Query psy3507
Match_columns 134
No_of_seqs 294 out of 1805
Neff 10.2
Searched_HMMs 46136
Date Fri Aug 16 18:26:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3507.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3507hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 1.3E-28 2.7E-33 164.0 5.8 114 18-131 129-264 (279)
2 KOG2462|consensus 99.9 1.2E-27 2.5E-32 159.3 6.4 98 35-134 128-239 (279)
3 KOG1074|consensus 99.8 1.2E-19 2.7E-24 135.7 2.1 81 54-134 605-692 (958)
4 KOG3608|consensus 99.7 4.6E-19 9.9E-24 122.1 2.5 107 26-134 196-316 (467)
5 KOG3576|consensus 99.7 1.6E-18 3.5E-23 111.4 1.8 77 54-130 117-193 (267)
6 KOG3576|consensus 99.7 4.3E-18 9.3E-23 109.5 1.8 100 34-133 114-235 (267)
7 KOG1074|consensus 99.7 8.7E-18 1.9E-22 126.0 2.6 52 83-134 880-931 (958)
8 KOG3623|consensus 99.7 6.6E-18 1.4E-22 125.2 1.2 82 50-131 890-971 (1007)
9 KOG3623|consensus 99.6 3.8E-17 8.3E-22 121.2 0.8 94 38-131 211-330 (1007)
10 KOG3608|consensus 99.5 1.8E-14 4E-19 99.6 2.8 81 49-130 287-372 (467)
11 PHA00733 hypothetical protein 99.3 8.3E-13 1.8E-17 81.2 3.2 79 52-132 38-121 (128)
12 PLN03086 PRLI-interacting fact 99.3 7.4E-12 1.6E-16 92.8 7.8 73 43-120 441-514 (567)
13 PLN03086 PRLI-interacting fact 99.2 6.4E-11 1.4E-15 87.9 8.5 102 25-130 441-560 (567)
14 PHA02768 hypothetical protein; 99.2 5.6E-12 1.2E-16 65.3 1.0 43 54-98 5-47 (55)
15 PHA00733 hypothetical protein 99.1 5.3E-11 1.1E-15 73.2 3.4 72 34-107 37-124 (128)
16 PHA02768 hypothetical protein; 99.1 4.5E-11 9.8E-16 61.9 2.2 43 82-126 5-47 (55)
17 PF13465 zf-H2C2_2: Zinc-finge 99.0 1.8E-10 3.8E-15 51.3 1.8 24 98-121 2-25 (26)
18 PF13465 zf-H2C2_2: Zinc-finge 98.9 1.9E-09 4.1E-14 48.0 2.8 26 69-94 1-26 (26)
19 KOG3993|consensus 98.8 7.6E-10 1.6E-14 78.6 0.1 24 110-133 356-379 (500)
20 PHA00732 hypothetical protein 98.7 6.2E-09 1.3E-13 58.6 2.2 48 54-107 1-49 (79)
21 KOG3993|consensus 98.7 7.4E-09 1.6E-13 73.7 1.0 120 12-131 260-479 (500)
22 PHA00616 hypothetical protein 98.6 8.9E-09 1.9E-13 50.9 0.9 32 55-86 2-33 (44)
23 PHA00616 hypothetical protein 98.6 2.8E-08 6E-13 49.2 1.6 34 82-115 1-34 (44)
24 PHA00732 hypothetical protein 98.5 9.2E-08 2E-12 53.9 3.1 46 82-133 1-47 (79)
25 PF00096 zf-C2H2: Zinc finger, 98.5 6E-08 1.3E-12 41.8 1.8 23 111-133 1-23 (23)
26 PF05605 zf-Di19: Drought indu 98.3 9.3E-07 2E-11 46.3 3.8 47 83-132 3-51 (54)
27 PF12756 zf-C2H2_2: C2H2 type 98.3 4.8E-07 1E-11 53.1 2.6 73 56-133 1-73 (100)
28 PF05605 zf-Di19: Drought indu 98.3 1.7E-06 3.6E-11 45.3 4.1 50 54-106 2-53 (54)
29 PF00096 zf-C2H2: Zinc finger, 98.3 1E-06 2.2E-11 37.8 2.4 22 55-76 1-22 (23)
30 PF13912 zf-C2H2_6: C2H2-type 98.2 6.7E-07 1.4E-11 39.9 1.6 24 110-133 1-24 (27)
31 PF13894 zf-C2H2_4: C2H2-type 98.2 1.1E-06 2.5E-11 37.8 2.1 23 111-133 1-23 (24)
32 PF13894 zf-C2H2_4: C2H2-type 97.9 1.3E-05 2.8E-10 34.3 2.7 23 55-77 1-23 (24)
33 PF13912 zf-C2H2_6: C2H2-type 97.9 7.9E-06 1.7E-10 36.4 1.7 24 82-105 1-24 (27)
34 COG5189 SFP1 Putative transcri 97.9 3.4E-06 7.4E-11 58.5 0.6 52 80-131 347-419 (423)
35 smart00355 ZnF_C2H2 zinc finge 97.8 1.6E-05 3.4E-10 34.6 2.2 23 111-133 1-23 (26)
36 PF12874 zf-met: Zinc-finger o 97.6 4.9E-05 1.1E-09 33.0 1.5 23 111-133 1-23 (25)
37 COG5189 SFP1 Putative transcri 97.6 2.8E-05 6.2E-10 54.1 1.0 54 50-103 345-419 (423)
38 PRK04860 hypothetical protein; 97.4 0.00013 2.9E-09 46.5 2.5 38 82-123 119-156 (160)
39 PF09237 GAGA: GAGA factor; I 97.4 0.00018 3.8E-09 36.5 2.3 27 81-107 23-49 (54)
40 smart00355 ZnF_C2H2 zinc finge 97.4 0.00025 5.5E-09 30.6 2.6 22 56-77 2-23 (26)
41 PF12874 zf-met: Zinc-finger o 97.2 0.00022 4.7E-09 30.9 1.3 21 83-103 1-21 (25)
42 PF12171 zf-C2H2_jaz: Zinc-fin 97.1 0.00012 2.5E-09 32.5 -0.1 21 111-131 2-22 (27)
43 PF09237 GAGA: GAGA factor; I 97.1 0.0012 2.5E-08 33.6 3.3 33 50-82 20-52 (54)
44 PF13909 zf-H2C2_5: C2H2-type 97.0 0.00061 1.3E-08 29.2 1.9 22 111-133 1-22 (24)
45 PF13909 zf-H2C2_5: C2H2-type 97.0 0.00095 2.1E-08 28.6 2.3 22 55-77 1-22 (24)
46 PRK04860 hypothetical protein; 96.9 0.00086 1.9E-08 42.9 2.4 39 53-95 118-156 (160)
47 PF12171 zf-C2H2_jaz: Zinc-fin 96.7 0.00066 1.4E-08 30.0 0.9 22 83-104 2-23 (27)
48 TIGR00622 ssl1 transcription f 96.7 0.0037 7.9E-08 37.4 4.1 89 38-133 2-104 (112)
49 PF13913 zf-C2HC_2: zinc-finge 96.7 0.0015 3.2E-08 28.4 1.8 21 111-132 3-23 (25)
50 PF12756 zf-C2H2_2: C2H2 type 96.6 0.003 6.6E-08 36.6 3.3 23 82-104 50-72 (100)
51 smart00451 ZnF_U1 U1-like zinc 96.1 0.0053 1.2E-07 28.6 1.9 22 110-131 3-24 (35)
52 KOG2893|consensus 96.0 0.0027 5.8E-08 42.9 0.9 48 55-106 11-59 (341)
53 PRK14890 putative Zn-ribbon RN 95.9 0.012 2.7E-07 30.9 2.8 10 81-90 47-56 (59)
54 COG2888 Predicted Zn-ribbon RN 95.2 0.018 3.8E-07 30.3 2.0 47 39-90 11-58 (61)
55 smart00451 ZnF_U1 U1-like zinc 95.1 0.021 4.6E-07 26.5 2.0 22 54-75 3-24 (35)
56 PRK00398 rpoP DNA-directed RNA 95.0 0.02 4.4E-07 28.6 1.9 28 37-64 3-31 (46)
57 KOG2231|consensus 94.9 0.063 1.4E-06 41.7 5.0 91 38-133 100-205 (669)
58 COG5236 Uncharacterized conser 94.8 0.0058 1.3E-07 43.4 -0.7 76 54-131 151-241 (493)
59 cd00350 rubredoxin_like Rubred 94.7 0.024 5.3E-07 26.3 1.6 9 109-117 16-24 (33)
60 COG4049 Uncharacterized protei 94.6 0.026 5.7E-07 29.2 1.6 25 79-103 14-38 (65)
61 PF09538 FYDLN_acid: Protein o 94.5 0.029 6.3E-07 33.5 2.0 30 38-67 10-39 (108)
62 COG5048 FOG: Zn-finger [Genera 94.3 0.012 2.6E-07 42.7 -0.0 63 53-115 288-356 (467)
63 COG5048 FOG: Zn-finger [Genera 94.2 0.0087 1.9E-07 43.4 -0.9 54 81-134 288-347 (467)
64 smart00659 RPOLCX RNA polymera 94.2 0.045 9.7E-07 27.2 1.9 26 38-63 3-28 (44)
65 PF13717 zinc_ribbon_4: zinc-r 94.1 0.052 1.1E-06 25.7 2.0 10 39-48 4-13 (36)
66 PF03604 DNA_RNApol_7kD: DNA d 94.0 0.05 1.1E-06 25.1 1.7 26 38-63 1-26 (32)
67 KOG2893|consensus 94.0 0.011 2.4E-07 39.9 -0.6 42 84-129 12-53 (341)
68 COG2888 Predicted Zn-ribbon RN 93.9 0.13 2.7E-06 27.1 3.3 41 21-61 11-57 (61)
69 TIGR02098 MJ0042_CXXC MJ0042 f 93.9 0.054 1.2E-06 25.8 1.9 10 39-48 4-13 (38)
70 PRK14890 putative Zn-ribbon RN 93.9 0.14 3.1E-06 27.0 3.5 10 37-46 25-34 (59)
71 KOG1146|consensus 93.7 0.02 4.3E-07 47.2 0.1 70 53-132 464-540 (1406)
72 PF13719 zinc_ribbon_5: zinc-r 93.5 0.068 1.5E-06 25.5 1.8 10 83-92 26-35 (37)
73 cd00729 rubredoxin_SM Rubredox 92.9 0.082 1.8E-06 24.7 1.5 24 38-62 3-26 (34)
74 KOG2186|consensus 92.8 0.084 1.8E-06 36.1 2.0 51 54-107 3-53 (276)
75 PF10571 UPF0547: Uncharacteri 92.6 0.11 2.4E-06 22.7 1.6 9 56-64 16-24 (26)
76 PF09723 Zn-ribbon_8: Zinc rib 92.5 0.093 2E-06 25.7 1.5 25 38-62 6-34 (42)
77 KOG1146|consensus 92.4 0.038 8.2E-07 45.7 0.0 19 113-131 1331-1349(1406)
78 PF07754 DUF1610: Domain of un 92.4 0.15 3.2E-06 21.8 1.8 8 54-61 16-23 (24)
79 smart00834 CxxC_CXXC_SSSS Puta 92.4 0.11 2.4E-06 25.0 1.7 25 38-62 6-34 (41)
80 TIGR02300 FYDLN_acid conserved 92.3 0.11 2.5E-06 31.7 1.9 34 38-71 10-43 (129)
81 KOG2907|consensus 92.0 0.13 2.8E-06 30.7 1.9 30 19-48 7-36 (116)
82 KOG2482|consensus 91.7 0.2 4.3E-06 35.9 2.8 79 54-132 195-356 (423)
83 PRK00464 nrdR transcriptional 91.5 0.12 2.6E-06 32.9 1.5 13 55-67 29-41 (154)
84 TIGR00622 ssl1 transcription f 91.2 0.42 9.1E-06 28.7 3.5 49 56-106 57-105 (112)
85 KOG2231|consensus 91.1 0.29 6.2E-06 38.2 3.5 71 55-133 183-262 (669)
86 PF09986 DUF2225: Uncharacteri 91.1 0.079 1.7E-06 35.6 0.4 12 111-122 49-60 (214)
87 PF08274 PhnA_Zn_Ribbon: PhnA 90.7 0.16 3.5E-06 23.0 1.1 24 39-62 4-27 (30)
88 TIGR02605 CxxC_CxxC_SSSS putat 90.6 0.18 3.9E-06 25.7 1.5 11 38-48 6-16 (52)
89 PF09986 DUF2225: Uncharacteri 90.4 0.27 5.8E-06 33.1 2.5 14 35-48 3-16 (214)
90 KOG4173|consensus 90.1 0.11 2.5E-06 34.4 0.5 73 55-130 80-166 (253)
91 PF02892 zf-BED: BED zinc fing 90.1 0.31 6.7E-06 23.9 2.0 22 109-130 15-40 (45)
92 COG4049 Uncharacterized protei 90.0 0.19 4.1E-06 26.1 1.2 29 49-77 12-40 (65)
93 PF14353 CpXC: CpXC protein 89.6 0.28 6.1E-06 30.1 2.0 10 39-48 3-12 (128)
94 PHA00626 hypothetical protein 89.5 0.42 9.1E-06 24.9 2.2 11 54-64 23-33 (59)
95 COG5151 SSL1 RNA polymerase II 89.3 0.4 8.7E-06 33.9 2.7 91 38-133 309-411 (421)
96 COG1592 Rubrerythrin [Energy p 89.0 0.28 6.2E-06 31.6 1.7 24 37-62 134-157 (166)
97 TIGR00373 conserved hypothetic 88.9 0.52 1.1E-05 30.2 2.9 31 80-119 107-137 (158)
98 smart00531 TFIIE Transcription 88.4 0.48 1E-05 29.9 2.4 36 53-92 98-133 (147)
99 PF00301 Rubredoxin: Rubredoxi 87.8 0.34 7.3E-06 24.4 1.2 11 38-48 2-12 (47)
100 smart00614 ZnF_BED BED zinc fi 87.1 0.38 8.3E-06 24.4 1.2 21 111-131 19-44 (50)
101 cd00730 rubredoxin Rubredoxin; 86.8 0.42 9E-06 24.4 1.2 11 38-48 2-12 (50)
102 COG1996 RPC10 DNA-directed RNA 86.7 0.48 1E-05 24.1 1.4 28 36-63 5-33 (49)
103 COG1198 PriA Primosomal protei 86.7 0.5 1.1E-05 37.5 2.1 40 20-63 445-484 (730)
104 COG1997 RPL43A Ribosomal prote 86.7 0.39 8.4E-06 27.4 1.1 30 37-66 35-65 (89)
105 PRK00432 30S ribosomal protein 86.4 0.62 1.4E-05 23.8 1.7 24 40-63 23-46 (50)
106 TIGR00373 conserved hypothetic 86.2 0.61 1.3E-05 29.9 2.0 32 52-92 107-138 (158)
107 PRK06266 transcription initiat 85.7 0.83 1.8E-05 29.9 2.5 30 81-119 116-145 (178)
108 PF05443 ROS_MUCR: ROS/MUCR tr 85.7 0.56 1.2E-05 29.1 1.6 23 108-133 70-92 (132)
109 TIGR00595 priA primosomal prot 85.6 0.61 1.3E-05 35.5 2.1 39 21-63 224-262 (505)
110 KOG2785|consensus 85.5 1 2.2E-05 32.8 3.0 78 54-131 3-89 (390)
111 PF02176 zf-TRAF: TRAF-type zi 85.5 0.88 1.9E-05 23.7 2.1 40 81-121 8-53 (60)
112 PRK06266 transcription initiat 85.2 0.56 1.2E-05 30.7 1.5 31 53-92 116-146 (178)
113 COG1773 Rubredoxin [Energy pro 84.9 0.58 1.3E-05 24.3 1.2 12 37-48 3-14 (55)
114 smart00531 TFIIE Transcription 84.8 2.4 5.3E-05 26.7 4.2 38 79-120 96-133 (147)
115 TIGR00686 phnA alkylphosphonat 83.7 0.8 1.7E-05 27.2 1.6 30 39-68 4-33 (109)
116 PRK03824 hypA hydrogenase nick 83.5 0.78 1.7E-05 28.6 1.5 11 38-48 71-81 (135)
117 KOG4167|consensus 83.4 0.37 8.1E-06 37.9 0.1 24 110-133 792-815 (907)
118 KOG2807|consensus 83.4 2.1 4.6E-05 30.6 3.8 34 37-73 276-309 (378)
119 PRK09678 DNA-binding transcrip 83.3 0.34 7.3E-06 26.8 -0.1 41 55-97 2-44 (72)
120 smart00734 ZnF_Rad18 Rad18-lik 83.0 1.3 2.9E-05 19.2 1.8 19 112-131 3-21 (26)
121 PRK10220 hypothetical protein; 82.9 1.1 2.5E-05 26.6 2.0 30 39-68 5-34 (111)
122 TIGR01206 lysW lysine biosynth 82.9 1.1 2.4E-05 23.3 1.7 11 38-48 3-13 (54)
123 KOG2186|consensus 82.9 0.87 1.9E-05 31.3 1.7 21 54-75 29-49 (276)
124 COG4530 Uncharacterized protei 82.8 0.86 1.9E-05 27.2 1.4 28 39-66 11-38 (129)
125 PF08271 TF_Zn_Ribbon: TFIIB z 81.9 1.3 2.9E-05 21.6 1.8 8 55-62 20-27 (43)
126 PF14369 zf-RING_3: zinc-finge 81.7 1.4 3.1E-05 20.6 1.7 8 40-47 24-31 (35)
127 PF06524 NOA36: NOA36 protein; 81.6 1.2 2.6E-05 30.8 2.0 88 39-128 127-227 (314)
128 COG1198 PriA Primosomal protei 81.2 1.8 3.9E-05 34.5 3.1 8 39-46 437-444 (730)
129 PRK03681 hypA hydrogenase nick 81.1 0.97 2.1E-05 27.3 1.3 27 36-62 69-95 (114)
