarity=0.301 Sum_probs=29.5
Q ss_pred ccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhc
Q psy8167 54 IPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGA 94 (167)
Q Consensus 54 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~ 94 (167)
|.|+.||+.|.....|..|+ ++|+ ++++|..|++.|..
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~-r~H~--k~~kc~~C~k~f~~ 43 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHL-RKHN--TNLKLSNCKRISLR 43 (55)
T ss_pred cCcchhCCeeccHHHHHHHH-HhcC--CcccCCcccceecc
Confidence 79999999999999999999 6686 56555555544443
No 16
>KOG3993|consensus
Probab=98.78 E-value=1.5e-09 Score=81.07 Aligned_cols=83 Identities=18% Similarity=0.221 Sum_probs=64.6
Q ss_pred CcccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccccCceecccccccccChhHHHHHHHhhcC---
Q psy8167 52 DRIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRIFHG--- 128 (167)
Q Consensus 52 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~h~~--- 128 (167)
.-|.|+.|...|.+-..|.+|. -.. .....|+|+.|+|+|.-..+|-.|.|.|..
T Consensus 266 GdyiCqLCK~kYeD~F~LAQHr-C~R---------------------IV~vEYrCPEC~KVFsCPANLASHRRWHKPR~e 323 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQHR-CPR---------------------IVHVEYRCPECDKVFSCPANLASHRRWHKPRPE 323 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhcc-CCe---------------------eEEeeecCCcccccccCchhhhhhhcccCCchh
Confidence 3478888888888887777774 211 114458999999999999999999998742
Q ss_pred -----C-------------------------CCCCCCchhhhcCCHHHHHHHHhhcCC
Q psy8167 129 -----G-------------------------ADPKLMDEQMARGSADFLEVVLNEDGE 156 (167)
Q Consensus 129 -----~-------------------------~~~~C~~C~~~f~~~~~l~~H~~~~~~ 156 (167)
. .-|.|.+|+|.|.+...|+.|+.+|+.
T Consensus 324 aa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 324 AAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred hhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 1 127899999999999999999988774
No 17
>PHA00616 hypothetical protein
Probab=98.73 E-value=8.1e-09 Score=53.27 Aligned_cols=33 Identities=21% Similarity=0.310 Sum_probs=18.8
Q ss_pred eecccccccccChhHHHHHHHhhcCCCCCCCCc
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGGADPKLMD 136 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~ 136 (167)
|.|..||+.|..++.|.+|++.||+++++.|+.
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 455555555555555555555555555555543
No 18
>PHA00732 hypothetical protein
Probab=98.73 E-value=7.2e-09 Score=61.19 Aligned_cols=48 Identities=19% Similarity=0.135 Sum_probs=40.4
Q ss_pred ceecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCCHHHHHHHHhhcC
Q psy8167 103 RIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSADFLEVVLNEDG 155 (167)
Q Consensus 103 ~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 155 (167)
+|.|..||+.|.....|..|++.+|. ++.|..|++.|. .|..|..++.
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 47899999999999999999985343 468999999998 4789987654
No 19
>PHA00616 hypothetical protein
Probab=98.72 E-value=5.6e-09 Score=53.85 Aligned_cols=34 Identities=3% Similarity=-0.215 Sum_probs=31.3
Q ss_pred CCCCCchhhhcCCHHHHHHHHhhcCCCCCccccc
Q psy8167 131 DPKLMDEQMARGSADFLEVVLNEDGEGEPVSITV 164 (167)
Q Consensus 131 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~ 164 (167)
||+|..||+.|....+|.+|++.||+.+|..+.-
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999887653
No 20
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.72 E-value=5.5e-08 Score=76.66 Aligned_cols=99 Identities=13% Similarity=0.286 Sum_probs=59.2
Q ss_pred CcccccccccccCCHHHHHHHHHHhcCCCCcccccc--hhhhhhccccccccCceecccccccccChhHHHHHHHhhcCC
Q psy8167 52 DRIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNV--IEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRIFHGG 129 (167)
Q Consensus 52 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~--c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~h~~~ 129 (167)
..-.|..|........ |..|. ... ....-.|+. |+..|.. ..+.+.+.|+.||+.|. ...|..|+.+||
T Consensus 406 ~~V~C~NC~~~i~l~~-l~lHe-~~C-~r~~V~Cp~~~Cg~v~~r---~el~~H~~C~~Cgk~f~-~s~LekH~~~~H-- 476 (567)
T PLN03086 406 DTVECRNCKHYIPSRS-IALHE-AYC-SRHNVVCPHDGCGIVLRV---EEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH-- 476 (567)
T ss_pred CeEECCCCCCccchhH-HHHHH-hhC-CCcceeCCcccccceeec---cccccCccCCCCCCccc-hHHHHHHHHhcC--
Confidence 3457999988755544 66887 433 333445653 6666632 33344456777776664 456666766654
Q ss_pred CCCCCCchhhhcCCHHHHHHHHhhcCCCCCcc
Q psy8167 130 ADPKLMDEQMARGSADFLEVVLNEDGEGEPVS 161 (167)
Q Consensus 130 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~ 161 (167)
+++.|+ ||+.+ ....|..|++.|.+.+|..
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~ 506 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLIT 506 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCcee
Confidence 566676 76544 4566666766666665543
No 21
>PHA00733 hypothetical protein
Probab=98.61 E-value=8.2e-08 Score=62.19 Aligned_cols=54 Identities=31% Similarity=0.551 Sum_probs=45.7
Q ss_pred CCcccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccccCceecccccccccChhHHHHHHHhhcC
Q psy8167 51 IDRIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRIFHG 128 (167)
Q Consensus 51 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~h~~ 128 (167)
.++|.|..|++.|.....|..|+ ..|. . +|.|.+|++.|.....|..|+...|+
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~-r~h~--~---------------------~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHI-RYTE--H---------------------SKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHH-hcCC--c---------------------CccCCCCCCccCCHHHHHHHHHHhcC
Confidence 57899999999999999999998 5442 1 26899999999999999999998775
No 22
>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=98.46 E-value=7.3e-08 Score=44.63 Aligned_cols=25 Identities=20% Similarity=0.375 Sum_probs=20.1
Q ss_pred HHHHHHHHhcCCCCcccccchhhhhh
Q psy8167 68 SLKKHIRIFHTQNQPQHTNVIEVALG 93 (167)
Q Consensus 68 ~l~~H~~~~h~~~~~~~c~~c~~~~~ 93 (167)
+|.+|+ +.|++++||.|+.|++.|.
T Consensus 1 ~l~~H~-~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHM-RTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHH-HHHSSSSSEEESSSSEEES
T ss_pred CHHHHh-hhcCCCCCCCCCCCcCeeC
Confidence 488999 6799999987777776664
No 23
>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=98.36 E-value=8.5e-07 Score=48.67 Aligned_cols=51 Identities=20% Similarity=0.129 Sum_probs=40.4
Q ss_pred ceecccccccccChhHHHHHHHhhcCC--CCCCCCchhhhcCCHHHHHHHHhhcCC
Q psy8167 103 RIRCELCDKSFTRKDSLKKHNRIFHGG--ADPKLMDEQMARGSADFLEVVLNEDGE 156 (167)
Q Consensus 103 ~~~C~~C~k~f~~~~~l~~H~~~h~~~--~~~~C~~C~~~f~~~~~l~~H~~~~~~ 156 (167)
.|.|++||+. .....|..|....|.. +.+.|++|...+.. +|.+|+..+|+
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~--~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVTD--NLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhhh--HHHHHHHHhcC
Confidence 4889999994 5567899998776653 46999999987664 89999987663
No 24
>KOG3993|consensus
Probab=98.32 E-value=3.1e-07 Score=69.00 Aligned_cols=76 Identities=26% Similarity=0.433 Sum_probs=49.0
Q ss_pred CcccccccccccCCHHHHHHHHHHhcCCCCc-c--cccchhhhhhccc---------cccccCceecccccccccChhHH
Q psy8167 52 DRIPCTLCDKTFTRKDSLKKHIRIFHTQNQP-Q--HTNVIEVALGARA---------NAAFIDRIRCELCDKSFTRKDSL 119 (167)
Q Consensus 52 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~-~--~c~~c~~~~~~~~---------~~~l~k~~~C~~C~k~f~~~~~l 119 (167)
..|+|+.|++.|.-..+|..|.+| |.-... - .-+.-.+....+. ...-..-|.|.+|+|.|.+..-|
T Consensus 294 vEYrCPEC~KVFsCPANLASHRRW-HKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYL 372 (500)
T KOG3993|consen 294 VEYRCPECDKVFSCPANLASHRRW-HKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYL 372 (500)
T ss_pred eeecCCcccccccCchhhhhhhcc-cCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHH
Confidence 459999999999999999999977 533221 1 0000000000000 00113358999999999999999
Q ss_pred HHHHHhhcC
Q psy8167 120 KKHNRIFHG 128 (167)
Q Consensus 120 ~~H~~~h~~ 128 (167)
+.|+-+|+.
T Consensus 373 rKHqlthq~ 381 (500)
T KOG3993|consen 373 RKHQLTHQR 381 (500)
T ss_pred HHhHHhhhc
Confidence 999887753
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=98.32 E-value=1.6e-06 Score=47.54 Aligned_cols=53 Identities=26% Similarity=0.479 Sum_probs=40.1
Q ss_pred cccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccccCceecccccccccChhHHHHHHHhhcC
Q psy8167 53 RIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRIFHG 128 (167)
Q Consensus 53 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~h~~ 128 (167)
.|.|++|++ ..+...|..|....|..+. +.+.|++|...+. .+|..|+..+|+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~--------------------~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSES--------------------KNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCC--------------------CCccCCCchhhhh--hHHHHHHHHhcC
Confidence 489999999 5667889999988887653 1256777776544 489999988764
No 26
>PHA00732 hypothetical protein
Probab=98.26 E-value=7.1e-07 Score=52.73 Aligned_cols=46 Identities=33% Similarity=0.582 Sum_probs=35.5
Q ss_pred cccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccccCceecccccccccChhHHHHHHHh
Q psy8167 53 RIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRI 125 (167)
Q Consensus 53 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~ 125 (167)
+|.|..|++.|.....|..|++..|.+ +.|+.||+.|. .+..|+++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~------------------------~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL------------------------TKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC------------------------CccCCCCCEeC---Chhhhhcc
Confidence 488999999999999999999434542 35778888887 36667754
No 27
>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=98.24 E-value=9.1e-07 Score=39.65 Aligned_cols=22 Identities=45% Similarity=0.934 Sum_probs=13.7
Q ss_pred eecccccccccChhHHHHHHHh
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRI 125 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~ 125 (167)
|.|+.|++.|..+..|..|++.
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 4566666666666666666655
No 28
>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=98.14 E-value=8.1e-07 Score=39.81 Aligned_cols=23 Identities=13% Similarity=-0.148 Sum_probs=21.2
Q ss_pred CCCCchhhhcCCHHHHHHHHhhc
Q psy8167 132 PKLMDEQMARGSADFLEVVLNED 154 (167)
Q Consensus 132 ~~C~~C~~~f~~~~~l~~H~~~~ 154 (167)
|.|..|++.|.....|..|++.|
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 67999999999999999999874
No 29
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.02 E-value=5.4e-06 Score=37.24 Aligned_cols=22 Identities=41% Similarity=0.890 Sum_probs=10.7
Q ss_pred ecccccccccChhHHHHHHHhh
Q psy8167 105 RCELCDKSFTRKDSLKKHNRIF 126 (167)
Q Consensus 105 ~C~~C~k~f~~~~~l~~H~~~h 126 (167)
.|++|++.|.....|..|+++|
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHHhh
Confidence 4555555555555555555544
No 30
>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=97.99 E-value=3.1e-06 Score=38.07 Aligned_cols=24 Identities=8% Similarity=-0.236 Sum_probs=20.3
Q ss_pred CCCCchhhhcCCHHHHHHHHhhcC
Q psy8167 132 PKLMDEQMARGSADFLEVVLNEDG 155 (167)
Q Consensus 132 ~~C~~C~~~f~~~~~l~~H~~~~~ 155 (167)
|.|++|++.|.+...|..|++.||
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 579999999999999999999875
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.91 E-value=5.4e-06 Score=51.19 Aligned_cols=49 Identities=24% Similarity=0.349 Sum_probs=21.3
Q ss_pred cccccccccChhHHHHHHHhhcC-----------------------CCCCCCCchhhhcCCHHHHHHHHhhc
Q psy8167 106 CELCDKSFTRKDSLKKHNRIFHG-----------------------GADPKLMDEQMARGSADFLEVVLNED 154 (167)
Q Consensus 106 C~~C~k~f~~~~~l~~H~~~h~~-----------------------~~~~~C~~C~~~f~~~~~l~~H~~~~ 154 (167)
|..|+..|.....|..|+...|+ ...+.|..|++.|.+...|..|++.+
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -----------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 66677777777777777655443 12488999999999999999999964
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.89 E-value=9.8e-06 Score=50.01 Aligned_cols=72 Identities=25% Similarity=0.520 Sum_probs=21.8
Q ss_pred cccccccccCCHHHHHHHHHHhcCCCCcccccc-hhhhhhccccccccCceecccccccccChhHHHHHHHhh
Q psy8167 55 PCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNV-IEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRIF 126 (167)
Q Consensus 55 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~-c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~h 126 (167)
.|..|+..|.....|..|+...|.-..+-.-.. -...+.......+...+.|..|++.|.....|..||+.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 489999999999999999988785543310000 000111100111234589999999999999999999974
No 33
>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=97.89 E-value=5.6e-06 Score=38.55 Aligned_cols=23 Identities=30% Similarity=0.788 Sum_probs=11.4
Q ss_pred eecccccccccChhHHHHHHHhh
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIF 126 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h 126 (167)
|.|..|++.|.....|..|++.|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 44555555555555555554443
No 34
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.85 E-value=6.6e-06 Score=43.45 Aligned_cols=33 Identities=9% Similarity=-0.172 Sum_probs=21.8
Q ss_pred CCCCCCCCchhhhcCCHHHHHHHHhhcCCCCCc
Q psy8167 128 GGADPKLMDEQMARGSADFLEVVLNEDGEGEPV 160 (167)
Q Consensus 128 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 160 (167)
.+.|..|++|+..+....+|++|+...|+.+|.
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~~ 53 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKPG 53 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS--
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccCC
Confidence 456788888888888888888888888877764
No 35
>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=97.80 E-value=1.6e-05 Score=36.95 Aligned_cols=26 Identities=8% Similarity=-0.202 Sum_probs=23.9
Q ss_pred CCCCCchhhhcCCHHHHHHHHhhcCC
Q psy8167 131 DPKLMDEQMARGSADFLEVVLNEDGE 156 (167)
Q Consensus 131 ~~~C~~C~~~f~~~~~l~~H~~~~~~ 156 (167)
+|.|..|++.|.+...|..|++.|+.
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 57899999999999999999998864
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.58 E-value=6.1e-05 Score=55.08 Aligned_cols=69 Identities=25% Similarity=0.459 Sum_probs=43.9
Q ss_pred CCcccccc--cccccCCHHHHHHHHHHhcCCCCccccc--chhhhhhccccccccCceecccccccccChhHHHHHHH
Q psy8167 51 IDRIPCTL--CDKTFTRKDSLKKHIRIFHTQNQPQHTN--VIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNR 124 (167)
Q Consensus 51 ~~~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~~c~--~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~ 124 (167)
++||+|++ |++.|+....|.-|+..-|...+...-+ .--..| ..-.|+|+|++|+|.|.....|+-|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F-----~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIF-----SAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccc-----cccCCceeccccchhhccCccceeccc
Confidence 48999987 9999999999999983323211111111 000001 111577888888888888888877754
No 37
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.54 E-value=0.0001 Score=39.03 Aligned_cols=31 Identities=19% Similarity=0.383 Sum_probs=23.0
Q ss_pred cCceecccccccccChhHHHHHHHhhcCCCC
Q psy8167 101 IDRIRCELCDKSFTRKDSLKKHNRIFHGGAD 131 (167)
Q Consensus 101 ~k~~~C~~C~k~f~~~~~l~~H~~~h~~~~~ 131 (167)
..+-.|++|+..+.+..+|++|+.++|+.+|
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 5567899999999999999999999998775
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.52 E-value=0.0001 Score=33.43 Aligned_cols=23 Identities=9% Similarity=-0.092 Sum_probs=13.1
Q ss_pred CCCCchhhhcCCHHHHHHHHhhc
Q psy8167 132 PKLMDEQMARGSADFLEVVLNED 154 (167)
Q Consensus 132 ~~C~~C~~~f~~~~~l~~H~~~~ 154 (167)
|.|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 34555666666666666665543
No 39
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.35 E-value=5e-05 Score=55.50 Aligned_cols=53 Identities=15% Similarity=0.151 Sum_probs=44.6
Q ss_pred cCceeccc--ccccccChhHHHHHHHhhc-------------------CCCCCCCCchhhhcCCHHHHHHHHhh
Q psy8167 101 IDRIRCEL--CDKSFTRKDSLKKHNRIFH-------------------GGADPKLMDEQMARGSADFLEVVLNE 153 (167)
Q Consensus 101 ~k~~~C~~--C~k~f~~~~~l~~H~~~h~-------------------~~~~~~C~~C~~~f~~~~~l~~H~~~ 153 (167)
+|+|+|++ |.|.|.....|+-|+..-| ..|||.|.+|+|.+..-.-|+-|...
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~H 420 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKH 420 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecccc
Confidence 58899987 8999999999999976433 14899999999999999988888764
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.33 E-value=0.0002 Score=32.39 Aligned_cols=24 Identities=42% Similarity=0.737 Sum_probs=21.4
Q ss_pred eecccccccccChhHHHHHHHhhc
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFH 127 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~ 127 (167)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 479999999999999999999754
No 41
>PRK04860 hypothetical protein; Provisional
Probab=97.22 E-value=0.00019 Score=48.27 Aligned_cols=38 Identities=21% Similarity=0.368 Sum_probs=33.6
Q ss_pred ceecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCCH
Q psy8167 103 RIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSA 144 (167)
Q Consensus 103 ~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 144 (167)
+|.|. |++ ....+++|.++|.++++|.|..|+..|...
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 58998 997 777889999999999999999999988754
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.19 E-value=0.00036 Score=31.30 Aligned_cols=23 Identities=35% Similarity=0.670 Sum_probs=11.1
Q ss_pred eecccccccccChhHHHHHHHhhc
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFH 127 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~ 127 (167)
|+|+.|..... ...|.+|++.+|
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 34555555554 555555555544
No 43
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.15 E-value=0.00014 Score=32.72 Aligned_cols=24 Identities=13% Similarity=-0.042 Sum_probs=19.3
Q ss_pred CCCCchhhhcCCHHHHHHHHhhcCC
Q psy8167 132 PKLMDEQMARGSADFLEVVLNEDGE 156 (167)
Q Consensus 132 ~~C~~C~~~f~~~~~l~~H~~~~~~ 156 (167)
|+|..|++... ...|.+|++.+|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 68999999998 9999999998653
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.12 E-value=0.00019 Score=32.58 Aligned_cols=21 Identities=14% Similarity=-0.137 Sum_probs=12.8
Q ss_pred CCCchhhhcCCHHHHHHHHhh
Q psy8167 133 KLMDEQMARGSADFLEVVLNE 153 (167)
Q Consensus 133 ~C~~C~~~f~~~~~l~~H~~~ 153 (167)
.|.+|++.|.+...|+.|++.
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCcCCHHHHHHHHCc
Confidence 466666666666666666653
No 45
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.91 E-value=0.0008 Score=30.41 Aligned_cols=23 Identities=39% Similarity=0.869 Sum_probs=20.8
Q ss_pred eecccccccccChhHHHHHHHhh
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIF 126 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h 126 (167)
|.|.+|++.|.....|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 57999999999999999999863
No 46
>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=96.64 E-value=0.00046 Score=31.94 Aligned_cols=21 Identities=10% Similarity=-0.189 Sum_probs=12.5
Q ss_pred CCCCchhhhcCCHHHHHHHHh
Q psy8167 132 PKLMDEQMARGSADFLEVVLN 152 (167)
Q Consensus 132 ~~C~~C~~~f~~~~~l~~H~~ 152 (167)
|.|..|++.|.+...|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 456666666666666666554
No 47
>KOG1146|consensus
Probab=96.50 E-value=0.00073 Score=58.00 Aligned_cols=103 Identities=15% Similarity=0.132 Sum_probs=71.2
Q ss_pred CCCcccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhcc----ccccccCceecccccccccChhHHHHHHHh
Q psy8167 50 PIDRIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGAR----ANAAFIDRIRCELCDKSFTRKDSLKKHNRI 125 (167)
Q Consensus 50 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~----~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~ 125 (167)
..+.++|+.|+..|++...|..||+..|.....-.|.. +..-... ....-.++|.|..|...+..+.+|.+|+..
T Consensus 462 ~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~-gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 462 FFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKA-GQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred ccccccCCccchhhhhHHHhhhcccccccccchhHhHh-ccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 35779999999999999999999977675443312211 0000000 001116778999999999999999998764
Q ss_pred hcC-------------------------------------------CCCCCCCchhhhcCCHHHHHHHHhh
Q psy8167 126 FHG-------------------------------------------GADPKLMDEQMARGSADFLEVVLNE 153 (167)
Q Consensus 126 h~~-------------------------------------------~~~~~C~~C~~~f~~~~~l~~H~~~ 153 (167)
-.. .-.+.|.+|++--.-..+|+-|+..
T Consensus 541 ~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmts 611 (1406)
T KOG1146|consen 541 DLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTA 611 (1406)
T ss_pred HhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhcccccccc
Confidence 210 1137899999988888889889874
No 48
>PRK04860 hypothetical protein; Provisional
Probab=96.29 E-value=0.0021 Score=43.29 Aligned_cols=38 Identities=11% Similarity=0.121 Sum_probs=31.5
Q ss_pred CcccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhc
Q psy8167 52 DRIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGA 94 (167)
Q Consensus 52 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~ 94 (167)
-+|.|. |+. ....+.+|. ++|.++++|.|..|+..|..
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~-ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHN-RVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHH-HHhcCCccEECCCCCceeEE
Confidence 469998 997 677788999 88999999888888777654
No 49
>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=96.15 E-value=0.0023 Score=29.52 Aligned_cols=22 Identities=36% Similarity=0.833 Sum_probs=20.1
Q ss_pred eecccccccccChhHHHHHHHh
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRI 125 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~ 125 (167)
|.|..|++.|.....+..|++.
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 6799999999999999999875
No 50
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=95.94 E-value=0.0034 Score=33.85 Aligned_cols=29 Identities=10% Similarity=-0.138 Sum_probs=21.2
Q ss_pred cCCCCCCCCchhhhcCCHHHHHHHHhhcC
Q psy8167 127 HGGADPKLMDEQMARGSADFLEVVLNEDG 155 (167)
Q Consensus 127 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 155 (167)
.|+.-+.|+.||+.|.....+.+|+...|
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 45666778888888888888888876433
No 51
>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=95.82 E-value=0.022 Score=35.79 Aligned_cols=27 Identities=19% Similarity=0.415 Sum_probs=20.6
Q ss_pred CcccccccccccCCHHHHHHHHHHhcCC
Q psy8167 52 DRIPCTLCDKTFTRKDSLKKHIRIFHTQ 79 (167)
Q Consensus 52 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 79 (167)
+...|..|+.+..- ..+..|++..|..
T Consensus 10 ~vlIC~~C~~av~~-~~v~~HL~~~H~~ 36 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-SEVESHLRKRHHI 36 (109)
T ss_pred CEEEeCCCCcccCc-hHHHHHHHHhccc
Confidence 55789999987666 7788999756643
No 52
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.75 E-value=0.0083 Score=27.16 Aligned_cols=19 Identities=16% Similarity=-0.225 Sum_probs=9.0
Q ss_pred CCCchhhhcCCHHHHHHHHh
Q psy8167 133 KLMDEQMARGSADFLEVVLN 152 (167)
Q Consensus 133 ~C~~C~~~f~~~~~l~~H~~ 152 (167)
.|..||+.| ....|.+|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 345555555 4444444443
No 53
>KOG1146|consensus
Probab=95.56 E-value=0.012 Score=50.90 Aligned_cols=52 Identities=17% Similarity=0.275 Sum_probs=43.4
Q ss_pred CceecccccccccChhHHHHHHHhhc-------------------------CCCCCCCCchhhhcCCHHHHHHHHhh
Q psy8167 102 DRIRCELCDKSFTRKDSLKKHNRIFH-------------------------GGADPKLMDEQMARGSADFLEVVLNE 153 (167)
Q Consensus 102 k~~~C~~C~k~f~~~~~l~~H~~~h~-------------------------~~~~~~C~~C~~~f~~~~~l~~H~~~ 153 (167)
+.+.|+.|+-.|.....|..|||.-| +.++|.|..|..++....+|..|+..
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 45788888888888888888888722 24689999999999999999999963
No 54
>KOG2231|consensus
Probab=95.55 E-value=0.021 Score=46.63 Aligned_cols=100 Identities=22% Similarity=0.280 Sum_probs=62.5
Q ss_pred ccccccccccC---------------CHHHHHHHHHHhcCCCCcccccchhhh---hhc------cccccc---------
Q psy8167 54 IPCTLCDKTFT---------------RKDSLKKHIRIFHTQNQPQHTNVIEVA---LGA------RANAAF--------- 100 (167)
Q Consensus 54 ~~C~~C~~~f~---------------~~~~l~~H~~~~h~~~~~~~c~~c~~~---~~~------~~~~~l--------- 100 (167)
+.|.+|++.|. ....|..|+...|. .+.|..|... |.. +..+..
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---LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDD 176 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhh---hhccccccccceeeeeeeehehHHHHHHHHhcCCCcc
Confidence 55888888773 67899999977774 3555555432 211 000000
Q ss_pred ---cCceecccccccccChhHHHHHHHhhcCCCCCCC---CchhhhcCCHHHHHHHHhhcCCC
Q psy8167 101 ---IDRIRCELCDKSFTRKDSLKKHNRIFHGGADPKL---MDEQMARGSADFLEVVLNEDGEG 157 (167)
Q Consensus 101 ---~k~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C---~~C~~~f~~~~~l~~H~~~~~~~ 157 (167)
...-.|..|...|.....|.+|++.+|-. -.-| +.++..|.....|..|-+.+|..