130 PF05191 ADK_lid: Adenylate ki 81.0 0.39 8.6E-06 22.7 -0.3 10 39-48 3-12 (36)
131 COG4957 Predicted transcriptio 80.1 0.85 1.9E-05 28.3 0.8 20 111-133 77-96 (148)
132 PRK04023 DNA polymerase II lar 80.1 2.5 5.3E-05 34.9 3.5 8 83-90 664-671 (1121)
133 PRK14873 primosome assembly pr 79.9 1.5 3.2E-05 34.7 2.2 39 20-63 393-431 (665)
134 PF09845 DUF2072: Zn-ribbon co 79.7 0.92 2E-05 28.0 0.9 26 37-62 1-27 (131)
135 COG3357 Predicted transcriptio 79.6 1.3 2.8E-05 25.5 1.4 26 36-61 57-83 (97)
136 PF08792 A2L_zn_ribbon: A2L zi 79.5 1.1 2.3E-05 20.8 0.9 27 21-47 5-31 (33)
137 COG5236 Uncharacterized conser 79.5 1.2 2.6E-05 32.2 1.5 68 55-130 221-301 (493)
138 PF12760 Zn_Tnp_IS1595: Transp 79.1 1.2 2.5E-05 22.2 1.0 25 38-62 19-45 (46)
139 PF11781 RRN7: RNA polymerase 78.9 1.4 3E-05 20.8 1.2 25 38-62 9-33 (36)
140 PF01363 FYVE: FYVE zinc finge 78.5 1.5 3.2E-05 23.6 1.4 25 38-63 10-34 (69)
141 PF07282 OrfB_Zn_ribbon: Putat 78.3 1.6 3.5E-05 23.5 1.5 27 39-65 30-57 (69)
142 PRK00564 hypA hydrogenase nick 77.8 1.4 3E-05 26.8 1.2 26 37-62 71-96 (117)
143 KOG1280|consensus 77.8 6.6 0.00014 28.5 4.7 42 49-90 74-117 (381)
144 smart00440 ZnF_C2C2 C2C2 Zinc 77.3 2.5 5.5E-05 20.3 1.9 9 55-63 29-37 (40)
145 PRK14873 primosome assembly pr 76.3 2.5 5.3E-05 33.5 2.5 8 39-46 385-392 (665)
146 PF01780 Ribosomal_L37ae: Ribo 76.2 1.1 2.4E-05 25.9 0.5 29 37-65 35-64 (90)
147 PRK05580 primosome assembly pr 75.9 2.2 4.8E-05 33.8 2.2 39 21-63 392-430 (679)
148 PF01155 HypA: Hydrogenase exp 75.3 0.8 1.7E-05 27.6 -0.2 25 38-63 71-95 (113)
149 smart00661 RPOL9 RNA polymeras 75.3 2.4 5.2E-05 21.3 1.6 10 54-63 20-29 (52)
150 PF07649 C1_3: C1-like domain; 75.3 2 4.4E-05 19.1 1.2 9 53-61 14-22 (30)
151 PF13240 zinc_ribbon_2: zinc-r 75.2 2.5 5.4E-05 17.7 1.3 7 40-46 2-8 (23)
152 PF03107 C1_2: C1 domain; Int 74.8 3.1 6.8E-05 18.5 1.7 21 39-61 2-22 (30)
153 COG0068 HypF Hydrogenase matur 74.7 0.19 4.2E-06 39.3 -3.7 68 16-90 98-181 (750)
154 smart00154 ZnF_AN1 AN1-like Zi 74.6 3.2 6.8E-05 19.9 1.8 7 39-45 14-20 (39)
155 PTZ00255 60S ribosomal protein 74.6 1.4 3.1E-05 25.4 0.7 30 37-66 36-66 (90)
156 TIGR00280 L37a ribosomal prote 73.3 1.4 2.9E-05 25.5 0.4 30 37-66 35-65 (91)
157 PF09297 zf-NADH-PPase: NADH p 73.2 1.8 3.8E-05 19.7 0.7 24 22-45 6-29 (32)
158 KOG2785|consensus 73.0 6.5 0.00014 28.8 3.7 26 54-79 166-191 (390)
159 COG1571 Predicted DNA-binding 72.9 2.6 5.6E-05 31.4 1.8 31 38-68 351-381 (421)
160 PF04959 ARS2: Arsenite-resist 72.9 2.5 5.4E-05 28.6 1.6 24 108-131 75-98 (214)
161 PF01096 TFIIS_C: Transcriptio 72.8 1.9 4.1E-05 20.6 0.8 9 55-63 29-37 (39)
162 PF04959 ARS2: Arsenite-resist 72.3 2 4.4E-05 29.0 1.1 29 50-78 73-101 (214)
163 PF10013 DUF2256: Uncharacteri 72.1 2.7 5.8E-05 20.6 1.2 15 112-126 10-24 (42)
164 COG3364 Zn-ribbon containing p 72.1 1.2 2.5E-05 26.3 -0.1 26 37-62 2-28 (112)
165 KOG4173|consensus 72.0 1.4 3E-05 29.5 0.2 53 55-107 107-172 (253)
166 PF12013 DUF3505: Protein of u 71.9 3.4 7.4E-05 24.5 1.9 23 111-133 81-107 (109)
167 PF12013 DUF3505: Protein of u 71.9 4.8 0.0001 23.9 2.5 26 54-79 80-109 (109)
168 PF05290 Baculo_IE-1: Baculovi 71.4 2.7 5.8E-05 26.1 1.3 58 33-97 76-136 (140)
169 smart00249 PHD PHD zinc finger 71.3 6.3 0.00014 18.7 2.6 11 37-47 14-24 (47)
170 PF15269 zf-C2H2_7: Zinc-finge 71.3 3.3 7.2E-05 20.5 1.4 21 111-131 21-41 (54)
171 cd00065 FYVE FYVE domain; Zinc 71.0 3.6 7.7E-05 21.1 1.7 26 40-66 5-30 (57)
172 PRK12380 hydrogenase nickel in 70.2 2.7 6E-05 25.3 1.2 25 37-62 70-94 (113)
173 PF06524 NOA36: NOA36 protein; 70.0 2.6 5.7E-05 29.2 1.2 96 8-105 114-232 (314)
174 KOG2593|consensus 70.0 6.1 0.00013 29.4 3.1 35 80-117 126-160 (436)
175 PF13453 zf-TFIIB: Transcripti 69.8 5.4 0.00012 19.2 2.0 16 55-70 20-35 (41)
176 PRK03976 rpl37ae 50S ribosomal 69.2 1.8 3.9E-05 25.0 0.3 30 37-66 36-66 (90)
177 KOG4167|consensus 69.2 0.95 2.1E-05 35.8 -1.1 27 53-79 791-817 (907)
178 PRK14714 DNA polymerase II lar 68.6 6 0.00013 33.6 3.1 21 39-63 681-701 (1337)
179 PF13878 zf-C2H2_3: zinc-finge 68.3 7.2 0.00016 18.9 2.3 24 55-78 14-39 (41)
180 KOG2807|consensus 68.2 8 0.00017 27.9 3.3 25 81-105 344-368 (378)
181 PF14446 Prok-RING_1: Prokaryo 68.1 5.1 0.00011 20.8 1.8 25 38-63 6-30 (54)
182 KOG2593|consensus 67.0 4.1 8.9E-05 30.3 1.8 31 33-63 124-162 (436)
183 PF14803 Nudix_N_2: Nudix N-te 66.8 5.3 0.00011 18.6 1.5 7 55-61 23-29 (34)
184 PRK04023 DNA polymerase II lar 66.7 7 0.00015 32.5 3.1 9 55-63 664-672 (1121)
185 KOG3507|consensus 66.5 4.9 0.00011 21.2 1.5 27 37-63 20-46 (62)
186 PF00130 C1_1: Phorbol esters/ 65.9 5.5 0.00012 20.0 1.7 26 37-62 11-36 (53)
187 KOG3408|consensus 65.6 6 0.00013 24.2 2.0 23 110-132 57-79 (129)
188 COG0068 HypF Hydrogenase matur 65.6 1.6 3.4E-05 34.5 -0.6 75 38-119 102-182 (750)
189 TIGR00244 transcriptional regu 65.2 4.4 9.6E-05 25.6 1.4 14 55-68 29-42 (147)
190 PF08790 zf-LYAR: LYAR-type C2 64.4 2.2 4.7E-05 19.0 -0.0 10 83-92 1-10 (28)
191 PF04810 zf-Sec23_Sec24: Sec23 63.9 6.3 0.00014 18.9 1.6 7 55-61 25-31 (40)
192 TIGR00100 hypA hydrogenase nic 63.2 4.8 0.0001 24.3 1.3 25 37-62 70-94 (115)
193 PF15616 TerY-C: TerY-C metal 63.1 6.9 0.00015 24.3 2.0 15 49-63 100-114 (131)
194 PRK00420 hypothetical protein; 63.0 7.5 0.00016 23.5 2.1 28 38-65 24-51 (112)
195 PF07975 C1_4: TFIIH C1-like d 62.9 1.2 2.7E-05 22.8 -1.1 15 55-69 22-36 (51)
196 PF01286 XPA_N: XPA protein N- 62.3 6.2 0.00013 18.4 1.3 10 39-48 5-14 (34)
197 PF07295 DUF1451: Protein of u 61.6 7 0.00015 24.7 1.9 27 37-64 112-140 (146)
198 COG2331 Uncharacterized protei 61.4 1.9 4.1E-05 24.0 -0.6 8 55-62 13-20 (82)
199 COG5216 Uncharacterized conser 61.2 5.9 0.00013 20.9 1.2 11 79-89 41-51 (67)
200 COG4888 Uncharacterized Zn rib 61.1 6.2 0.00013 23.3 1.4 30 35-64 20-56 (104)
201 PF10058 DUF2296: Predicted in 60.8 11 0.00023 19.6 2.2 30 16-45 19-52 (54)
202 COG1327 Predicted transcriptio 60.7 5.4 0.00012 25.4 1.2 10 39-48 30-39 (156)
203 PF12773 DZR: Double zinc ribb 59.8 15 0.00033 18.2 2.7 9 38-46 30-38 (50)
204 COG1571 Predicted DNA-binding 59.7 5.9 0.00013 29.5 1.5 28 21-49 352-379 (421)
205 PF03563 Bunya_G2: Bunyavirus 59.4 12 0.00026 26.2 2.8 36 39-75 236-271 (285)
206 COG3677 Transposase and inacti 59.3 7.2 0.00016 24.1 1.6 11 38-48 54-64 (129)
207 PRK12722 transcriptional activ 59.0 7 0.00015 25.8 1.6 27 18-44 133-161 (187)
208 COG3091 SprT Zn-dependent meta 58.8 6.4 0.00014 25.1 1.3 34 81-119 116-149 (156)
209 PF15135 UPF0515: Uncharacteri 58.3 9.5 0.00021 26.4 2.2 49 19-67 112-168 (278)
210 COG1998 RPS31 Ribosomal protei 57.8 9.4 0.0002 19.4 1.6 9 54-62 37-45 (51)
211 PF09082 DUF1922: Domain of un 57.8 3.2 6.8E-05 22.6 -0.1 27 20-48 4-30 (68)
212 TIGR01053 LSD1 zinc finger dom 57.8 9.2 0.0002 17.3 1.5 23 22-44 4-26 (31)
213 PRK12496 hypothetical protein; 56.7 8.4 0.00018 24.9 1.7 26 38-64 128-153 (164)
214 PRK04351 hypothetical protein; 56.6 9.4 0.0002 24.2 1.9 33 54-94 112-144 (149)
215 PF13824 zf-Mss51: Zinc-finger 56.1 10 0.00022 19.8 1.6 11 53-63 13-23 (55)
216 KOG2071|consensus 56.1 6.9 0.00015 30.3 1.4 26 108-133 416-441 (579)
217 PF00628 PHD: PHD-finger; Int 56.0 13 0.00029 18.4 2.1 11 37-47 14-24 (51)
218 smart00064 FYVE Protein presen 55.8 9.7 0.00021 20.3 1.6 26 39-65 12-37 (68)
219 PRK00762 hypA hydrogenase nick 54.9 7.2 0.00016 23.9 1.1 9 38-47 71-79 (124)
220 PF14634 zf-RING_5: zinc-RING 54.4 19 0.00041 17.4 2.4 8 82-89 36-43 (44)
221 KOG0717|consensus 53.7 8.1 0.00018 29.2 1.4 21 111-131 293-313 (508)
222 PRK12860 transcriptional activ 52.6 10 0.00023 25.1 1.6 28 17-44 132-161 (189)
223 PRK11032 hypothetical protein; 52.4 10 0.00022 24.4 1.5 26 38-63 125-151 (160)
224 cd00029 C1 Protein kinase C co 52.4 11 0.00023 18.5 1.4 22 40-61 14-35 (50)
225 PF01428 zf-AN1: AN1-like Zinc 51.8 4.3 9.3E-05 19.8 -0.2 13 109-121 12-24 (43)
226 PF02318 FYVE_2: FYVE-type zin 51.8 3.7 8E-05 24.9 -0.5 24 38-61 55-78 (118)
227 PF01927 Mut7-C: Mut7-C RNAse 51.5 18 0.00038 22.8 2.5 17 82-98 124-140 (147)
228 KOG3408|consensus 51.2 9 0.0002 23.4 1.1 23 82-104 57-79 (129)
229 PF05495 zf-CHY: CHY zinc fing 51.0 6.3 0.00014 21.6 0.4 27 37-63 41-70 (71)
230 KOG2906|consensus 51.0 11 0.00024 22.1 1.4 34 83-120 66-103 (105)
231 PF13248 zf-ribbon_3: zinc-rib 50.9 12 0.00027 15.9 1.2 6 40-45 5-10 (26)
232 PF09416 UPF1_Zn_bind: RNA hel 49.8 28 0.00061 22.2 3.2 21 55-75 15-41 (152)
233 COG2824 PhnA Uncharacterized Z 49.8 11 0.00024 22.4 1.3 29 39-67 5-33 (112)
234 KOG2482|consensus 49.1 9.7 0.00021 27.7 1.1 51 82-132 144-217 (423)
235 PRK05452 anaerobic nitric oxid 48.6 11 0.00024 28.7 1.5 13 36-48 424-436 (479)
236 PF10263 SprT-like: SprT-like 48.4 12 0.00025 23.6 1.4 9 83-91 144-152 (157)
237 PF11793 FANCL_C: FANCL C-term 47.9 15 0.00033 20.0 1.6 8 84-91 57-64 (70)
238 KOG0978|consensus 47.5 4.1 8.8E-05 32.3 -1.0 16 83-98 679-694 (698)
239 cd02249 ZZ Zinc finger, ZZ typ 47.5 20 0.00042 17.6 1.8 21 38-61 1-21 (46)
240 PF05129 Elf1: Transcription e 47.1 12 0.00026 21.1 1.1 9 36-44 21-29 (81)
241 cd02337 ZZ_CBP Zinc finger, ZZ 46.9 21 0.00046 17.2 1.9 9 53-61 12-20 (41)
242 PF09332 Mcm10: Mcm10 replicat 46.6 6.2 0.00013 28.7 -0.1 27 36-62 284-311 (344)
243 PF04216 FdhE: Protein involve 46.3 4.6 9.9E-05 28.5 -0.8 26 35-63 195-220 (290)
244 PF13451 zf-trcl: Probable zin 46.3 7.7 0.00017 19.7 0.2 15 108-122 2-16 (49)
245 PF02150 RNA_POL_M_15KD: RNA p 46.0 15 0.00032 17.1 1.2 8 56-63 22-29 (35)
246 KOG2636|consensus 46.0 14 0.00031 27.8 1.6 28 103-130 394-422 (497)
247 PF11672 DUF3268: Protein of u 46.0 20 0.00042 21.3 1.9 7 55-61 32-38 (102)
248 TIGR01384 TFS_arch transcripti 45.6 19 0.00042 21.0 1.9 38 82-121 62-101 (104)
249 PF10276 zf-CHCC: Zinc-finger 45.5 9.2 0.0002 18.5 0.4 12 36-47 28-39 (40)
250 cd00924 Cyt_c_Oxidase_Vb Cytoc 44.6 11 0.00023 22.1 0.7 12 36-47 78-89 (97)
251 PF12907 zf-met2: Zinc-binding 44.5 9.5 0.00021 18.5 0.4 20 84-103 3-25 (40)
252 PTZ00448 hypothetical protein; 44.4 17 0.00037 26.7 1.8 23 110-132 314-336 (373)
253 smart00731 SprT SprT homologue 44.3 16 0.00035 22.8 1.5 29 36-64 111-143 (146)
254 KOG0957|consensus 43.9 20 0.00044 27.6 2.1 48 16-66 541-601 (707)
255 COG1675 TFA1 Transcription ini 43.6 37 0.00081 22.3 3.1 32 79-119 110-141 (176)
256 cd02341 ZZ_ZZZ3 Zinc finger, Z 43.3 24 0.00052 17.7 1.8 8 54-61 15-22 (48)
257 PRK03564 formate dehydrogenase 43.2 23 0.0005 25.4 2.3 26 34-62 209-234 (309)
258 PF06397 Desulfoferrod_N: Desu 42.6 13 0.00028 17.6 0.7 12 37-48 6-17 (36)
259 cd04476 RPA1_DBD_C RPA1_DBD_C: 42.4 21 0.00045 22.8 1.9 12 36-47 50-61 (166)
260 PF04780 DUF629: Protein of un 42.1 19 0.00042 27.3 1.8 21 111-131 58-78 (466)
261 COG1656 Uncharacterized conser 41.9 28 0.00062 22.5 2.3 13 83-95 131-143 (165)
262 PF04780 DUF629: Protein of un 41.5 19 0.00041 27.4 1.7 26 82-107 57-83 (466)
263 smart00586 ZnF_DBF Zinc finger 41.2 22 0.00048 18.0 1.4 20 108-130 3-22 (49)