T Consensus 177 ~s~rGhp~C~~C~~~fld~~el~rH~~~~h~~-chfC~~~~~~neyy~~~~dLe~HfR~~Hfl 238 (669)
T KOG2231|consen 177 ESCRGHPLCKFCHERFLDDDELYRHLRFDHEF-CHFCDYKTGQNEYYNDYDDLEEHFRKGHFL 238 (669)
T ss_pred ccccCCccchhhhhhhccHHHHHHhhccceeh-eeecCcccccchhcccchHHHHHhhhcCcc
Confidence 11125888888999998988888875522 1222 22357777888888888876643
No 55
>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=95.45 E-value=0.01 Score=29.00 Aligned_cols=23 Identities=9% Similarity=-0.224 Sum_probs=17.9
Q ss_pred CCCCCchhhhcCCHHHHHHHHhh
Q psy8167 131 DPKLMDEQMARGSADFLEVVLNE 153 (167)
Q Consensus 131 ~~~C~~C~~~f~~~~~l~~H~~~ 153 (167)
+|.|.+|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 56788888888888888888763
No 56
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=95.25 E-value=0.011 Score=31.89 Aligned_cols=32 Identities=19% Similarity=0.384 Sum_probs=27.5
Q ss_pred ccCCCCcccccccccccCCHHHHHHHHHHhcC
Q psy8167 47 PVVPIDRIPCTLCDKTFTRKDSLKKHIRIFHT 78 (167)
Q Consensus 47 ~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 78 (167)
...++..+.|+-|++.|.....+.+|....|.
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 34567789999999999999999999977774
No 57
>KOG2893|consensus
Probab=94.80 E-value=0.0095 Score=42.22 Aligned_cols=32 Identities=19% Similarity=0.387 Sum_probs=24.1
Q ss_pred cccccccccCCHHHHHHHHHHhcCCCCcccccchhhh
Q psy8167 55 PCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVA 91 (167)
Q Consensus 55 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~ 91 (167)
.|=+|++.|....-|..|++..| |+|-+|-+.
T Consensus 12 wcwycnrefddekiliqhqkakh-----fkchichkk 43 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAKH-----FKCHICHKK 43 (341)
T ss_pred eeeecccccchhhhhhhhhhhcc-----ceeeeehhh
Confidence 48899999999999999996655 445544443
No 58
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=94.35 E-value=0.072 Score=33.47 Aligned_cols=25 Identities=4% Similarity=-0.120 Sum_probs=23.0
Q ss_pred CCC----CchhhhcCCHHHHHHHHhhcCC
Q psy8167 132 PKL----MDEQMARGSADFLEVVLNEDGE 156 (167)
Q Consensus 132 ~~C----~~C~~~f~~~~~l~~H~~~~~~ 156 (167)
|.| ..|++.+.+...|++|++.+|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 9999999999999999998774
No 59
>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=93.95 E-value=0.055 Score=26.29 Aligned_cols=21 Identities=38% Similarity=0.749 Sum_probs=19.3
Q ss_pred cccccccccccCCHHHHHHHH
Q psy8167 53 RIPCTLCDKTFTRKDSLKKHI 73 (167)
Q Consensus 53 ~~~C~~C~~~f~~~~~l~~H~ 73 (167)
+|.|..|++.|.....+..|+
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~ 23 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHL 23 (35)
T ss_pred CeEccccCCccCCHHHHHHHH
Confidence 588999999999999998988
No 60
>KOG2186|consensus
Probab=93.85 E-value=0.033 Score=39.85 Aligned_cols=46 Identities=15% Similarity=0.156 Sum_probs=34.8
Q ss_pred eecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCCHHHHHHHHh
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSADFLEVVLN 152 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 152 (167)
|.|..||-...- ..+.+|+.. .....|.|..|++.|-. ..++.|..
T Consensus 4 FtCnvCgEsvKK-p~vekH~sr-Crn~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSR-CRNAYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHh-ccCCeeEEeeccccccc-chhhhhhh
Confidence 678888866544 456678877 44478999999999988 78888875
No 61
>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=93.24 E-value=0.065 Score=25.94 Aligned_cols=10 Identities=10% Similarity=-0.546 Sum_probs=5.9
Q ss_pred CCCCCCchhh
Q psy8167 130 ADPKLMDEQM 139 (167)
Q Consensus 130 ~~~~C~~C~~ 139 (167)
.+..|++|+.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 4566666653
No 62
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.07 E-value=0.016 Score=44.62 Aligned_cols=59 Identities=20% Similarity=0.158 Sum_probs=52.9
Q ss_pred CceecccccccccChhHHHHHHH--hhcCC--CCCCCC--chhhhcCCHHHHHHHHhhcCCCCCc
Q psy8167 102 DRIRCELCDKSFTRKDSLKKHNR--IFHGG--ADPKLM--DEQMARGSADFLEVVLNEDGEGEPV 160 (167)
Q Consensus 102 k~~~C~~C~k~f~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~ 160 (167)
..+.|..|...|.....+..|.+ .|.++ +++.|. .|++.|.+...+.+|...|....+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPA 352 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcc
Confidence 36789999999999999999999 78999 899999 7999999999999999988765543
No 63
>KOG2482|consensus
Probab=93.06 E-value=0.14 Score=38.36 Aligned_cols=100 Identities=19% Similarity=0.334 Sum_probs=65.0
Q ss_pred cccccccccccCCHHHHHHHHHHhcCCC-Ccccccchhhh-----------------------hhc--cc---cccc---
Q psy8167 53 RIPCTLCDKTFTRKDSLKKHIRIFHTQN-QPQHTNVIEVA-----------------------LGA--RA---NAAF--- 100 (167)
Q Consensus 53 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~-~~~~c~~c~~~-----------------------~~~--~~---~~~l--- 100 (167)
.+.|-.|.+.|..+..|..||+.....+ .| +-....+- +.. .+ +..+
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinP-knreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed 273 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINP-KNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNED 273 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCC-CccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcC
Confidence 4889999999999999999995532111 12 11111110 000 00 0000
Q ss_pred ---cCceecccccccccChhHHHHHHHhhcC---------------------------CCCCCCCchhhhcCCHHHHHHH
Q psy8167 101 ---IDRIRCELCDKSFTRKDSLKKHNRIFHG---------------------------GADPKLMDEQMARGSADFLEVV 150 (167)
Q Consensus 101 ---~k~~~C~~C~k~f~~~~~l~~H~~~h~~---------------------------~~~~~C~~C~~~f~~~~~l~~H 150 (167)
.-...|-.|.........|..||.+-|. .+...|..|.-.|-....|..|
T Consensus 274 ~a~a~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~h 353 (423)
T KOG2482|consen 274 DAEALSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIH 353 (423)
T ss_pred CCCccceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhh
Confidence 1113799999888888899999987663 1235588899999999999999
Q ss_pred Hhh
Q psy8167 151 LNE 153 (167)
Q Consensus 151 ~~~ 153 (167)
+..
T Consensus 354 m~e 356 (423)
T KOG2482|consen 354 MVE 356 (423)
T ss_pred ccc
Confidence 963
No 64
>KOG4173|consensus
Probab=92.87 E-value=0.053 Score=37.65 Aligned_cols=75 Identities=17% Similarity=0.318 Sum_probs=56.2
Q ss_pred cccccc--cccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccccCceecccccccccChhHHHHHHHhhc---
Q psy8167 53 RIPCTL--CDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRIFH--- 127 (167)
Q Consensus 53 ~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~h~--- 127 (167)
.|.|++ |-..|.....+..|....|+ ..|..|.+.|.....|..|+..-|
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~-------------------------~sCs~C~r~~Pt~hLLd~HI~E~HDs~ 133 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHG-------------------------NSCSFCKRAFPTGHLLDAHILEWHDSL 133 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhccc-------------------------chhHHHHHhCCchhhhhHHHHHHHHHH
Confidence 366776 66777777777777633332 258999999999999988876544
Q ss_pred -------CCCCCCCCc--hhhhcCCHHHHHHHHh
Q psy8167 128 -------GGADPKLMD--EQMARGSADFLEVVLN 152 (167)
Q Consensus 128 -------~~~~~~C~~--C~~~f~~~~~l~~H~~ 152 (167)
|...|+|-+ |+-.|.+...-+.|+-
T Consensus 134 Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I 167 (253)
T KOG4173|consen 134 FQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMI 167 (253)
T ss_pred HHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHH
Confidence 345688987 9999999999888884
No 65
>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=92.44 E-value=0.068 Score=33.57 Aligned_cols=30 Identities=17% Similarity=0.275 Sum_probs=17.6
Q ss_pred ccccchhhhhhccccccccCceecccccccccCh
Q psy8167 83 QHTNVIEVALGARANAAFIDRIRCELCDKSFTRK 116 (167)
Q Consensus 83 ~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~ 116 (167)
..|+.||..|.. ... .+..|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYD--Lnk--~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD--LNK--DPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc--CCC--CCccCCCCCCccCcc
Confidence 456666666665 332 445577777666554
No 66
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=92.05 E-value=0.087 Score=26.23 Aligned_cols=33 Identities=21% Similarity=0.371 Sum_probs=19.6
Q ss_pred eecccccccccChhHHHHHHHhhcCCCCCCCCchhhhc
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMAR 141 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 141 (167)
..|+.|+..|.-... ++..++...+|+.|+..|
T Consensus 3 i~CP~C~~~f~v~~~-----~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDD-----KLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHH-----HcccCCcEEECCCCCcEe
Confidence 357777777666544 112344467777777666
No 67
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=91.66 E-value=0.029 Score=39.77 Aligned_cols=43 Identities=21% Similarity=0.258 Sum_probs=26.6
Q ss_pred CceecccccccccChhHHHHHHHhhc----------CCCC-----CCCCchhhhcCCH
Q psy8167 102 DRIRCELCDKSFTRKDSLKKHNRIFH----------GGAD-----PKLMDEQMARGSA 144 (167)
Q Consensus 102 k~~~C~~C~k~f~~~~~l~~H~~~h~----------~~~~-----~~C~~C~~~f~~~ 144 (167)
+.+.|++|++.|..........+.-. +.-| ..|+.||.+|...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 45678888887777655444443211 1112 5699999988755
No 68
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=91.34 E-value=0.13 Score=25.44 Aligned_cols=33 Identities=18% Similarity=0.248 Sum_probs=20.6
Q ss_pred eecccccccccChhHHHHHHHhhcCCCCCCCCchhhhc
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMAR 141 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 141 (167)
+.|+.|+..|.-.... +-..+...+|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHH-----CCCCCcEEECCCCCCEe
Confidence 4677777777766552 22334467777777766
No 69
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.13 E-value=0.11 Score=40.09 Aligned_cols=108 Identities=18% Similarity=0.181 Sum_probs=71.6
Q ss_pred CcccccccccccCCHHHHHHHHHH-hcCCC--Cccccc--chhhhhhccccccc--------------------------
Q psy8167 52 DRIPCTLCDKTFTRKDSLKKHIRI-FHTQN--QPQHTN--VIEVALGARANAAF-------------------------- 100 (167)
Q Consensus 52 ~~~~C~~C~~~f~~~~~l~~H~~~-~h~~~--~~~~c~--~c~~~~~~~~~~~l-------------------------- 100 (167)
.++.|..|...|.....|..|.+. .|.++ +++.|+ .|++.|.. ...+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSR--NDALKRHILLHTSISPAKEKLLNSSSKFSP 365 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccc--cccccCCcccccCCCccccccccCcccccc
Confidence 368889999999999999999842 78888 888888 78888866 3322
Q ss_pred ------------------cCceec--ccccccccChhHHHHHHHhhcCCC--CCCCCchhhhcCCHHHHHHHHhhcCCCC
Q psy8167 101 ------------------IDRIRC--ELCDKSFTRKDSLKKHNRIFHGGA--DPKLMDEQMARGSADFLEVVLNEDGEGE 158 (167)
Q Consensus 101 ------------------~k~~~C--~~C~k~f~~~~~l~~H~~~h~~~~--~~~C~~C~~~f~~~~~l~~H~~~~~~~~ 158 (167)
.+.+.+ ..|...+.....+..|...|.... .+.+..|.+.|.....+..|++.+....
T Consensus 366 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 (467)
T COG5048 366 LLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHA 445 (467)
T ss_pred ccCCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccCC
Confidence 000111 224445555555555555544444 4556678888888888888888776555
Q ss_pred Ccc
Q psy8167 159 PVS 161 (167)
Q Consensus 159 ~~~ 161 (167)
++.
T Consensus 446 ~~~ 448 (467)
T COG5048 446 PLL 448 (467)
T ss_pred cee
Confidence 443
No 70
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.78 E-value=0.13 Score=26.89 Aligned_cols=9 Identities=33% Similarity=1.040 Sum_probs=4.9
Q ss_pred eeccccccc
Q psy8167 104 IRCELCDKS 112 (167)
Q Consensus 104 ~~C~~C~k~ 112 (167)
++|+.||..
T Consensus 22 ~~Cp~CG~~ 30 (46)
T PRK00398 22 VRCPYCGYR 30 (46)
T ss_pred eECCCCCCe
Confidence 456666543
No 71
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.63 E-value=0.15 Score=27.98 Aligned_cols=31 Identities=10% Similarity=0.084 Sum_probs=16.2
Q ss_pred eecccccccccChhHHHHHHHhhcCCCCCCCCchhh
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQM 139 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 139 (167)
|.|+.||..-..+..--+ .-..+|.|+.||.
T Consensus 28 F~CPnCGe~~I~Rc~~CR-----k~g~~Y~Cp~CGF 58 (61)
T COG2888 28 FPCPNCGEVEIYRCAKCR-----KLGNPYRCPKCGF 58 (61)
T ss_pred eeCCCCCceeeehhhhHH-----HcCCceECCCcCc
Confidence 556666644444332111 1234788888875
No 72
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=90.36 E-value=0.38 Score=36.26 Aligned_cols=78 Identities=19% Similarity=0.171 Sum_probs=46.5
Q ss_pred cccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccccCceecccccccccChhHHHHHHHhhcCCCCCCC
Q psy8167 55 PCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRIFHGGADPKL 134 (167)
Q Consensus 55 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C 134 (167)
.|..|...|-....|..|++..| -.|-+|.+.-.. .. .-|.....|..|.+. .-|.|
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~H-----E~ChICD~v~p~--~~------------QYFK~Y~~Le~HF~~----~hy~c 278 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRH-----EACHICDMVGPI--RY------------QYFKSYEDLEAHFRN----AHYCC 278 (493)
T ss_pred hhhhccceecChHHHHHHHHhhh-----hhhhhhhccCcc--ch------------hhhhCHHHHHHHhhc----CceEE
Confidence 59999999999999999997766 345555443211 00 134444555555443 23555
Q ss_pred Cc--h----hhhcCCHHHHHHHHhhcC
Q psy8167 135 MD--E----QMARGSADFLEVVLNEDG 155 (167)
Q Consensus 135 ~~--C----~~~f~~~~~l~~H~~~~~ 155 (167)
.. | -..|.....|..|+...|
T Consensus 279 t~qtc~~~k~~vf~~~~el~~h~~~~h 305 (493)
T COG5236 279 TFQTCRVGKCYVFPYHTELLEHLTRFH 305 (493)
T ss_pred EEEEEecCcEEEeccHHHHHHHHHHHh
Confidence 53 3 145666667777765433
No 73
>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=90.14 E-value=0.15 Score=25.40 Aligned_cols=33 Identities=24% Similarity=0.261 Sum_probs=16.4
Q ss_pred eecccccccccChhHHHHHHHhhcCCCCCCCCchhhhc
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMAR 141 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 141 (167)
+.|+.|+..|.-..... ...+....|+.|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~-----~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-----GANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHc-----CCCCCEEECCCCCCEE
Confidence 45666666655543321 1112245666666555
No 74
>KOG2893|consensus
Probab=89.91 E-value=0.058 Score=38.38 Aligned_cols=41 Identities=20% Similarity=0.216 Sum_probs=33.1
Q ss_pred cccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCCHHHHHHH
Q psy8167 106 CELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSADFLEVV 150 (167)
Q Consensus 106 C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H 150 (167)
|=+|++.|.....|.+|++. +-|+|.+|-|...+.--|.-|
T Consensus 13 cwycnrefddekiliqhqka----khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceee
Confidence 78899999999999999876 679999998776665555444
No 75
>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=89.89 E-value=0.17 Score=23.09 Aligned_cols=9 Identities=33% Similarity=0.962 Sum_probs=5.0
Q ss_pred ccccccccc
Q psy8167 106 CELCDKSFT 114 (167)
Q Consensus 106 C~~C~k~f~ 114 (167)
|+.||..|.
T Consensus 17 Cp~CG~~F~ 25 (26)
T PF10571_consen 17 CPHCGYDFE 25 (26)
T ss_pred CCCCCCCCc
Confidence 555655553
No 76
>KOG2231|consensus
Probab=89.75 E-value=0.43 Score=39.32 Aligned_cols=53 Identities=25% Similarity=0.465 Sum_probs=33.6
Q ss_pred cccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccccCceecccccccccChhHHHHHHHhhc
Q psy8167 55 PCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRIFH 127 (167)
Q Consensus 55 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~h~ 127 (167)
.|..|...|.....|.+|++..| |.|..|.+. ..++.-|.....|..|-+.+|
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h-----~~chfC~~~---------------~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH-----EFCHFCDYK---------------TGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce-----eheeecCcc---------------cccchhcccchHHHHHhhhcC
Confidence 58888888888888888885544 445554321 112345666677777777655
No 77
>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=89.36 E-value=0.28 Score=23.88 Aligned_cols=9 Identities=11% Similarity=-0.382 Sum_probs=5.3
Q ss_pred CCCCCchhh
Q psy8167 131 DPKLMDEQM 139 (167)
Q Consensus 131 ~~~C~~C~~ 139 (167)
|..|++|+.
T Consensus 18 p~~CP~Cg~ 26 (34)
T cd00729 18 PEKCPICGA 26 (34)
T ss_pred CCcCcCCCC
Confidence 456666654
No 78
>KOG2482|consensus
Probab=89.34 E-value=0.37 Score=36.23 Aligned_cols=70 Identities=26% Similarity=0.524 Sum_probs=41.1
Q ss_pred ccccccccccC-CHHHHHHHHHHhcCCC--CcccccchhhhhhccccccccCceecccccccccChhHHHHHHHh
Q psy8167 54 IPCTLCDKTFT-RKDSLKKHIRIFHTQN--QPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRI 125 (167)
Q Consensus 54 ~~C~~C~~~f~-~~~~l~~H~~~~h~~~--~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~ 125 (167)
..|-.|+..+. .++....|+...|.-. .|-.--.+.+.... ...-...+.|-.|.+.|..+..|+.||+.
T Consensus 145 lqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLeh--LkekL~r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 145 LQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEH--LKEKLERLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred eEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHH--HHHHHhhheeeeeccccCCcHHHHHHHHh
Confidence 56888887655 6677778876666322 11111111111100 00002346899999999999999999985
No 79
>PHA00626 hypothetical protein
Probab=88.83 E-value=0.075 Score=28.78 Aligned_cols=14 Identities=14% Similarity=-0.055 Sum_probs=8.9
Q ss_pred CCCCCchhhhcCCH
Q psy8167 131 DPKLMDEQMARGSA 144 (167)
Q Consensus 131 ~~~C~~C~~~f~~~ 144 (167)
.|+|..||+.|..-
T Consensus 23 rYkCkdCGY~ft~~ 36 (59)
T PHA00626 23 DYVCCDCGYNDSKD 36 (59)
T ss_pred ceEcCCCCCeechh
Confidence 56666676666544
No 80
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.35 E-value=0.77 Score=28.96 Aligned_cols=22 Identities=18% Similarity=0.434 Sum_probs=17.7
Q ss_pred CcccccccccccCCHHHHHHHH
Q psy8167 52 DRIPCTLCDKTFTRKDSLKKHI 73 (167)
Q Consensus 52 ~~~~C~~C~~~f~~~~~l~~H~ 73 (167)
-|..|+.||-.......|.+-.
T Consensus 14 LP~~CpiCgLtLVss~HLARSy 35 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSY 35 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhh
Confidence 4577999999888888887765
No 81
>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=88.30 E-value=0.096 Score=37.01 Aligned_cols=23 Identities=4% Similarity=-0.158 Sum_probs=10.6
Q ss_pred CCCCCchhhhcCCHHHHHHHHhh
Q psy8167 131 DPKLMDEQMARGSADFLEVVLNE 153 (167)
Q Consensus 131 ~~~C~~C~~~f~~~~~l~~H~~~ 153 (167)
+|.|..|+|.|......+.|+..
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHH
T ss_pred EECCCCCCcccCChHHHHHHHhh
Confidence 35555555555555555555543
No 82
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=88.09 E-value=0.13 Score=35.34 Aligned_cols=29 Identities=14% Similarity=0.192 Sum_probs=14.8
Q ss_pred cccccchhhhhhccccccccCceeccccccc
Q psy8167 82 PQHTNVIEVALGARANAAFIDRIRCELCDKS 112 (167)
Q Consensus 82 ~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~ 112 (167)
-|.|+.|+..|.. ..++...|.|+.||..
T Consensus 117 ~Y~Cp~C~~rytf--~eA~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 117 FFFCPNCHIRFTF--DEAMEYGFRCPQCGEM 145 (178)
T ss_pred EEECCCCCcEEeH--HHHhhcCCcCCCCCCC
Confidence 3555555555554 3344444555555543
No 83
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=87.76 E-value=0.48 Score=34.02 Aligned_cols=12 Identities=25% Similarity=0.684 Sum_probs=8.8
Q ss_pred CCCccccccccc
Q psy8167 50 PIDRIPCTLCDK 61 (167)
Q Consensus 50 ~~~~~~C~~C~~ 61 (167)
..+.|.|..|..
T Consensus 109 ~drqFaC~~Cd~ 120 (278)
T PF15135_consen 109 VDRQFACSSCDH 120 (278)
T ss_pred cceeeeccccch
Confidence 346788888875
No 84
>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=87.69 E-value=0.16 Score=36.64 Aligned_cols=89 Identities=13% Similarity=0.203 Sum_probs=50.5
Q ss_pred CCCcccccccccccCCHHHHHHHHHHhc-CCCCcccccchhhhhhccccccccCceecccccccccChhHHHHHHHh---
Q psy8167 50 PIDRIPCTLCDKTFTRKDSLKKHIRIFH-TQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRI--- 125 (167)
Q Consensus 50 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h-~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~--- 125 (167)
+.+.|+|.+|+...-....| .|+..-. .....|+|..|.+.- + |.|..|.-.|-.. |.+.
T Consensus 139 GGrif~CsfC~~flCEDDQF-EHQAsCQvLe~E~~KC~SCNrlG-q---------~sCLRCK~cfCdd-----HvrrKg~ 202 (314)
T PF06524_consen 139 GGRIFKCSFCDNFLCEDDQF-EHQASCQVLESETFKCQSCNRLG-Q---------YSCLRCKICFCDD-----HVRRKGF 202 (314)
T ss_pred CCeEEEeecCCCeeeccchh-hhhhhhhhhhccccccccccccc-c---------hhhhheeeeehhh-----hhhhccc
Confidence 34678888888655555544 6662211 223467777776432 2 3455554444332 3332
Q ss_pred -hcCCCCCCCCchhhhcCCHHHHHHHHhhc
Q psy8167 126 -FHGGADPKLMDEQMARGSADFLEVVLNED 154 (167)
Q Consensus 126 -h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 154 (167)
-...+++.|+.|++-...-..|..-.|.|
T Consensus 203 ky~k~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 203 KYEKGKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred ccccCCCCCCCCCCCcccccccceeeeecc
Confidence 13457888999988777777665555544
No 85
>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=87.56 E-value=0.17 Score=27.08 Aligned_cols=29 Identities=14% Similarity=0.244 Sum_probs=16.1
Q ss_pred eecccccccccChhHHHHHHHhhcCCCCCCCCchhh
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQM 139 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 139 (167)
|+|..||..|.....+. .+....|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~-------~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMS-------DDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecC-------CCCCCCCCCCCC
Confidence 66777777666442211 134556777765
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=87.29 E-value=0.34 Score=32.64 Aligned_cols=29 Identities=17% Similarity=0.111 Sum_probs=15.2
Q ss_pred cccccchhhhhhccccccccCceeccccccc
Q psy8167 82 PQHTNVIEVALGARANAAFIDRIRCELCDKS 112 (167)
Q Consensus 82 ~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~ 112 (167)
-|.|+.|+..|.. .-++...|.|+.||..
T Consensus 109 ~Y~Cp~c~~r~tf--~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 109 FFICPNMCVRFTF--NEAMELNFTCPRCGAM 137 (158)
T ss_pred eEECCCCCcEeeH--HHHHHcCCcCCCCCCE
Confidence 4555555555555 4444444566666543
No 87
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=87.06 E-value=0.38 Score=32.60 Aligned_cols=23 Identities=17% Similarity=0.174 Sum_probs=15.5
Q ss_pred ceecccccccccChhHHHHHHHhhcCCCCCCCCchh
Q psy8167 103 RIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQ 138 (167)
Q Consensus 103 ~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~ 138 (167)
.|.|++||.. +-++.|-+|++||
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCC
Confidence 4778888743 3456677788886
No 88
>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=86.09 E-value=0.28 Score=25.09 Aligned_cols=13 Identities=38% Similarity=0.807 Sum_probs=7.0
Q ss_pred eecccccccccCh
Q psy8167 104 IRCELCDKSFTRK 116 (167)
Q Consensus 104 ~~C~~C~k~f~~~ 116 (167)
|+|..||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 6 YRCEECGHEFEVL 18 (42)
T ss_pred EEeCCCCCEEEEE
Confidence 4555555555543
No 89
>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=86.04 E-value=0.79 Score=23.56 Aligned_cols=27 Identities=26% Similarity=0.604 Sum_probs=17.5
Q ss_pred CCcccccccccccCCH----HHHHHHHHHhc
Q psy8167 51 IDRIPCTLCDKTFTRK----DSLKKHIRIFH 77 (167)
Q Consensus 51 ~~~~~C~~C~~~f~~~----~~l~~H~~~~h 77 (167)
.....|..|++.+... ..|.+|++..|
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 3567899999988875 78888885544
No 90
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=85.93 E-value=0.72 Score=24.50 Aligned_cols=21 Identities=33% Similarity=0.893 Sum_probs=16.0
Q ss_pred eecccccccccCh-----hHHHHHHH
Q psy8167 104 IRCELCDKSFTRK-----DSLKKHNR 124 (167)
Q Consensus 104 ~~C~~C~k~f~~~-----~~l~~H~~ 124 (167)
-.|..|++.+... ++|.+|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 3688888888665 58888887
No 91
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=85.80 E-value=1.6 Score=33.08 Aligned_cols=92 Identities=20% Similarity=0.234 Sum_probs=62.1
Q ss_pred ccccc--cccccCCHHHHHHHHHHhcCCCCcccccchhh---hhhccccccc---------------cCce----ecccc
Q psy8167 54 IPCTL--CDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEV---ALGARANAAF---------------IDRI----RCELC 109 (167)
Q Consensus 54 ~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~---~~~~~~~~~l---------------~k~~----~C~~C 109 (167)
|.|+. |.........|..|.+..|. -+-|..|-. .|.. ...| +..| .|..|
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~---~~~C~~C~~nKk~F~~--E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC 226 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHG---FVLCSECIGNKKDFWN--EIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFC 226 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC---cEEhHhhhcCcccCcc--ceeeeecccccccccCCccccCcCCCchhhhc
Confidence 77874 77777778889999866663 355655543 2222 1111 1112 59999
Q ss_pred cccccChhHHHHHHHhhcCCCCCCCCchh-------hhcCCHHHHHHHHhhc
Q psy8167 110 DKSFTRKDSLKKHNRIFHGGADPKLMDEQ-------MARGSADFLEVVLNED 154 (167)
Q Consensus 110 ~k~f~~~~~l~~H~~~h~~~~~~~C~~C~-------~~f~~~~~l~~H~~~~ 154 (167)
.+.|-....|..|+|..| -.|-+|+ +.|....+|..|-+.-
T Consensus 227 ~~~FYdDDEL~~HcR~~H----E~ChICD~v~p~~~QYFK~Y~~Le~HF~~~ 274 (493)
T COG5236 227 KIYFYDDDELRRHCRLRH----EACHICDMVGPIRYQYFKSYEDLEAHFRNA 274 (493)
T ss_pred cceecChHHHHHHHHhhh----hhhhhhhccCccchhhhhCHHHHHHHhhcC
Confidence 999999999999998744 2455664 5788999999998743
No 92
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=85.74 E-value=0.33 Score=31.61 Aligned_cols=23 Identities=43% Similarity=0.700 Sum_probs=13.2
Q ss_pred eecccccccccChhHHHHHHHhhcCC
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGG 129 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~ 129 (167)
..|-+||+.|... .+|++.|||.
T Consensus 73 i~clecGk~~k~L---krHL~~~~gl 95 (132)
T PF05443_consen 73 IICLECGKKFKTL---KRHLRTHHGL 95 (132)
T ss_dssp EE-TBT--EESBH---HHHHHHTT-S
T ss_pred eEEccCCcccchH---HHHHHHccCC
Confidence 4677788777663 6777777665
No 93
>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=85.58 E-value=0.42 Score=30.71 Aligned_cols=30 Identities=3% Similarity=-0.120 Sum_probs=15.5
Q ss_pred ccccchhhhhhccccccccCceecccccccccCh
Q psy8167 83 QHTNVIEVALGARANAAFIDRIRCELCDKSFTRK 116 (167)
Q Consensus 83 ~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~ 116 (167)
..|+.||..|.. .. ..+..|+.||..|...
T Consensus 10 r~Cp~cg~kFYD--Ln--k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYD--LN--RRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccc--cC--CCCccCCCcCCccCcc
Confidence 455566655554 22 1334566666655444
No 94
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=84.98 E-value=0.29 Score=32.56 Aligned_cols=13 Identities=23% Similarity=0.639 Sum_probs=7.2
Q ss_pred eecccccccccCh
Q psy8167 104 IRCELCDKSFTRK 116 (167)
Q Consensus 104 ~~C~~C~k~f~~~ 116 (167)
|.|+.|+..|...
T Consensus 100 Y~Cp~C~~~y~~~ 112 (147)
T smart00531 100 YKCPNCQSKYTFL 112 (147)
T ss_pred EECcCCCCEeeHH
Confidence 5566666555543
No 95
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=84.88 E-value=0.41 Score=32.47 Aligned_cols=23 Identities=13% Similarity=0.114 Sum_probs=16.4
Q ss_pred cccccchhhhhhccccccccCceeccccc
Q psy8167 82 PQHTNVIEVALGARANAAFIDRIRCELCD 110 (167)
Q Consensus 82 ~~~c~~c~~~~~~~~~~~l~k~~~C~~C~ 110 (167)
.|.|++||..+.. +-|-.|++||
T Consensus 134 ~~vC~vCGy~~~g------e~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTHEG------EAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCcccC------CCCCcCCCCC
Confidence 4777777777665 5556788887
No 96
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=84.46 E-value=0.49 Score=26.07 Aligned_cols=10 Identities=0% Similarity=-0.323 Sum_probs=7.0
Q ss_pred CCCCCCchhh
Q psy8167 130 ADPKLMDEQM 139 (167)
Q Consensus 130 ~~~~C~~C~~ 139 (167)
.+|.|+.||.
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 4777777775
No 97
>KOG2785|consensus
Probab=83.84 E-value=1.2 Score=34.01 Aligned_cols=50 Identities=18% Similarity=0.125 Sum_probs=43.3
Q ss_pred eecccccccccChhHHHHHHHhhcCC-----------------------CCCCCCchh---hhcCCHHHHHHHHhh
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGG-----------------------ADPKLMDEQ---MARGSADFLEVVLNE 153 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~ 153 (167)
-.|-.|++.+........||..+|+- .-+-|-.|+ +.|.+-...+.||..
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 46999999999999999999999872 236788898 999999999999973
No 98
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=83.82 E-value=0.46 Score=31.88 Aligned_cols=12 Identities=0% Similarity=-0.114 Sum_probs=6.3
Q ss_pred ccccchhhhhhc
Q psy8167 83 QHTNVIEVALGA 94 (167)
Q Consensus 83 ~~c~~c~~~~~~ 94 (167)
+.|+.||++|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 455555555544
No 99
>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=83.68 E-value=0.69 Score=30.16 Aligned_cols=31 Identities=6% Similarity=-0.187 Sum_probs=19.8
Q ss_pred cCCCCCCCCchhhhcCCHHHHHHHHhhcCCCCCc
Q psy8167 127 HGGADPKLMDEQMARGSADFLEVVLNEDGEGEPV 160 (167)
Q Consensus 127 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 160 (167)
..+....|-+||+.|..- ++|++.||+..|.
T Consensus 68 I~~d~i~clecGk~~k~L---krHL~~~~gltp~ 98 (132)
T PF05443_consen 68 ITPDYIICLECGKKFKTL---KRHLRTHHGLTPE 98 (132)
T ss_dssp B-SS-EE-TBT--EESBH---HHHHHHTT-S-HH
T ss_pred cccCeeEEccCCcccchH---HHHHHHccCCCHH
Confidence 455678899999999885 9999999876654
No 100
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=83.60 E-value=0.53 Score=28.29 Aligned_cols=27 Identities=15% Similarity=0.354 Sum_probs=13.2
Q ss_pred CcccccchhhhhhccccccccCceeccccc
Q psy8167 81 QPQHTNVIEVALGARANAAFIDRIRCELCD 110 (167)
Q Consensus 81 ~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~ 110 (167)
+|-.|..||+.|.. ..+.++-+|+.|.
T Consensus 57 ~Pa~CkkCGfef~~---~~ik~pSRCP~CK 83 (97)
T COG3357 57 RPARCKKCGFEFRD---DKIKKPSRCPKCK 83 (97)
T ss_pred cChhhcccCccccc---cccCCcccCCcch
Confidence 35556666555544 2233344555553
No 101
>KOG2785|consensus
Probab=83.49 E-value=1.5 Score=33.60 Aligned_cols=73 Identities=19% Similarity=0.248 Sum_probs=46.4
Q ss_pred CCcccccccccccCCHHHHHHHHHHhcCCCCc---ccccchhhhhhccccccccCceeccccc---ccccChhHHHHHHH
Q psy8167 51 IDRIPCTLCDKTFTRKDSLKKHIRIFHTQNQP---QHTNVIEVALGARANAAFIDRIRCELCD---KSFTRKDSLKKHNR 124 (167)
Q Consensus 51 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~---~~c~~c~~~~~~~~~~~l~k~~~C~~C~---k~f~~~~~l~~H~~ 124 (167)
..|--|-.|+..+.....-..||...|.---| |--..=|-.-.- ...+...|.|-.|. +.|......+.||.
T Consensus 164 ~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YL--geKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 164 LIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYL--GEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred cCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHH--HHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 34567999999999999999999665532111 111111100000 11115557788888 99999999999997
Q ss_pred h
Q psy8167 125 I 125 (167)
Q Consensus 125 ~ 125 (167)
-
T Consensus 242 ~ 242 (390)
T KOG2785|consen 242 D 242 (390)
T ss_pred h
Confidence 4
No 102
>KOG2186|consensus
Probab=83.07 E-value=0.68 Score=33.38 Aligned_cols=38 Identities=11% Similarity=0.237 Sum_probs=23.4
Q ss_pred cccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhh
Q psy8167 53 RIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALG 93 (167)
Q Consensus 53 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~ 93 (167)
.|.|..||....-. .+.+|+.+.+. .-|.|..|+..|.
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCrn--~~fSCIDC~k~F~ 40 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCRN--AYFSCIDCGKTFE 40 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhccC--CeeEEeecccccc
Confidence 58899999876544 46679855442 3444544444443
No 103
>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=82.96 E-value=0.53 Score=23.62 Aligned_cols=12 Identities=42% Similarity=0.935 Sum_probs=6.7
Q ss_pred eecccccccccC
Q psy8167 104 IRCELCDKSFTR 115 (167)
Q Consensus 104 ~~C~~C~k~f~~ 115 (167)
|+|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (41)
T smart00834 6 YRCEDCGHTFEV 17 (41)
T ss_pred EEcCCCCCEEEE
Confidence 456666655544
No 104
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=82.84 E-value=0.15 Score=36.20 Aligned_cols=22 Identities=32% Similarity=0.703 Sum_probs=15.3
Q ss_pred CcccccccccccCCHHHHHHHH
Q psy8167 52 DRIPCTLCDKTFTRKDSLKKHI 73 (167)
Q Consensus 52 ~~~~C~~C~~~f~~~~~l~~H~ 73 (167)
+...|++|+..|....-.....
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~ 25 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKI 25 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCc
Confidence 4578999999888775443333
No 105
>KOG4167|consensus
Probab=82.63 E-value=0.34 Score=40.06 Aligned_cols=27 Identities=22% Similarity=0.406 Sum_probs=23.8
Q ss_pred cCceecccccccccChhHHHHHHHhhc
Q psy8167 101 IDRIRCELCDKSFTRKDSLKKHNRIFH 127 (167)
Q Consensus 101 ~k~~~C~~C~k~f~~~~~l~~H~~~h~ 127 (167)
..-|.|..|+|.|..-..+..||++|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 344899999999999999999999975
No 106
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=82.48 E-value=0.86 Score=23.62 Aligned_cols=11 Identities=0% Similarity=-0.408 Sum_probs=5.0
Q ss_pred ccccchhhhhh
Q psy8167 83 QHTNVIEVALG 93 (167)
Q Consensus 83 ~~c~~c~~~~~ 93 (167)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 44444444443
No 107
>PF14353 CpXC: CpXC protein
Probab=82.30 E-value=0.63 Score=30.07 Aligned_cols=11 Identities=27% Similarity=0.776 Sum_probs=6.6
Q ss_pred cccccccccCC
Q psy8167 55 PCTLCDKTFTR 65 (167)
Q Consensus 55 ~C~~C~~~f~~ 65 (167)
.|+.|+..|..
T Consensus 3 tCP~C~~~~~~ 13 (128)
T PF14353_consen 3 TCPHCGHEFEF 13 (128)
T ss_pred CCCCCCCeeEE
Confidence 46666665543
No 108
>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=82.29 E-value=1.3 Score=20.07 Aligned_cols=19 Identities=16% Similarity=0.546 Sum_probs=13.5
Q ss_pred ecccccccccChhHHHHHHH
Q psy8167 105 RCELCDKSFTRKDSLKKHNR 124 (167)
Q Consensus 105 ~C~~C~k~f~~~~~l~~H~~ 124 (167)
.|++|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 578888777 5567777765
No 109
>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=82.16 E-value=0.65 Score=24.82 Aligned_cols=9 Identities=33% Similarity=0.925 Sum_probs=4.7
Q ss_pred Cceeccccc
Q psy8167 102 DRIRCELCD 110 (167)
Q Consensus 102 k~~~C~~C~ 110 (167)
..|.|++|+
T Consensus 33 ~~w~CP~C~ 41 (50)
T cd00730 33 DDWVCPVCG 41 (50)
T ss_pred CCCCCCCCC
Confidence 335555555
No 110
>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=82.02 E-value=0.98 Score=32.02 Aligned_cols=31 Identities=32% Similarity=0.568 Sum_probs=23.9
Q ss_pred CCCcccccccccccCCHHHHHHHHHHhcCCC
Q psy8167 50 PIDRIPCTLCDKTFTRKDSLKKHIRIFHTQN 80 (167)
Q Consensus 50 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 80 (167)
.+..|.|..|+|.|.-......|+...|...
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 3456999999999999999999998888653
No 111
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=80.62 E-value=0.8 Score=24.29 Aligned_cols=7 Identities=57% Similarity=1.488 Sum_probs=3.7
Q ss_pred eeccccc
Q psy8167 104 IRCELCD 110 (167)
Q Consensus 104 ~~C~~C~ 110 (167)
.+|+.||
T Consensus 25 irCp~Cg 31 (49)
T COG1996 25 IRCPYCG 31 (49)
T ss_pred eeCCCCC
Confidence 4555555
No 112
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=79.15 E-value=1.4 Score=29.33 Aligned_cols=33 Identities=6% Similarity=0.079 Sum_probs=16.4
Q ss_pred cccccchhhhhhccccccc---cCceeccccccccc
Q psy8167 82 PQHTNVIEVALGARANAAF---IDRIRCELCDKSFT 114 (167)
Q Consensus 82 ~~~c~~c~~~~~~~~~~~l---~k~~~C~~C~k~f~ 114 (167)
-|.|+.|+..|.......+ ...|.|+.||....
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELE 134 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEE
Confidence 4566666655554111111 22277777776543
No 113
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=78.53 E-value=1.2 Score=26.58 Aligned_cols=12 Identities=25% Similarity=0.794 Sum_probs=6.6
Q ss_pred eecccccccccC
Q psy8167 104 IRCELCDKSFTR 115 (167)
Q Consensus 104 ~~C~~C~k~f~~ 115 (167)
+.|..||..|..
T Consensus 54 W~C~kCg~~fAG 65 (89)
T COG1997 54 WKCRKCGAKFAG 65 (89)
T ss_pred EEcCCCCCeecc
Confidence 456666655543
No 114
>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=77.95 E-value=1.5 Score=29.57 Aligned_cols=33 Identities=9% Similarity=-0.077 Sum_probs=26.4
Q ss_pred cCceecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcC
Q psy8167 101 IDRIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARG 142 (167)
Q Consensus 101 ~k~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 142 (167)
...|.|+.|+..|+....+. .-|.|+.||....
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEee
Confidence 45588999999999888875 2799999986543
No 115
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=77.18 E-value=1.4 Score=30.33 Aligned_cols=34 Identities=12% Similarity=0.054 Sum_probs=26.6
Q ss_pred cCceecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCC
Q psy8167 101 IDRIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGS 143 (167)
Q Consensus 101 ~k~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 143 (167)
...|.|+.|+..|.....+. .-|.|+.||-....
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 45588999999998887653 37999999876544
No 116
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=76.66 E-value=0.58 Score=27.06 Aligned_cols=17 Identities=0% Similarity=-0.246 Sum_probs=9.7
Q ss_pred CCCCCCC--chhhhcCCHH
Q psy8167 129 GADPKLM--DEQMARGSAD 145 (167)
Q Consensus 129 ~~~~~C~--~C~~~f~~~~ 145 (167)
+.-++|. .||..|....
T Consensus 25 ~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 25 ERYHQCQNVNCSATFITYE 43 (72)
T ss_pred eeeeecCCCCCCCEEEEEE
Confidence 3456666 5666665543
No 117
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=76.47 E-value=0.63 Score=39.02 Aligned_cols=15 Identities=0% Similarity=-0.093 Sum_probs=11.3
Q ss_pred hcCCCCCCCCchhhh
Q psy8167 126 FHGGADPKLMDEQMA 140 (167)
Q Consensus 126 h~~~~~~~C~~C~~~ 140 (167)
+....|..|+.||-.
T Consensus 470 ~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 470 YQEPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCCCC
Confidence 455678999999854
No 118
>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=76.28 E-value=1.2 Score=23.47 Aligned_cols=10 Identities=30% Similarity=0.747 Sum_probs=3.7
Q ss_pred cCceeccccc
Q psy8167 101 IDRIRCELCD 110 (167)
Q Consensus 101 ~k~~~C~~C~ 110 (167)
...|.|++|+
T Consensus 32 p~~w~CP~C~ 41 (47)
T PF00301_consen 32 PDDWVCPVCG 41 (47)
T ss_dssp -TT-B-TTTS
T ss_pred CCCCcCcCCC
Confidence 3445566555
No 119
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=75.82 E-value=2.4 Score=22.52 Aligned_cols=39 Identities=15% Similarity=0.244 Sum_probs=22.6
Q ss_pred CcccccccccccCCHHHHHHHHHHhcCCCCcccccchhh
Q psy8167 52 DRIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEV 90 (167)
Q Consensus 52 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~ 90 (167)
+.+.|..||..|.--..-+......-....|-.|+.|..
T Consensus 3 k~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR~ 41 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCRQ 41 (49)
T ss_pred eeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHHH
Confidence 568899999888766554444422122234555655543
No 120
>KOG4167|consensus
Probab=75.66 E-value=1.6 Score=36.41 Aligned_cols=28 Identities=32% Similarity=0.572 Sum_probs=23.9
Q ss_pred CCcccccccccccCCHHHHHHHHHHhcCC
Q psy8167 51 IDRIPCTLCDKTFTRKDSLKKHIRIFHTQ 79 (167)
Q Consensus 51 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 79 (167)
...|.|..|++.|....++..|| +.|..
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHM-K~Hr~ 817 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHM-KTHRQ 817 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHH-HHHHH
Confidence 46799999999999999999999 55643
No 121
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.95 E-value=0.73 Score=32.79 Aligned_cols=41 Identities=22% Similarity=0.332 Sum_probs=26.5
Q ss_pred cCceecccccccccChhHHHHHHHhhcCCCC---------------CCCCchhhhc
Q psy8167 101 IDRIRCELCDKSFTRKDSLKKHNRIFHGGAD---------------PKLMDEQMAR 141 (167)
Q Consensus 101 ~k~~~C~~C~k~f~~~~~l~~H~~~h~~~~~---------------~~C~~C~~~f 141 (167)
.+.+.|++|+..|....-+..-.|+-.++.. ..|+.|..+-
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~yAa 72 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYYAA 72 (267)
T ss_pred hceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhHHH
Confidence 5667888888888877655555555444321 4599997653
No 122
>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=73.88 E-value=1.9 Score=24.40 Aligned_cols=8 Identities=50% Similarity=1.481 Sum_probs=2.1
Q ss_pred cccccccc
Q psy8167 56 CTLCDKTF 63 (167)
Q Consensus 56 C~~C~~~f 63 (167)
|..|++.|
T Consensus 12 C~~C~~~F 19 (69)
T PF01363_consen 12 CMICGKKF 19 (69)
T ss_dssp -TTT--B-
T ss_pred CcCcCCcC
Confidence 55555554
No 123
>PF12907 zf-met2: Zinc-binding
Probab=73.07 E-value=2.9 Score=21.17 Aligned_cols=32 Identities=34% Similarity=0.611 Sum_probs=22.8
Q ss_pred cccccccccc---CCHHHHHHHHHHhcCCCCcccc
Q psy8167 54 IPCTLCDKTF---TRKDSLKKHIRIFHTQNQPQHT 85 (167)
Q Consensus 54 ~~C~~C~~~f---~~~~~l~~H~~~~h~~~~~~~c 85 (167)
+.|.+|...| .....|..|....|.......|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~~C 36 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTFEEC 36 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHHHc
Confidence 5799999544 5667899999778876544333
No 124
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=73.06 E-value=1.5 Score=19.28 Aligned_cols=6 Identities=33% Similarity=1.093 Sum_probs=3.1
Q ss_pred cccccc
Q psy8167 106 CELCDK 111 (167)
Q Consensus 106 C~~C~k 111 (167)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 555553
No 125
>KOG0978|consensus
Probab=73.01 E-value=1.1 Score=37.30 Aligned_cols=14 Identities=14% Similarity=0.821 Sum_probs=8.7
Q ss_pred CcccccccccccCC
Q psy8167 52 DRIPCTLCDKTFTR 65 (167)
Q Consensus 52 ~~~~C~~C~~~f~~ 65 (167)
...+|+.|+..++.
T Consensus 642 ~~LkCs~Cn~R~Kd 655 (698)
T KOG0978|consen 642 ELLKCSVCNTRWKD 655 (698)
T ss_pred hceeCCCccCchhh
Confidence 34678888854443
No 126
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=71.70 E-value=1.6 Score=26.42 Aligned_cols=32 Identities=16% Similarity=0.244 Sum_probs=16.7
Q ss_pred CcccccchhhhhhccccccccCceecccccccccC
Q psy8167 81 QPQHTNVIEVALGARANAAFIDRIRCELCDKSFTR 115 (167)
Q Consensus 81 ~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~ 115 (167)
..|.|+.|++.-..+.... -+.|..|++.|..
T Consensus 34 ~ky~Cp~Cgk~~vkR~a~G---IW~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKRVATG---IWKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSEEEEEETT---EEEETTTTEEEE-
T ss_pred CCCcCCCCCCceeEEeeeE---EeecCCCCCEEeC
Confidence 3577777776543311111 1677777776653
No 127
>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=71.34 E-value=11 Score=19.42 Aligned_cols=27 Identities=19% Similarity=0.160 Sum_probs=11.9
Q ss_pred ccccchhhhhhccccccccCceecccccc
Q psy8167 83 QHTNVIEVALGARANAAFIDRIRCELCDK 111 (167)
Q Consensus 83 ~~c~~c~~~~~~~~~~~l~k~~~C~~C~k 111 (167)
+.|+.|+..-.. ...-...|+|..|++
T Consensus 19 ~~CP~Cg~~~~~--~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHY--RLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeE--EeCCCCeEECCCCCC
Confidence 446666654111 111134456666553
No 128
>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=68.78 E-value=0.76 Score=30.61 Aligned_cols=12 Identities=25% Similarity=0.722 Sum_probs=5.9
Q ss_pred ecccccccccCh
Q psy8167 105 RCELCDKSFTRK 116 (167)
Q Consensus 105 ~C~~C~k~f~~~ 116 (167)
-|..||+.|+|-
T Consensus 70 YC~~CGkpyPWt 81 (158)
T PF10083_consen 70 YCHNCGKPYPWT 81 (158)
T ss_pred hHHhCCCCCchH
Confidence 355555555444
No 129
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=68.68 E-value=0.88 Score=27.92 Aligned_cols=39 Identities=8% Similarity=0.031 Sum_probs=18.0
Q ss_pred ccCceecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcC
Q psy8167 100 FIDRIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARG 142 (167)
Q Consensus 100 l~k~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 142 (167)
|.+.|.|+.||..-...-.+. .-...-...|..||.+|.
T Consensus 19 L~k~FtCp~Cghe~vs~ctvk----k~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVK----KTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred CCceEecCccCCeeeeEEEEE----ecCceeEEEcccCcceEE
Confidence 456667777764433322211 101112345666666654
No 130
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=68.64 E-value=2 Score=36.22 Aligned_cols=46 Identities=13% Similarity=0.192 Sum_probs=29.8
Q ss_pred ccccccccccCCH---HHHHHHHHHhcCCCCcccccchhhhhhccccccccCceeccccccc
Q psy8167 54 IPCTLCDKTFTRK---DSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKS 112 (167)
Q Consensus 54 ~~C~~C~~~f~~~---~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~ 112 (167)
..|..||..+.-. ..| ..|.......|-.||..- ..+..|+.||-.
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~l-----t~H~~~~~L~CH~Cg~~~--------~~p~~Cp~Cgs~ 484 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPL-----TLHKATGQLRCHYCGYQE--------PIPQSCPECGSE 484 (730)
T ss_pred eecccCCCcccCCCCCcce-----EEecCCCeeEeCCCCCCC--------CCCCCCCCCCCC
Confidence 4577777655533 233 445566778999998662 345789999954
No 131
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=68.01 E-value=2.2 Score=19.20 Aligned_cols=6 Identities=33% Similarity=1.065 Sum_probs=3.0
Q ss_pred cccccc
Q psy8167 106 CELCDK 111 (167)
Q Consensus 106 C~~C~k 111 (167)
|+.||.
T Consensus 19 C~~CG~ 24 (26)
T PF13248_consen 19 CPNCGA 24 (26)
T ss_pred ChhhCC
Confidence 555553
No 132
>PRK04023 DNA polymerase II large subunit; Validated
Probab=68.00 E-value=2.7 Score=36.44 Aligned_cols=12 Identities=0% Similarity=-0.205 Sum_probs=7.6
Q ss_pred CCCCCchhhhcC
Q psy8167 131 DPKLMDEQMARG 142 (167)
Q Consensus 131 ~~~C~~C~~~f~ 142 (167)
++.|+.||..-.