264 KOG2272|consensus 41.1 36 0.00077 23.8 2.8 14 81-94 220-233 (332)
265 COG5415 Predicted integral mem 41.0 17 0.00036 24.6 1.2 41 6-46 179-223 (251)
266 PRK11823 DNA repair protein Ra 40.9 22 0.00047 26.9 2.0 25 37-64 7-31 (446)
267 KOG2636|consensus 40.8 22 0.00048 26.9 1.9 28 76-103 395-423 (497)
268 PF04641 Rtf2: Rtf2 RING-finge 40.6 39 0.00085 23.5 3.1 53 34-95 110-163 (260)
269 COG1655 Uncharacterized protei 40.1 9.3 0.0002 26.2 -0.0 23 81-103 18-40 (267)
270 PRK05978 hypothetical protein; 39.5 23 0.00051 22.5 1.7 6 57-62 55-60 (148)
271 KOG1280|consensus 39.5 33 0.00071 25.1 2.5 38 80-117 77-116 (381)
272 PF11023 DUF2614: Protein of u 39.5 19 0.00041 21.7 1.2 28 38-66 70-97 (114)
273 PF11789 zf-Nse: Zinc-finger o 39.4 48 0.001 17.2 2.6 45 35-87 9-53 (57)
274 PF06943 zf-LSD1: LSD1 zinc fi 39.3 31 0.00068 14.8 1.6 21 24-44 3-23 (25)
275 COG4338 Uncharacterized protei 39.3 12 0.00026 18.9 0.3 16 112-127 14-29 (54)
276 KOG3002|consensus 39.2 29 0.00064 24.8 2.3 91 16-116 45-142 (299)
277 smart00109 C1 Protein kinase C 39.2 27 0.00059 16.7 1.7 23 38-61 12-34 (49)
278 PF13901 DUF4206: Domain of un 39.1 25 0.00054 23.5 1.9 29 36-64 151-182 (202)
279 TIGR00416 sms DNA repair prote 38.9 24 0.00053 26.7 2.0 26 37-65 7-32 (454)
280 PF13005 zf-IS66: zinc-finger 38.8 17 0.00036 17.8 0.8 9 40-48 5-13 (47)
281 COG4306 Uncharacterized protei 38.7 30 0.00065 21.3 2.0 32 37-68 39-82 (160)
282 cd01121 Sms Sms (bacterial rad 38.5 27 0.00058 25.7 2.1 24 38-64 1-24 (372)
283 PF13445 zf-RING_UBOX: RING-ty 38.3 42 0.0009 16.4 2.2 27 40-68 1-27 (43)
284 KOG0696|consensus 38.2 12 0.00025 28.4 0.2 59 51-118 70-129 (683)
285 PRK07591 threonine synthase; V 37.5 23 0.00049 26.5 1.6 22 38-61 19-40 (421)
286 PRK11827 hypothetical protein; 37.5 25 0.00054 18.7 1.3 28 21-48 10-37 (60)
287 COG1779 C4-type Zn-finger prot 37.4 14 0.00031 24.6 0.5 11 38-48 44-54 (201)
288 PF08646 Rep_fac-A_C: Replicat 37.4 18 0.0004 22.5 1.0 27 20-47 19-47 (146)
289 KOG0717|consensus 37.2 21 0.00046 27.1 1.4 22 83-104 293-314 (508)
290 PRK06450 threonine synthase; V 37.0 22 0.00047 25.8 1.4 23 38-62 4-26 (338)
291 PHA02942 putative transposase; 37.0 39 0.00085 25.0 2.8 11 82-92 342-352 (383)
292 PF04423 Rad50_zn_hook: Rad50 37.0 13 0.00027 19.0 0.2 11 112-122 22-32 (54)
293 COG5112 UFD2 U1-like Zn-finger 36.8 28 0.00061 20.8 1.6 21 111-131 56-76 (126)
294 PLN02294 cytochrome c oxidase 36.8 17 0.00037 23.6 0.8 19 102-121 134-152 (174)
295 TIGR00627 tfb4 transcription f 36.3 28 0.0006 24.6 1.8 24 38-64 256-279 (279)
296 KOG3799|consensus 36.3 17 0.00037 22.7 0.7 42 19-62 65-115 (169)
297 PF14311 DUF4379: Domain of un 36.2 34 0.00073 17.4 1.7 12 83-94 29-40 (55)
298 TIGR03830 CxxCG_CxxCG_HTH puta 36.1 30 0.00066 20.7 1.8 31 42-73 20-50 (127)
299 PF07503 zf-HYPF: HypF finger; 35.6 3.5 7.5E-05 19.3 -1.9 11 110-120 21-31 (35)
300 cd02335 ZZ_ADA2 Zinc finger, Z 35.5 41 0.00088 16.8 1.9 8 53-60 14-21 (49)
301 PLN02748 tRNA dimethylallyltra 35.3 27 0.00059 26.6 1.7 24 109-132 417-441 (468)
302 PHA02998 RNA polymerase subuni 35.3 35 0.00076 22.5 2.0 11 83-93 172-182 (195)
303 PLN03238 probable histone acet 35.3 37 0.0008 24.1 2.3 24 108-131 46-69 (290)
304 PRK14559 putative protein seri 35.2 56 0.0012 26.1 3.4 52 3-67 3-54 (645)
305 KOG2923|consensus 35.0 25 0.00053 18.9 1.1 11 79-89 41-51 (67)
306 PRK14892 putative transcriptio 34.9 39 0.00084 19.9 2.0 12 54-65 42-53 (99)
307 PF06220 zf-U1: U1 zinc finger 34.6 35 0.00076 16.1 1.5 11 54-64 3-13 (38)
308 PF07191 zinc-ribbons_6: zinc- 34.2 22 0.00048 19.5 0.9 12 37-48 17-28 (70)
309 PF09963 DUF2197: Uncharacteri 34.2 16 0.00035 19.1 0.3 10 81-90 30-39 (56)
310 PRK12286 rpmF 50S ribosomal pr 33.1 34 0.00074 17.9 1.4 20 38-61 28-47 (57)
311 PF01485 IBR: IBR domain; Int 32.6 34 0.00074 17.5 1.5 27 21-47 20-50 (64)
312 COG1594 RPB9 DNA-directed RNA 32.5 34 0.00074 20.6 1.6 9 19-27 22-30 (113)
313 PRK12775 putative trifunctiona 32.5 28 0.00061 29.2 1.6 45 19-63 796-847 (1006)
314 PF10122 Mu-like_Com: Mu-like 32.3 25 0.00054 18.0 0.8 30 19-48 4-35 (51)
315 PF07535 zf-DBF: DBF zinc fing 31.8 36 0.00078 17.2 1.3 19 109-130 4-22 (49)
316 TIGR01562 FdhE formate dehydro 31.4 40 0.00086 24.2 2.0 26 34-62 207-232 (305)
317 PF10083 DUF2321: Uncharacteri 30.9 45 0.00097 21.4 1.9 20 49-68 63-82 (158)
318 COG5188 PRP9 Splicing factor 3 30.9 37 0.0008 25.0 1.7 28 103-130 367-395 (470)
319 TIGR01031 rpmF_bact ribosomal 30.8 36 0.00079 17.6 1.3 8 38-45 27-34 (55)
320 PF08209 Sgf11: Sgf11 (transcr 30.4 50 0.0011 15.2 1.6 21 82-103 4-24 (33)
321 COG1645 Uncharacterized Zn-fin 30.0 30 0.00066 21.5 1.0 23 21-45 30-52 (131)
322 COG1439 Predicted nucleic acid 29.9 28 0.00062 22.8 1.0 23 38-63 140-162 (177)
323 PF09855 DUF2082: Nucleic-acid 29.7 36 0.00078 18.3 1.2 7 38-44 1-7 (64)
324 PRK00415 rps27e 30S ribosomal 29.7 49 0.0011 17.5 1.7 9 55-63 31-39 (59)
325 COG5151 SSL1 RNA polymerase II 29.5 68 0.0015 23.2 2.8 25 81-105 387-411 (421)
326 PF13639 zf-RING_2: Ring finge 29.4 74 0.0016 15.1 2.5 8 40-47 3-10 (44)
327 TIGR03831 YgiT_finger YgiT-typ 29.2 25 0.00055 16.7 0.5 12 36-47 31-42 (46)
328 KOG1842|consensus 29.0 26 0.00057 26.5 0.8 24 54-77 15-38 (505)
329 PF05180 zf-DNL: DNL zinc fing 28.9 7.8 0.00017 21.0 -1.5 12 78-89 25-36 (66)
330 PRK00418 DNA gyrase inhibitor; 28.8 45 0.00098 17.8 1.5 11 38-48 7-17 (62)
331 KOG2071|consensus 28.8 42 0.00091 26.3 1.8 26 53-78 417-442 (579)
332 PF02591 DUF164: Putative zinc 28.7 21 0.00046 18.3 0.2 12 34-45 43-54 (56)
333 PF02748 PyrI_C: Aspartate car 28.3 26 0.00055 18.0 0.5 16 33-48 31-46 (52)
334 PRK06260 threonine synthase; V 28.3 40 0.00088 24.9 1.7 25 38-63 4-28 (397)
335 PF05741 zf-nanos: Nanos RNA b 28.2 52 0.0011 17.2 1.6 10 37-46 33-42 (55)
336 KOG0402|consensus 28.2 21 0.00045 20.3 0.1 29 38-66 37-66 (92)
337 TIGR03844 cysteate_syn cysteat 28.0 39 0.00085 25.1 1.5 22 38-61 3-24 (398)
338 PF07227 DUF1423: Protein of u 27.8 34 0.00074 25.8 1.2 53 38-91 129-192 (446)
339 PF14255 Cys_rich_CPXG: Cystei 27.7 30 0.00065 17.8 0.7 10 39-48 2-11 (52)
340 TIGR03826 YvyF flagellar opero 27.2 42 0.00091 21.1 1.4 21 2-25 4-24 (137)
341 KOG3362|consensus 27.1 20 0.00044 22.6 -0.1 20 54-73 129-148 (156)
342 KOG4727|consensus 27.1 57 0.0012 21.4 1.9 27 49-75 70-96 (193)
343 PLN00104 MYST -like histone ac 26.9 51 0.0011 25.1 2.0 23 109-131 197-219 (450)
344 smart00291 ZnF_ZZ Zinc-binding 26.7 77 0.0017 15.3 2.0 21 38-61 5-25 (44)
345 PF01783 Ribosomal_L32p: Ribos 26.7 67 0.0015 16.6 1.9 15 18-32 25-39 (56)
346 COG4357 Zinc finger domain con 26.7 19 0.00042 21.0 -0.2 33 36-68 61-94 (105)
347 TIGR00319 desulf_FeS4 desulfof 26.7 31 0.00068 15.6 0.6 13 36-48 6-18 (34)
348 PLN03239 histone acetyltransfe 26.7 57 0.0012 23.9 2.1 24 108-131 104-127 (351)
349 cd00974 DSRD Desulforedoxin (D 26.5 32 0.0007 15.6 0.6 13 36-48 3-15 (34)
350 COG4640 Predicted membrane pro 26.5 61 0.0013 24.3 2.2 16 56-71 17-32 (465)
351 TIGR00515 accD acetyl-CoA carb 26.3 24 0.00052 25.0 0.2 30 38-67 27-58 (285)
352 PF00569 ZZ: Zinc finger, ZZ t 26.2 52 0.0011 16.1 1.4 23 37-61 4-26 (46)
353 COG3809 Uncharacterized protei 26.2 92 0.002 17.6 2.4 38 39-76 3-43 (88)
354 cd02340 ZZ_NBR1_like Zinc fing 26.1 75 0.0016 15.4 1.9 7 54-60 14-20 (43)
355 COG1326 Uncharacterized archae 25.8 71 0.0015 21.4 2.2 11 82-92 30-40 (201)
356 PF05280 FlhC: Flagellar trans 25.7 33 0.00072 22.5 0.7 28 17-44 132-161 (175)
357 PRK08222 hydrogenase 4 subunit 25.5 48 0.001 21.7 1.5 19 109-127 113-131 (181)
358 CHL00174 accD acetyl-CoA carbo 25.5 25 0.00055 25.1 0.2 30 38-67 39-70 (296)
359 PTZ00448 hypothetical protein; 25.3 56 0.0012 24.1 1.9 23 54-76 314-336 (373)
360 PF14206 Cys_rich_CPCC: Cystei 25.1 67 0.0014 18.1 1.8 9 38-46 2-10 (78)
361 PTZ00064 histone acetyltransfe 25.1 63 0.0014 25.0 2.1 24 108-131 278-301 (552)
362 KOG0782|consensus 24.9 14 0.00029 29.0 -1.3 51 68-124 239-290 (1004)
363 PF11931 DUF3449: Domain of un 24.8 24 0.00053 23.5 0.0 21 81-101 100-121 (196)
364 COG2816 NPY1 NTP pyrophosphohy 24.5 52 0.0011 23.3 1.5 28 21-48 113-140 (279)
365 smart00504 Ubox Modified RING 24.1 1.1E+02 0.0025 15.5 4.1 45 38-93 2-46 (63)
366 COG4896 Uncharacterized protei 23.8 58 0.0013 17.4 1.3 39 56-94 4-43 (68)
367 COG2051 RPS27A Ribosomal prote 23.6 55 0.0012 17.8 1.2 8 56-63 40-47 (67)
368 COG4391 Uncharacterized protei 23.2 86 0.0019 16.7 1.9 20 28-47 15-34 (62)
369 PF11494 Ta0938: Ta0938; Inte 23.2 77 0.0017 18.6 1.8 34 34-67 11-50 (105)
370 COG1545 Predicted nucleic-acid 22.8 59 0.0013 20.3 1.4 23 38-63 30-52 (140)
371 PRK05654 acetyl-CoA carboxylas 22.7 29 0.00063 24.7 0.1 30 38-67 28-59 (292)
372 KOG2747|consensus 22.4 59 0.0013 24.3 1.5 25 108-132 156-180 (396)
373 smart00647 IBR In Between Ring 22.3 74 0.0016 16.2 1.6 8 38-45 41-48 (64)
374 PF04438 zf-HIT: HIT zinc fing 22.3 38 0.00082 15.1 0.4 11 36-46 12-22 (30)
375 cd00122 MBD MeCP2, MBD1, MBD2, 21.5 90 0.0019 16.3 1.8 23 111-133 28-50 (62)
376 PRK08359 transcription factor; 21.2 32 0.0007 22.6 0.0 27 38-64 7-40 (176)
377 COG0675 Transposase and inacti 21.0 60 0.0013 22.8 1.4 24 39-66 311-334 (364)
378 PRK14811 formamidopyrimidine-D 20.8 74 0.0016 22.3 1.8 26 39-64 237-265 (269)
379 KOG4124|consensus 20.8 14 0.00031 26.9 -1.8 47 81-127 348-415 (442)
380 PF02891 zf-MIZ: MIZ/SP-RING z 20.7 57 0.0012 16.4 0.9 8 83-90 42-49 (50)
381 PF14319 Zn_Tnp_IS91: Transpos 20.6 97 0.0021 18.5 2.0 62 34-101 39-101 (111)
382 KOG1729|consensus 20.2 12 0.00026 26.5 -2.2 28 38-66 169-197 (288)
383 PLN03238 probable histone acet 20.1 1.1E+02 0.0024 21.9 2.4 25 51-75 45-69 (290)
384 KOG0320|consensus 20.1 22 0.00049 23.3 -0.8 51 35-94 129-179 (187)
385 PRK00241 nudC NADH pyrophospha 20.0 69 0.0015 22.3 1.4 28 21-48 101-128 (256)
No 1
>KOG2462|consensus
Probab=99.95 E-value=1.3e-28 Score=163.95 Aligned_cols=114 Identities=23% Similarity=0.448 Sum_probs=100.1
Q ss_pred ceecCccccc----------ccccCCC---CccccCCCCCCccc---------CCCCcceeeCCCCCccCChHHHHHHHH
Q psy3507 18 TLATCIHCRL----------LLVPTAE---ELMYHCKTCSTVSH---------PNISYKYTCYACDYHTLMSEDMKKHMR 75 (134)
Q Consensus 18 ~~~~C~~C~~----------h~~~h~~---~~~~~C~~C~~~f~---------~~~~~~~~C~~C~~~f~~~~~l~~H~~ 75 (134)
..++|+.|++ |..+|.. .+.+.|++||+.|. .+...+++|.+||+.|...-.|..|++
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiR 208 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIR 208 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccc
Confidence 3577888844 4444432 67799999999998 445578999999999999999999999
Q ss_pred HhcCCCceeccccCccccCchhHHHHhhhcCCCCCeecCcChhhhcCHHHHHHHHH
Q psy3507 76 KHTGEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 76 ~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~F~~~~~l~~H~~ 131 (134)
+|+||+||.|+.|+++|..+++|+.|+++|.+.|+|+|..|+|+|...+.|.+|..