T Consensus 663 ~y~CPKCG~El~ 674 (1121)
T PRK04023 663 EDECEKCGREPT 674 (1121)
T ss_pred CCcCCCCCCCCC
Confidence 466888865443
No 133
>PRK14873 primosome assembly protein PriA; Provisional
Probab=67.68 E-value=2 Score=35.90 Aligned_cols=26 Identities=15% Similarity=0.208 Sum_probs=13.8
Q ss_pred cCCCCcccccchhhhhhccccccccCceecccccc
Q psy8167 77 HTQNQPQHTNVIEVALGARANAAFIDRIRCELCDK 111 (167)
Q Consensus 77 h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k 111 (167)
|.......|..||.... ++.|+.||.
T Consensus 405 h~~~~~l~Ch~CG~~~~---------p~~Cp~Cgs 430 (665)
T PRK14873 405 PSAGGTPRCRWCGRAAP---------DWRCPRCGS 430 (665)
T ss_pred ecCCCeeECCCCcCCCc---------CccCCCCcC
Confidence 43444566666664322 256666664
No 134
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.63 E-value=2.6 Score=26.37 Aligned_cols=10 Identities=30% Similarity=0.391 Sum_probs=5.0
Q ss_pred eecccccccc
Q psy8167 104 IRCELCDKSF 113 (167)
Q Consensus 104 ~~C~~C~k~f 113 (167)
.-|++||++|
T Consensus 27 iVsPytG~s~ 36 (129)
T COG4530 27 IVSPYTGKSY 36 (129)
T ss_pred cccCcccccc
Confidence 3455555555
No 135
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=67.35 E-value=3.3 Score=22.52 Aligned_cols=7 Identities=29% Similarity=0.871 Sum_probs=3.0
Q ss_pred ccccccc
Q psy8167 55 PCTLCDK 61 (167)
Q Consensus 55 ~C~~C~~ 61 (167)
.|+.||.
T Consensus 4 ~CP~CG~ 10 (54)
T TIGR01206 4 ECPDCGA 10 (54)
T ss_pred CCCCCCC
Confidence 3444444
No 136
>KOG3408|consensus
Probab=66.86 E-value=4.3 Score=25.93 Aligned_cols=23 Identities=9% Similarity=-0.129 Sum_probs=18.6
Q ss_pred CCCCCchhhhcCCHHHHHHHHhh
Q psy8167 131 DPKLMDEQMARGSADFLEVVLNE 153 (167)
Q Consensus 131 ~~~C~~C~~~f~~~~~l~~H~~~ 153 (167)
.|-|..|.+.|.....|..|.++
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhc
Confidence 47788888888888888888863
No 137
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=64.61 E-value=5.2 Score=26.52 Aligned_cols=19 Identities=21% Similarity=0.443 Sum_probs=12.8
Q ss_pred ceecccccccccChhHHHH
Q psy8167 103 RIRCELCDKSFTRKDSLKK 121 (167)
Q Consensus 103 ~~~C~~C~k~f~~~~~l~~ 121 (167)
-+.|+.||+.|..-+++.+
T Consensus 124 f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred EEECCCCCCEecccccHHH
Confidence 3567777777777666554
No 138
>KOG4602|consensus
Probab=64.38 E-value=11 Score=27.43 Aligned_cols=46 Identities=11% Similarity=0.280 Sum_probs=23.5
Q ss_pred CCcccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccccCceecccccc
Q psy8167 51 IDRIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDK 111 (167)
Q Consensus 51 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k 111 (167)
.++.-|.+|...-....-+.. |..+.++.--.|.+ .+.|-|++||-
T Consensus 231 ~r~l~CvFC~nN~E~~A~y~t-----H~lkd~dgRVLCPk----------LR~YVCPiCGA 276 (318)
T KOG4602|consen 231 PRPLCCVFCFNNAEEFARYHT-----HPLKDKDGRVLCPK----------LRSYVCPICGA 276 (318)
T ss_pred CCceeEEeecCCCchhhheec-----ccccCCCCcEechh----------HhhhcCccccc
Confidence 355678888764444444333 43333332222222 34468888883
No 139
>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=63.49 E-value=5.8 Score=31.59 Aligned_cols=30 Identities=23% Similarity=0.377 Sum_probs=26.5
Q ss_pred CcccccccccccCCHHHHHHHHHHhcCCCC
Q psy8167 52 DRIPCTLCDKTFTRKDSLKKHIRIFHTQNQ 81 (167)
Q Consensus 52 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 81 (167)
+.|.|+.|.+.|.....+..|+...|.+.-
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~l 85 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAGL 85 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhhc
Confidence 458899999999999999999988897763
No 140
>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=63.23 E-value=3.9 Score=18.18 Aligned_cols=7 Identities=29% Similarity=0.937 Sum_probs=4.3
Q ss_pred eeccccc
Q psy8167 104 IRCELCD 110 (167)
Q Consensus 104 ~~C~~C~ 110 (167)
|.|+.||
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 5666665
No 141
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=63.21 E-value=3.1 Score=19.58 Aligned_cols=10 Identities=30% Similarity=0.962 Sum_probs=4.2
Q ss_pred eecccccccc
Q psy8167 104 IRCELCDKSF 113 (167)
Q Consensus 104 ~~C~~C~k~f 113 (167)
|.|+.|+..+
T Consensus 14 Y~Cp~C~~~~ 23 (30)
T PF04438_consen 14 YRCPRCGARY 23 (30)
T ss_dssp EE-TTT--EE
T ss_pred EECCCcCCce
Confidence 6676666543
No 142
>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=62.61 E-value=2.5 Score=29.55 Aligned_cols=22 Identities=27% Similarity=0.744 Sum_probs=0.0
Q ss_pred cCceeccccc-ccccChhHHHHH
Q psy8167 101 IDRIRCELCD-KSFTRKDSLKKH 122 (167)
Q Consensus 101 ~k~~~C~~C~-k~f~~~~~l~~H 122 (167)
.+.|.|.+|| ..|..+..+.+|
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp -----------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHh
Confidence 3335555555 345555555555
No 143
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=61.65 E-value=4.4 Score=24.53 Aligned_cols=31 Identities=16% Similarity=0.213 Sum_probs=16.0
Q ss_pred cccccchhhhhhccccccccCceecccccccccC
Q psy8167 82 PQHTNVIEVALGARANAAFIDRIRCELCDKSFTR 115 (167)
Q Consensus 82 ~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~ 115 (167)
.|.|+.|++.-..+.. ..-+.|..|++.|..
T Consensus 36 ~y~CpfCgk~~vkR~a---~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 36 KYFCPFCGKHAVKRQA---VGIWRCKGCKKTVAG 66 (90)
T ss_pred CccCCCCCCCceeeee---eEEEEcCCCCCEEeC
Confidence 5677777643222001 122567777776654
No 144
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=61.63 E-value=4 Score=36.35 Aligned_cols=11 Identities=0% Similarity=-0.233 Sum_probs=6.7
Q ss_pred CCCCCchhhhc
Q psy8167 131 DPKLMDEQMAR 141 (167)
Q Consensus 131 ~~~C~~C~~~f 141 (167)
...|+.|+...
T Consensus 709 a~~CP~CGtpl 719 (1337)
T PRK14714 709 RVECPRCDVEL 719 (1337)
T ss_pred cccCCCCCCcc
Confidence 34688887443
No 145
>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=61.18 E-value=4.2 Score=24.67 Aligned_cols=32 Identities=13% Similarity=0.140 Sum_probs=16.4
Q ss_pred cccccchhhhhhccccccccCceecccccccccCh
Q psy8167 82 PQHTNVIEVALGARANAAFIDRIRCELCDKSFTRK 116 (167)
Q Consensus 82 ~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~ 116 (167)
.|.|+.|++.-..+.. ..-+.|..|++.|..-
T Consensus 35 ~y~CpfCgk~~vkR~a---~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 35 KYVCPFCGKKTVKRGS---TGIWTCRKCGAKFAGG 66 (91)
T ss_pred CccCCCCCCCceEEEe---eEEEEcCCCCCEEeCC
Confidence 5677777643222111 1125677777766543
No 146
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=61.06 E-value=3.2 Score=26.99 Aligned_cols=22 Identities=36% Similarity=0.380 Sum_probs=13.4
Q ss_pred ecccccccccChhHHHHHHHhhcCC
Q psy8167 105 RCELCDKSFTRKDSLKKHNRIFHGG 129 (167)
Q Consensus 105 ~C~~C~k~f~~~~~l~~H~~~h~~~ 129 (167)
-|-.+|+.|. .|++|+.+|++-
T Consensus 78 icLEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 78 ICLEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred EEeccCcchH---HHHHHHhcccCC
Confidence 4666666664 356666666654
No 147
>KOG2593|consensus
Probab=61.01 E-value=7.1 Score=30.61 Aligned_cols=31 Identities=10% Similarity=0.127 Sum_probs=18.3
Q ss_pred Ccccccchhhhhhccccccc----cCceecccccc
Q psy8167 81 QPQHTNVIEVALGARANAAF----IDRIRCELCDK 111 (167)
Q Consensus 81 ~~~~c~~c~~~~~~~~~~~l----~k~~~C~~C~k 111 (167)
.-|.|+.|.+.|..-....| ...|.|..|+-
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGG 161 (436)
T ss_pred ccccCCccccchhhhHHHHhhcccCceEEEecCCC
Confidence 34777777777766333333 34577777764
No 148
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=60.95 E-value=5.3 Score=20.31 Aligned_cols=9 Identities=22% Similarity=0.641 Sum_probs=4.1
Q ss_pred eeccccccc
Q psy8167 104 IRCELCDKS 112 (167)
Q Consensus 104 ~~C~~C~k~ 112 (167)
+-|..||..
T Consensus 20 ~vC~~CG~V 28 (43)
T PF08271_consen 20 LVCPNCGLV 28 (43)
T ss_dssp EEETTT-BB
T ss_pred EECCCCCCE
Confidence 455555543
No 149
>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=60.78 E-value=5.5 Score=21.39 Aligned_cols=12 Identities=33% Similarity=0.861 Sum_probs=5.9
Q ss_pred ceeccccccccc
Q psy8167 103 RIRCELCDKSFT 114 (167)
Q Consensus 103 ~~~C~~C~k~f~ 114 (167)
.+.|..||+.|-
T Consensus 18 k~~Cr~Cg~~~C 29 (57)
T cd00065 18 RHHCRNCGRIFC 29 (57)
T ss_pred ccccCcCcCCcC
Confidence 345555555443
No 150
>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=60.42 E-value=3.5 Score=33.31 Aligned_cols=47 Identities=11% Similarity=0.269 Sum_probs=24.2
Q ss_pred cccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccccCceecccccc
Q psy8167 55 PCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDK 111 (167)
Q Consensus 55 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k 111 (167)
.|..||....-..= ...+ ..|.......|..||....- +..|+.||.
T Consensus 215 ~C~~Cg~~~~C~~C-~~~l-~~h~~~~~l~Ch~Cg~~~~~--------~~~Cp~C~s 261 (505)
T TIGR00595 215 LCRSCGYILCCPNC-DVSL-TYHKKEGKLRCHYCGYQEPI--------PKTCPQCGS 261 (505)
T ss_pred EhhhCcCccCCCCC-CCce-EEecCCCeEEcCCCcCcCCC--------CCCCCCCCC
Confidence 46666654332200 0122 34555556777777755432 246777774
No 151
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=59.99 E-value=3.3 Score=26.89 Aligned_cols=13 Identities=31% Similarity=0.751 Sum_probs=6.8
Q ss_pred ccccccccccCCH
Q psy8167 54 IPCTLCDKTFTRK 66 (167)
Q Consensus 54 ~~C~~C~~~f~~~ 66 (167)
++|..||+.|..-
T Consensus 2 H~Ct~Cg~~f~dg 14 (131)
T PF09845_consen 2 HQCTKCGRVFEDG 14 (131)
T ss_pred cccCcCCCCcCCC
Confidence 4555555555543
No 152
>PF15269 zf-C2H2_7: Zinc-finger
Probab=59.95 E-value=7.3 Score=20.15 Aligned_cols=22 Identities=23% Similarity=0.424 Sum_probs=18.0
Q ss_pred eecccccccccChhHHHHHHHh
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRI 125 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~ 125 (167)
|+|-+|.....-++.|-.||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 4788888888888889888875
No 153
>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=59.87 E-value=4.6 Score=19.33 Aligned_cols=6 Identities=50% Similarity=1.359 Sum_probs=2.4
Q ss_pred eccccc
Q psy8167 105 RCELCD 110 (167)
Q Consensus 105 ~C~~C~ 110 (167)
+|+.||
T Consensus 19 rC~~CG 24 (32)
T PF03604_consen 19 RCPECG 24 (32)
T ss_dssp SBSSSS
T ss_pred ECCcCC
Confidence 344444
No 154
>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=59.83 E-value=5.4 Score=20.36 Aligned_cols=17 Identities=24% Similarity=0.743 Sum_probs=14.0
Q ss_pred ecccccccccChhHHHH
Q psy8167 105 RCELCDKSFTRKDSLKK 121 (167)
Q Consensus 105 ~C~~C~k~f~~~~~l~~ 121 (167)
.|.+||+.|..+....+
T Consensus 10 ~C~~C~rpf~WRKKW~~ 26 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWAR 26 (42)
T ss_pred cCcccCCcchHHHHHHH
Confidence 49999999999877654
No 155
>COG2879 Uncharacterized small protein [Function unknown]
Probab=59.74 E-value=11 Score=21.10 Aligned_cols=18 Identities=11% Similarity=0.078 Sum_probs=11.7
Q ss_pred CHHHHHHHHhhcCCCCCc
Q psy8167 143 SADFLEVVLNEDGEGEPV 160 (167)
Q Consensus 143 ~~~~l~~H~~~~~~~~~~ 160 (167)
..+++..|++.+|+.+|+
T Consensus 24 dYdnYVehmr~~hPd~p~ 41 (65)
T COG2879 24 DYDNYVEHMRKKHPDKPP 41 (65)
T ss_pred cHHHHHHHHHHhCcCCCc
Confidence 556666777776666664
No 156
>KOG3214|consensus
Probab=59.52 E-value=3 Score=25.58 Aligned_cols=41 Identities=7% Similarity=-0.011 Sum_probs=20.4
Q ss_pred cCceecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCCHH
Q psy8167 101 IDRIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSAD 145 (167)
Q Consensus 101 ~k~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~ 145 (167)
...|.|+.|..--.-.-. +..-+..-...|.+|+.+|....
T Consensus 21 dt~FnClfcnHek~v~~~----~Dk~~~iG~~sC~iC~esFqt~i 61 (109)
T KOG3214|consen 21 DTQFNCLFCNHEKSVSCT----LDKKHNIGKASCRICEESFQTTI 61 (109)
T ss_pred heeeccCccccccceeee----ehhhcCcceeeeeehhhhhccch
Confidence 444667766632222111 11122233567778887777643
No 157
>KOG3408|consensus
Probab=59.32 E-value=6.9 Score=25.01 Aligned_cols=25 Identities=24% Similarity=0.505 Sum_probs=22.0
Q ss_pred CCCcccccccccccCCHHHHHHHHH
Q psy8167 50 PIDRIPCTLCDKTFTRKDSLKKHIR 74 (167)
Q Consensus 50 ~~~~~~C~~C~~~f~~~~~l~~H~~ 74 (167)
|...|.|-.|.+.|.+...|..|.+
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHh
Confidence 4467999999999999999999983
No 158
>KOG2593|consensus
Probab=57.72 E-value=6.2 Score=30.94 Aligned_cols=39 Identities=18% Similarity=0.331 Sum_probs=29.1
Q ss_pred CcccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhc
Q psy8167 52 DRIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGA 94 (167)
Q Consensus 52 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~ 94 (167)
.-|.|+.|.+.|.....++ ..-.....|.|..|+.....
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~----L~~~~~~~F~C~~C~gelve 165 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQ----LLDNETGEFHCENCGGELVE 165 (436)
T ss_pred ccccCCccccchhhhHHHH----hhcccCceEEEecCCCchhc
Confidence 4499999999999888763 22333557999999876644
No 159
>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=57.61 E-value=3.4 Score=19.12 Aligned_cols=17 Identities=47% Similarity=0.825 Sum_probs=8.0
Q ss_pred ecccccccccChhHHHHH
Q psy8167 105 RCELCDKSFTRKDSLKKH 122 (167)
Q Consensus 105 ~C~~C~k~f~~~~~l~~H 122 (167)
.|-.|++.| ....++.|
T Consensus 2 sCiDC~~~F-~~~~y~~H 18 (28)
T PF08790_consen 2 SCIDCSKDF-DGDSYKSH 18 (28)
T ss_dssp EETTTTEEE-EGGGTTT-
T ss_pred eeecCCCCc-CcCCcCCC
Confidence 455666666 33333444
No 160
>PRK04023 DNA polymerase II large subunit; Validated
Probab=57.45 E-value=6.1 Score=34.46 Aligned_cols=11 Identities=36% Similarity=0.788 Sum_probs=8.1
Q ss_pred Ccccccccccc
Q psy8167 52 DRIPCTLCDKT 62 (167)
Q Consensus 52 ~~~~C~~C~~~ 62 (167)
....|+.||..
T Consensus 625 g~RfCpsCG~~ 635 (1121)
T PRK04023 625 GRRKCPSCGKE 635 (1121)
T ss_pred cCccCCCCCCc
Confidence 45678888875
No 161
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=57.23 E-value=5.3 Score=24.18 Aligned_cols=31 Identities=16% Similarity=0.215 Sum_probs=16.8
Q ss_pred cccccchhhhhhccccccccCceecccccccccC
Q psy8167 82 PQHTNVIEVALGARANAAFIDRIRCELCDKSFTR 115 (167)
Q Consensus 82 ~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~ 115 (167)
.|.|+.|++.-..+.. ..-+.|..|++.|..
T Consensus 36 ~y~CpfCgk~~vkR~a---~GIW~C~~C~~~~AG 66 (90)
T PRK03976 36 KHVCPVCGRPKVKRVG---TGIWECRKCGAKFAG 66 (90)
T ss_pred CccCCCCCCCceEEEE---EEEEEcCCCCCEEeC
Confidence 5777777643322111 112577777777654
No 162
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=57.01 E-value=10 Score=20.42 Aligned_cols=15 Identities=13% Similarity=0.521 Sum_probs=10.2
Q ss_pred eecccccccccChhH
Q psy8167 104 IRCELCDKSFTRKDS 118 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~ 118 (167)
++|+.||..|...-.
T Consensus 29 W~C~~Cgh~w~~~v~ 43 (55)
T PF14311_consen 29 WKCPKCGHEWKASVN 43 (55)
T ss_pred EECCCCCCeeEccHh
Confidence 578888777666543
No 163
>KOG1280|consensus
Probab=56.93 E-value=5 Score=30.49 Aligned_cols=29 Identities=17% Similarity=0.208 Sum_probs=16.4
Q ss_pred ceecccccccccChhHHHHHHHhhcCCCC
Q psy8167 103 RIRCELCDKSFTRKDSLKKHNRIFHGGAD 131 (167)
Q Consensus 103 ~~~C~~C~k~f~~~~~l~~H~~~h~~~~~ 131 (167)
.|.|++|++.-.....|..|...-|.+..
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hpda~ 107 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHPEAS 107 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCcccC
Confidence 45566666655555566666555554443
No 164
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=56.54 E-value=3.6 Score=35.03 Aligned_cols=13 Identities=0% Similarity=-0.360 Sum_probs=0.0
Q ss_pred cccccchhhhhhc
Q psy8167 82 PQHTNVIEVALGA 94 (167)
Q Consensus 82 ~~~c~~c~~~~~~ 94 (167)
.+.|+.|+.....
T Consensus 655 ~r~Cp~Cg~~t~~ 667 (900)
T PF03833_consen 655 RRRCPKCGKETFY 667 (900)
T ss_dssp -------------
T ss_pred cccCcccCCcchh
Confidence 3566666665444
No 165
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=56.05 E-value=8.1 Score=20.30 Aligned_cols=10 Identities=20% Similarity=0.488 Sum_probs=4.9
Q ss_pred eecccccccc
Q psy8167 104 IRCELCDKSF 113 (167)
Q Consensus 104 ~~C~~C~k~f 113 (167)
+.|+.||..+
T Consensus 21 ~vC~~Cg~~~ 30 (52)
T smart00661 21 FVCRKCGYEE 30 (52)
T ss_pred EECCcCCCeE
Confidence 4455555443
No 166
>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 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=55.73 E-value=6.1 Score=25.07 Aligned_cols=12 Identities=25% Similarity=0.681 Sum_probs=6.8
Q ss_pred eecccccccccC
Q psy8167 104 IRCELCDKSFTR 115 (167)
Q Consensus 104 ~~C~~C~k~f~~ 115 (167)
+.|..||..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (115)
T TIGR00100 71 CECEDCSEEVSP 82 (115)
T ss_pred EEcccCCCEEec
Confidence 456666655544
No 168
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=55.51 E-value=5.3 Score=26.16 Aligned_cols=16 Identities=19% Similarity=0.586 Sum_probs=11.2
Q ss_pred cCceecccccccccCh
Q psy8167 101 IDRIRCELCDKSFTRK 116 (167)
Q Consensus 101 ~k~~~C~~C~k~f~~~ 116 (167)
...+.|..||..|...
T Consensus 68 p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 68 EAVLKCRNCGNEWSLK 83 (135)
T ss_pred ceEEECCCCCCEEecc
Confidence 3457888888777654
No 169
>KOG0782|consensus
Probab=55.18 E-value=4 Score=33.29 Aligned_cols=49 Identities=20% Similarity=0.366 Sum_probs=33.8
Q ss_pred HHHHHHHHHHhcCCCCcccccchhhhhhccccccc----cCceecccccccccChh
Q psy8167 66 KDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAF----IDRIRCELCDKSFTRKD 117 (167)
Q Consensus 66 ~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l----~k~~~C~~C~k~f~~~~ 117 (167)
...|.+|. +.|.....=+|+.|++.|-+ ...+ ..-..|..|...|-.+-
T Consensus 238 E~~fvrHH-WVHrrRqeGkC~~CgKgFQQ--Kf~FhsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 238 ESGFVRHH-WVHRRRQEGKCNTCGKGFQQ--KFFFHSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred cccchHHh-HhhHhhhccccchhhhhhhh--heeeccccEEEEEehHHHHHhhcch
Confidence 34788887 77877777788888888877 4433 12236888877776664
No 170
>KOG0717|consensus
Probab=54.82 E-value=6.4 Score=31.19 Aligned_cols=22 Identities=14% Similarity=-0.176 Sum_probs=19.9
Q ss_pred CCCCchhhhcCCHHHHHHHHhh
Q psy8167 132 PKLMDEQMARGSADFLEVVLNE 153 (167)
Q Consensus 132 ~~C~~C~~~f~~~~~l~~H~~~ 153 (167)
+-|.+|+|+|.+..+|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999999863
No 171
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=54.37 E-value=7.5 Score=24.19 Aligned_cols=23 Identities=4% Similarity=-0.253 Sum_probs=19.3
Q ss_pred CCCCCchhhhcCCHHHHHHHHhh
Q psy8167 131 DPKLMDEQMARGSADFLEVVLNE 153 (167)
Q Consensus 131 ~~~C~~C~~~f~~~~~l~~H~~~ 153 (167)
.+-|..|.+.|.+...|..|.+.
T Consensus 55 qhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhcc
Confidence 46788999999999999998863
No 172
>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=53.85 E-value=8.3 Score=30.77 Aligned_cols=22 Identities=5% Similarity=-0.266 Sum_probs=11.9
Q ss_pred CCCCchhhhcCCHHHHHHHHhh
Q psy8167 132 PKLMDEQMARGSADFLEVVLNE 153 (167)
Q Consensus 132 ~~C~~C~~~f~~~~~l~~H~~~ 153 (167)
+.|+.|.+.|.....+..|+..
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHH
Confidence 4455555555555555555553
No 173
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=53.71 E-value=3.9 Score=22.25 Aligned_cols=40 Identities=10% Similarity=0.066 Sum_probs=25.0
Q ss_pred eeccc--ccccccChhHHHHHHHhhcCCCCCCCCc----hhhhcCCH
Q psy8167 104 IRCEL--CDKSFTRKDSLKKHNRIFHGGADPKLMD----EQMARGSA 144 (167)
Q Consensus 104 ~~C~~--C~k~f~~~~~l~~H~~~h~~~~~~~C~~----C~~~f~~~ 144 (167)
..|+. |...+. +..|..|+...-...+..|.. |+..+...
T Consensus 10 v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~ 55 (60)
T PF02176_consen 10 VPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVPRE 55 (60)
T ss_dssp EE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEEHH
T ss_pred eeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccchh
Confidence 56877 444444 558889998667777888998 88877544
No 174
>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=52.45 E-value=4.4 Score=32.76 Aligned_cols=14 Identities=0% Similarity=-0.273 Sum_probs=9.4
Q ss_pred cCCCCCCCCchhhh
Q psy8167 127 HGGADPKLMDEQMA 140 (167)
Q Consensus 127 ~~~~~~~C~~C~~~ 140 (167)
....|..|+.|+..
T Consensus 249 ~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 249 QEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCCCCCCC
Confidence 33457788888753
No 175
>PRK14873 primosome assembly protein PriA; Provisional
Probab=52.27 E-value=4.5 Score=33.87 Aligned_cols=11 Identities=9% Similarity=-0.215 Sum_probs=8.4
Q ss_pred CCCCCCchhhh
Q psy8167 130 ADPKLMDEQMA 140 (167)
Q Consensus 130 ~~~~C~~C~~~ 140 (167)
.+..|+.||..
T Consensus 421 ~p~~Cp~Cgs~ 431 (665)
T PRK14873 421 PDWRCPRCGSD 431 (665)
T ss_pred cCccCCCCcCC
Confidence 47889999764
No 176
>KOG2636|consensus
Probab=52.11 E-value=9.2 Score=30.19 Aligned_cols=23 Identities=17% Similarity=0.514 Sum_probs=17.0
Q ss_pred cCceeccccc-ccccChhHHHHHH
Q psy8167 101 IDRIRCELCD-KSFTRKDSLKKHN 123 (167)
Q Consensus 101 ~k~~~C~~C~-k~f~~~~~l~~H~ 123 (167)
.+.|.|.+|| +++..+..+.+|-
T Consensus 399 ~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 399 DIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred CcccceeeccCccccCcHHHHHHh
Confidence 4556788888 7777888888773
No 177
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=51.74 E-value=16 Score=18.43 Aligned_cols=23 Identities=22% Similarity=0.554 Sum_probs=17.0
Q ss_pred ccccccccccCC--HHHHHHHHHHhc
Q psy8167 54 IPCTLCDKTFTR--KDSLKKHIRIFH 77 (167)
Q Consensus 54 ~~C~~C~~~f~~--~~~l~~H~~~~h 77 (167)
-.|+.||+.|.. ...-..|. +.|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~-~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHK-KYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHH-HHH
Confidence 479999998874 46667776 545
No 178
>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=51.51 E-value=6 Score=25.01 Aligned_cols=13 Identities=31% Similarity=0.787 Sum_probs=6.7
Q ss_pred eecccccccccCh
Q psy8167 104 IRCELCDKSFTRK 116 (167)
Q Consensus 104 ~~C~~C~k~f~~~ 116 (167)
+.|..||+.|.-.
T Consensus 71 ~~C~~Cg~~~~~~ 83 (113)
T PF01155_consen 71 ARCRDCGHEFEPD 83 (113)
T ss_dssp EEETTTS-EEECH
T ss_pred EECCCCCCEEecC
Confidence 4566666655543
No 179
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=51.40 E-value=7.8 Score=28.09 Aligned_cols=28 Identities=14% Similarity=0.060 Sum_probs=15.3
Q ss_pred cccccchhhhhhccccccccCceecccccc
Q psy8167 82 PQHTNVIEVALGARANAAFIDRIRCELCDK 111 (167)
Q Consensus 82 ~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k 111 (167)
.|.|+.|+..|.. ...+..+-.|-.|+.
T Consensus 155 ef~C~~C~h~F~G--~~qm~v~sPCy~C~~ 182 (278)
T PF15135_consen 155 EFHCPKCRHNFRG--FAQMGVPSPCYGCGN 182 (278)
T ss_pred eeecccccccchh--hhhcCCCCCccCCCC
Confidence 4666666666655 444444445555553
No 180
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=51.32 E-value=8.1 Score=17.87 Aligned_cols=7 Identities=57% Similarity=1.383 Sum_probs=2.4
Q ss_pred eeccccc
Q psy8167 104 IRCELCD 110 (167)
Q Consensus 104 ~~C~~C~ 110 (167)
|.|.+|.
T Consensus 16 Y~C~~Cd 22 (30)
T PF07649_consen 16 YRCSECD 22 (30)
T ss_dssp EE-TTT-
T ss_pred EECccCC
Confidence 4454444
No 181
>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=50.62 E-value=6.3 Score=19.39 Aligned_cols=8 Identities=25% Similarity=1.103 Sum_probs=3.4
Q ss_pred cccccccc
Q psy8167 106 CELCDKSF 113 (167)
Q Consensus 106 C~~C~k~f 113 (167)
|+.||+.|
T Consensus 4 C~~Cg~~Y 11 (36)
T PF05191_consen 4 CPKCGRIY 11 (36)
T ss_dssp ETTTTEEE
T ss_pred cCCCCCcc
Confidence 44444443
No 182
>COG1773 Rubredoxin [Energy production and conversion]
Probab=50.53 E-value=8 Score=21.07 Aligned_cols=15 Identities=27% Similarity=0.789 Sum_probs=11.5
Q ss_pred ceecccccccccChh
Q psy8167 103 RIRCELCDKSFTRKD 117 (167)
Q Consensus 103 ~~~C~~C~k~f~~~~ 117 (167)
.|+|.+||..|.-..
T Consensus 3 ~~~C~~CG~vYd~e~ 17 (55)
T COG1773 3 RWRCSVCGYVYDPEK 17 (55)
T ss_pred ceEecCCceEecccc
Confidence 578999998876543
No 183
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=50.31 E-value=6.4 Score=26.26 Aligned_cols=35 Identities=20% Similarity=0.369 Sum_probs=23.2
Q ss_pred cCceecccccccccChhHHHHHHHhhcCCCCCCCCchhhh
Q psy8167 101 IDRIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMA 140 (167)
Q Consensus 101 ~k~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 140 (167)
.-.|.|. |+..|.+. ++|-..-.|+ .|.|..|+-.
T Consensus 115 ~~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 115 TYPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred ceeEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 3457899 99886654 4454443444 8999999743
No 184
>KOG2636|consensus
Probab=50.04 E-value=11 Score=29.76 Aligned_cols=29 Identities=3% Similarity=-0.118 Sum_probs=24.0
Q ss_pred HhhcCCCCCCCCchh-hhcCCHHHHHHHHh
Q psy8167 124 RIFHGGADPKLMDEQ-MARGSADFLEVVLN 152 (167)
Q Consensus 124 ~~h~~~~~~~C~~C~-~~f~~~~~l~~H~~ 152 (167)
+.|--+..|.|.+|| +++.....+.+|-.
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 455556789999999 99999999999874
No 185
>KOG0978|consensus
Probab=49.88 E-value=4 Score=34.09 Aligned_cols=22 Identities=18% Similarity=0.095 Sum_probs=16.1
Q ss_pred CCCCCCCchhhhcCCHHHHHHH
Q psy8167 129 GADPKLMDEQMARGSADFLEVV 150 (167)
Q Consensus 129 ~~~~~C~~C~~~f~~~~~l~~H 150 (167)
-+.-+|+.|+.+|...+.++-|
T Consensus 676 tRqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 676 TRQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred HhcCCCCCCCCCCCcccccccC
Confidence 3567899999999877665544
No 186
>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=49.72 E-value=4.6 Score=19.03 Aligned_cols=8 Identities=0% Similarity=-0.546 Sum_probs=3.5
Q ss_pred CCCCCchh
Q psy8167 131 DPKLMDEQ 138 (167)
Q Consensus 131 ~~~C~~C~ 138 (167)
-+.|+.|+
T Consensus 19 ~~vCp~C~ 26 (30)
T PF08274_consen 19 LLVCPECG 26 (30)
T ss_dssp SEEETTTT
T ss_pred EEeCCccc
Confidence 34444443
No 187
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=49.37 E-value=8.4 Score=24.55 Aligned_cols=12 Identities=25% Similarity=0.825 Sum_probs=6.3
Q ss_pred eecccccccccC
Q psy8167 104 IRCELCDKSFTR 115 (167)
Q Consensus 104 ~~C~~C~k~f~~ 115 (167)
+.|..||..|..
T Consensus 72 ~~C~~Cg~~~~~ 83 (117)
T PRK00564 72 LECKDCSHVFKP 83 (117)
T ss_pred EEhhhCCCcccc
Confidence 456666644433
No 188
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=49.01 E-value=12 Score=28.10 Aligned_cols=48 Identities=8% Similarity=-0.067 Sum_probs=24.9
Q ss_pred ecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCCHHHHHHHHhhc
Q psy8167 105 RCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSADFLEVVLNED 154 (167)
Q Consensus 105 ~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 154 (167)
.|-.|.-.|.-...-.. ......-.|+|..|...|-...+.--|..-|
T Consensus 364 ~Cf~CQ~~fp~~~~~~~--~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 364 HCFVCQGPFPKPPVSPF--DESTSSGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred cceeccCCCCCCCCCcc--cccccccceechhhhhhhhhhhHHHHHHHHh
Confidence 36666655555432111 1112233577777777777666665565433
No 189
>PHA02998 RNA polymerase subunit; Provisional
Probab=48.97 E-value=2.4 Score=29.00 Aligned_cols=38 Identities=11% Similarity=0.003 Sum_probs=23.0
Q ss_pred ceecccccccccChhHHHHHHHhhcCCCC----CCCCchhhhcCCH
Q psy8167 103 RIRCELCDKSFTRKDSLKKHNRIFHGGAD----PKLMDEQMARGSA 144 (167)
Q Consensus 103 ~~~C~~C~k~f~~~~~l~~H~~~h~~~~~----~~C~~C~~~f~~~ 144 (167)
...|+.|+..=.... .+++...++| |.|..||+.|.-.
T Consensus 143 ~v~CPkCg~~~A~f~----qlQTRSADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 143 NTPCPNCKSKNTTPM----MIQTRAADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCCceEEE----EEeeccCCCCceEEEEcCCCCCccCCc
Confidence 347999984322211 1233345555 8999999988765
No 190
>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=48.75 E-value=31 Score=23.31 Aligned_cols=61 Identities=15% Similarity=0.240 Sum_probs=39.6
Q ss_pred ceecccccccccChhHHHHHHHhhcCCCCCCCCchhhhc-CCHHHHHHHHhhcC-CCCCccccc
Q psy8167 103 RIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMAR-GSADFLEVVLNEDG-EGEPVSITV 164 (167)
Q Consensus 103 ~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f-~~~~~l~~H~~~~~-~~~~~~~~~ 164 (167)
...|+.|.-........ ...|.+...|+-.|..=+=.| .+...|++|.+..| ...|..+.+
T Consensus 80 ~L~CPLCRG~V~GWtvv-e~AR~~LN~K~RsC~~e~C~F~GtY~eLrKHar~~HP~~rP~~vDP 142 (162)
T PF07800_consen 80 ELACPLCRGEVKGWTVV-EPARRFLNAKKRSCSQESCSFSGTYSELRKHARSEHPSARPSEVDP 142 (162)
T ss_pred cccCccccCceeceEEc-hHHHHHhccCCccCcccccccccCHHHHHHHHHhhCCCCCCccCCH
Confidence 35799987444433333 346777788888888733333 35678999999644 666766544
No 191
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=48.59 E-value=10 Score=18.48 Aligned_cols=9 Identities=22% Similarity=0.586 Sum_probs=4.7
Q ss_pred ecccccccc
Q psy8167 105 RCELCDKSF 113 (167)
Q Consensus 105 ~C~~C~k~f 113 (167)
.|..|++.+
T Consensus 22 ~C~~C~Y~~ 30 (35)
T PF02150_consen 22 ACRTCGYEE 30 (35)
T ss_dssp EESSSS-EE
T ss_pred CCCCCCCcc
Confidence 566666544
No 192
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=48.28 E-value=5 Score=30.66 Aligned_cols=39 Identities=13% Similarity=0.036 Sum_probs=13.6
Q ss_pred ccccccccccCCHHHHHHHHHHhcCC------CCcccccchhhhhhc
Q psy8167 54 IPCTLCDKTFTRKDSLKKHIRIFHTQ------NQPQHTNVIEVALGA 94 (167)
Q Consensus 54 ~~C~~C~~~f~~~~~l~~H~~~~h~~------~~~~~c~~c~~~~~~ 94 (167)
+.|..|.+.+-.....-.- ..|.. .+-|.|..|++....
T Consensus 253 v~C~~C~yt~~~~~~~C~~--~~H~l~~~~a~KRFFkC~~C~~Rt~s 297 (344)
T PF09332_consen 253 VTCKQCKYTAFKPSDRCKE--EGHPLKWHDAVKRFFKCKDCGNRTIS 297 (344)
T ss_dssp EEETTT--EESS--HHHHH--TT--EEEEEEE-EEEE-T-TS-EEEE
T ss_pred EEcCCCCCcccCcchhHHh--cCCceEEeeeeeeeEECCCCCCeeee
Confidence 6677777644443332211 11322 234666666665444
No 193
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.12 E-value=6.9 Score=20.56 Aligned_cols=19 Identities=16% Similarity=0.576 Sum_probs=15.0
Q ss_pred ecccccccccChhHHHHHH
Q psy8167 105 RCELCDKSFTRKDSLKKHN 123 (167)
Q Consensus 105 ~C~~C~k~f~~~~~l~~H~ 123 (167)
-|++|++.|.++....+-.
T Consensus 14 ICpvCqRPFsWRkKW~~cW 32 (54)
T COG4338 14 ICPVCQRPFSWRKKWARCW 32 (54)
T ss_pred hhhhhcCchHHHHHHHHHH
Confidence 4999999999987766543
No 194
>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=48.09 E-value=6.9 Score=19.03 Aligned_cols=9 Identities=0% Similarity=-0.182 Sum_probs=2.5
Q ss_pred ccchhhhhh
Q psy8167 85 TNVIEVALG 93 (167)
Q Consensus 85 c~~c~~~~~ 93 (167)
|..|++.|.
T Consensus 6 C~eC~~~f~ 14 (34)
T PF01286_consen 6 CDECGKPFM 14 (34)
T ss_dssp -TTT--EES
T ss_pred HhHhCCHHH
Confidence 444444443
No 195
>KOG4173|consensus
Probab=48.08 E-value=15 Score=25.97 Aligned_cols=47 Identities=17% Similarity=0.305 Sum_probs=36.2
Q ss_pred ceeccc--ccccccChhHHHHHHHhhcCCCCCCCCchhhhcCCHHHHHHHHh
Q psy8167 103 RIRCEL--CDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSADFLEVVLN 152 (167)
Q Consensus 103 ~~~C~~--C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 152 (167)
.|.|++ |-..|.....+..|--+.| --.|..|.+.|.+...|.-|+.
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h---~~sCs~C~r~~Pt~hLLd~HI~ 127 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLH---GNSCSFCKRAFPTGHLLDAHIL 127 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcc---cchhHHHHHhCCchhhhhHHHH
Confidence 356766 5577777777777755544 4579999999999999999986
No 196
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=47.99 E-value=12 Score=25.83 Aligned_cols=30 Identities=13% Similarity=0.138 Sum_probs=18.1
Q ss_pred CcccccchhhhhhccccccccCceeccccccc
Q psy8167 81 QPQHTNVIEVALGARANAAFIDRIRCELCDKS 112 (167)
Q Consensus 81 ~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~ 112 (167)
.-|.|+.|...++. .-++...|.|+.||-.
T Consensus 112 ~~y~C~~~~~r~sf--deA~~~~F~Cp~Cg~~ 141 (176)
T COG1675 112 NYYVCPNCHVKYSF--DEAMELGFTCPKCGED 141 (176)
T ss_pred CceeCCCCCCcccH--HHHHHhCCCCCCCCch
Confidence 44677666666665 4444444777777754
No 197
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=47.85 E-value=12 Score=25.40 Aligned_cols=17 Identities=24% Similarity=0.616 Sum_probs=9.3
Q ss_pred eecccccccccChhHHH
Q psy8167 104 IRCELCDKSFTRKDSLK 120 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~ 120 (167)
+.|+.||+.|..-+++.
T Consensus 131 ~~C~~CgkiYW~GsHw~ 147 (165)
T COG1656 131 YRCPKCGKIYWKGSHWR 147 (165)
T ss_pred eECCCCcccccCchHHH
Confidence 34666666555555544
No 198
>PF12773 DZR: Double zinc ribbon
Probab=47.80 E-value=13 Score=19.40 Aligned_cols=9 Identities=0% Similarity=-0.315 Sum_probs=4.2
Q ss_pred CCCCCchhh
Q psy8167 131 DPKLMDEQM 139 (167)
Q Consensus 131 ~~~C~~C~~ 139 (167)
...|..|+.
T Consensus 29 ~~~C~~Cg~ 37 (50)
T PF12773_consen 29 KKICPNCGA 37 (50)
T ss_pred CCCCcCCcC
Confidence 344555544
No 199
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=47.63 E-value=16 Score=30.57 Aligned_cols=7 Identities=29% Similarity=0.923 Sum_probs=3.6
Q ss_pred ccccccc
Q psy8167 106 CELCDKS 112 (167)
Q Consensus 106 C~~C~k~ 112 (167)
|+.||..
T Consensus 44 C~~CG~~ 50 (645)
T PRK14559 44 CPNCGAE 50 (645)
T ss_pred ccccCCc
Confidence 5555543
No 200
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=47.19 E-value=8 Score=27.05 Aligned_cols=48 Identities=13% Similarity=0.032 Sum_probs=27.3
Q ss_pred CcccccchhhhhhccccccccCceecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCC
Q psy8167 81 QPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGS 143 (167)
Q Consensus 81 ~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 143 (167)
-||.|-+|.+.|.. ---..||..|-..-.++... +-..|.+|++....
T Consensus 195 IPF~C~iCKkdy~s---------pvvt~CGH~FC~~Cai~~y~------kg~~C~~Cgk~t~G 242 (259)
T COG5152 195 IPFLCGICKKDYES---------PVVTECGHSFCSLCAIRKYQ------KGDECGVCGKATYG 242 (259)
T ss_pred Cceeehhchhhccc---------hhhhhcchhHHHHHHHHHhc------cCCcceecchhhcc
Confidence 36888888777665 11234565555554444332 24568888775433
No 201
>KOG4118|consensus
Probab=46.82 E-value=14 Score=20.78 Aligned_cols=30 Identities=10% Similarity=0.055 Sum_probs=21.8
Q ss_pred CCCCCchhhhcCCHHHHHHHHhhcCCCCCc
Q psy8167 131 DPKLMDEQMARGSADFLEVVLNEDGEGEPV 160 (167)
Q Consensus 131 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 160 (167)
-|+|.+|--.......+..|....|+..|+
T Consensus 38 ~~kCtVC~~~mpdpktfkqhfe~kHpk~~~ 67 (74)
T KOG4118|consen 38 HHKCTVCMVQMPDPKTFKQHFENKHPKEPL 67 (74)
T ss_pred HhhhHhhHhhCCCCchHHHHHhhcCCCCCC
Confidence 377888877777777777887776665554
No 202
>KOG1842|consensus
Probab=46.64 E-value=13 Score=29.30 Aligned_cols=29 Identities=17% Similarity=0.457 Sum_probs=26.1
Q ss_pred cccccccccccCCHHHHHHHHHHhcCCCC
Q psy8167 53 RIPCTLCDKTFTRKDSLKKHIRIFHTQNQ 81 (167)
Q Consensus 53 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 81 (167)
-|.|++|..-|.....|..|....|.++.
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEED 43 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhccccc
Confidence 48999999999999999999988887763
No 203
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=46.54 E-value=11 Score=18.88 Aligned_cols=10 Identities=20% Similarity=0.740 Sum_probs=4.3
Q ss_pred Cceecccccc
Q psy8167 102 DRIRCELCDK 111 (167)
Q Consensus 102 k~~~C~~C~k 111 (167)
+.+.|+.|+.
T Consensus 23 ~~w~C~~C~~ 32 (40)
T PF04810_consen 23 KTWICNFCGT 32 (40)
T ss_dssp TEEEETTT--
T ss_pred CEEECcCCCC
Confidence 3455555554
No 204
>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=45.81 E-value=5.1 Score=21.48 Aligned_cols=24 Identities=25% Similarity=0.527 Sum_probs=11.1
Q ss_pred ceecccccccccChhHHHHHHHhh
Q psy8167 103 RIRCELCDKSFTRKDSLKKHNRIF 126 (167)
Q Consensus 103 ~~~C~~C~k~f~~~~~l~~H~~~h 126 (167)
.|.|+.|+..|=..-.+-.|..+|
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTTTS-
T ss_pred eEECCCCCCccccCcChhhhcccc
Confidence 467777777776666655555543
No 205
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=45.46 E-value=9.7 Score=19.04 Aligned_cols=15 Identities=20% Similarity=0.600 Sum_probs=11.6
Q ss_pred cccccccccccCCHH
Q psy8167 53 RIPCTLCDKTFTRKD 67 (167)
Q Consensus 53 ~~~C~~C~~~f~~~~ 67 (167)
+|.|..|++.|-..-
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 688999998887653
No 206
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=44.78 E-value=11 Score=20.59 Aligned_cols=44 Identities=9% Similarity=0.172 Sum_probs=21.0
Q ss_pred CcccccchhhhhhccccccccCceecccccccccChhHHHHHHHhhcCCCCCCCCc
Q psy8167 81 QPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMD 136 (167)
Q Consensus 81 ~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~ 136 (167)
..+.|+.....| ..|.....||..|...+-+. ++ ......+|+.
T Consensus 10 ~~~~CPiT~~~~--------~~PV~s~~C~H~fek~aI~~-~i---~~~~~~~CPv 53 (57)
T PF11789_consen 10 ISLKCPITLQPF--------EDPVKSKKCGHTFEKEAILQ-YI---QRNGSKRCPV 53 (57)
T ss_dssp --SB-TTTSSB---------SSEEEESSS--EEEHHHHHH-HC---TTTS-EE-SC
T ss_pred eccCCCCcCChh--------hCCcCcCCCCCeecHHHHHH-HH---HhcCCCCCCC
Confidence 356666654443 33567778888887765543 43 2334566766
No 207
>KOG2807|consensus
Probab=43.82 E-value=36 Score=25.93 Aligned_cols=21 Identities=24% Similarity=0.569 Sum_probs=12.4
Q ss_pred cccccccccccCCHHHHHHHH
Q psy8167 53 RIPCTLCDKTFTRKDSLKKHI 73 (167)
Q Consensus 53 ~~~C~~C~~~f~~~~~l~~H~ 73 (167)
|..|+.|+-.......|.+-.
T Consensus 290 P~eCpiC~ltLVss~hLARSy 310 (378)
T KOG2807|consen 290 PIECPICSLTLVSSPHLARSY 310 (378)
T ss_pred CccCCccceeEecchHHHHHH
Confidence 445666666666666665544
No 208
>KOG1701|consensus
Probab=43.65 E-value=18 Score=28.53 Aligned_cols=45 Identities=18% Similarity=0.217 Sum_probs=27.9
Q ss_pred ccccccccccCCHHHHHHHHHH-hcCCCCcccccchhhhhhccccccc
Q psy8167 54 IPCTLCDKTFTRKDSLKKHIRI-FHTQNQPQHTNVIEVALGARANAAF 100 (167)
Q Consensus 54 ~~C~~C~~~f~~~~~l~~H~~~-~h~~~~~~~c~~c~~~~~~~~~~~l 100 (167)
-.|-.|++...-...-..=|.+ .| ..=|.|..|.+.+.-++..++
T Consensus 275 ~iC~~C~K~V~g~~~ac~Am~~~fH--v~CFtC~~C~r~L~Gq~FY~v 320 (468)
T KOG1701|consen 275 GICAFCHKTVSGQGLAVEAMDQLFH--VQCFTCRTCRRQLAGQSFYQV 320 (468)
T ss_pred hhhhhcCCcccCcchHHHHhhhhhc--ccceehHhhhhhhcccccccc
Confidence 3699999866655443333322 34 335899999888776444444
No 209
>KOG1280|consensus
Probab=42.96 E-value=27 Score=26.75 Aligned_cols=39 Identities=10% Similarity=0.176 Sum_probs=29.1
Q ss_pred CCcccccccccccCCHHHHHHHHHHhcCCCC-cccccchh
Q psy8167 51 IDRIPCTLCDKTFTRKDSLKKHIRIFHTQNQ-PQHTNVIE 89 (167)
Q Consensus 51 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~-~~~c~~c~ 89 (167)
..-|.|++|+..=.....|..|....|.... ..-|+.|+
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 3469999999988888899999988886654 23455553
No 210
>PF04641 Rtf2: Rtf2 RING-finger
Probab=42.88 E-value=2.9 Score=30.61 Aligned_cols=17 Identities=29% Similarity=0.524 Sum_probs=11.6
Q ss_pred CCCcccccccccccCCH
Q psy8167 50 PIDRIPCTLCDKTFTRK 66 (167)
Q Consensus 50 ~~~~~~C~~C~~~f~~~ 66 (167)
....|.|++.+..|...
T Consensus 110 ~~~~~~CPvt~~~~~~~ 126 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGK 126 (260)
T ss_pred CCceeECCCCCcccCCc
Confidence 34668898888776433
No 211
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=42.60 E-value=11 Score=23.33 Aligned_cols=11 Identities=27% Similarity=0.827 Sum_probs=5.5
Q ss_pred eeccccccccc
Q psy8167 104 IRCELCDKSFT 114 (167)
Q Consensus 104 ~~C~~C~k~f~ 114 (167)
+.|..||..|.
T Consensus 3 H~CtrCG~vf~ 13 (112)
T COG3364 3 HQCTRCGEVFD 13 (112)
T ss_pred ceecccccccc
Confidence 34555555443
No 212
>PTZ00448 hypothetical protein; Provisional
Probab=42.38 E-value=24 Score=27.26 Aligned_cols=22 Identities=23% Similarity=0.628 Sum_probs=11.4
Q ss_pred eecccccccccChhHHHHHHHh
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRI 125 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~ 125 (167)
|.|..|+-.|......+.|+++
T Consensus 315 ~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 315 LLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred ccccccccccCCHHHHHHHhhh
Confidence 4455555555544555555544
No 213
>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=41.63 E-value=11 Score=20.17 Aligned_cols=12 Identities=25% Similarity=0.863 Sum_probs=6.3
Q ss_pred ecccccccccCh
Q psy8167 105 RCELCDKSFTRK 116 (167)
Q Consensus 105 ~C~~C~k~f~~~ 116 (167)
.|++|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 799999888765
No 214
>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=41.51 E-value=15 Score=27.74 Aligned_cols=77 Identities=16% Similarity=0.091 Sum_probs=41.2
Q ss_pred cccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccccCceecccccccccChhHHHHHHHhhc-----
Q psy8167 53 RIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRIFH----- 127 (167)
Q Consensus 53 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~h~----- 127 (167)
.-.|++||..-. ..+.... ....|.+-..|..|+..-.. .+..|..||.. ..|. ......