T Consensus 209 THTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 209 THTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred cccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999975
No 2
>KOG2462|consensus
Probab=99.94 E-value=1.2e-27 Score=159.34 Aligned_cols=98 Identities=28% Similarity=0.604 Sum_probs=91.3
Q ss_pred CccccCCCCCCcccCCC--------------CcceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccCchhHHH
Q psy3507 35 ELMYHCKTCSTVSHPNI--------------SYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKI 100 (134)
Q Consensus 35 ~~~~~C~~C~~~f~~~~--------------~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~ 100 (134)
...|+|++||+.+.... .+.+.|++|++.|.+-..|++|+++|. .+++|.+||+.|.++.-|+.
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQG 205 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQG 205 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhc
Confidence 45699999999998433 567999999999999999999999997 67999999999999999999
Q ss_pred HhhhcCCCCCeecCcChhhhcCHHHHHHHHHhcC
Q psy3507 101 HERKHTGDKPYICQQCRDTFSSLYLFRNRLQSHG 134 (134)
Q Consensus 101 H~~~h~~~~~~~C~~C~~~F~~~~~l~~H~~~H~ 134 (134)
|+|+|+|||||.|+.|+|+|..+++|+.||+||+
T Consensus 206 HiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS 239 (279)
T KOG2462|consen 206 HIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHS 239 (279)
T ss_pred ccccccCCCCccCCcccchhcchHHHHHHHHhhc
Confidence 9999999999999999999999999999999995
No 3
>KOG1074|consensus
Probab=99.76 E-value=1.2e-19 Score=135.65 Aligned_cols=81 Identities=26% Similarity=0.565 Sum_probs=73.3
Q ss_pred ceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccCchhHHHHhhhcCCCC----CeecC---cChhhhcCHHHH
Q psy3507 54 KYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHTGDK----PYICQ---QCRDTFSSLYLF 126 (134)
Q Consensus 54 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~----~~~C~---~C~~~F~~~~~l 126 (134)
+-+|-+|.++..-++.|+.|.++|+|++||+|.+||++|.++.+|+.|+.+|...- +|.|+ +|-+.|...-.|
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~l 684 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTL 684 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccc
Confidence 47899999999999999999999999999999999999999999999999887643 48899 899999999999
Q ss_pred HHHHHhcC
Q psy3507 127 RNRLQSHG 134 (134)
Q Consensus 127 ~~H~~~H~ 134 (134)
..|+++|+
T Consensus 685 pQhIriH~ 692 (958)
T KOG1074|consen 685 PQHIRIHL 692 (958)
T ss_pred cceEEeec
Confidence 99999884
No 4
>KOG3608|consensus
Probab=99.75 E-value=4.6e-19 Score=122.08 Aligned_cols=107 Identities=24% Similarity=0.512 Sum_probs=96.3
Q ss_pred ccccccCCCCccccCCCCCCccc-------------CCCCcceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccc
Q psy3507 26 RLLLVPTAEELMYHCKTCSTVSH-------------PNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSC 92 (134)
Q Consensus 26 ~~h~~~h~~~~~~~C~~C~~~f~-------------~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 92 (134)
+.|.++|+++|...|+.||..|. .....+|.|..|.+.|.+...|..|+..|.. .|+|+.|+.+.
T Consensus 196 reH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn--~ykCplCdmtc 273 (467)
T KOG3608|consen 196 REHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN--CYKCPLCDMTC 273 (467)
T ss_pred HHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh--cccccccccCC
Confidence 66999999999999999999998 2223479999999999999999999998874 59999999999
Q ss_pred cCchhHHHHhhh-cCCCCCeecCcChhhhcCHHHHHHHHHhcC
Q psy3507 93 TQSSALKIHERK-HTGDKPYICQQCRDTFSSLYLFRNRLQSHG 134 (134)
Q Consensus 93 ~~~~~l~~H~~~-h~~~~~~~C~~C~~~F~~~~~l~~H~~~H~ 134 (134)
..+++|..|++. |..++||+|..|++.|.+.+.|.+|+.+|+
T Consensus 274 ~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 274 SSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred CChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 999999999885 888999999999999999999999999885
No 5
>KOG3576|consensus
Probab=99.72 E-value=1.6e-18 Score=111.43 Aligned_cols=77 Identities=27% Similarity=0.626 Sum_probs=44.0
Q ss_pred ceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccCchhHHHHhhhcCCCCCeecCcChhhhcCHHHHHHHH
Q psy3507 54 KYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLFRNRL 130 (134)
Q Consensus 54 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~F~~~~~l~~H~ 130 (134)
.|.|.+|++.|.....|.+|++.|...+.+-|..||+.|...-.|++|+++|+|.+||+|..|+++|..+-+|..|+
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 35555555555555555555555555555555555555555555555555555555555555555555555555554
No 6
>KOG3576|consensus
Probab=99.70 E-value=4.3e-18 Score=109.49 Aligned_cols=100 Identities=29% Similarity=0.545 Sum_probs=89.5
Q ss_pred CCccccCCCCCCccc-----------CCCCcceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccCchhHHHHh
Q psy3507 34 EELMYHCKTCSTVSH-----------PNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHE 102 (134)
Q Consensus 34 ~~~~~~C~~C~~~f~-----------~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 102 (134)
+...|.|.+|++.|. +...+.+.|..||+.|.+.-+|++|+++|+|.+||+|..|+++|.++-+|..|+
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 345699999999998 667778999999999999999999999999999999999999999999999997
Q ss_pred hh-cC----------CCCCeecCcChhhhcCHHHHHHHHHhc
Q psy3507 103 RK-HT----------GDKPYICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 103 ~~-h~----------~~~~~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
+. |. .++.|.|+.||.+-.....+..|++.|
T Consensus 194 ~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~ 235 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLH 235 (267)
T ss_pred HHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhc
Confidence 75 43 245699999999999999999998876
No 7
>KOG1074|consensus
Probab=99.69 E-value=8.7e-18 Score=125.95 Aligned_cols=52 Identities=33% Similarity=0.695 Sum_probs=49.8
Q ss_pred eeccccCccccCchhHHHHhhhcCCCCCeecCcChhhhcCHHHHHHHHHhcC
Q psy3507 83 YKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLFRNRLQSHG 134 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~F~~~~~l~~H~~~H~ 134 (134)
..|.+|++.|...+.|..|+++|++++||.|..|++.|..+.+|+.||.+|.
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~ 931 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHM 931 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhcccc
Confidence 3699999999999999999999999999999999999999999999999984
No 8
>KOG3623|consensus
Probab=99.68 E-value=6.6e-18 Score=125.22 Aligned_cols=82 Identities=27% Similarity=0.639 Sum_probs=77.9
Q ss_pred CCCcceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccCchhHHHHhhhcCCCCCeecCcChhhhcCHHHHHHH
Q psy3507 50 NISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLFRNR 129 (134)
Q Consensus 50 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~F~~~~~l~~H 129 (134)
..+.+|.|+.|++.|...+.|.+|.--|+|.+||+|.+|.++|..+-.|..|+|.|.|+|||+|..|+|+|....++..|
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQH 969 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQH 969 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhh
Confidence 33457999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HH
Q psy3507 130 LQ 131 (134)
Q Consensus 130 ~~ 131 (134)
|.
T Consensus 970 MN 971 (1007)
T KOG3623|consen 970 MN 971 (1007)
T ss_pred hc
Confidence 84
No 9
>KOG3623|consensus
Probab=99.63 E-value=3.8e-17 Score=121.23 Aligned_cols=94 Identities=24% Similarity=0.594 Sum_probs=83.3
Q ss_pred ccCCCCCCccc-------------CCCCcceeeCCCCCccCChHHHHHHHHHhcCC-------------CceeccccCcc
Q psy3507 38 YHCKTCSTVSH-------------PNISYKYTCYACDYHTLMSEDMKKHMRKHTGE-------------KPYKCEYCAYS 91 (134)
Q Consensus 38 ~~C~~C~~~f~-------------~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~-------------~~~~C~~C~~~ 91 (134)
.+|++|.+.+. ...+..|.|..|..+|..+..|.+||.+|... +.|+|.+||++
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKA 290 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKA 290 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchh
Confidence 67888888776 33445689999999999999999999988532 44999999999
Q ss_pred ccCchhHHHHhhhcCCCCCeecCcChhhhcCHHHHHHHHH
Q psy3507 92 CTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 92 f~~~~~l~~H~~~h~~~~~~~C~~C~~~F~~~~~l~~H~~ 131 (134)
|..+-.|+.|+|+|.|+|||.|+.|+|+|....++..||.
T Consensus 291 FKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 291 FKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred hhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 9999999999999999999999999999999999999874
No 10
>KOG3608|consensus
Probab=99.48 E-value=1.8e-14 Score=99.64 Aligned_cols=81 Identities=27% Similarity=0.576 Sum_probs=44.6
Q ss_pred CCCCcceeeCCCCCccCChHHHHHHHHHhcCCCceeccc--cCccccCchhHHHHhhh-cCCC--CCeecCcChhhhcCH
Q psy3507 49 PNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEY--CAYSCTQSSALKIHERK-HTGD--KPYICQQCRDTFSSL 123 (134)
Q Consensus 49 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~-h~~~--~~~~C~~C~~~F~~~ 123 (134)
+...++|+|+.|++.+.+.+.|.+|..+|+ +..|.|+. |...+.+...+..|++. |.|. .+|.|..|++.|++-
T Consensus 287 Hs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G 365 (467)
T KOG3608|consen 287 HSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSG 365 (467)
T ss_pred hccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccc
Confidence 444455555555555555555555555554 33455544 55555555555555443 2232 336777777777777
Q ss_pred HHHHHHH
Q psy3507 124 YLFRNRL 130 (134)
Q Consensus 124 ~~l~~H~ 130 (134)
.+|.+|+
T Consensus 366 ~~L~~HL 372 (467)
T KOG3608|consen 366 KSLSAHL 372 (467)
T ss_pred hhHHHHH
Confidence 7777775
No 11
>PHA00733 hypothetical protein
Probab=99.34 E-value=8.3e-13 Score=81.17 Aligned_cols=79 Identities=15% Similarity=0.280 Sum_probs=62.9
Q ss_pred CcceeeCCCCCccCChHHHHHH--HH---HhcCCCceeccccCccccCchhHHHHhhhcCCCCCeecCcChhhhcCHHHH
Q psy3507 52 SYKYTCYACDYHTLMSEDMKKH--MR---KHTGEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLF 126 (134)
Q Consensus 52 ~~~~~C~~C~~~f~~~~~l~~H--~~---~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~F~~~~~l 126 (134)
.+++.|.+|...|..+..|..+ +. .+.+.+||.|+.|++.|.+...|..|++.+ +.+|.|..|++.|.....|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHH
Confidence 4456777777777666665554 11 234578999999999999999999999876 4579999999999999999
Q ss_pred HHHHHh
Q psy3507 127 RNRLQS 132 (134)
Q Consensus 127 ~~H~~~ 132 (134)
.+|+..
T Consensus 116 ~~H~~~ 121 (128)
T PHA00733 116 LDHVCK 121 (128)
T ss_pred HHHHHH
Confidence 999854
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.32 E-value=7.4e-12 Score=92.76 Aligned_cols=73 Identities=21% Similarity=0.466 Sum_probs=32.8
Q ss_pred CCCccc-CCCCcceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccCchhHHHHhhhcCCCCCeecCcChhhh
Q psy3507 43 CSTVSH-PNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTF 120 (134)
Q Consensus 43 C~~~f~-~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~F 120 (134)
||..|. ...+..+.|+.|++.|. ...|..|+..++ .++.|+ |+..+ .+..|..|+.+|.+++++.|..|++.|
T Consensus 441 Cg~v~~r~el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v 514 (567)
T PLN03086 441 CGIVLRVEEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMV 514 (567)
T ss_pred ccceeeccccccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCcc
Confidence 444444 22223344555554443 344445544432 344454 54332 334444454444444555555555444
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.22 E-value=6.4e-11 Score=87.88 Aligned_cols=102 Identities=17% Similarity=0.342 Sum_probs=82.1
Q ss_pred cccccccCCCCccccCCCCCCcccC--------CCCcceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccC--
Q psy3507 25 CRLLLVPTAEELMYHCKTCSTVSHP--------NISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQ-- 94 (134)
Q Consensus 25 C~~h~~~h~~~~~~~C~~C~~~f~~--------~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~-- 94 (134)
|+..++....++.+.|+.|++.|.. .-..++.|+ |++.+ .+..|..|+.+|.+.+++.|+.|++.+..
T Consensus 441 Cg~v~~r~el~~H~~C~~Cgk~f~~s~LekH~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~ 518 (567)
T PLN03086 441 CGIVLRVEEAKNHVHCEKCGQAFQQGEMEKHMKVFHEPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGG 518 (567)
T ss_pred ccceeeccccccCccCCCCCCccchHHHHHHHHhcCCCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCc
Confidence 5666666666778999999999871 113678999 99755 67999999999999999999999999852
Q ss_pred --------chhHHHHhhhcCCCCCeecCcChhhhcCHHHHHHHH
Q psy3507 95 --------SSALKIHERKHTGDKPYICQQCRDTFSSLYLFRNRL 130 (134)
Q Consensus 95 --------~~~l~~H~~~h~~~~~~~C~~C~~~F~~~~~l~~H~ 130 (134)
.+.|..|.... |.+++.|..||+.|..+ .|..|+
T Consensus 519 ~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~ 560 (567)
T PLN03086 519 SAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQ 560 (567)
T ss_pred cccchhhhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHH
Confidence 35799998885 89999999999998754 566665
No 14
>PHA02768 hypothetical protein; Provisional
Probab=99.19 E-value=5.6e-12 Score=65.27 Aligned_cols=43 Identities=23% Similarity=0.441 Sum_probs=24.6
Q ss_pred ceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccCchhH
Q psy3507 54 KYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSAL 98 (134)
Q Consensus 54 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l 98 (134)
.|+|+.||+.|...++|..|+++|. ++++|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 3556666666666666666666655 455566666655554443
No 15
>PHA00733 hypothetical protein
Probab=99.12 E-value=5.3e-11 Score=73.21 Aligned_cols=72 Identities=19% Similarity=0.237 Sum_probs=61.2
Q ss_pred CCccccCCCCCCccc----------------CCCCcceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccCchh
Q psy3507 34 EELMYHCKTCSTVSH----------------PNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSA 97 (134)
Q Consensus 34 ~~~~~~C~~C~~~f~----------------~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~ 97 (134)
..+++.|.+|.+.|. ..+..+|.|+.|++.|.....|..|++.+ +.+|.|+.|++.|.....