T Consensus 184 ~~~CPvCGs~P~--~s~~~~~-~~~~G~RyL~CslC~teW~~-------~R~~C~~Cg~~----~~l~-y~~~e~~~~~~ 248 (305)
T TIGR01562 184 RTLCPACGSPPV--ASMVRQG-GKETGLRYLSCSLCATEWHY-------VRVKCSHCEES----KHLA-YLSLEHDAEKA 248 (305)
T ss_pred CCcCCCCCChhh--hhhhccc-CCCCCceEEEcCCCCCcccc-------cCccCCCCCCC----Ccee-eEeecCCCCCc
Confidence 347999996321 1111110 11456678899999754332 34689999953 1222 111111
Q ss_pred CCCCCCCCchhhhcCCH
Q psy8167 128 GGADPKLMDEQMARGSA 144 (167)
Q Consensus 128 ~~~~~~C~~C~~~f~~~ 144 (167)
+.+-..|..|+...+.-
T Consensus 249 ~~r~e~C~~C~~YlK~~ 265 (305)
T TIGR01562 249 VLKAETCDSCQGYLKIL 265 (305)
T ss_pred ceEEeeccccccchhhh
Confidence 12345788888766654
No 215
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=41.31 E-value=13 Score=29.96 Aligned_cols=7 Identities=29% Similarity=0.904 Sum_probs=3.1
Q ss_pred eeccccc
Q psy8167 104 IRCELCD 110 (167)
Q Consensus 104 ~~C~~C~ 110 (167)
|.|+.||
T Consensus 459 ~~cp~c~ 465 (479)
T PRK05452 459 FLCPECS 465 (479)
T ss_pred CcCcCCC
Confidence 3444444
No 216
>KOG2071|consensus
Probab=41.13 E-value=13 Score=30.38 Aligned_cols=28 Identities=0% Similarity=-0.114 Sum_probs=20.1
Q ss_pred CCCCCCCCchhhhcCCHHHHHHHHhhcC
Q psy8167 128 GGADPKLMDEQMARGSADFLEVVLNEDG 155 (167)
Q Consensus 128 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 155 (167)
...+-+|..||..|........|+..|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 4556778888888887777777776554
No 217
>COG4640 Predicted membrane protein [Function unknown]
Probab=40.73 E-value=16 Score=28.47 Aligned_cols=16 Identities=31% Similarity=0.837 Sum_probs=10.4
Q ss_pred eecccccccccChhHH
Q psy8167 104 IRCELCDKSFTRKDSL 119 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l 119 (167)
..|.+||..|......
T Consensus 16 ~qC~qCG~~~t~~~sq 31 (465)
T COG4640 16 VQCTQCGHKFTSRQSQ 31 (465)
T ss_pred ccccccCCcCCchhhh
Confidence 4488888777666443
No 218
>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=40.48 E-value=8.5 Score=19.20 Aligned_cols=9 Identities=22% Similarity=0.549 Sum_probs=4.3
Q ss_pred eeccccccc
Q psy8167 104 IRCELCDKS 112 (167)
Q Consensus 104 ~~C~~C~k~ 112 (167)
|.|..||+.
T Consensus 29 y~C~~C~~~ 37 (39)
T PF01096_consen 29 YVCCNCGHR 37 (39)
T ss_dssp EEESSSTEE
T ss_pred EEeCCCCCe
Confidence 445555543
No 219
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=40.44 E-value=30 Score=18.70 Aligned_cols=29 Identities=7% Similarity=-0.033 Sum_probs=16.4
Q ss_pred cccccccChhHHHHHHHhhcCCCCCCCCchhhhcC
Q psy8167 108 LCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARG 142 (167)
Q Consensus 108 ~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 142 (167)
-||..|.+.. +..+++. ...|+.|++.+.
T Consensus 18 ~~G~v~~~~~-i~~~~~~-----~~~cP~~~~~~~ 46 (63)
T smart00504 18 PSGQTYERRA-IEKWLLS-----HGTDPVTGQPLT 46 (63)
T ss_pred CCCCEEeHHH-HHHHHHH-----CCCCCCCcCCCC
Confidence 4566665443 3445443 346888877764
No 220
>PRK12496 hypothetical protein; Provisional
Probab=40.04 E-value=11 Score=25.52 Aligned_cols=11 Identities=0% Similarity=-0.212 Sum_probs=5.8
Q ss_pred ccccchhhhhh
Q psy8167 83 QHTNVIEVALG 93 (167)
Q Consensus 83 ~~c~~c~~~~~ 93 (167)
+.|.-|++.|.
T Consensus 128 ~~C~gC~~~~~ 138 (164)
T PRK12496 128 KVCKGCKKKYP 138 (164)
T ss_pred EECCCCCcccc
Confidence 44555555553
No 221
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=39.92 E-value=17 Score=19.69 Aligned_cols=25 Identities=12% Similarity=0.248 Sum_probs=13.0
Q ss_pred ccccchhhhhhccccccccCceeccccccc
Q psy8167 83 QHTNVIEVALGARANAAFIDRIRCELCDKS 112 (167)
Q Consensus 83 ~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~ 112 (167)
-.|..|++.|.. ...+ -.|+.||..
T Consensus 6 ~~C~~Cg~~~~~--~dDi---VvCp~Cgap 30 (54)
T PF14446_consen 6 CKCPVCGKKFKD--GDDI---VVCPECGAP 30 (54)
T ss_pred ccChhhCCcccC--CCCE---EECCCCCCc
Confidence 356666666643 1111 357777744
No 222
>PRK05580 primosome assembly protein PriA; Validated
Probab=39.81 E-value=7.8 Score=32.57 Aligned_cols=13 Identities=0% Similarity=-0.276 Sum_probs=8.3
Q ss_pred CCCCCCCCchhhh
Q psy8167 128 GGADPKLMDEQMA 140 (167)
Q Consensus 128 ~~~~~~C~~C~~~ 140 (167)
...+..|+.|+..
T Consensus 418 ~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 418 EPIPKACPECGST 430 (679)
T ss_pred CCCCCCCCCCcCC
Confidence 3446778888654
No 223
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=39.72 E-value=4.5 Score=25.65 Aligned_cols=16 Identities=13% Similarity=0.420 Sum_probs=11.4
Q ss_pred CcccccccccccCCHH
Q psy8167 52 DRIPCTLCDKTFTRKD 67 (167)
Q Consensus 52 ~~~~C~~C~~~f~~~~ 67 (167)
..+.|..||..+....
T Consensus 21 ~~l~C~kCgye~~~~~ 36 (113)
T COG1594 21 GKLVCRKCGYEEEASN 36 (113)
T ss_pred cEEECCCCCcchhccc
Confidence 3688999998666553
No 224
>PRK00420 hypothetical protein; Validated
Probab=39.41 E-value=18 Score=22.89 Aligned_cols=29 Identities=17% Similarity=0.189 Sum_probs=16.5
Q ss_pred ccccchhhhhhccccccccCceecccccccccC
Q psy8167 83 QHTNVIEVALGARANAAFIDRIRCELCDKSFTR 115 (167)
Q Consensus 83 ~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~ 115 (167)
-.|+.||..+.. . -.....|+.||....-
T Consensus 24 ~~CP~Cg~pLf~--l--k~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 24 KHCPVCGLPLFE--L--KDGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCCCccee--c--CCCceECCCCCCeeee
Confidence 567777765442 1 0223468888875544
No 225
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=38.89 E-value=3.8 Score=29.54 Aligned_cols=37 Identities=11% Similarity=0.143 Sum_probs=12.3
Q ss_pred Ccccccchhhhh-hccccccccCceecccccccccChh
Q psy8167 81 QPQHTNVIEVAL-GARANAAFIDRIRCELCDKSFTRKD 117 (167)
Q Consensus 81 ~~~~c~~c~~~~-~~~~~~~l~k~~~C~~C~k~f~~~~ 117 (167)
+...|+.||..- ..-........|-|..|+..|..++
T Consensus 30 ~n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELKS 67 (254)
T PF06044_consen 30 ENMYCPNCGSKPLSKFENNRPVADFYCPNCNEEYELKS 67 (254)
T ss_dssp HH---TTT--SS-EE--------EEE-TTT--EEEEEE
T ss_pred HCCcCCCCCChhHhhccCCCccceeECCCCchHHhhhh
Confidence 345677776652 1111122255677888877776554
No 226
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=38.66 E-value=17 Score=27.50 Aligned_cols=78 Identities=18% Similarity=0.147 Sum_probs=43.3
Q ss_pred CcccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccccCceecccccccccChhHHHHH-HHhh-cCC
Q psy8167 52 DRIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKH-NRIF-HGG 129 (167)
Q Consensus 52 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H-~~~h-~~~ 129 (167)
..-.|++||..-. ..+ .+. ....|.+-..|..|+..-.. .+..|..||.. ..|.-+ ...- ...
T Consensus 186 ~~~~CPvCGs~P~--~s~-v~~-~~~~G~RyL~CslC~teW~~-------~R~~C~~Cg~~----~~l~y~~~~~~~~~~ 250 (309)
T PRK03564 186 QRQFCPVCGSMPV--SSV-VQI-GTTQGLRYLHCNLCESEWHV-------VRVKCSNCEQS----GKLHYWSLDSEQAAV 250 (309)
T ss_pred CCCCCCCCCCcch--hhe-eec-cCCCCceEEEcCCCCCcccc-------cCccCCCCCCC----CceeeeeecCCCcce
Confidence 3467999996322 111 122 22456778899999754332 33589999952 222211 1100 112
Q ss_pred CCCCCCchhhhcCCH
Q psy8167 130 ADPKLMDEQMARGSA 144 (167)
Q Consensus 130 ~~~~C~~C~~~f~~~ 144 (167)
+-..|..|+..++.-
T Consensus 251 r~e~C~~C~~YlK~~ 265 (309)
T PRK03564 251 KAESCGDCGTYLKIL 265 (309)
T ss_pred Eeeecccccccceec
Confidence 347799998777664
No 227
>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=38.61 E-value=13 Score=22.84 Aligned_cols=20 Identities=5% Similarity=-0.184 Sum_probs=14.0
Q ss_pred HHhhcCCCCCCCCchhhhcCC
Q psy8167 123 NRIFHGGADPKLMDEQMARGS 143 (167)
Q Consensus 123 ~~~h~~~~~~~C~~C~~~f~~ 143 (167)
+..+ .++++.|..||..|.-
T Consensus 72 ~~l~-~g~~~rC~eCG~~fkL 91 (97)
T cd00924 72 MWLE-KGKPKRCPECGHVFKL 91 (97)
T ss_pred EEEe-CCCceeCCCCCcEEEE
Confidence 4443 3478999999888753
No 228
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=38.11 E-value=22 Score=18.98 Aligned_cols=9 Identities=33% Similarity=0.955 Sum_probs=5.3
Q ss_pred eeccccccc
Q psy8167 104 IRCELCDKS 112 (167)
Q Consensus 104 ~~C~~C~k~ 112 (167)
++|+.|+..
T Consensus 25 IKCpRC~ti 33 (51)
T PF10122_consen 25 IKCPRCKTI 33 (51)
T ss_pred EECCCCCcc
Confidence 456666644
No 229
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=38.08 E-value=17 Score=28.68 Aligned_cols=14 Identities=0% Similarity=-0.221 Sum_probs=8.6
Q ss_pred CCCCCchhhhcCCH
Q psy8167 131 DPKLMDEQMARGSA 144 (167)
Q Consensus 131 ~~~C~~C~~~f~~~ 144 (167)
-|+|..||..+...
T Consensus 367 g~rC~kCg~~~~~~ 380 (421)
T COG1571 367 GFRCKKCGTRARET 380 (421)
T ss_pred CcccccccccCCcc
Confidence 56666666665554
No 230
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=37.92 E-value=16 Score=31.33 Aligned_cols=33 Identities=9% Similarity=0.000 Sum_probs=14.8
Q ss_pred cccchhhhhhccccccccCceecccccccccCh
Q psy8167 84 HTNVIEVALGARANAAFIDRIRCELCDKSFTRK 116 (167)
Q Consensus 84 ~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~ 116 (167)
.|..|++.|..-...-..+++.|..||..|-..
T Consensus 462 tC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~ 494 (1374)
T PTZ00303 462 SCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVF 494 (1374)
T ss_pred cccCcCCcccccccccccccccccCCccccCcc
Confidence 355666555431011112445566666544443
No 231
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=37.89 E-value=31 Score=25.74 Aligned_cols=22 Identities=9% Similarity=-0.422 Sum_probs=11.1
Q ss_pred CCCCCchhhhcCCHHHHHHHHh
Q psy8167 131 DPKLMDEQMARGSADFLEVVLN 152 (167)
Q Consensus 131 ~~~C~~C~~~f~~~~~l~~H~~ 152 (167)
-|-|..|=+.|.+...|.+|+.
T Consensus 48 lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 48 LYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred EEEcCCCcchhCCHHHHHHHHH
Confidence 3445555555555555555544
No 232
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=37.71 E-value=3.5 Score=21.56 Aligned_cols=12 Identities=0% Similarity=-0.427 Sum_probs=6.7
Q ss_pred CCCCCc--hhhhcC
Q psy8167 131 DPKLMD--EQMARG 142 (167)
Q Consensus 131 ~~~C~~--C~~~f~ 142 (167)
-++|.. ||..|.
T Consensus 25 Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 25 YCQCTNPECGHTFV 38 (47)
T ss_pred EEEECCCcCCCEEE
Confidence 355554 666654
No 233
>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=37.71 E-value=15 Score=18.66 Aligned_cols=15 Identities=40% Similarity=0.758 Sum_probs=8.9
Q ss_pred CceecccccccccCh
Q psy8167 102 DRIRCELCDKSFTRK 116 (167)
Q Consensus 102 k~~~C~~C~k~f~~~ 116 (167)
-++.|..|++.|=..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 357899999888654
No 234
>KOG0402|consensus
Probab=37.36 E-value=16 Score=21.67 Aligned_cols=30 Identities=13% Similarity=0.174 Sum_probs=15.5
Q ss_pred cccccchhhhhhccccccccCceeccccccccc
Q psy8167 82 PQHTNVIEVALGARANAAFIDRIRCELCDKSFT 114 (167)
Q Consensus 82 ~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~ 114 (167)
.|.|..||+....+.... -+.|..|.+.|.
T Consensus 36 ky~CsfCGK~~vKR~AvG---iW~C~~C~kv~a 65 (92)
T KOG0402|consen 36 KYTCSFCGKKTVKRKAVG---IWKCGSCKKVVA 65 (92)
T ss_pred hhhhhhcchhhhhhhcee---EEecCCccceec
Confidence 366777766544311111 256666666554
No 235
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.35 E-value=27 Score=20.53 Aligned_cols=40 Identities=15% Similarity=0.172 Sum_probs=23.8
Q ss_pred ccchhhhhhccccccccCceecccccccccChhHHHHHHHh
Q psy8167 85 TNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRI 125 (167)
Q Consensus 85 c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~ 125 (167)
|++|+-.........++.. .|+.|+-....+..|..-+..
T Consensus 4 CP~C~v~l~~~~rs~vEiD-~CPrCrGVWLDrGELdKli~r 43 (88)
T COG3809 4 CPICGVELVMSVRSGVEID-YCPRCRGVWLDRGELDKLIER 43 (88)
T ss_pred cCcCCceeeeeeecCceee-eCCccccEeecchhHHHHHHH
Confidence 5555544333222333333 399999998888888766554
No 236
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=37.26 E-value=16 Score=29.19 Aligned_cols=7 Identities=29% Similarity=0.947 Sum_probs=4.0
Q ss_pred eeccccc
Q psy8167 104 IRCELCD 110 (167)
Q Consensus 104 ~~C~~C~ 110 (167)
.+|+.|+
T Consensus 22 g~Cp~C~ 28 (454)
T TIGR00416 22 GKCPACH 28 (454)
T ss_pred EECcCCC
Confidence 4566665
No 237
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=37.19 E-value=15 Score=23.67 Aligned_cols=11 Identities=27% Similarity=0.510 Sum_probs=5.1
Q ss_pred cccccccccccC
Q psy8167 53 RIPCTLCDKTFT 64 (167)
Q Consensus 53 ~~~C~~C~~~f~ 64 (167)
.+.| .||..|.
T Consensus 70 ~~~C-~Cg~~~~ 80 (124)
T PRK00762 70 EIEC-ECGYEGV 80 (124)
T ss_pred eEEe-eCcCccc
Confidence 3445 5554433
No 238
>KOG2071|consensus
Probab=37.18 E-value=20 Score=29.46 Aligned_cols=28 Identities=21% Similarity=0.418 Sum_probs=23.5
Q ss_pred CCcccccccccccCCHHHHHHHHHHhcCC
Q psy8167 51 IDRIPCTLCDKTFTRKDSLKKHIRIFHTQ 79 (167)
Q Consensus 51 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 79 (167)
..+-.|..||.+|.+......|| ..|..
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~m-d~H~d 443 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHM-DIHDD 443 (579)
T ss_pred CCcchhcccccccccchhhhhHh-hhhhh
Confidence 45688999999999999999998 66754
No 239
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=37.12 E-value=15 Score=18.62 Aligned_cols=10 Identities=20% Similarity=0.956 Sum_probs=8.0
Q ss_pred eecccccccc
Q psy8167 104 IRCELCDKSF 113 (167)
Q Consensus 104 ~~C~~C~k~f 113 (167)
-.|++||..|
T Consensus 30 ~~CpYCg~~y 39 (40)
T PF10276_consen 30 VVCPYCGTRY 39 (40)
T ss_dssp EEETTTTEEE
T ss_pred EECCCCCCEE
Confidence 5788888776
No 240
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=37.08 E-value=9.3 Score=32.07 Aligned_cols=72 Identities=13% Similarity=0.105 Sum_probs=37.4
Q ss_pred cccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccc--cCc------e-ecccccccccChhHHHHHH
Q psy8167 53 RIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAF--IDR------I-RCELCDKSFTRKDSLKKHN 123 (167)
Q Consensus 53 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l--~k~------~-~C~~C~k~f~~~~~l~~H~ 123 (167)
.-.|+.|-+.+.+..+=+-+. .--.|..||=+|.- .-.| .+. | -|+.|.+.|....+-+-|
T Consensus 101 ~a~C~~Cl~Ei~dp~~rrY~Y-------PF~~CT~CGPRfTI--i~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfH- 170 (750)
T COG0068 101 AATCEDCLEEIFDPNSRRYLY-------PFINCTNCGPRFTI--IEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFH- 170 (750)
T ss_pred hhhhHHHHHHhcCCCCcceec-------cccccCCCCcceee--eccCCCCcccCccccCcCCHHHHHHhcCccccccc-
Confidence 345777765444443311110 11357777766654 2222 111 2 388888877776664333
Q ss_pred HhhcCCCCCCCCchhh
Q psy8167 124 RIFHGGADPKLMDEQM 139 (167)
Q Consensus 124 ~~h~~~~~~~C~~C~~ 139 (167)
. .|..|+.||=
T Consensus 171 ----A-Qp~aCp~CGP 181 (750)
T COG0068 171 ----A-QPIACPKCGP 181 (750)
T ss_pred ----c-ccccCcccCC
Confidence 2 2777888863
No 241
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=37.08 E-value=17 Score=19.78 Aligned_cols=7 Identities=29% Similarity=0.952 Sum_probs=3.6
Q ss_pred eeccccc
Q psy8167 104 IRCELCD 110 (167)
Q Consensus 104 ~~C~~C~ 110 (167)
|.|+.||
T Consensus 15 ~~Cp~cG 21 (55)
T PF13824_consen 15 FECPDCG 21 (55)
T ss_pred CcCCCCC
Confidence 4555555
No 242
>PRK04351 hypothetical protein; Provisional
Probab=36.44 E-value=17 Score=24.34 Aligned_cols=33 Identities=15% Similarity=0.170 Sum_probs=22.5
Q ss_pred ceecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCC
Q psy8167 103 RIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGS 143 (167)
Q Consensus 103 ~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 143 (167)
.|.|..||..+.+. +. +....|.|..|+-.+..
T Consensus 112 ~Y~C~~Cg~~~~r~-------Rr-~n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 112 LYECQSCGQQYLRK-------RR-INTKRYRCGKCRGKLKL 144 (149)
T ss_pred EEECCCCCCEeeee-------ee-cCCCcEEeCCCCcEeee
Confidence 37898899776542 22 34478999999866543
No 243
>PLN02294 cytochrome c oxidase subunit Vb
Probab=36.40 E-value=14 Score=25.27 Aligned_cols=21 Identities=5% Similarity=-0.276 Sum_probs=15.7
Q ss_pred HHhhcCCCCCCCCchhhhcCCH
Q psy8167 123 NRIFHGGADPKLMDEQMARGSA 144 (167)
Q Consensus 123 ~~~h~~~~~~~C~~C~~~f~~~ 144 (167)
+.. +.+++..|..||..|.-.
T Consensus 134 f~L-~kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 134 FWL-EKGKSFECPVCTQYFELE 154 (174)
T ss_pred EEe-cCCCceeCCCCCCEEEEE
Confidence 444 456799999999988643
No 244
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=36.38 E-value=22 Score=25.97 Aligned_cols=34 Identities=24% Similarity=0.442 Sum_probs=22.3
Q ss_pred CceecccccccccChhHHHHHHHhhcCCCCCCCCchhh
Q psy8167 102 DRIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQM 139 (167)
Q Consensus 102 k~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 139 (167)
..+.|..|+..+......... ....+..|+.|+.
T Consensus 121 ~~~~C~~C~~~~~~~~~~~~~----~~~~~p~C~~Cg~ 154 (250)
T COG0846 121 KRVRCSKCGNQYYDEDVIKFI----EDGLIPRCPKCGG 154 (250)
T ss_pred eeeEeCCCcCccchhhhhhhc----ccCCCCcCccCCC
Confidence 445799999888755422211 2226889999987
No 245
>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=35.96 E-value=24 Score=19.74 Aligned_cols=9 Identities=0% Similarity=-0.286 Sum_probs=3.6
Q ss_pred CCCCchhhh
Q psy8167 132 PKLMDEQMA 140 (167)
Q Consensus 132 ~~C~~C~~~ 140 (167)
+.|+.||..
T Consensus 47 ~~C~~Cg~~ 55 (69)
T PF07282_consen 47 FTCPNCGFE 55 (69)
T ss_pred EEcCCCCCE
Confidence 344444433
No 246
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=35.89 E-value=25 Score=18.67 Aligned_cols=7 Identities=0% Similarity=-0.610 Sum_probs=2.9
Q ss_pred CCCCchh
Q psy8167 132 PKLMDEQ 138 (167)
Q Consensus 132 ~~C~~C~ 138 (167)
+.|..||
T Consensus 38 ~~C~~Cg 44 (50)
T PRK00432 38 WHCGKCG 44 (50)
T ss_pred EECCCcC
Confidence 3344443
No 247
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=35.82 E-value=16 Score=24.41 Aligned_cols=12 Identities=0% Similarity=-0.175 Sum_probs=6.9
Q ss_pred ccccchhhhhhc
Q psy8167 83 QHTNVIEVALGA 94 (167)
Q Consensus 83 ~~c~~c~~~~~~ 94 (167)
-.|..|+..|..
T Consensus 29 ReC~~C~~RFTT 40 (156)
T COG1327 29 RECLECGERFTT 40 (156)
T ss_pred hcccccccccch
Confidence 456666665555
No 248
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=35.56 E-value=19 Score=30.85 Aligned_cols=33 Identities=12% Similarity=0.165 Sum_probs=19.0
Q ss_pred ecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCCH
Q psy8167 105 RCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSA 144 (167)
Q Consensus 105 ~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 144 (167)
.|..|++.|...... .+.+++.|..||..|-..
T Consensus 462 tC~~C~kkFfSlsK~-------L~~RKHHCRkCGrVFC~~ 494 (1374)
T PTZ00303 462 SCPSCGRAFISLSRP-------LGTRAHHCRSCGIRLCVF 494 (1374)
T ss_pred cccCcCCcccccccc-------cccccccccCCccccCcc
Confidence 599999999764210 122345566666555443
No 249
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=35.46 E-value=18 Score=24.05 Aligned_cols=11 Identities=36% Similarity=0.863 Sum_probs=5.1
Q ss_pred ecccccccccC
Q psy8167 105 RCELCDKSFTR 115 (167)
Q Consensus 105 ~C~~C~k~f~~ 115 (167)
.|..||+.|..
T Consensus 30 eC~~C~~RFTT 40 (147)
T TIGR00244 30 ECLECHERFTT 40 (147)
T ss_pred cCCccCCccce
Confidence 34444444444
No 250
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=35.33 E-value=17 Score=18.21 Aligned_cols=8 Identities=0% Similarity=-0.484 Sum_probs=3.3
Q ss_pred CCCCchhh
Q psy8167 132 PKLMDEQM 139 (167)
Q Consensus 132 ~~C~~C~~ 139 (167)
|.|..|++
T Consensus 29 y~C~~C~~ 36 (40)
T smart00440 29 YVCTKCGH 36 (40)
T ss_pred EEeCCCCC
Confidence 44444443
No 251
>KOG1729|consensus
Probab=35.30 E-value=5.6 Score=29.63 Aligned_cols=6 Identities=0% Similarity=-0.861 Sum_probs=2.9
Q ss_pred CCCchh
Q psy8167 133 KLMDEQ 138 (167)
Q Consensus 133 ~C~~C~ 138 (167)
.|+.|-
T Consensus 216 vC~~CF 221 (288)
T KOG1729|consen 216 VCDICF 221 (288)
T ss_pred ecHHHH
Confidence 455553
No 252
>PRK11823 DNA repair protein RadA; Provisional
Probab=35.15 E-value=18 Score=28.81 Aligned_cols=7 Identities=43% Similarity=0.952 Sum_probs=3.6
Q ss_pred eeccccc
Q psy8167 104 IRCELCD 110 (167)
Q Consensus 104 ~~C~~C~ 110 (167)
.+|+.|+
T Consensus 22 g~Cp~C~ 28 (446)
T PRK11823 22 GRCPECG 28 (446)
T ss_pred eeCcCCC
Confidence 3455554
No 253
>KOG2907|consensus
Probab=35.02 E-value=29 Score=21.92 Aligned_cols=8 Identities=25% Similarity=0.787 Sum_probs=6.5
Q ss_pred cccccccc
Q psy8167 54 IPCTLCDK 61 (167)
Q Consensus 54 ~~C~~C~~ 61 (167)
.+|+.||-
T Consensus 75 ~kCpkCgh 82 (116)
T KOG2907|consen 75 HKCPKCGH 82 (116)
T ss_pred ccCcccCC
Confidence 67999985
No 254
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=34.86 E-value=23 Score=23.38 Aligned_cols=33 Identities=15% Similarity=0.116 Sum_probs=21.4
Q ss_pred ceecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcC
Q psy8167 103 RIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARG 142 (167)
Q Consensus 103 ~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 142 (167)
.|.|..|+..+.+ +.+ +.....|.|..|+-.+.