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~s 114 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDS 114 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHH
Confidence 356788999987776 34467899999999999999999999876 357999999999999999
Q ss_pred HHHHhhhcCC
Q psy3507 98 LKIHERKHTG 107 (134)
Q Consensus 98 l~~H~~~h~~ 107 (134)
|..|+...++
T Consensus 115 L~~H~~~~h~ 124 (128)
T PHA00733 115 TLDHVCKKHN 124 (128)
T ss_pred HHHHHHHhcC
Confidence 9999886543
No 16
>PHA02768 hypothetical protein; Provisional
Probab=99.10 E-value=4.5e-11 Score=61.91 Aligned_cols=43 Identities=19% Similarity=0.358 Sum_probs=39.5
Q ss_pred ceeccccCccccCchhHHHHhhhcCCCCCeecCcChhhhcCHHHH
Q psy3507 82 PYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLF 126 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~F~~~~~l 126 (134)
-|.|+.||+.|...++|..|+++|+ ++|+|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 3899999999999999999999998 699999999999977665
No 17
>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=99.01 E-value=1.8e-10 Score=51.33 Aligned_cols=24 Identities=54% Similarity=1.092 Sum_probs=14.9
Q ss_pred HHHHhhhcCCCCCeecCcChhhhc
Q psy3507 98 LKIHERKHTGDKPYICQQCRDTFS 121 (134)
Q Consensus 98 l~~H~~~h~~~~~~~C~~C~~~F~ 121 (134)
|..|+++|++++||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 556666666666666666666654
No 18
>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=1.9e-09 Score=47.96 Aligned_cols=26 Identities=58% Similarity=1.258 Sum_probs=23.9
Q ss_pred HHHHHHHHhcCCCceeccccCccccC
Q psy3507 69 DMKKHMRKHTGEKPYKCEYCAYSCTQ 94 (134)
Q Consensus 69 ~l~~H~~~h~~~~~~~C~~C~~~f~~ 94 (134)
+|..|+++|++++||.|+.|++.|.+
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 58899999999999999999999863
No 19
>KOG3993|consensus
Probab=98.81 E-value=7.6e-10 Score=78.58 Aligned_cols=24 Identities=21% Similarity=0.552 Sum_probs=22.2
Q ss_pred CeecCcChhhhcCHHHHHHHHHhc
Q psy3507 110 PYICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 110 ~~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
.|.|..|++.|.+...|+.|+.+|
T Consensus 356 i~~C~~C~KkFrRqAYLrKHqlth 379 (500)
T KOG3993|consen 356 IFSCHTCGKKFRRQAYLRKHQLTH 379 (500)
T ss_pred eeecHHhhhhhHHHHHHHHhHHhh
Confidence 499999999999999999998877
No 20
>PHA00732 hypothetical protein
Probab=98.73 E-value=6.2e-09 Score=58.62 Aligned_cols=48 Identities=29% Similarity=0.525 Sum_probs=37.3
Q ss_pred ceeeCCCCCccCChHHHHHHHHH-hcCCCceeccccCccccCchhHHHHhhhcCC
Q psy3507 54 KYTCYACDYHTLMSEDMKKHMRK-HTGEKPYKCEYCAYSCTQSSALKIHERKHTG 107 (134)
Q Consensus 54 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 107 (134)
+|.|+.|++.|.....|..|++. |. ++.|+.|++.|. .+..|.++...
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccCC
Confidence 47899999999999999999874 54 357999999887 47788765443
No 21
>KOG3993|consensus
Probab=98.65 E-value=7.4e-09 Score=73.68 Aligned_cols=120 Identities=19% Similarity=0.295 Sum_probs=76.1
Q ss_pred ccCCccceecCccccc----------ccccCCCCccccCCCCCCccc----------------------------C----
Q psy3507 12 GLKNPFTLATCIHCRL----------LLVPTAEELMYHCKTCSTVSH----------------------------P---- 49 (134)
Q Consensus 12 ~~~~~~~~~~C~~C~~----------h~~~h~~~~~~~C~~C~~~f~----------------------------~---- 49 (134)
+..|+...++|..|+. |.-.-....-|+|++|+++|+ .
T Consensus 260 ~i~n~iGdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~r 339 (500)
T KOG3993|consen 260 GIPNVIGDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETR 339 (500)
T ss_pred cCcccHHHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhh
Confidence 5567777788888833 222222223488888888887 0
Q ss_pred ------------CCCcceeeCCCCCccCChHHHHHHHHHhcCCC------------------------------------
Q psy3507 50 ------------NISYKYTCYACDYHTLMSEDMKKHMRKHTGEK------------------------------------ 81 (134)
Q Consensus 50 ------------~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~------------------------------------ 81 (134)
..+..|.|.+|++.|.....|+.|+.+|....
T Consensus 340 ae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~ 419 (500)
T KOG3993|consen 340 AEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGD 419 (500)
T ss_pred hhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhccccccccccccccccccccccc
Confidence 11224888888888888888888876654210
Q ss_pred ----------ceeccccCccccCchhHHHHhhhcCCCCCeecCcChhhhcCHHHHHHHHH
Q psy3507 82 ----------PYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 82 ----------~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~F~~~~~l~~H~~ 131 (134)
.-.++.++..+.++..-..+.+.-..+.-|.|..|..+|.+...|.+|+.
T Consensus 420 ~vl~~a~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin 479 (500)
T KOG3993|consen 420 EVLYVAGSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHIN 479 (500)
T ss_pred ceeeeeccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhh
Confidence 01234444444444443344444344556899999999999999999974
No 22
>PHA00616 hypothetical protein
Probab=98.65 E-value=8.9e-09 Score=50.91 Aligned_cols=32 Identities=16% Similarity=0.318 Sum_probs=16.2
Q ss_pred eeeCCCCCccCChHHHHHHHHHhcCCCceecc
Q psy3507 55 YTCYACDYHTLMSEDMKKHMRKHTGEKPYKCE 86 (134)
Q Consensus 55 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~ 86 (134)
|+|+.||+.|...+.|..|++.|++++++.|+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 44555555555555555555555555544443
No 23
>PHA00616 hypothetical protein
Probab=98.58 E-value=2.8e-08 Score=49.17 Aligned_cols=34 Identities=12% Similarity=0.143 Sum_probs=31.8
Q ss_pred ceeccccCccccCchhHHHHhhhcCCCCCeecCc
Q psy3507 82 PYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQ 115 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~ 115 (134)
||+|+.||+.|...++|..|++.|++++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999998864
No 24
>PHA00732 hypothetical protein
Probab=98.53 E-value=9.2e-08 Score=53.87 Aligned_cols=46 Identities=28% Similarity=0.640 Sum_probs=39.2
Q ss_pred ceeccccCccccCchhHHHHhhh-cCCCCCeecCcChhhhcCHHHHHHHHHhc
Q psy3507 82 PYKCEYCAYSCTQSSALKIHERK-HTGDKPYICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
||.|+.|++.|.+...|..|++. |. ++.|+.||+.|.+ |..|+++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~---l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRR---LNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCC---hhhhhccc
Confidence 58899999999999999999985 65 3689999999984 88887654
No 25
>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=98.52 E-value=6e-08 Score=41.77 Aligned_cols=23 Identities=30% Similarity=0.691 Sum_probs=17.9
Q ss_pred eecCcChhhhcCHHHHHHHHHhc
Q psy3507 111 YICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 111 ~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
|.|+.|++.|.+...|.+|++.|
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 57788888888888888887765
No 26
>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=98.34 E-value=9.3e-07 Score=46.28 Aligned_cols=47 Identities=26% Similarity=0.528 Sum_probs=22.6
Q ss_pred eeccccCccccCchhHHHHhhh-cCCC-CCeecCcChhhhcCHHHHHHHHHh
Q psy3507 83 YKCEYCAYSCTQSSALKIHERK-HTGD-KPYICQQCRDTFSSLYLFRNRLQS 132 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~-h~~~-~~~~C~~C~~~F~~~~~l~~H~~~ 132 (134)
|.|+.|++ ..+...|..|... |..+ +.+.|++|...+. .+|..|+..
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~ 51 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNS 51 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHH
Confidence 45555555 2334455555333 3332 3355555555433 255555543
No 27
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.31 E-value=4.8e-07 Score=53.06 Aligned_cols=73 Identities=23% Similarity=0.373 Sum_probs=20.5
Q ss_pred eeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccCchhHHHHhhhcCCCCCeecCcChhhhcCHHHHHHHHHhc
Q psy3507 56 TCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 56 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
+|..|+..|.+...|..|+...++... + ....+.....+..+++.-. ...+.|..|++.|.+...|..||+.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~---~-~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDI---P-DQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Ccccccccccccccccccccccccccc---c-ccccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 488999999999999999975443211 1 1112223334444433222 23689999999999999999999764
No 28
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.29 E-value=1.7e-06 Score=45.30 Aligned_cols=50 Identities=24% Similarity=0.460 Sum_probs=39.2
Q ss_pred ceeeCCCCCccCChHHHHHHHHH-hcCC-CceeccccCccccCchhHHHHhhhcC
Q psy3507 54 KYTCYACDYHTLMSEDMKKHMRK-HTGE-KPYKCEYCAYSCTQSSALKIHERKHT 106 (134)
Q Consensus 54 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~-~~~~C~~C~~~f~~~~~l~~H~~~h~ 106 (134)
.|.|+.|++ ..+...|..|... |..+ +.+.|++|...+. .+|..|+..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 488999999 5677899999775 5543 5699999998654 48999988654
No 29
>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=98.26 E-value=1e-06 Score=37.81 Aligned_cols=22 Identities=32% Similarity=0.727 Sum_probs=13.5
Q ss_pred eeeCCCCCccCChHHHHHHHHH
Q psy3507 55 YTCYACDYHTLMSEDMKKHMRK 76 (134)
Q Consensus 55 ~~C~~C~~~f~~~~~l~~H~~~ 76 (134)
|+|+.|++.|.+...|..|++.
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 4566666666666666666654
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.23 E-value=6.7e-07 Score=39.95 Aligned_cols=24 Identities=46% Similarity=0.912 Sum_probs=19.8
Q ss_pred CeecCcChhhhcCHHHHHHHHHhc
Q psy3507 110 PYICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 110 ~~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
||+|..|++.|.+..+|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 578888888888888888888776
No 31
>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=98.21 E-value=1.1e-06 Score=37.80 Aligned_cols=23 Identities=26% Similarity=0.683 Sum_probs=15.9
Q ss_pred eecCcChhhhcCHHHHHHHHHhc
Q psy3507 111 YICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 111 ~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
|.|+.|++.|.+...|+.|+++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 56777777777777777777765
No 32
>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=97.93 E-value=1.3e-05 Score=34.34 Aligned_cols=23 Identities=26% Similarity=0.686 Sum_probs=12.2
Q ss_pred eeeCCCCCccCChHHHHHHHHHh
Q psy3507 55 YTCYACDYHTLMSEDMKKHMRKH 77 (134)
Q Consensus 55 ~~C~~C~~~f~~~~~l~~H~~~h 77 (134)
|.|+.|++.|.+...|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 45566666666666666665544
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=97.90 E-value=7.9e-06 Score=36.35 Aligned_cols=24 Identities=38% Similarity=0.863 Sum_probs=13.5
Q ss_pred ceeccccCccccCchhHHHHhhhc
Q psy3507 82 PYKCEYCAYSCTQSSALKIHERKH 105 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~h 105 (134)
+|.|..|++.|.+...|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 355555555555555555555544
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.89 E-value=3.4e-06 Score=58.49 Aligned_cols=52 Identities=33% Similarity=0.692 Sum_probs=36.5
Q ss_pred CCceeccc--cCccccCchhHHHHhhh-c------------------CCCCCeecCcChhhhcCHHHHHHHHH
Q psy3507 80 EKPYKCEY--CAYSCTQSSALKIHERK-H------------------TGDKPYICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 80 ~~~~~C~~--C~~~f~~~~~l~~H~~~-h------------------~~~~~~~C~~C~~~F~~~~~l~~H~~ 131 (134)
++||+|++ |++.+.....|+.|+.- | ...|||.|++|+|.|+....|+-|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 36666655 66666666666666542 2 23589999999999999888887753
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.84 E-value=1.6e-05 Score=34.62 Aligned_cols=23 Identities=26% Similarity=0.746 Sum_probs=18.0
Q ss_pred eecCcChhhhcCHHHHHHHHHhc
Q psy3507 111 YICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 111 ~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
|.|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 46788888888888888888765
No 36
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.56 E-value=4.9e-05 Score=33.05 Aligned_cols=23 Identities=35% Similarity=0.726 Sum_probs=15.9
Q ss_pred eecCcChhhhcCHHHHHHHHHhc
Q psy3507 111 YICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 111 ~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
|.|..|++.|.+...|+.|++.+
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 56777777777777777777543
No 37
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.56 E-value=2.8e-05 Score=54.07 Aligned_cols=54 Identities=30% Similarity=0.605 Sum_probs=44.7
Q ss_pred CCCcceeeCC--CCCccCChHHHHHHHHH-hc------------------CCCceeccccCccccCchhHHHHhh
Q psy3507 50 NISYKYTCYA--CDYHTLMSEDMKKHMRK-HT------------------GEKPYKCEYCAYSCTQSSALKIHER 103 (134)
Q Consensus 50 ~~~~~~~C~~--C~~~f~~~~~l~~H~~~-h~------------------~~~~~~C~~C~~~f~~~~~l~~H~~ 103 (134)
.++++|+|++ |.+.+.....|+.|+.- |. ..+||+|++|++.+.....|+.|+.
T Consensus 345 ~d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 345 KDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred ecCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 3458899988 99999999999999862 31 2488999999999999999998854
No 38
>PRK04860 hypothetical protein; Provisional
Probab=97.39 E-value=0.00013 Score=46.55 Aligned_cols=38 Identities=29% Similarity=0.771 Sum_probs=30.6
Q ss_pred ceeccccCccccCchhHHHHhhhcCCCCCeecCcChhhhcCH
Q psy3507 82 PYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSL 123 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~F~~~ 123 (134)
+|.|. |+. ....+..|.++|+++++|.|..|+..|...
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 58887 876 566788888889888889999998887643
No 39
>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=97.37 E-value=0.00018 Score=36.55 Aligned_cols=27 Identities=26% Similarity=0.373 Sum_probs=10.0
Q ss_pred CceeccccCccccCchhHHHHhhhcCC
Q psy3507 81 KPYKCEYCAYSCTQSSALKIHERKHTG 107 (134)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~~h~~ 107 (134)
.|-.|++|+..+.+..+|.+|+...++
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhc
Confidence 334444444444444444444444333
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.36 E-value=0.00025 Score=30.56 Aligned_cols=22 Identities=32% Similarity=0.581 Sum_probs=12.9
Q ss_pred eeCCCCCccCChHHHHHHHHHh
Q psy3507 56 TCYACDYHTLMSEDMKKHMRKH 77 (134)
Q Consensus 56 ~C~~C~~~f~~~~~l~~H~~~h 77 (134)
.|+.|++.|.....|..|++.|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHh
Confidence 4556666666666666665544
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.19 E-value=0.00022 Score=30.93 Aligned_cols=21 Identities=29% Similarity=0.692 Sum_probs=11.9
Q ss_pred eeccccCccccCchhHHHHhh
Q psy3507 83 YKCEYCAYSCTQSSALKIHER 103 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~ 103 (134)
|.|++|+..|.+...|..|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 345555555555555555554
No 42
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.09 E-value=0.00012 Score=32.54 Aligned_cols=21 Identities=24% Similarity=0.672 Sum_probs=11.2
Q ss_pred eecCcChhhhcCHHHHHHHHH
Q psy3507 111 YICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 111 ~~C~~C~~~F~~~~~l~~H~~ 131 (134)
|.|..|++.|.+...|..|++
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 445555555555555555543
No 43
>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=97.06 E-value=0.0012 Score=33.62 Aligned_cols=33 Identities=21% Similarity=0.360 Sum_probs=23.2
Q ss_pred CCCcceeeCCCCCccCChHHHHHHHHHhcCCCc
Q psy3507 50 NISYKYTCYACDYHTLMSEDMKKHMRKHTGEKP 82 (134)
Q Consensus 50 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 82 (134)
..+.+-.|++|+..+....+|.+|+...++.+|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 345678999999999999999999988777665
No 44
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.01 E-value=0.00061 Score=29.20 Aligned_cols=22 Identities=27% Similarity=0.578 Sum_probs=15.1
Q ss_pred eecCcChhhhcCHHHHHHHHHhc
Q psy3507 111 YICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 111 ~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
|+|+.|+.... ...|.+|++.|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 67888887776 77888888764
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.97 E-value=0.00095 Score=28.59 Aligned_cols=22 Identities=36% Similarity=1.013 Sum_probs=12.6
Q ss_pred eeeCCCCCccCChHHHHHHHHHh
Q psy3507 55 YTCYACDYHTLMSEDMKKHMRKH 77 (134)
Q Consensus 55 ~~C~~C~~~f~~~~~l~~H~~~h 77 (134)
|.|+.|+.... +..|..|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 45666666665 66666666654
No 46
>PRK04860 hypothetical protein; Provisional
Probab=96.87 E-value=0.00086 Score=42.89 Aligned_cols=39 Identities=26% Similarity=0.635 Sum_probs=33.8
Q ss_pred cceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccCc
Q psy3507 53 YKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQS 95 (134)
Q Consensus 53 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 95 (134)
.+|.|. |+. ....+..|.++|.++++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 469998 987 667889999999999999999999987654
No 47
>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=96.75 E-value=0.00066 Score=30.05 Aligned_cols=22 Identities=23% Similarity=0.548 Sum_probs=16.7
Q ss_pred eeccccCccccCchhHHHHhhh
Q psy3507 83 YKCEYCAYSCTQSSALKIHERK 104 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~ 104 (134)
|.|+.|++.|.+...+..|++.