T Consensus 112 ~y~C~~C~~~~~~------~rr-~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRYLR------VRR-SNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCCce------Ecc-ccCcceEEcCCCCCEEE
Confidence 5789889977642 222 22226799999986553
No 255
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=34.82 E-value=25 Score=23.03 Aligned_cols=57 Identities=12% Similarity=0.158 Sum_probs=32.8
Q ss_pred CCCCcccccchhhhhhccccccccCceec---ccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCCHH
Q psy8167 78 TQNQPQHTNVIEVALGARANAAFIDRIRC---ELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSAD 145 (167)
Q Consensus 78 ~~~~~~~c~~c~~~~~~~~~~~l~k~~~C---~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~ 145 (167)
...+-|+|.+|..+... ...| ||-.| .+|+--+ .+|..|-. .-.+|+.|.-+|.+..
T Consensus 76 ~d~~lYeCnIC~etS~e--e~FL-KPneCCgY~iCn~Cy---a~LWK~~~-----~ypvCPvCkTSFKss~ 135 (140)
T PF05290_consen 76 LDPKLYECNICKETSAE--ERFL-KPNECCGYSICNACY---ANLWKFCN-----LYPVCPVCKTSFKSSS 135 (140)
T ss_pred cCCCceeccCcccccch--hhcC-CcccccchHHHHHHH---HHHHHHcc-----cCCCCCcccccccccc
Confidence 44577999999887766 3222 23333 1232222 23444433 3568999998888764
No 256
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=34.75 E-value=17 Score=26.60 Aligned_cols=27 Identities=26% Similarity=0.381 Sum_probs=21.1
Q ss_pred ecccccccccChhHHHHHHHhhcCCCCCCCCchh
Q psy8167 105 RCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQ 138 (167)
Q Consensus 105 ~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~ 138 (167)
.|+.||........| |..-.|+|+.|-
T Consensus 222 ~CP~Cg~~W~L~~pl-------h~iFdFKCD~CR 248 (258)
T PF10071_consen 222 KCPSCGGDWRLKEPL-------HDIFDFKCDPCR 248 (258)
T ss_pred CCCCCCCccccCCch-------hhceeccCCcce
Confidence 699999887776665 455689999985
No 257
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=34.35 E-value=10 Score=23.40 Aligned_cols=12 Identities=0% Similarity=-0.344 Sum_probs=6.7
Q ss_pred CCCCchhhhcCC
Q psy8167 132 PKLMDEQMARGS 143 (167)
Q Consensus 132 ~~C~~C~~~f~~ 143 (167)
..|..||..+..
T Consensus 43 ~~C~~CG~y~~~ 54 (99)
T PRK14892 43 ITCGNCGLYTEF 54 (99)
T ss_pred EECCCCCCccCE
Confidence 456666655543
No 258
>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=34.22 E-value=14 Score=23.02 Aligned_cols=8 Identities=0% Similarity=-0.429 Sum_probs=5.3
Q ss_pred CCCCchhh
Q psy8167 132 PKLMDEQM 139 (167)
Q Consensus 132 ~~C~~C~~ 139 (167)
|.|..|+-
T Consensus 32 y~C~~C~A 39 (102)
T PF11672_consen 32 YVCTPCDA 39 (102)
T ss_pred EECCCCCc
Confidence 67777753
No 259
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=33.67 E-value=88 Score=24.22 Aligned_cols=22 Identities=18% Similarity=0.643 Sum_probs=11.1
Q ss_pred Ccccccccc-cccCCHHHHHHHH
Q psy8167 52 DRIPCTLCD-KTFTRKDSLKKHI 73 (167)
Q Consensus 52 ~~~~C~~C~-~~f~~~~~l~~H~ 73 (167)
+.|.|.+|| +.+.-+..|.+|.
T Consensus 373 ~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 373 IEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred cceeeeecccccccchHHHHhhh
Confidence 345566665 4444444454443
No 260
>PRK05978 hypothetical protein; Provisional
Probab=33.66 E-value=21 Score=23.82 Aligned_cols=8 Identities=25% Similarity=0.742 Sum_probs=4.9
Q ss_pred cccccccc
Q psy8167 54 IPCTLCDK 61 (167)
Q Consensus 54 ~~C~~C~~ 61 (167)
-+|+.||+
T Consensus 34 grCP~CG~ 41 (148)
T PRK05978 34 GRCPACGE 41 (148)
T ss_pred CcCCCCCC
Confidence 45666665
No 261
>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=33.66 E-value=16 Score=24.16 Aligned_cols=31 Identities=16% Similarity=0.223 Sum_probs=18.9
Q ss_pred ceecccccccccChhHHHHHHHhhcCCCCCCCCchhhhc
Q psy8167 103 RIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMAR 141 (167)
Q Consensus 103 ~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 141 (167)
.|.|..|+..+.... +. ....|.|..|+-.|
T Consensus 123 ~~~C~~C~~~~~r~~------~~--~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 123 VYRCPSCGREYKRHR------RS--KRKRYRCGRCGGPL 153 (157)
T ss_pred EEEcCCCCCEeeeec------cc--chhhEECCCCCCEE
Confidence 467888887764432 22 22358888887554
No 262
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.63 E-value=19 Score=23.21 Aligned_cols=13 Identities=23% Similarity=0.654 Sum_probs=9.3
Q ss_pred ecccccccccChh
Q psy8167 105 RCELCDKSFTRKD 117 (167)
Q Consensus 105 ~C~~C~k~f~~~~ 117 (167)
-|..||+.|.+-.
T Consensus 70 fchncgs~fpwte 82 (160)
T COG4306 70 FCHNCGSRFPWTE 82 (160)
T ss_pred hhhcCCCCCCcHH
Confidence 4778888887753
No 263
>KOG1994|consensus
Probab=33.54 E-value=23 Score=25.40 Aligned_cols=21 Identities=19% Similarity=0.616 Sum_probs=18.5
Q ss_pred CcccccccccccCCHHHHHHH
Q psy8167 52 DRIPCTLCDKTFTRKDSLKKH 72 (167)
Q Consensus 52 ~~~~C~~C~~~f~~~~~l~~H 72 (167)
.-|.|-+||..|.....|..|
T Consensus 238 eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 238 EHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred cceEEEEeccccCCHHHHHHh
Confidence 348899999999999999776
No 264
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=33.16 E-value=17 Score=25.42 Aligned_cols=9 Identities=44% Similarity=1.099 Sum_probs=6.3
Q ss_pred ccccccccc
Q psy8167 54 IPCTLCDKT 62 (167)
Q Consensus 54 ~~C~~C~~~ 62 (167)
..|+.||..
T Consensus 15 ~~CPvCg~~ 23 (201)
T COG1779 15 IDCPVCGGT 23 (201)
T ss_pred ecCCcccce
Confidence 558888863
No 265
>PF15616 TerY-C: TerY-C metal binding domain
Probab=32.47 E-value=26 Score=22.87 Aligned_cols=9 Identities=0% Similarity=-0.525 Sum_probs=4.3
Q ss_pred CCCCCchhh
Q psy8167 131 DPKLMDEQM 139 (167)
Q Consensus 131 ~~~C~~C~~ 139 (167)
...|+.|++
T Consensus 105 ~~~CPwCg~ 113 (131)
T PF15616_consen 105 EVTCPWCGN 113 (131)
T ss_pred CEECCCCCC
Confidence 444555543
No 266
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=31.63 E-value=24 Score=27.43 Aligned_cols=21 Identities=10% Similarity=0.003 Sum_probs=11.1
Q ss_pred ccccchhhhhhccccccccCceeccccc
Q psy8167 83 QHTNVIEVALGARANAAFIDRIRCELCD 110 (167)
Q Consensus 83 ~~c~~c~~~~~~~~~~~l~k~~~C~~C~ 110 (167)
|.|..||..... + -.+|+.|+
T Consensus 1 ~~c~~cg~~~~~--~-----~g~cp~c~ 21 (372)
T cd01121 1 YVCSECGYVSPK--W-----LGKCPECG 21 (372)
T ss_pred CCCCCCCCCCCC--c-----cEECcCCC
Confidence 456666654443 1 14566666
No 267
>KOG3990|consensus
Probab=31.45 E-value=29 Score=25.35 Aligned_cols=15 Identities=20% Similarity=0.481 Sum_probs=8.5
Q ss_pred cccccccccccCCHH
Q psy8167 53 RIPCTLCDKTFTRKD 67 (167)
Q Consensus 53 ~~~C~~C~~~f~~~~ 67 (167)
.|.|..|..+|....
T Consensus 6 L~aCtkC~~r~p~ea 20 (305)
T KOG3990|consen 6 LYACTKCRQRLPFEA 20 (305)
T ss_pred HHHHHhHhhhCcHHH
Confidence 456666666655443
No 268
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.43 E-value=19 Score=20.04 Aligned_cols=12 Identities=17% Similarity=0.741 Sum_probs=9.0
Q ss_pred eecccccccccC
Q psy8167 104 IRCELCDKSFTR 115 (167)
Q Consensus 104 ~~C~~C~k~f~~ 115 (167)
-.|++|++.|..
T Consensus 49 v~CPYC~t~y~l 60 (62)
T COG4391 49 VVCPYCSTRYRL 60 (62)
T ss_pred EecCccccEEEe
Confidence 468888888764
No 269
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.40 E-value=24 Score=22.92 Aligned_cols=16 Identities=38% Similarity=0.719 Sum_probs=9.7
Q ss_pred CCcccccccccccCCH
Q psy8167 51 IDRIPCTLCDKTFTRK 66 (167)
Q Consensus 51 ~~~~~C~~C~~~f~~~ 66 (167)
...|+|+.|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 3456666666666554
No 270
>PTZ00448 hypothetical protein; Provisional
Probab=30.80 E-value=36 Score=26.35 Aligned_cols=23 Identities=0% Similarity=-0.229 Sum_probs=20.7
Q ss_pred CCCCCchhhhcCCHHHHHHHHhh
Q psy8167 131 DPKLMDEQMARGSADFLEVVLNE 153 (167)
Q Consensus 131 ~~~C~~C~~~f~~~~~l~~H~~~ 153 (167)
.|.|..|+-.|......+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999999999999974
No 271
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=30.66 E-value=31 Score=18.03 Aligned_cols=6 Identities=50% Similarity=1.492 Sum_probs=2.5
Q ss_pred eecccc
Q psy8167 104 IRCELC 109 (167)
Q Consensus 104 ~~C~~C 109 (167)
|+|..|
T Consensus 16 ~~C~~C 21 (49)
T cd02335 16 IKCAEC 21 (49)
T ss_pred EECCCC
Confidence 444433
No 272
>PTZ00064 histone acetyltransferase; Provisional
Probab=30.57 E-value=45 Score=27.07 Aligned_cols=31 Identities=13% Similarity=-0.323 Sum_probs=21.8
Q ss_pred CCCCCCchhhhcCCHHHHHHHHhhcCCCCCc
Q psy8167 130 ADPKLMDEQMARGSADFLEVVLNEDGEGEPV 160 (167)
Q Consensus 130 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 160 (167)
.-|-|..|=+.|.....|.+|+.......|+
T Consensus 279 ~LYICEfCLkY~~s~~~l~rH~~~C~~rhPP 309 (552)
T PTZ00064 279 TLHFCEYCLDFFCFEDELIRHLSRCQLRHPP 309 (552)
T ss_pred eEEEccchhhhhCCHHHHHHHHhcCCCCCCC
Confidence 4577888888888888888888754433444
No 273
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=30.51 E-value=43 Score=26.77 Aligned_cols=31 Identities=6% Similarity=-0.254 Sum_probs=23.7
Q ss_pred CCCCCchhhhcCCHHHHHHHHhhcCCCCCcc
Q psy8167 131 DPKLMDEQMARGSADFLEVVLNEDGEGEPVS 161 (167)
Q Consensus 131 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~ 161 (167)
-|-|..|=+.|.....|.+|+....-..|.-
T Consensus 198 lyiCe~Cl~y~~~~~~~~~H~~~C~~~~PPG 228 (450)
T PLN00104 198 LYFCEFCLKFMKRKEQLQRHMKKCDLKHPPG 228 (450)
T ss_pred EEEchhhhhhhcCHHHHHHHHhcCCCCCCCc
Confidence 4779999999999999999997555444443
No 274
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=30.29 E-value=26 Score=24.55 Aligned_cols=8 Identities=25% Similarity=0.800 Sum_probs=4.2
Q ss_pred cccccccc
Q psy8167 55 PCTLCDKT 62 (167)
Q Consensus 55 ~C~~C~~~ 62 (167)
.|+.|+..
T Consensus 2 ~Cp~C~~~ 9 (192)
T TIGR00310 2 DCPSCGGE 9 (192)
T ss_pred cCCCCCCC
Confidence 35666543
No 275
>PLN02748 tRNA dimethylallyltransferase
Probab=30.11 E-value=36 Score=27.42 Aligned_cols=24 Identities=8% Similarity=-0.273 Sum_probs=20.1
Q ss_pred CCCCCCchhh-hcCCHHHHHHHHhh
Q psy8167 130 ADPKLMDEQM-ARGSADFLEVVLNE 153 (167)
Q Consensus 130 ~~~~C~~C~~-~f~~~~~l~~H~~~ 153 (167)
+.|.|..|++ .+....++..|++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 5678999997 89999999999863
No 276
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=30.05 E-value=8.7 Score=21.90 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=10.9
Q ss_pred ccccchhhhhhccccccccCceecccccccc
Q psy8167 83 QHTNVIEVALGARANAAFIDRIRCELCDKSF 113 (167)
Q Consensus 83 ~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f 113 (167)
|.| .||.....+.. .+.-+| .||+..
T Consensus 4 frC-~Cgr~lya~e~---~kTkkC-~CG~~l 29 (68)
T PF09082_consen 4 FRC-DCGRYLYAKEG---AKTKKC-VCGKTL 29 (68)
T ss_dssp EEE-TTS--EEEETT----SEEEE-TTTEEE
T ss_pred EEe-cCCCEEEecCC---cceeEe-cCCCee
Confidence 455 46655443111 122357 777653
No 277
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=29.45 E-value=34 Score=17.98 Aligned_cols=6 Identities=33% Similarity=1.126 Sum_probs=2.4
Q ss_pred eecccc
Q psy8167 104 IRCELC 109 (167)
Q Consensus 104 ~~C~~C 109 (167)
|+|..|
T Consensus 16 ~~C~~C 21 (48)
T cd02341 16 YHCSEC 21 (48)
T ss_pred EECCCC
Confidence 344443
No 278
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.39 E-value=22 Score=26.10 Aligned_cols=33 Identities=12% Similarity=-0.031 Sum_probs=19.5
Q ss_pred eecccccccccChhHHHHHHHhhcCCCCCCCCchhhh
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMA 140 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 140 (167)
..|.-||..|-+.-.+..- +..+.-.|+.|-..
T Consensus 228 ps~t~CgHlFC~~Cl~~~~----t~~k~~~CplCRak 260 (271)
T COG5574 228 PSCTPCGHLFCLSCLLISW----TKKKYEFCPLCRAK 260 (271)
T ss_pred cccccccchhhHHHHHHHH----HhhccccCchhhhh
Confidence 4577788888777666541 22233338888543
No 279
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=29.31 E-value=35 Score=26.29 Aligned_cols=30 Identities=3% Similarity=-0.165 Sum_probs=22.6
Q ss_pred HHhhcCCCCCCCCchh-hhcCCHHHHHHHHh
Q psy8167 123 NRIFHGGADPKLMDEQ-MARGSADFLEVVLN 152 (167)
Q Consensus 123 ~~~h~~~~~~~C~~C~-~~f~~~~~l~~H~~ 152 (167)
.+.|--++.|.|.+|| +.+.....+.+|-.
T Consensus 366 ~klhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 366 CKLHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred HHhcCCCcceeeeecccccccchHHHHhhhh
Confidence 4555667889999998 77777777777764
No 280
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=29.21 E-value=45 Score=16.51 Aligned_cols=10 Identities=0% Similarity=-0.656 Sum_probs=2.5
Q ss_pred CCCCchhhhc
Q psy8167 132 PKLMDEQMAR 141 (167)
Q Consensus 132 ~~C~~C~~~f 141 (167)
|=|+.|+..|
T Consensus 4 yyCdyC~~~~ 13 (38)
T PF06220_consen 4 YYCDYCKKYL 13 (38)
T ss_dssp -B-TTT--B-
T ss_pred eeccccccee
Confidence 4455555444
No 281
>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=28.63 E-value=28 Score=17.16 Aligned_cols=11 Identities=27% Similarity=0.688 Sum_probs=5.6
Q ss_pred ceecccccccc
Q psy8167 103 RIRCELCDKSF 113 (167)
Q Consensus 103 ~~~C~~C~k~f 113 (167)
-|+|..||...
T Consensus 6 ~YkC~~CGniV 16 (36)
T PF06397_consen 6 FYKCEHCGNIV 16 (36)
T ss_dssp EEE-TTT--EE
T ss_pred EEEccCCCCEE
Confidence 37899988643
No 282
>KOG3362|consensus
Probab=28.55 E-value=16 Score=24.19 Aligned_cols=22 Identities=9% Similarity=-0.099 Sum_probs=13.0
Q ss_pred CCCCCchhhhcCCHHHHHHHHh
Q psy8167 131 DPKLMDEQMARGSADFLEVVLN 152 (167)
Q Consensus 131 ~~~C~~C~~~f~~~~~l~~H~~ 152 (167)
+|.|.-||-.+-+..-|..|..
T Consensus 129 ~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 129 KYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred hhHHHhcCCceeechhhhhccc
Confidence 4566666666666655555543
No 283
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=28.52 E-value=28 Score=17.98 Aligned_cols=13 Identities=15% Similarity=0.296 Sum_probs=8.0
Q ss_pred eecccccccccCh
Q psy8167 104 IRCELCDKSFTRK 116 (167)
Q Consensus 104 ~~C~~C~k~f~~~ 116 (167)
|-|..|+..+-..
T Consensus 12 ~~CL~C~~~~c~~ 24 (50)
T smart00290 12 WLCLTCGQVGCGR 24 (50)
T ss_pred EEecCCCCcccCC
Confidence 5677777665544
No 284
>KOG1842|consensus
Probab=28.49 E-value=34 Score=27.23 Aligned_cols=29 Identities=17% Similarity=0.370 Sum_probs=24.0
Q ss_pred cCceecccccccccChhHHHHHHHhhcCC
Q psy8167 101 IDRIRCELCDKSFTRKDSLKKHNRIFHGG 129 (167)
Q Consensus 101 ~k~~~C~~C~k~f~~~~~l~~H~~~h~~~ 129 (167)
...|.|++|+..|.....|..|...-|.+
T Consensus 13 ~egflCPiC~~dl~~~~~L~~H~d~eH~~ 41 (505)
T KOG1842|consen 13 LEGFLCPICLLDLPNLSALNDHLDVEHFE 41 (505)
T ss_pred hhcccCchHhhhhhhHHHHHHHHhhhccc
Confidence 34478999999999999999998876654
No 285
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=28.27 E-value=24 Score=23.23 Aligned_cols=12 Identities=0% Similarity=-0.260 Sum_probs=7.9
Q ss_pred ccccchhhhhhc
Q psy8167 83 QHTNVIEVALGA 94 (167)
Q Consensus 83 ~~c~~c~~~~~~ 94 (167)
-+|..||..|..
T Consensus 30 ~kC~~CG~v~~P 41 (140)
T COG1545 30 TKCKKCGRVYFP 41 (140)
T ss_pred EEcCCCCeEEcC
Confidence 467777766655
No 286
>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=28.22 E-value=26 Score=26.07 Aligned_cols=78 Identities=12% Similarity=0.021 Sum_probs=28.1
Q ss_pred ccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhccccccccCceecccccccccChhHHHHHHHhhcCCCCCC
Q psy8167 54 IPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKHNRIFHGGADPK 133 (167)
Q Consensus 54 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~ 133 (167)
-.|++||..-. -+.+..-. ..|.+-..|..|+..-.. .+..|+.||-.-...-.+.. ...--+.+-+.
T Consensus 173 g~CPvCGs~P~-~s~l~~~~---~~G~R~L~Cs~C~t~W~~-------~R~~Cp~Cg~~~~~~l~~~~-~e~~~~~rve~ 240 (290)
T PF04216_consen 173 GYCPVCGSPPV-LSVLRGGE---REGKRYLHCSLCGTEWRF-------VRIKCPYCGNTDHEKLEYFT-VEGEPAYRVEV 240 (290)
T ss_dssp SS-TTT---EE-EEEEE---------EEEEEETTT--EEE---------TTS-TTT---SS-EEE---------SEEEEE
T ss_pred CcCCCCCCcCc-eEEEecCC---CCccEEEEcCCCCCeeee-------cCCCCcCCCCCCCcceeeEe-cCCCCcEEEEE
Confidence 46999985311 11111111 125567888888754332 23579999955333222110 01101122366
Q ss_pred CCchhhhcCC
Q psy8167 134 LMDEQMARGS 143 (167)
Q Consensus 134 C~~C~~~f~~ 143 (167)
|..|+..++.
T Consensus 241 C~~C~~YlK~ 250 (290)
T PF04216_consen 241 CESCGSYLKT 250 (290)
T ss_dssp ETTTTEEEEE
T ss_pred CCcccchHHH
Confidence 8888765543
No 287
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=27.76 E-value=23 Score=20.92 Aligned_cols=11 Identities=36% Similarity=1.068 Sum_probs=4.6
Q ss_pred ecccccccccC
Q psy8167 105 RCELCDKSFTR 115 (167)
Q Consensus 105 ~C~~C~k~f~~ 115 (167)
.|..||..|..
T Consensus 48 ~C~~Cg~~~~~ 58 (81)
T PF05129_consen 48 SCRVCGESFQT 58 (81)
T ss_dssp EESSS--EEEE
T ss_pred EecCCCCeEEE
Confidence 45555555443
No 288
>KOG4317|consensus
Probab=27.59 E-value=15 Score=27.72 Aligned_cols=12 Identities=0% Similarity=-0.161 Sum_probs=7.6
Q ss_pred ccccchhhhhhc
Q psy8167 83 QHTNVIEVALGA 94 (167)
Q Consensus 83 ~~c~~c~~~~~~ 94 (167)
|.|+-|...+.+
T Consensus 20 YtCPRCn~~YCs 31 (383)
T KOG4317|consen 20 YTCPRCNLLYCS 31 (383)
T ss_pred ccCCCCCcccee
Confidence 667776665555
No 289
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=27.46 E-value=35 Score=16.53 Aligned_cols=6 Identities=0% Similarity=-0.546 Sum_probs=2.3
Q ss_pred CCCchh
Q psy8167 133 KLMDEQ 138 (167)
Q Consensus 133 ~C~~C~ 138 (167)
.|+.||
T Consensus 24 vC~~Cg 29 (34)
T PF14803_consen 24 VCPACG 29 (34)
T ss_dssp EETTTT
T ss_pred ECCCCC
Confidence 333333
No 290
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=27.33 E-value=26 Score=23.69 Aligned_cols=6 Identities=33% Similarity=1.110 Sum_probs=3.5
Q ss_pred cccccc
Q psy8167 56 CTLCDK 61 (167)
Q Consensus 56 C~~C~~ 61 (167)
|+.|+.
T Consensus 3 Cp~C~~ 8 (160)
T smart00709 3 CPSCGG 8 (160)
T ss_pred CCCCCC
Confidence 666654
No 291
>KOG0782|consensus
Probab=26.54 E-value=21 Score=29.41 Aligned_cols=30 Identities=10% Similarity=0.071 Sum_probs=15.8
Q ss_pred HHHHHHHhhcCCCCCCCCchhhhcCCHHHH
Q psy8167 118 SLKKHNRIFHGGADPKLMDEQMARGSADFL 147 (167)
Q Consensus 118 ~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l 147 (167)
.+.+|.=.|.....-+|..|+|.|..+..+
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQKf~F 269 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQKFFF 269 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhhheee
Confidence 455554444444445666666666655433
No 292
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=26.44 E-value=41 Score=15.51 Aligned_cols=7 Identities=29% Similarity=0.814 Sum_probs=4.0
Q ss_pred eeccccc
Q psy8167 104 IRCELCD 110 (167)
Q Consensus 104 ~~C~~C~ 110 (167)
|.|..|+
T Consensus 16 Y~C~~c~ 22 (30)
T PF03107_consen 16 YHCSECC 22 (30)
T ss_pred EEeCCCC
Confidence 5565555
No 293
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=26.35 E-value=70 Score=22.44 Aligned_cols=12 Identities=17% Similarity=0.639 Sum_probs=8.1
Q ss_pred Cccccccccccc
Q psy8167 52 DRIPCTLCDKTF 63 (167)
Q Consensus 52 ~~~~C~~C~~~f 63 (167)
+.+.|.+|-..+
T Consensus 17 ~~~~CpICld~~ 28 (193)
T PLN03208 17 GDFDCNICLDQV 28 (193)
T ss_pred CccCCccCCCcC
Confidence 457788887654
No 294
>KOG1819|consensus
Probab=26.00 E-value=37 Score=27.51 Aligned_cols=8 Identities=0% Similarity=-0.263 Sum_probs=3.4
Q ss_pred ccchhhhh
Q psy8167 85 TNVIEVAL 92 (167)
Q Consensus 85 c~~c~~~~ 92 (167)
|..||..|
T Consensus 920 crncggif 927 (990)
T KOG1819|consen 920 CRNCGGIF 927 (990)
T ss_pred hcccCcee
Confidence 44444443
No 295
>KOG1044|consensus
Probab=25.52 E-value=30 Score=28.44 Aligned_cols=36 Identities=22% Similarity=0.396 Sum_probs=21.7
Q ss_pred ecccccccccChhHHHHHHHhhcCCCC-----CCCCchhhhcCCHHHH
Q psy8167 105 RCELCDKSFTRKDSLKKHNRIFHGGAD-----PKLMDEQMARGSADFL 147 (167)
Q Consensus 105 ~C~~C~k~f~~~~~l~~H~~~h~~~~~-----~~C~~C~~~f~~~~~l 147 (167)
+|..|.+-+..+- |+ .|++. -.|..|+..|.....|
T Consensus 194 kc~~c~~fisgkv-Lq------ag~kh~HPtCARCsRCgqmF~eGEEM 234 (670)
T KOG1044|consen 194 KCEECEKFISGKV-LQ------AGDKHFHPTCARCSRCGQMFGEGEEM 234 (670)
T ss_pred ehHHhhhhhhhhh-hh------ccCcccCcchhhhhhhccccccchhe
Confidence 6788876555542 22 33333 3477788888776554
No 296
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=25.50 E-value=40 Score=23.46 Aligned_cols=51 Identities=12% Similarity=0.032 Sum_probs=27.2
Q ss_pred eeccc----ccccccChhHHHHHHHhhcCCCCCCCCc----hhhhcCCHHHHHHHHhhcCCC
Q psy8167 104 IRCEL----CDKSFTRKDSLKKHNRIFHGGADPKLMD----EQMARGSADFLEVVLNEDGEG 157 (167)
Q Consensus 104 ~~C~~----C~k~f~~~~~l~~H~~~h~~~~~~~C~~----C~~~f~~~~~l~~H~~~~~~~ 157 (167)
++|.. |...+... ....|.+. ..-+|+.|+. |+..-.. ..|..|....|..
T Consensus 15 ~pC~~~~~GC~~~~~~~-~~~~HE~~-C~~~p~~CP~~~~~C~~~G~~-~~l~~Hl~~~H~~ 73 (198)
T PF03145_consen 15 FPCKNAKYGCTETFPYS-EKREHEEE-CPFRPCSCPFPGSGCDWQGSY-KELLDHLRDKHSW 73 (198)
T ss_dssp EE-CCGGGT---EE-GG-GHHHHHHT--TTSEEE-SSSSTT---EEEC-CCHHHHHHHHTTT
T ss_pred ecCCCCCCCCccccccc-ChhhHhcc-CCCcCCcCCCCCCCccccCCH-HHHHHHHHHHCCC
Confidence 45655 66665444 55668775 6677888987 7665543 4677899876655
No 297
>PRK06450 threonine synthase; Validated
Probab=25.31 E-value=31 Score=26.34 Aligned_cols=10 Identities=30% Similarity=0.527 Sum_probs=5.2
Q ss_pred cccccccccc
Q psy8167 54 IPCTLCDKTF 63 (167)
Q Consensus 54 ~~C~~C~~~f 63 (167)
++|..||+.|
T Consensus 4 ~~C~~Cg~~~ 13 (338)
T PRK06450 4 EVCMKCGKER 13 (338)
T ss_pred eEECCcCCcC
Confidence 4555555543
No 298
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=25.29 E-value=68 Score=23.75 Aligned_cols=34 Identities=18% Similarity=0.281 Sum_probs=18.7
Q ss_pred eecccccccccChhHHHHHHHhhcCCCCCCCCchh
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQ 138 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~ 138 (167)
..|..|+..+.....+...+.......+..|+ ||
T Consensus 138 ~~C~~C~~~~~~~~~~~~~~~~~~~~~~P~C~-Cg 171 (271)
T PTZ00409 138 ARCCTCRKTIQLNKIMLQKTSHFMHQLPPECP-CG 171 (271)
T ss_pred ceeCCCCCCcccCHHHHhhhhhhccCCCCCCC-CC
Confidence 47999998876544433221111122356788 86
No 299
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=25.24 E-value=45 Score=16.24 Aligned_cols=9 Identities=22% Similarity=0.892 Sum_probs=4.1
Q ss_pred ecccccccc
Q psy8167 105 RCELCDKSF 113 (167)
Q Consensus 105 ~C~~C~k~f 113 (167)
.|..||-.+
T Consensus 23 sC~~CGPr~ 31 (35)
T PF07503_consen 23 SCTNCGPRY 31 (35)
T ss_dssp -BTTCC-SC
T ss_pred cCCCCCCCE
Confidence 466666544
No 300
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=24.80 E-value=24 Score=25.21 Aligned_cols=28 Identities=21% Similarity=0.265 Sum_probs=0.0
Q ss_pred eecccccccccChhHHHHHHHhhcCCCCC
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGGADP 132 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~~~~ 132 (167)
..|++||....- +.|..|||+...+..|
T Consensus 169 ~~cPitGe~IP~-~e~~eHmRi~LlDP~w 196 (229)
T PF12230_consen 169 IICPITGEMIPA-DEMDEHMRIELLDPRW 196 (229)
T ss_dssp -----------------------------
T ss_pred cccccccccccc-cccccccccccccccc
Confidence 578888877654 4778899987765444
No 301
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=24.55 E-value=38 Score=18.15 Aligned_cols=16 Identities=25% Similarity=0.733 Sum_probs=10.0
Q ss_pred cCceecccccccccCh
Q psy8167 101 IDRIRCELCDKSFTRK 116 (167)
Q Consensus 101 ~k~~~C~~C~k~f~~~ 116 (167)
...|+|.+|++.+...
T Consensus 33 ~~~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 33 PIKLRCHYCERIITED 48 (52)
T ss_dssp TCEEEETTT--EEEHH
T ss_pred CCEEEeeCCCCEeccc
Confidence 4557899999877654
No 302
>PLN03239 histone acetyltransferase; Provisional
Probab=24.49 E-value=67 Score=24.77 Aligned_cols=23 Identities=4% Similarity=-0.492 Sum_probs=13.7
Q ss_pred CCCCCCchhhhcCCHHHHHHHHh
Q psy8167 130 ADPKLMDEQMARGSADFLEVVLN 152 (167)
Q Consensus 130 ~~~~C~~C~~~f~~~~~l~~H~~ 152 (167)
.-|-|..|-+.|.+...|.+|+.
T Consensus 105 ~lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 105 VLYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred eEEEeccchhhhcCHHHHHHHHH
Confidence 34666666666666666666654
No 303
>KOG0320|consensus
Probab=24.35 E-value=29 Score=23.96 Aligned_cols=10 Identities=10% Similarity=-0.161 Sum_probs=5.4
Q ss_pred CCCCCchhhh
Q psy8167 131 DPKLMDEQMA 140 (167)
Q Consensus 131 ~~~C~~C~~~ 140 (167)
..+|+.|++.
T Consensus 167 ~~~CP~C~kk 176 (187)
T KOG0320|consen 167 TNKCPTCRKK 176 (187)
T ss_pred CCCCCCcccc
Confidence 4556666553
No 304
>cd01396 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
Probab=24.33 E-value=64 Score=18.83 Aligned_cols=18 Identities=17% Similarity=-0.051 Sum_probs=10.0
Q ss_pred hhhhcCCHHHHHHHHhhc
Q psy8167 137 EQMARGSADFLEVVLNED 154 (167)
Q Consensus 137 C~~~f~~~~~l~~H~~~~ 154 (167)
||+.|.+...|.+.+..+
T Consensus 34 ~Gkk~RS~~ev~~yL~~~ 51 (77)
T cd01396 34 TGKKFRSKVELARYLEKN 51 (77)
T ss_pred CCCEEECHHHHHHHHHhC
Confidence 455555555555555544
No 305
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=24.32 E-value=74 Score=24.43 Aligned_cols=53 Identities=11% Similarity=0.059 Sum_probs=32.8
Q ss_pred ecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCCHHHHHHHHhh-cCCCCCccccccc
Q psy8167 105 RCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSADFLEVVLNE-DGEGEPVSITVYL 166 (167)
Q Consensus 105 ~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~-~~~~~~~~~~~~~ 166 (167)
.|..|...|...... .-.+.|+.||..+.....-+.-... -.++.|..--+||
T Consensus 248 AC~rC~t~y~le~A~---------~~~wrCpkCGg~ikKGV~dRv~ELad~~~~~p~~RPPYl 301 (403)
T COG1379 248 ACSRCYTRYSLEEAK---------SLRWRCPKCGGKIKKGVSDRVLELADTEPEHPKHRPPYL 301 (403)
T ss_pred HHHHhhhccCcchhh---------hhcccCcccccchhhhHHHHHHHhhccCcccCCCCCCce
Confidence 378887777654332 1257899998877766555444332 2356666666775
No 306
>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=23.92 E-value=25 Score=26.21 Aligned_cols=11 Identities=18% Similarity=0.661 Sum_probs=7.8
Q ss_pred ccccccccccc
Q psy8167 53 RIPCTLCDKTF 63 (167)
Q Consensus 53 ~~~C~~C~~~f 63 (167)
..+|+.|+...
T Consensus 26 ~~~c~~c~~~~ 36 (285)
T TIGR00515 26 WTKCPKCGQVL 36 (285)
T ss_pred eeECCCCcchh
Confidence 56788888643
No 307
>PLN02748 tRNA dimethylallyltransferase
Probab=23.48 E-value=55 Score=26.40 Aligned_cols=25 Identities=16% Similarity=0.389 Sum_probs=20.8
Q ss_pred cCceecccccc-cccChhHHHHHHHh
Q psy8167 101 IDRIRCELCDK-SFTRKDSLKKHNRI 125 (167)
Q Consensus 101 ~k~~~C~~C~k-~f~~~~~l~~H~~~ 125 (167)
-+.|.|..|++ .+.....+..|++.
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhcc
Confidence 45678999997 79999999988764
No 308
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=23.22 E-value=27 Score=26.19 Aligned_cols=11 Identities=18% Similarity=0.392 Sum_probs=7.8
Q ss_pred ccccccccccc
Q psy8167 53 RIPCTLCDKTF 63 (167)
Q Consensus 53 ~~~C~~C~~~f 63 (167)
..+|+.|+...
T Consensus 38 w~kc~~C~~~~ 48 (296)
T CHL00174 38 WVQCENCYGLN 48 (296)
T ss_pred eeECCCccchh
Confidence 56788888643
No 309
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=23.03 E-value=76 Score=23.02 Aligned_cols=32 Identities=22% Similarity=0.362 Sum_probs=20.2
Q ss_pred eecccccccccChhHHHHHHHhhcCCCCCCCCchhh
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQM 139 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 139 (167)
..|..|++.|.....+. .........|+.|+-
T Consensus 120 ~~C~~C~~~~~~~~~~~----~~~~~~~p~Cp~Cgg 151 (244)
T PRK14138 120 YYCVRCGKRYTVEDVIE----KLEKSDVPRCDDCSG 151 (244)
T ss_pred eEECCCCCcccHHHHHH----HHhcCCCCCCCCCCC
Confidence 47999998887654433 112223577999973
No 310
>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=22.89 E-value=77 Score=19.68 Aligned_cols=37 Identities=8% Similarity=0.092 Sum_probs=24.8
Q ss_pred CcccccccccccCCHHHHHHHHHHhcCCCCcccccchhh
Q psy8167 52 DRIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEV 90 (167)
Q Consensus 52 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~ 90 (167)
..|.|+.-|..|.+...+...+ . .-..+.|.|...|+
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~-~-~y~~~vwtC~~TGk 38 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRM-I-LYNQRVWTCEITGK 38 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHH-H-HHhCCeeEEecCCC
Confidence 4688999999999988777666 3 22334555555443
No 311
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=22.84 E-value=38 Score=18.63 Aligned_cols=12 Identities=25% Similarity=0.922 Sum_probs=6.2
Q ss_pred eecccccccccC
Q psy8167 104 IRCELCDKSFTR 115 (167)
Q Consensus 104 ~~C~~C~k~f~~ 115 (167)
..|++||+.+..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 479999988776
No 312
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=22.77 E-value=59 Score=22.80 Aligned_cols=10 Identities=0% Similarity=-0.124 Sum_probs=5.1
Q ss_pred CCCCchhhhc
Q psy8167 132 PKLMDEQMAR 141 (167)
Q Consensus 132 ~~C~~C~~~f 141 (167)
..|..||..+
T Consensus 31 vrC~eCG~V~ 40 (201)
T COG1326 31 VRCEECGTVH 40 (201)
T ss_pred EEccCCCcEe
Confidence 4455555444
No 313
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=22.72 E-value=35 Score=27.04 Aligned_cols=6 Identities=33% Similarity=1.337 Sum_probs=3.5
Q ss_pred eccccc
Q psy8167 105 RCELCD 110 (167)
Q Consensus 105 ~C~~C~ 110 (167)
+|+.||
T Consensus 23 kCp~Cg 28 (456)
T COG1066 23 KCPACG 28 (456)
T ss_pred cCCCCC
Confidence 466665
No 314
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=22.39 E-value=50 Score=21.58 Aligned_cols=27 Identities=15% Similarity=0.160 Sum_probs=14.9
Q ss_pred cccccchhhhhhccccccccCceecccccccc
Q psy8167 82 PQHTNVIEVALGARANAAFIDRIRCELCDKSF 113 (167)
Q Consensus 82 ~~~c~~c~~~~~~~~~~~l~k~~~C~~C~k~f 113 (167)
...|+.||-.... -....-|++||+.+
T Consensus 28 ~~hCp~Cg~PLF~-----KdG~v~CPvC~~~~ 54 (131)
T COG1645 28 AKHCPKCGTPLFR-----KDGEVFCPVCGYRE 54 (131)
T ss_pred HhhCcccCCccee-----eCCeEECCCCCceE
Confidence 3567777765433 01223588888543
No 315
>PRK07218 replication factor A; Provisional
Probab=22.36 E-value=37 Score=26.93 Aligned_cols=7 Identities=29% Similarity=1.056 Sum_probs=3.4
Q ss_pred ccccccc
Q psy8167 55 PCTLCDK 61 (167)
Q Consensus 55 ~C~~C~~ 61 (167)
+|+.|++
T Consensus 299 rCP~C~r 305 (423)
T PRK07218 299 RCPECGR 305 (423)
T ss_pred cCcCccc
Confidence 3555554
No 316
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.35 E-value=43 Score=24.96 Aligned_cols=27 Identities=15% Similarity=0.162 Sum_probs=19.0
Q ss_pred cCceecccccccccChhHHHHHHHhhcCCCCCCCCchhhhc
Q psy8167 101 IDRIRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMAR 141 (167)
Q Consensus 101 ~k~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 141 (167)
...|-|++|.-.|-. .|..|..|+-.|
T Consensus 253 ~~GyvCs~Clsi~C~--------------~p~~C~~Cgt~f 279 (279)
T TIGR00627 253 SIGFVCSVCLSVLCQ--------------YTPICKTCKTAF 279 (279)
T ss_pred cceEECCCccCCcCC--------------CCCCCCCCCCCC
Confidence 444889999865543 356899998765
No 317
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.31 E-value=22 Score=20.76 Aligned_cols=9 Identities=33% Similarity=0.822 Sum_probs=5.3
Q ss_pred ccccccccc
Q psy8167 54 IPCTLCDKT 62 (167)
Q Consensus 54 ~~C~~C~~~ 62 (167)
|.|..|+..
T Consensus 13 Y~c~~cg~~ 21 (82)
T COG2331 13 YECTECGNR 21 (82)
T ss_pred EeecccchH
Confidence 566666653
No 318
>PRK07591 threonine synthase; Validated
Probab=21.90 E-value=40 Score=26.62 Aligned_cols=28 Identities=11% Similarity=0.161 Sum_probs=16.4
Q ss_pred cccccccccccCCHHHHHHHHHHhcCCCCcccccchhhhhhc
Q psy8167 53 RIPCTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGA 94 (167)
Q Consensus 53 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~c~~c~~~~~~ 94 (167)
.+.|..||+.|.. ... +.|+.|+..+.-
T Consensus 18 ~l~C~~Cg~~~~~-------------~~~-~~C~~cg~~l~~ 45 (421)
T PRK07591 18 ALKCRECGAEYPL-------------GPI-HVCEECFGPLEV 45 (421)
T ss_pred EEEeCCCCCcCCC-------------CCC-ccCCCCCCeEEE
Confidence 3778888875531 112 667777655443
No 319
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=21.80 E-value=37 Score=23.06 Aligned_cols=6 Identities=33% Similarity=1.392 Sum_probs=3.3
Q ss_pred cccccc
Q psy8167 56 CTLCDK 61 (167)
Q Consensus 56 C~~C~~ 61 (167)
|+.||.
T Consensus 1 CP~Cg~ 6 (163)
T TIGR00340 1 CPVCGS 6 (163)
T ss_pred CCCCCC
Confidence 555654
No 320
>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=21.80 E-value=26 Score=23.32 Aligned_cols=6 Identities=33% Similarity=1.088 Sum_probs=2.8
Q ss_pred eccccc
Q psy8167 105 RCELCD 110 (167)
Q Consensus 105 ~C~~C~ 110 (167)
+|+.||
T Consensus 132 ~Cp~C~ 137 (146)
T PF07295_consen 132 PCPKCG 137 (146)
T ss_pred CCCCCC
Confidence 345554
No 321
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, 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. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=21.71 E-value=78 Score=22.54 Aligned_cols=31 Identities=10% Similarity=0.173 Sum_probs=19.1
Q ss_pred eecccccccccChhHHHHHHHhhcCCCCCCCCchhh
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQM 139 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 139 (167)
..|..|++.|..... +.........|+.|+-
T Consensus 114 ~~C~~C~~~~~~~~~-----~~~~~~~~p~C~~Cgg 144 (222)
T cd01413 114 AYCVNCGSKYDLEEV-----KYAKKHEVPRCPKCGG 144 (222)
T ss_pred ceECCCCCCcchhHH-----HHhccCCCCcCCCCCC
Confidence 479999988765533 1112234578988863
No 322
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=21.70 E-value=30 Score=25.95 Aligned_cols=11 Identities=18% Similarity=0.480 Sum_probs=8.1
Q ss_pred Ccccccccccc
Q psy8167 52 DRIPCTLCDKT 62 (167)
Q Consensus 52 ~~~~C~~C~~~ 62 (167)
-..+|+.|+..
T Consensus 26 ~~~~c~~c~~~ 36 (292)
T PRK05654 26 LWTKCPSCGQV 36 (292)
T ss_pred CeeECCCccch
Confidence 35679999874
No 323
>KOG3352|consensus
Probab=21.69 E-value=38 Score=22.65 Aligned_cols=17 Identities=6% Similarity=-0.129 Sum_probs=13.3
Q ss_pred cCCCCCCCCchhhhcCC
Q psy8167 127 HGGADPKLMDEQMARGS 143 (167)
Q Consensus 127 ~~~~~~~C~~C~~~f~~ 143 (167)
+.++..+|..||..|.-
T Consensus 129 ~Kge~~rc~eCG~~fkL 145 (153)
T KOG3352|consen 129 EKGETQRCPECGHYFKL 145 (153)
T ss_pred EcCCcccCCcccceEEe
Confidence 55668889999988863
No 324
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=21.67 E-value=41 Score=16.54 Aligned_cols=16 Identities=25% Similarity=0.592 Sum_probs=8.8
Q ss_pred ecccccccccChhHHH
Q psy8167 105 RCELCDKSFTRKDSLK 120 (167)
Q Consensus 105 ~C~~C~k~f~~~~~l~ 120 (167)
.|+.|++.|-+.+.-+
T Consensus 4 ~CprC~kg~Hwa~~C~ 19 (36)
T PF14787_consen 4 LCPRCGKGFHWASECR 19 (36)
T ss_dssp C-TTTSSSCS-TTT--
T ss_pred cCcccCCCcchhhhhh
Confidence 4788888877765543
No 325
>PRK01343 zinc-binding protein; Provisional
Probab=21.54 E-value=47 Score=18.26 Aligned_cols=11 Identities=36% Similarity=0.600 Sum_probs=8.9
Q ss_pred eeccccccccc
Q psy8167 104 IRCELCDKSFT 114 (167)
Q Consensus 104 ~~C~~C~k~f~ 114 (167)
..|++|++.+.
T Consensus 10 ~~CP~C~k~~~ 20 (57)
T PRK01343 10 RPCPECGKPST 20 (57)
T ss_pred CcCCCCCCcCc
Confidence 46999999875
No 326
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=21.45 E-value=30 Score=23.43 Aligned_cols=8 Identities=38% Similarity=1.003 Sum_probs=2.5
Q ss_pred eecccccc
Q psy8167 104 IRCELCDK 111 (167)
Q Consensus 104 ~~C~~C~k 111 (167)
|.|+.||.
T Consensus 31 f~C~~CGy 38 (161)
T PF03367_consen 31 FECEHCGY 38 (161)
T ss_dssp EE-TTT--
T ss_pred eECCCCCC
Confidence 34555553
No 327
>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=21.42 E-value=47 Score=15.98 Aligned_cols=20 Identities=15% Similarity=0.511 Sum_probs=11.3
Q ss_pred eecccccccccChhHHHHHHH
Q psy8167 104 IRCELCDKSFTRKDSLKKHNR 124 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~ 124 (167)
+.|+.|++.+... -+-.|+.
T Consensus 5 ~~C~nC~R~v~a~-RfA~HLe 24 (33)
T PF08209_consen 5 VECPNCGRPVAAS-RFAPHLE 24 (33)
T ss_dssp EE-TTTSSEEEGG-GHHHHHH
T ss_pred EECCCCcCCcchh-hhHHHHH
Confidence 6788888766543 3334543
No 328
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=20.81 E-value=61 Score=16.02 Aligned_cols=15 Identities=27% Similarity=0.625 Sum_probs=8.1
Q ss_pred eecccccccccChhH
Q psy8167 104 IRCELCDKSFTRKDS 118 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~ 118 (167)
..|..|++.|.....
T Consensus 7 ~~C~~C~~~~~~~~~ 21 (43)
T PF06467_consen 7 KTCSYCKKYIPNKPT 21 (43)
T ss_dssp EE-TTT--EEECCC-
T ss_pred CcCcccCCcccCCCc
Confidence 468888888877664
No 329
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=20.60 E-value=89 Score=15.65 Aligned_cols=10 Identities=20% Similarity=-0.034 Sum_probs=5.3
Q ss_pred CCCCCCCchh
Q psy8167 129 GADPKLMDEQ 138 (167)
Q Consensus 129 ~~~~~C~~C~ 138 (167)
.....|++|+
T Consensus 34 ~~~~~CP~C~ 43 (44)
T PF14634_consen 34 GKSVKCPICR 43 (44)
T ss_pred CCCCCCcCCC
Confidence 3455566554
No 330
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=20.50 E-value=22 Score=30.04 Aligned_cols=68 Identities=10% Similarity=-0.015 Sum_probs=42.6
Q ss_pred ccccchhhhhhccccccccCce-ecccccccccChhHHHHHHHhhcC-CCCCCCCchhhhcCCHHHHHHHH
Q psy8167 83 QHTNVIEVALGARANAAFIDRI-RCELCDKSFTRKDSLKKHNRIFHG-GADPKLMDEQMARGSADFLEVVL 151 (167)
Q Consensus 83 ~~c~~c~~~~~~~~~~~l~k~~-~C~~C~k~f~~~~~l~~H~~~h~~-~~~~~C~~C~~~f~~~~~l~~H~ 151 (167)
-.|+.|-+-+.+...-....+| .|..||-.|+--..|--- |.++. ..-..|+.|.+-+....+=+=|-
T Consensus 102 a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~nRRfHA 171 (750)
T COG0068 102 ATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLNRRFHA 171 (750)
T ss_pred hhhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCcccccccc
Confidence 5677787766553333333333 599999999877665433 22232 23467999999888876655444
No 331
>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=20.34 E-value=27 Score=20.02 Aligned_cols=13 Identities=23% Similarity=0.501 Sum_probs=6.7
Q ss_pred ccccccccccCCH
Q psy8167 54 IPCTLCDKTFTRK 66 (167)
Q Consensus 54 ~~C~~C~~~f~~~ 66 (167)
++++-|++.|.=.
T Consensus 11 ~~~~cC~~~y~C~ 23 (71)
T PF05495_consen 11 IRFPCCGKYYPCR 23 (71)
T ss_dssp EEETTTTEEESSH
T ss_pred EECCcccCeecHH
Confidence 4455555555543
No 332
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=20.31 E-value=30 Score=23.58 Aligned_cols=31 Identities=13% Similarity=0.075 Sum_probs=20.4
Q ss_pred eecccccccccChhHHHHHHHhhcCCCCCCCCchhhhcCCH
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQMARGSA 144 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 144 (167)
..|+.|+..|..-. ....+.|..|-+.|.+.
T Consensus 75 l~C~~C~~Tfk~f~----------~~g~fGCaeCY~tf~~~ 105 (176)
T COG3880 75 LGCHNCGMTFKEFI----------QSGLFGCAECYKTFESQ 105 (176)
T ss_pred hcCccccccHHHHH----------HhcccchHHHHHHHHHH
Confidence 46888887665421 12368888888888765
No 333
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=20.14 E-value=49 Score=23.82 Aligned_cols=17 Identities=6% Similarity=-0.297 Sum_probs=14.5
Q ss_pred cCCCCCCCCchhhhcCC
Q psy8167 127 HGGADPKLMDEQMARGS 143 (167)
Q Consensus 127 ~~~~~~~C~~C~~~f~~ 143 (167)
+.+++..|..||..|.-
T Consensus 177 rEGkpqRCpECGqVFKL 193 (268)
T PTZ00043 177 REGFLYRCGECDQIFML 193 (268)
T ss_pred cCCCCccCCCCCcEEEE
Confidence 56679999999999975
No 334
>PRK12722 transcriptional activator FlhC; Provisional
Probab=20.05 E-value=61 Score=22.62 Aligned_cols=28 Identities=14% Similarity=0.067 Sum_probs=18.7
Q ss_pred eecccccccccChhHHHHHHHhhcCCCCCCCCchhh
Q psy8167 104 IRCELCDKSFTRKDSLKKHNRIFHGGADPKLMDEQM 139 (167)
Q Consensus 104 ~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 139 (167)
-.|..||-.|..... .....|.|+.|.-
T Consensus 135 ~~C~~Cgg~fv~~~~--------e~~~~f~CplC~~ 162 (187)
T PRK12722 135 SSCNCCGGHFVTHAH--------DPVGSFVCGLCQP 162 (187)
T ss_pred ccCCCCCCCeecccc--------ccCCCCcCCCCCC
Confidence 368889988875432 2234788999854
No 335
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=20.01 E-value=1e+02 Score=17.38 Aligned_cols=18 Identities=11% Similarity=0.067 Sum_probs=10.4
Q ss_pred CHHHHHHHHhhcCCCCCc
Q psy8167 143 SADFLEVVLNEDGEGEPV 160 (167)
Q Consensus 143 ~~~~l~~H~~~~~~~~~~ 160 (167)
....+..|++.||++.|+
T Consensus 24 ~Ye~Yv~H~~~~HP~~p~ 41 (65)
T PF04328_consen 24 DYERYVEHMRRHHPDEPP 41 (65)
T ss_pred HHHHHHHHHHHHCcCCCC
Confidence 344555677766655544
Done!