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 5678888888888888777664
No 48
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.71 E-value=0.0037 Score=37.42 Aligned_cols=89 Identities=18% Similarity=0.399 Sum_probs=55.7
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCccCChHHHHHHHHHhc-------CCCc-------eeccccCccccCchhHHHHhh
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYHTLMSEDMKKHMRKHT-------GEKP-------YKCEYCAYSCTQSSALKIHER 103 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~-------~~~~-------~~C~~C~~~f~~~~~l~~H~~ 103 (134)
|.|+.|+... -+.|-.|+.|+-.......|.+.- |+ .+.+ -.|-.|...|........ .
T Consensus 2 Y~CPrC~skv---C~LP~~CpiCgLtLVss~HLARSy--HHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~ 74 (112)
T TIGR00622 2 YFCPQCRAKV---CELPVECPICGLTLILSTHLARSY--HHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--D 74 (112)
T ss_pred ccCCCCCCCc---cCCCCcCCcCCCEEeccchHHHhh--hccCCCcccccccccccCCCCcccCcCCCCCCcccccc--c
Confidence 7788887653 456778888888888877777532 21 0111 137778888876431110 0
Q ss_pred hcCCCCCeecCcChhhhcCHHHHHHHHHhc
Q psy3507 104 KHTGDKPYICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 104 ~h~~~~~~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
.-.....|+|+.|...|-..-+.-.|...|
T Consensus 75 ~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 75 ELKDSHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred ccccccceeCCCCCCccccccchhhhhhcc
Confidence 012234688999988887777777776666
No 49
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.68 E-value=0.0015 Score=28.43 Aligned_cols=21 Identities=14% Similarity=0.276 Sum_probs=14.0
Q ss_pred eecCcChhhhcCHHHHHHHHHh
Q psy3507 111 YICQQCRDTFSSLYLFRNRLQS 132 (134)
Q Consensus 111 ~~C~~C~~~F~~~~~l~~H~~~ 132 (134)
..|+.||+.| ..+.|.+|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3577777777 56677777653
No 50
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.59 E-value=0.003 Score=36.64 Aligned_cols=23 Identities=30% Similarity=0.736 Sum_probs=17.5
Q ss_pred ceeccccCccccCchhHHHHhhh
Q psy3507 82 PYKCEYCAYSCTQSSALKIHERK 104 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~ 104 (134)
.+.|..|++.|.+...|..|++.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHcC
Confidence 57888888888888888888775
No 51
>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=96.08 E-value=0.0053 Score=28.65 Aligned_cols=22 Identities=23% Similarity=0.535 Sum_probs=14.7
Q ss_pred CeecCcChhhhcCHHHHHHHHH
Q psy3507 110 PYICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 110 ~~~C~~C~~~F~~~~~l~~H~~ 131 (134)
+|.|..|++.|.+...+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4667777777776667766663
No 52
>KOG2893|consensus
Probab=96.00 E-value=0.0027 Score=42.85 Aligned_cols=48 Identities=23% Similarity=0.439 Sum_probs=39.8
Q ss_pred eeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccCchhHHHH-hhhcC
Q psy3507 55 YTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIH-ERKHT 106 (134)
Q Consensus 55 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H-~~~h~ 106 (134)
-+|-+|++.|....-|.+|++. +.|+|.+|.+.+.+.-.|..| +.+|.
T Consensus 11 pwcwycnrefddekiliqhqka----khfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred ceeeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehhhhhh
Confidence 4688999999999999998875 349999999988888888888 66553
No 53
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=95.87 E-value=0.012 Score=30.89 Aligned_cols=10 Identities=40% Similarity=1.408 Sum_probs=6.5
Q ss_pred CceeccccCc
Q psy3507 81 KPYKCEYCAY 90 (134)
Q Consensus 81 ~~~~C~~C~~ 90 (134)
.+|.|+.||.
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 4577777764
No 54
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=95.21 E-value=0.018 Score=30.28 Aligned_cols=47 Identities=19% Similarity=0.537 Sum_probs=22.8
Q ss_pred cCCCCCCccc-CCCCcceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCc
Q psy3507 39 HCKTCSTVSH-PNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAY 90 (134)
Q Consensus 39 ~C~~C~~~f~-~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 90 (134)
.|.-||.... ......|.|+.||..--.+...- .....+|.|+.||.
T Consensus 11 ~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~C-----Rk~g~~Y~Cp~CGF 58 (61)
T COG2888 11 VCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKC-----RKLGNPYRCPKCGF 58 (61)
T ss_pred eeccCCCEeccCCceeEeeCCCCCceeeehhhhH-----HHcCCceECCCcCc
Confidence 4555555552 33334566666664333322211 11235677777774
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=95.11 E-value=0.021 Score=26.51 Aligned_cols=22 Identities=14% Similarity=0.425 Sum_probs=15.0
Q ss_pred ceeeCCCCCccCChHHHHHHHH
Q psy3507 54 KYTCYACDYHTLMSEDMKKHMR 75 (134)
Q Consensus 54 ~~~C~~C~~~f~~~~~l~~H~~ 75 (134)
+|.|+.|++.|.+...+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4667777777777777766654
No 56
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=95.01 E-value=0.02 Score=28.63 Aligned_cols=28 Identities=21% Similarity=0.489 Sum_probs=15.9
Q ss_pred cccCCCCCCcccCCCCc-ceeeCCCCCcc
Q psy3507 37 MYHCKTCSTVSHPNISY-KYTCYACDYHT 64 (134)
Q Consensus 37 ~~~C~~C~~~f~~~~~~-~~~C~~C~~~f 64 (134)
.|.|+.||..|...... ...|+.||..+
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeE
Confidence 46677777766522221 56677776543
No 57
>KOG2231|consensus
Probab=94.93 E-value=0.063 Score=41.69 Aligned_cols=91 Identities=22% Similarity=0.400 Sum_probs=54.6
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCccCChHHHHHHHH-HhcCCCceeccccC---------ccccCchhHHHHhhhcC-
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYHTLMSEDMKKHMR-KHTGEKPYKCEYCA---------YSCTQSSALKIHERKHT- 106 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~f~~~~~l~~H~~-~h~~~~~~~C~~C~---------~~f~~~~~l~~H~~~h~- 106 (134)
+.|.+|+..|...-. .-.|..| -.|.+...|+.|+. .|.. +.|.+|- ...-+...|..|+..--
T Consensus 100 ~~C~~C~~~~~~~~~-~~~~~~c-~~~~s~~~Lk~H~~~~H~~---~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~ 174 (669)
T KOG2231|consen 100 HSCHICDRRFRALYN-KKECLHC-TEFKSVENLKNHMRDQHKL---HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDP 174 (669)
T ss_pred hhcCccccchhhhcc-cCCCccc-cchhHHHHHHHHHHHhhhh---hccccccccceeeeeeeehehHHHHHHHHhcCCC
Confidence 668888887742111 2357777 67778889999985 4432 3333322 12234466777765421
Q ss_pred CCCC----eecCcChhhhcCHHHHHHHHHhc
Q psy3507 107 GDKP----YICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 107 ~~~~----~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
+++. -.|..|...|.....|.+|++.+
T Consensus 175 d~~s~rGhp~C~~C~~~fld~~el~rH~~~~ 205 (669)
T KOG2231|consen 175 DDESCRGHPLCKFCHERFLDDDELYRHLRFD 205 (669)
T ss_pred ccccccCCccchhhhhhhccHHHHHHhhccc
Confidence 1222 35777888888888888887643
No 58
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.80 E-value=0.0058 Score=43.44 Aligned_cols=76 Identities=21% Similarity=0.398 Sum_probs=40.3
Q ss_pred ceeeCC--CCCccCChHHHHHHHHHhcCCCceeccccCc---------cccCchhHHHHhhhcCCCCCe----ecCcChh
Q psy3507 54 KYTCYA--CDYHTLMSEDMKKHMRKHTGEKPYKCEYCAY---------SCTQSSALKIHERKHTGDKPY----ICQQCRD 118 (134)
Q Consensus 54 ~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~---------~f~~~~~l~~H~~~h~~~~~~----~C~~C~~ 118 (134)
.|.|+. |.........|..|.++.++. +.|.+|-. ...++..|..|......+.-| .|..|..
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~--~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~ 228 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGF--VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKI 228 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCc--EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccc
Confidence 366665 555555667777787764432 44554432 122334455554432222122 4666666
Q ss_pred hhcCHHHHHHHHH
Q psy3507 119 TFSSLYLFRNRLQ 131 (134)
Q Consensus 119 ~F~~~~~l~~H~~ 131 (134)
.|..-..|.+|++
T Consensus 229 ~FYdDDEL~~HcR 241 (493)
T COG5236 229 YFYDDDELRRHCR 241 (493)
T ss_pred eecChHHHHHHHH
Confidence 6666666666654
No 59
>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=94.71 E-value=0.024 Score=26.26 Aligned_cols=9 Identities=33% Similarity=1.283 Sum_probs=4.6
Q ss_pred CCeecCcCh
Q psy3507 109 KPYICQQCR 117 (134)
Q Consensus 109 ~~~~C~~C~ 117 (134)
.++.|+.||
T Consensus 16 ~~~~CP~Cg 24 (33)
T cd00350 16 APWVCPVCG 24 (33)
T ss_pred CCCcCcCCC
Confidence 345555554
No 60
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.56 E-value=0.026 Score=29.23 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=13.0
Q ss_pred CCCceeccccCccccCchhHHHHhh
Q psy3507 79 GEKPYKCEYCAYSCTQSSALKIHER 103 (134)
Q Consensus 79 ~~~~~~C~~C~~~f~~~~~l~~H~~ 103 (134)
|+..+.|+.|+..|....++..|..
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhh
Confidence 4444555555555555555555543
No 61
>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=94.53 E-value=0.029 Score=33.52 Aligned_cols=30 Identities=13% Similarity=0.191 Sum_probs=22.9
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCccCCh
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYHTLMS 67 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~f~~~ 67 (134)
..|+.||++|.--+..|-.|+.||..|...
T Consensus 10 R~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 568888888886666777788888877665
No 62
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.30 E-value=0.012 Score=42.65 Aligned_cols=63 Identities=29% Similarity=0.491 Sum_probs=51.9
Q ss_pred cceeeCCCCCccCChHHHHHHHH--HhcCC--Cceecc--ccCccccCchhHHHHhhhcCCCCCeecCc
Q psy3507 53 YKYTCYACDYHTLMSEDMKKHMR--KHTGE--KPYKCE--YCAYSCTQSSALKIHERKHTGDKPYICQQ 115 (134)
Q Consensus 53 ~~~~C~~C~~~f~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~C~~ 115 (134)
.++.|..|...|.....+..|.+ .|.++ +++.|+ .|++.|.....+..|...|.+..++.+..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccccc
Confidence 46788888888888888888888 78888 888888 78888888888888888888777665543
No 63
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.23 E-value=0.0087 Score=43.39 Aligned_cols=54 Identities=33% Similarity=0.615 Sum_probs=49.6
Q ss_pred CceeccccCccccCchhHHHHhh--hcCCC--CCeecC--cChhhhcCHHHHHHHHHhcC
Q psy3507 81 KPYKCEYCAYSCTQSSALKIHER--KHTGD--KPYICQ--QCRDTFSSLYLFRNRLQSHG 134 (134)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~F~~~~~l~~H~~~H~ 134 (134)
.++.|..|...|.....|..|.+ .|.++ +++.|+ .|++.|.+...+..|..+|+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~ 347 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHT 347 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCccccc
Confidence 36889999999999999999999 89999 999999 79999999999999988774
No 64
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=94.18 E-value=0.045 Score=27.21 Aligned_cols=26 Identities=23% Similarity=0.608 Sum_probs=15.1
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
|.|..||..|.-....+..|+.||..
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCce
Confidence 56666666665444445666666643
No 65
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=94.12 E-value=0.052 Score=25.70 Aligned_cols=10 Identities=20% Similarity=0.673 Sum_probs=5.0
Q ss_pred cCCCCCCccc
Q psy3507 39 HCKTCSTVSH 48 (134)
Q Consensus 39 ~C~~C~~~f~ 48 (134)
.|+.|+..|.
T Consensus 4 ~Cp~C~~~y~ 13 (36)
T PF13717_consen 4 TCPNCQAKYE 13 (36)
T ss_pred ECCCCCCEEe
Confidence 4555555544
No 66
>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=94.00 E-value=0.05 Score=25.07 Aligned_cols=26 Identities=19% Similarity=0.466 Sum_probs=13.5
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
|.|..||..+.-....+..|+.||..
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS-S
T ss_pred CCCCcCCCeeEcCCCCcEECCcCCCe
Confidence 45666666665444445566666643
No 67
>KOG2893|consensus
Probab=93.99 E-value=0.011 Score=39.93 Aligned_cols=42 Identities=21% Similarity=0.386 Sum_probs=34.1
Q ss_pred eccccCccccCchhHHHHhhhcCCCCCeecCcChhhhcCHHHHHHH
Q psy3507 84 KCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLFRNR 129 (134)
Q Consensus 84 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~F~~~~~l~~H 129 (134)
-|-.|++.|.....|.+|++ .+-|+|.+|-+...+-..|..|
T Consensus 12 wcwycnrefddekiliqhqk----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhh----hccceeeeehhhhccCCCceee
Confidence 47889999999999999987 4569999998877666666555
No 68
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=93.94 E-value=0.13 Score=27.12 Aligned_cols=41 Identities=22% Similarity=0.673 Sum_probs=18.0
Q ss_pred cCcccccccccCCCCccccCCCCCCccc------CCCCcceeeCCCC
Q psy3507 21 TCIHCRLLLVPTAEELMYHCKTCSTVSH------PNISYKYTCYACD 61 (134)
Q Consensus 21 ~C~~C~~h~~~h~~~~~~~C~~C~~~f~------~~~~~~~~C~~C~ 61 (134)
.|..|+.-+..-..--.|.|+.||+.-- .....+|+|+.||
T Consensus 11 ~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 11 VCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCG 57 (61)
T ss_pred eeccCCCEeccCCceeEeeCCCCCceeeehhhhHHHcCCceECCCcC
Confidence 3444444333333333455666653322 2223355666555
No 69
>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=93.93 E-value=0.054 Score=25.79 Aligned_cols=10 Identities=30% Similarity=0.783 Sum_probs=4.6
Q ss_pred cCCCCCCccc
Q psy3507 39 HCKTCSTVSH 48 (134)
Q Consensus 39 ~C~~C~~~f~ 48 (134)
.|+.|+..|.
T Consensus 4 ~CP~C~~~~~ 13 (38)
T TIGR02098 4 QCPNCKTSFR 13 (38)
T ss_pred ECCCCCCEEE
Confidence 4444444443
No 70
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=93.87 E-value=0.14 Score=26.95 Aligned_cols=10 Identities=30% Similarity=0.946 Sum_probs=4.6
Q ss_pred cccCCCCCCc
Q psy3507 37 MYHCKTCSTV 46 (134)
Q Consensus 37 ~~~C~~C~~~ 46 (134)
.|.|+.||+.
T Consensus 25 ~F~CPnCG~~ 34 (59)
T PRK14890 25 KFLCPNCGEV 34 (59)
T ss_pred EeeCCCCCCe
Confidence 3445555443
No 71
>KOG1146|consensus
Probab=93.68 E-value=0.02 Score=47.18 Aligned_cols=70 Identities=29% Similarity=0.548 Sum_probs=43.8
Q ss_pred cceeeCCCCCccCChHHHHHHHHH-hcCCCceeccccCccccCchhHHHHhhh------cCCCCCeecCcChhhhcCHHH
Q psy3507 53 YKYTCYACDYHTLMSEDMKKHMRK-HTGEKPYKCEYCAYSCTQSSALKIHERK------HTGDKPYICQQCRDTFSSLYL 125 (134)
Q Consensus 53 ~~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~------h~~~~~~~C~~C~~~F~~~~~ 125 (134)
+.+.|+.|+..|.....|..||+. |..... .+|. ..+.|.+. -.+.++|.|..|...+....+
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~---~~c~-------~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~ 533 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQS---AYCK-------AGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGN 533 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccch---hHhH-------hccccccccccccccCCCCcccceeeeeeeecchH
Confidence 557777777777777777777775 322111 1221 11112111 123468999999999999999
Q ss_pred HHHHHHh
Q psy3507 126 FRNRLQS 132 (134)
Q Consensus 126 l~~H~~~ 132 (134)
|.+|++.
T Consensus 534 LsihlqS 540 (1406)
T KOG1146|consen 534 LSIHLQS 540 (1406)
T ss_pred HHHHHHH
Confidence 9999863
No 72
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.55 E-value=0.068 Score=25.45 Aligned_cols=10 Identities=20% Similarity=0.617 Sum_probs=4.3
Q ss_pred eeccccCccc
Q psy3507 83 YKCEYCAYSC 92 (134)
Q Consensus 83 ~~C~~C~~~f 92 (134)
..|+.|+..|
T Consensus 26 vrC~~C~~~f 35 (37)
T PF13719_consen 26 VRCPKCGHVF 35 (37)
T ss_pred EECCCCCcEe
Confidence 4444444433
No 73
>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=92.92 E-value=0.082 Score=24.67 Aligned_cols=24 Identities=17% Similarity=0.470 Sum_probs=11.8
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCC
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDY 62 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~ 62 (134)
|.|..||..+.- .+.+..|++|+.
T Consensus 3 ~~C~~CG~i~~g-~~~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHEG-EEAPEKCPICGA 26 (34)
T ss_pred EECCCCCCEeEC-CcCCCcCcCCCC
Confidence 556666655431 123445655554
No 74
>KOG2186|consensus
Probab=92.80 E-value=0.084 Score=36.07 Aligned_cols=51 Identities=22% Similarity=0.415 Sum_probs=35.7
Q ss_pred ceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccCchhHHHHhhhcCC
Q psy3507 54 KYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHTG 107 (134)
Q Consensus 54 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 107 (134)
.|.|..||....- ..+.+|+..=.+ ..|.|..|++.|.. .++..|..--+.
T Consensus 3 ~FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCITE 53 (276)
T KOG2186|consen 3 FFTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCITE 53 (276)
T ss_pred EEehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcch
Confidence 4788888876654 445668775544 56889999998888 567777664443
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=92.56 E-value=0.11 Score=22.68 Aligned_cols=9 Identities=33% Similarity=0.851 Sum_probs=4.6
Q ss_pred eeCCCCCcc
Q psy3507 56 TCYACDYHT 64 (134)
Q Consensus 56 ~C~~C~~~f 64 (134)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 355555554
No 76
>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=92.52 E-value=0.093 Score=25.71 Aligned_cols=25 Identities=20% Similarity=0.509 Sum_probs=13.5
Q ss_pred ccCCCCCCccc----CCCCcceeeCCCCC
Q psy3507 38 YHCKTCSTVSH----PNISYKYTCYACDY 62 (134)
Q Consensus 38 ~~C~~C~~~f~----~~~~~~~~C~~C~~ 62 (134)
|.|..||..|. -.....-.|+.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 56666666665 11134455666654
No 77
>KOG1146|consensus
Probab=92.42 E-value=0.038 Score=45.67 Aligned_cols=19 Identities=16% Similarity=0.378 Sum_probs=12.4
Q ss_pred cCcChhhhcCHHHHHHHHH
Q psy3507 113 CQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 113 C~~C~~~F~~~~~l~~H~~ 131 (134)
|..|...|.....|+.||+
T Consensus 1331 c~~c~~~~~~~~alqihm~ 1349 (1406)
T KOG1146|consen 1331 CLACEVLLSGREALQIHMR 1349 (1406)
T ss_pred chHHHhhcchhHHHHHHHH
Confidence 6666666666666666664
No 78
>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=92.38 E-value=0.15 Score=21.85 Aligned_cols=8 Identities=25% Similarity=1.011 Sum_probs=3.2
Q ss_pred ceeeCCCC
Q psy3507 54 KYTCYACD 61 (134)
Q Consensus 54 ~~~C~~C~ 61 (134)
.|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 34444443
No 79
>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=92.36 E-value=0.11 Score=25.01 Aligned_cols=25 Identities=24% Similarity=0.486 Sum_probs=12.7
Q ss_pred ccCCCCCCccc----CCCCcceeeCCCCC
Q psy3507 38 YHCKTCSTVSH----PNISYKYTCYACDY 62 (134)
Q Consensus 38 ~~C~~C~~~f~----~~~~~~~~C~~C~~ 62 (134)
|.|..||..|. ......-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 56666666655 11123345666654
No 80
>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=92.28 E-value=0.11 Score=31.72 Aligned_cols=34 Identities=9% Similarity=-0.131 Sum_probs=25.8
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCccCChHHHH
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYHTLMSEDMK 71 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~f~~~~~l~ 71 (134)
..|+.||++|.--+..|..|+.||..|.....++
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCccCcchhhc
Confidence 5688889888877777888888888876654433
No 81
>KOG2907|consensus
Probab=91.96 E-value=0.13 Score=30.70 Aligned_cols=30 Identities=23% Similarity=0.424 Sum_probs=21.6
Q ss_pred eecCcccccccccCCCCccccCCCCCCccc
Q psy3507 19 LATCIHCRLLLVPTAEELMYHCKTCSTVSH 48 (134)
Q Consensus 19 ~~~C~~C~~h~~~h~~~~~~~C~~C~~~f~ 48 (134)
..-|..|+..+..........|..|+..+.
T Consensus 7 ~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~ 36 (116)
T KOG2907|consen 7 LDFCSDCGSLLEEPSAQSTVLCIRCKIEYP 36 (116)
T ss_pred cchhhhhhhhcccccccCceEeccccccCC
Confidence 456777877666666666677888888776
No 82
>KOG2482|consensus
Probab=91.66 E-value=0.2 Score=35.86 Aligned_cols=79 Identities=22% Similarity=0.325 Sum_probs=55.8
Q ss_pred ceeeCCCCCccCChHHHHHHHHH--hcCC---------------------------------------------------
Q psy3507 54 KYTCYACDYHTLMSEDMKKHMRK--HTGE--------------------------------------------------- 80 (134)
Q Consensus 54 ~~~C~~C~~~f~~~~~l~~H~~~--h~~~--------------------------------------------------- 80 (134)
.+.|-.|.+.|..+..|+.||+. |..-
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~ 274 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDD 274 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCC
Confidence 48899999999999999999973 3210
Q ss_pred -Cc--eeccccCccccCchhHHHHhhh-cCC--------------------------CCCeecCcChhhhcCHHHHHHHH
Q psy3507 81 -KP--YKCEYCAYSCTQSSALKIHERK-HTG--------------------------DKPYICQQCRDTFSSLYLFRNRL 130 (134)
Q Consensus 81 -~~--~~C~~C~~~f~~~~~l~~H~~~-h~~--------------------------~~~~~C~~C~~~F~~~~~l~~H~ 130 (134)
.+ ..|-.|.....+...|..|+.. |.- ...-.|-.|.-.|.....|..||
T Consensus 275 a~a~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm 354 (423)
T KOG2482|consen 275 AEALSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHM 354 (423)
T ss_pred CCccceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhc
Confidence 11 3677788877778888888774 310 11235777888888888888887
Q ss_pred Hh
Q psy3507 131 QS 132 (134)
Q Consensus 131 ~~ 132 (134)
..
T Consensus 355 ~e 356 (423)
T KOG2482|consen 355 VE 356 (423)
T ss_pred cc
Confidence 53
No 83
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=91.47 E-value=0.12 Score=32.93 Aligned_cols=13 Identities=23% Similarity=0.391 Sum_probs=6.7
Q ss_pred eeeCCCCCccCCh
Q psy3507 55 YTCYACDYHTLMS 67 (134)
Q Consensus 55 ~~C~~C~~~f~~~ 67 (134)
++|+.||.+|.+.
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 5555555555443
No 84
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.20 E-value=0.42 Score=28.73 Aligned_cols=49 Identities=16% Similarity=0.307 Sum_probs=30.5
Q ss_pred eeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccCchhHHHHhhhcC
Q psy3507 56 TCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHT 106 (134)
Q Consensus 56 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 106 (134)
.|--|...|........- .-.....|+|+.|...|--.-++..|...|.
T Consensus 57 ~C~~C~~~f~~~~~~~~~--~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFD--ELKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cccCcCCCCCCccccccc--ccccccceeCCCCCCccccccchhhhhhccC
Confidence 477888877654311100 0122346888888888888888888865553
No 85
>KOG2231|consensus
Probab=91.13 E-value=0.29 Score=38.23 Aligned_cols=71 Identities=24% Similarity=0.525 Sum_probs=47.7
Q ss_pred eeeCCCCCccCChHHHHHHHHHhcCCCceeccccC------ccccCchhHHHHhhhcCCCCCeecC--cCh-hhhcCHHH
Q psy3507 55 YTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCA------YSCTQSSALKIHERKHTGDKPYICQ--QCR-DTFSSLYL 125 (134)
Q Consensus 55 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~------~~f~~~~~l~~H~~~h~~~~~~~C~--~C~-~~F~~~~~ 125 (134)
-.|..|...|.....|..|++.++ |.|..|+ .-|.....|..|.+.++ |.|+ .|. +.|.....
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H----flCE~~~C~~~~f~~~~~ 254 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH----FLCEEEFCRTKKFYVAFE 254 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC----ccccccccccceeeehhH
Confidence 568899999999999999888654 5666663 45667788888877544 5666 453 34444445
Q ss_pred HHHHHHhc
Q psy3507 126 FRNRLQSH 133 (134)
Q Consensus 126 l~~H~~~H 133 (134)
+..+++.|
T Consensus 255 ~ei~lk~~ 262 (669)
T KOG2231|consen 255 LEIELKAH 262 (669)
T ss_pred HHHHHHhh
Confidence 55665543
No 86
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=91.06 E-value=0.079 Score=35.62 Aligned_cols=12 Identities=17% Similarity=0.642 Sum_probs=8.9
Q ss_pred eecCcChhhhcC
Q psy3507 111 YICQQCRDTFSS 122 (134)
Q Consensus 111 ~~C~~C~~~F~~ 122 (134)
..|+.||.+|..
T Consensus 49 ~vCP~CgyA~~~ 60 (214)
T PF09986_consen 49 WVCPHCGYAAFE 60 (214)
T ss_pred EECCCCCCcccc
Confidence 478888887754
No 87
>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=90.74 E-value=0.16 Score=23.00 Aligned_cols=24 Identities=17% Similarity=0.375 Sum_probs=9.6
Q ss_pred cCCCCCCcccCCCCcceeeCCCCC
Q psy3507 39 HCKTCSTVSHPNISYKYTCYACDY 62 (134)
Q Consensus 39 ~C~~C~~~f~~~~~~~~~C~~C~~ 62 (134)
+|+.|+..+.......+.|+.|+.
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----EE-SSSEEETTTTE
T ss_pred CCCCCCCcceeccCCEEeCCcccc
Confidence 466666666655555566666654
No 88
>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=90.63 E-value=0.18 Score=25.73 Aligned_cols=11 Identities=27% Similarity=0.842 Sum_probs=5.4
Q ss_pred ccCCCCCCccc
Q psy3507 38 YHCKTCSTVSH 48 (134)
Q Consensus 38 ~~C~~C~~~f~ 48 (134)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 44555555444
No 89
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.39 E-value=0.27 Score=33.11 Aligned_cols=14 Identities=14% Similarity=0.406 Sum_probs=10.1
Q ss_pred CccccCCCCCCccc
Q psy3507 35 ELMYHCKTCSTVSH 48 (134)
Q Consensus 35 ~~~~~C~~C~~~f~ 48 (134)
++.+.|+.|+..|.
T Consensus 3 ~k~~~CPvC~~~F~ 16 (214)
T PF09986_consen 3 DKKITCPVCGKEFK 16 (214)
T ss_pred CCceECCCCCCeee
Confidence 35577888888777
No 90
>KOG4173|consensus
Probab=90.15 E-value=0.11 Score=34.42 Aligned_cols=73 Identities=21% Similarity=0.489 Sum_probs=40.7
Q ss_pred eeeCC--CCCccCChHHHHHHHHHhcCCCceeccccCccccCchhHHHHhhh-c---------CCCCCeecCc--Chhhh
Q psy3507 55 YTCYA--CDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERK-H---------TGDKPYICQQ--CRDTF 120 (134)
Q Consensus 55 ~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~-h---------~~~~~~~C~~--C~~~F 120 (134)
+.|++ |...|........|-.+-++ -.|..|.+.|.+...|..|+.. | .|..-|+|-+ |+..|
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 44554 44556555555555443222 2566677777766666666542 2 2333366643 77777
Q ss_pred cCHHHHHHHH
Q psy3507 121 SSLYLFRNRL 130 (134)
Q Consensus 121 ~~~~~l~~H~ 130 (134)
.+...-..|+
T Consensus 157 kT~r~RkdH~ 166 (253)
T KOG4173|consen 157 KTSRDRKDHM 166 (253)
T ss_pred hhhhhhhhHH
Confidence 6666666664
No 91
>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=90.09 E-value=0.31 Score=23.94 Aligned_cols=22 Identities=18% Similarity=0.341 Sum_probs=10.8
Q ss_pred CCeecCcChhhhcCH----HHHHHHH
Q psy3507 109 KPYICQQCRDTFSSL----YLFRNRL 130 (134)
Q Consensus 109 ~~~~C~~C~~~F~~~----~~l~~H~ 130 (134)
....|..|++.+... +.|.+|+
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHH
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 345666666665543 5666666
No 92
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=89.96 E-value=0.19 Score=26.10 Aligned_cols=29 Identities=17% Similarity=0.212 Sum_probs=24.7
Q ss_pred CCCCcceeeCCCCCccCChHHHHHHHHHh
Q psy3507 49 PNISYKYTCYACDYHTLMSEDMKKHMRKH 77 (134)
Q Consensus 49 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 77 (134)
..++..+.|+-|+..|....++.+|...-
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKa 40 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKA 40 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHH
Confidence 45677799999999999999999998743
No 93
>PF14353 CpXC: CpXC protein
Probab=89.63 E-value=0.28 Score=30.08 Aligned_cols=10 Identities=20% Similarity=0.587 Sum_probs=5.8
Q ss_pred cCCCCCCccc
Q psy3507 39 HCKTCSTVSH 48 (134)
Q Consensus 39 ~C~~C~~~f~ 48 (134)
+|+.|+..|.
T Consensus 3 tCP~C~~~~~ 12 (128)
T PF14353_consen 3 TCPHCGHEFE 12 (128)
T ss_pred CCCCCCCeeE
Confidence 4666666555
No 94
>PHA00626 hypothetical protein
Probab=89.51 E-value=0.42 Score=24.87 Aligned_cols=11 Identities=36% Similarity=1.198 Sum_probs=5.2
Q ss_pred ceeeCCCCCcc
Q psy3507 54 KYTCYACDYHT 64 (134)
Q Consensus 54 ~~~C~~C~~~f 64 (134)
.|+|+.|+..|
T Consensus 23 rYkCkdCGY~f 33 (59)
T PHA00626 23 DYVCCDCGYND 33 (59)
T ss_pred ceEcCCCCCee
Confidence 34444444444
No 95
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=89.31 E-value=0.4 Score=33.95 Aligned_cols=91 Identities=22% Similarity=0.413 Sum_probs=55.8
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCccCChHHHHHHHHHhc-----CCC-------ceeccccCccccCchhHHHHhhhc
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYHTLMSEDMKKHMRKHT-----GEK-------PYKCEYCAYSCTQSSALKIHERKH 105 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~-----~~~-------~~~C~~C~~~f~~~~~l~~H~~~h 105 (134)
|.|+.|.... -..|..|+.|+-.......|.+-..--. .++ .-.|-.|...|.....-..- .-
T Consensus 309 y~CP~CktkV---CsLPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~~~~~--~~ 383 (421)
T COG5151 309 YECPVCKTKV---CSLPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPVSPFD--ES 383 (421)
T ss_pred eeCCccccee---ecCCccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCCCccc--cc
Confidence 8888887653 4567889999877666666654321100 111 12377777777664321111 11
Q ss_pred CCCCCeecCcChhhhcCHHHHHHHHHhc
Q psy3507 106 TGDKPYICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 106 ~~~~~~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
+..-.|+|+.|...|-.--+.-.|...|
T Consensus 384 ~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 384 TSSGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ccccceechhhhhhhhhhhHHHHHHHHh
Confidence 2234599999999998887777777665
No 96
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=88.96 E-value=0.28 Score=31.60 Aligned_cols=24 Identities=17% Similarity=0.445 Sum_probs=15.4
Q ss_pred cccCCCCCCcccCCCCcceeeCCCCC
Q psy3507 37 MYHCKTCSTVSHPNISYKYTCYACDY 62 (134)
Q Consensus 37 ~~~C~~C~~~f~~~~~~~~~C~~C~~ 62 (134)
.|.|+.||..+. ++.|-+||+|+-
T Consensus 134 ~~vC~vCGy~~~--ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTHE--GEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCccc--CCCCCcCCCCCC
Confidence 477777776643 356667777763
No 97
>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=88.91 E-value=0.52 Score=30.16 Aligned_cols=31 Identities=16% Similarity=0.400 Sum_probs=20.8
Q ss_pred CCceeccccCccccCchhHHHHhhhcCCCCCeecCcChhh
Q psy3507 80 EKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDT 119 (134)
Q Consensus 80 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 119 (134)
..-|.|+.|+..|+...++. .-|.|+.||..
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 34577887877777666653 25788888764
No 98
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=88.41 E-value=0.48 Score=29.91 Aligned_cols=36 Identities=17% Similarity=0.384 Sum_probs=19.0
Q ss_pred cceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccc
Q psy3507 53 YKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSC 92 (134)
Q Consensus 53 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 92 (134)
.-|.|+.|+..|.....+.. ... ...|.|+.||...
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEE
Confidence 34667777666665443321 011 2337777777654
No 99
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=87.78 E-value=0.34 Score=24.42 Aligned_cols=11 Identities=36% Similarity=0.963 Sum_probs=6.5
Q ss_pred ccCCCCCCccc
Q psy3507 38 YHCKTCSTVSH 48 (134)
Q Consensus 38 ~~C~~C~~~f~ 48 (134)
|+|..||.++.
T Consensus 2 y~C~~CgyvYd 12 (47)
T PF00301_consen 2 YQCPVCGYVYD 12 (47)
T ss_dssp EEETTTSBEEE
T ss_pred cCCCCCCEEEc
Confidence 55666665555
No 100
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=87.08 E-value=0.38 Score=24.36 Aligned_cols=21 Identities=24% Similarity=0.448 Sum_probs=12.7
Q ss_pred eecCcChhhhcCH-----HHHHHHHH
Q psy3507 111 YICQQCRDTFSSL-----YLFRNRLQ 131 (134)
Q Consensus 111 ~~C~~C~~~F~~~-----~~l~~H~~ 131 (134)
-.|..|++.+... +.|.+|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 4566666655443 56777776
No 101
>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=86.82 E-value=0.42 Score=24.41 Aligned_cols=11 Identities=27% Similarity=1.011 Sum_probs=7.2
Q ss_pred ccCCCCCCccc
Q psy3507 38 YHCKTCSTVSH 48 (134)
Q Consensus 38 ~~C~~C~~~f~ 48 (134)
|+|..||..|.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 56666666665
No 102
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=86.70 E-value=0.48 Score=24.05 Aligned_cols=28 Identities=18% Similarity=0.487 Sum_probs=15.9
Q ss_pred ccccCCCCCCccc-CCCCcceeeCCCCCc
Q psy3507 36 LMYHCKTCSTVSH-PNISYKYTCYACDYH 63 (134)
Q Consensus 36 ~~~~C~~C~~~f~-~~~~~~~~C~~C~~~ 63 (134)
..|.|..||+.|. ........|+.||..
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 3466666666665 233344666666643
No 103
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=86.67 E-value=0.5 Score=37.51 Aligned_cols=40 Identities=20% Similarity=0.407 Sum_probs=29.8
Q ss_pred ecCcccccccccCCCCccccCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 20 ATCIHCRLLLVPTAEELMYHCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 20 ~~C~~C~~h~~~h~~~~~~~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
.+|..|..-+..|.......|..||.. ...+..|+.||..
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~----~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQ----EPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCC----CCCCCCCCCCCCC
Confidence 456667777777777778888888875 4567788888865
No 104
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=86.65 E-value=0.39 Score=27.40 Aligned_cols=30 Identities=13% Similarity=0.244 Sum_probs=16.2
Q ss_pred cccCCCCCCccc-CCCCcceeeCCCCCccCC
Q psy3507 37 MYHCKTCSTVSH-PNISYKYTCYACDYHTLM 66 (134)
Q Consensus 37 ~~~C~~C~~~f~-~~~~~~~~C~~C~~~f~~ 66 (134)
.|.|+.|++.-. ......+.|..|+..|..
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCeecc
Confidence 366666665522 233334666666666654
No 105
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=86.40 E-value=0.62 Score=23.76 Aligned_cols=24 Identities=21% Similarity=0.605 Sum_probs=10.1
Q ss_pred CCCCCCcccCCCCcceeeCCCCCc
Q psy3507 40 CKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 40 C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
|+.||..|.......+.|..|+..
T Consensus 23 CP~Cg~~~m~~~~~r~~C~~Cgyt 46 (50)
T PRK00432 23 CPRCGSGFMAEHLDRWHCGKCGYT 46 (50)
T ss_pred CcCCCcchheccCCcEECCCcCCE
Confidence 455544333222234445555443
No 106
>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=86.21 E-value=0.61 Score=29.86 Aligned_cols=32 Identities=16% Similarity=0.329 Sum_probs=22.0
Q ss_pred CcceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccc
Q psy3507 52 SYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSC 92 (134)
Q Consensus 52 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 92 (134)
..-|.|+.|+..|+...++. .-|.|+.||...
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 34577888887777777664 147888888643
No 107
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=85.70 E-value=0.83 Score=29.88 Aligned_cols=30 Identities=23% Similarity=0.532 Sum_probs=17.6
Q ss_pred CceeccccCccccCchhHHHHhhhcCCCCCeecCcChhh
Q psy3507 81 KPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDT 119 (134)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 119 (134)
.-|.|+.|+..|+...++. .-|.|+.||..
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~ 145 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME---------YGFRCPQCGEM 145 (178)
T ss_pred CEEECCCCCcEEeHHHHhh---------cCCcCCCCCCC
Confidence 3466777776666554432 24677777654
No 108
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=85.68 E-value=0.56 Score=29.10 Aligned_cols=23 Identities=26% Similarity=0.723 Sum_probs=15.7
Q ss_pred CCCeecCcChhhhcCHHHHHHHHHhc
Q psy3507 108 DKPYICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 108 ~~~~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
+....|-+||+.|.. |.+|+++|
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~ 92 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTH 92 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHT
T ss_pred cCeeEEccCCcccch---HHHHHHHc
Confidence 344789999999987 69999888
No 109
>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=85.60 E-value=0.61 Score=35.49 Aligned_cols=39 Identities=23% Similarity=0.488 Sum_probs=30.6
Q ss_pred cCcccccccccCCCCccccCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 21 TCIHCRLLLVPTAEELMYHCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 21 ~C~~C~~h~~~h~~~~~~~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
.|..|...+..|.......|..||... ..+..|+.|+..
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~----~~~~~Cp~C~s~ 262 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHYCGYQE----PIPKTCPQCGSE 262 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCCCcCcC----CCCCCCCCCCCC
Confidence 577777788888888889999999763 346789999864
No 110
>KOG2785|consensus
Probab=85.52 E-value=1 Score=32.81 Aligned_cols=78 Identities=17% Similarity=0.303 Sum_probs=42.0
Q ss_pred ceeeCCCCCccCChHHHHHHHHH--hcC---CCceec-cccCccccCchhHHHH-hh--hcCCCCCeecCcChhhhcCHH
Q psy3507 54 KYTCYACDYHTLMSEDMKKHMRK--HTG---EKPYKC-EYCAYSCTQSSALKIH-ER--KHTGDKPYICQQCRDTFSSLY 124 (134)
Q Consensus 54 ~~~C~~C~~~f~~~~~l~~H~~~--h~~---~~~~~C-~~C~~~f~~~~~l~~H-~~--~h~~~~~~~C~~C~~~F~~~~ 124 (134)
.|.|..|...|.+....+.|+++ |.- .+...= ++-...|..+..-..- .. .-.++-++.|..|.+.|.+..
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~ 82 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPK 82 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChh
Confidence 47899999999999888889873 421 000000 1111222221111000 00 122344577777777777777
Q ss_pred HHHHHHH
Q psy3507 125 LFRNRLQ 131 (134)
Q Consensus 125 ~l~~H~~ 131 (134)
....|+.
T Consensus 83 a~~~hl~ 89 (390)
T KOG2785|consen 83 AHENHLK 89 (390)
T ss_pred hHHHHHH
Confidence 7777764
No 111
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=85.48 E-value=0.88 Score=23.72 Aligned_cols=40 Identities=20% Similarity=0.513 Sum_probs=22.2
Q ss_pred Cceeccc--cCccccCchhHHHHhhhcCCCCCeecCc----Chhhhc
Q psy3507 81 KPYKCEY--CAYSCTQSSALKIHERKHTGDKPYICQQ----CRDTFS 121 (134)
Q Consensus 81 ~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~----C~~~F~ 121 (134)
.+..|+. |...+. +..|..|+..--..++..|+. |+..+.
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred CEeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 4566766 444343 456778877655566777887 777665
No 112
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=85.21 E-value=0.56 Score=30.65 Aligned_cols=31 Identities=19% Similarity=0.501 Sum_probs=19.2
Q ss_pred cceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccc
Q psy3507 53 YKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSC 92 (134)
Q Consensus 53 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 92 (134)
.-|.|+.|+..|....++. .-|.|+.||...
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L 146 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME---------YGFRCPQCGEML 146 (178)
T ss_pred CEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCC
Confidence 3467777777766665542 247777777643
No 113
>COG1773 Rubredoxin [Energy production and conversion]
Probab=84.91 E-value=0.58 Score=24.35 Aligned_cols=12 Identities=25% Similarity=0.736 Sum_probs=9.1
Q ss_pred cccCCCCCCccc
Q psy3507 37 MYHCKTCSTVSH 48 (134)
Q Consensus 37 ~~~C~~C~~~f~ 48 (134)
.|+|..||..|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 477888888776
No 114
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=84.81 E-value=2.4 Score=26.71 Aligned_cols=38 Identities=24% Similarity=0.552 Sum_probs=25.7
Q ss_pred CCCceeccccCccccCchhHHHHhhhcCCCCCeecCcChhhh
Q psy3507 79 GEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTF 120 (134)
Q Consensus 79 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~F 120 (134)
+...|.|+.|+..|.....+.. ... ...|.|+.||...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEE
Confidence 3456999999999886544332 011 3349999999765
No 115
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=83.73 E-value=0.8 Score=27.25 Aligned_cols=30 Identities=20% Similarity=0.386 Sum_probs=24.2
Q ss_pred cCCCCCCcccCCCCcceeeCCCCCccCChH
Q psy3507 39 HCKTCSTVSHPNISYKYTCYACDYHTLMSE 68 (134)
Q Consensus 39 ~C~~C~~~f~~~~~~~~~C~~C~~~f~~~~ 68 (134)
.|+.|+..|.......|.|+.|+..+....
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYEWNENE 33 (109)
T ss_pred cCCcCCCcceEecCCeeECccccccccccc
Confidence 588999988877777899999998876553
No 116
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=83.49 E-value=0.78 Score=28.58 Aligned_cols=11 Identities=18% Similarity=0.676 Sum_probs=5.8
Q ss_pred ccCCCCCCccc
Q psy3507 38 YHCKTCSTVSH 48 (134)
Q Consensus 38 ~~C~~C~~~f~ 48 (134)
+.|..||..|.
T Consensus 71 ~~C~~CG~~~~ 81 (135)
T PRK03824 71 LKCRNCGNEWS 81 (135)
T ss_pred EECCCCCCEEe
Confidence 55555555544
No 117
>KOG4167|consensus
Probab=83.38 E-value=0.37 Score=37.89 Aligned_cols=24 Identities=17% Similarity=0.524 Sum_probs=22.3
Q ss_pred CeecCcChhhhcCHHHHHHHHHhc
Q psy3507 110 PYICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 110 ~~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
-|.|..|+|.|..-.++..||++|
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHH
Confidence 399999999999999999999998
No 118
>KOG2807|consensus
Probab=83.38 E-value=2.1 Score=30.63 Aligned_cols=34 Identities=21% Similarity=0.488 Sum_probs=27.4
Q ss_pred cccCCCCCCcccCCCCcceeeCCCCCccCChHHHHHH
Q psy3507 37 MYHCKTCSTVSHPNISYKYTCYACDYHTLMSEDMKKH 73 (134)
Q Consensus 37 ~~~C~~C~~~f~~~~~~~~~C~~C~~~f~~~~~l~~H 73 (134)
-|.|+.|+... -+.|-+|+.|+-.......|.+-
T Consensus 276 Gy~CP~Ckakv---CsLP~eCpiC~ltLVss~hLARS 309 (378)
T KOG2807|consen 276 GYFCPQCKAKV---CSLPIECPICSLTLVSSPHLARS 309 (378)
T ss_pred ceeCCcccCee---ecCCccCCccceeEecchHHHHH
Confidence 38899998764 55788999999998888888754
No 119
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=83.26 E-value=0.34 Score=26.77 Aligned_cols=41 Identities=15% Similarity=0.292 Sum_probs=20.1
Q ss_pred eeeCCCCCccCChHHHHHHHHHhcCCCceecc--ccCccccCchh
Q psy3507 55 YTCYACDYHTLMSEDMKKHMRKHTGEKPYKCE--YCAYSCTQSSA 97 (134)
Q Consensus 55 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~--~C~~~f~~~~~ 97 (134)
+.|+.|+........-.... -..+..++|. .||..|.....
T Consensus 2 m~CP~Cg~~a~irtSr~~s~--~~~~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITD--TTKERYHQCQNVNCSATFITYES 44 (72)
T ss_pred ccCCCCCCccEEEEChhcCh--hhheeeeecCCCCCCCEEEEEEE
Confidence 45777775543222221111 1233456676 67777766543
No 120
>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=83.00 E-value=1.3 Score=19.17 Aligned_cols=19 Identities=21% Similarity=0.419 Sum_probs=10.6
Q ss_pred ecCcChhhhcCHHHHHHHHH
Q psy3507 112 ICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 112 ~C~~C~~~F~~~~~l~~H~~ 131 (134)
.|+.|++.+ ....+.+|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 466666665 4455555553
No 121
>PRK10220 hypothetical protein; Provisional
Probab=82.90 E-value=1.1 Score=26.64 Aligned_cols=30 Identities=23% Similarity=0.407 Sum_probs=24.3
Q ss_pred cCCCCCCcccCCCCcceeeCCCCCccCChH
Q psy3507 39 HCKTCSTVSHPNISYKYTCYACDYHTLMSE 68 (134)
Q Consensus 39 ~C~~C~~~f~~~~~~~~~C~~C~~~f~~~~ 68 (134)
.|+.|+..|.......|.|+.|+..+...+
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHEWNDAE 34 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCcCCccc
Confidence 588999888877777899999998776654
No 122
>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=82.90 E-value=1.1 Score=23.27 Aligned_cols=11 Identities=18% Similarity=0.776 Sum_probs=4.9
Q ss_pred ccCCCCCCccc
Q psy3507 38 YHCKTCSTVSH 48 (134)
Q Consensus 38 ~~C~~C~~~f~ 48 (134)
++|+.||..+.
T Consensus 3 ~~CP~CG~~ie 13 (54)
T TIGR01206 3 FECPDCGAEIE 13 (54)
T ss_pred cCCCCCCCEEe
Confidence 34444444443
No 123
>KOG2186|consensus
Probab=82.85 E-value=0.87 Score=31.32 Aligned_cols=21 Identities=19% Similarity=0.445 Sum_probs=11.4
Q ss_pred ceeeCCCCCccCChHHHHHHHH
Q psy3507 54 KYTCYACDYHTLMSEDMKKHMR 75 (134)
Q Consensus 54 ~~~C~~C~~~f~~~~~l~~H~~ 75 (134)
.|.|-.|++.|.. ..+..|..
T Consensus 29 ~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 29 YFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred eeEEeeccccccc-chhhhhhh
Confidence 3556666666655 44455544
No 124
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.80 E-value=0.86 Score=27.19 Aligned_cols=28 Identities=0% Similarity=-0.441 Sum_probs=22.7
Q ss_pred cCCCCCCcccCCCCcceeeCCCCCccCC
Q psy3507 39 HCKTCSTVSHPNISYKYTCYACDYHTLM 66 (134)
Q Consensus 39 ~C~~C~~~f~~~~~~~~~C~~C~~~f~~ 66 (134)
.|+.||+.|.--...|..|++||++|..
T Consensus 11 idPetg~KFYDLNrdPiVsPytG~s~P~ 38 (129)
T COG4530 11 IDPETGKKFYDLNRDPIVSPYTGKSYPR 38 (129)
T ss_pred cCccccchhhccCCCccccCcccccchH
Confidence 4788888888777788889999988843
No 125
>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=81.86 E-value=1.3 Score=21.57 Aligned_cols=8 Identities=25% Similarity=0.820 Sum_probs=3.3
Q ss_pred eeeCCCCC
Q psy3507 55 YTCYACDY 62 (134)
Q Consensus 55 ~~C~~C~~ 62 (134)
+.|..||.
T Consensus 20 ~vC~~CG~ 27 (43)
T PF08271_consen 20 LVCPNCGL 27 (43)
T ss_dssp EEETTT-B
T ss_pred EECCCCCC
Confidence 44555543
No 126
>PF14369 zf-RING_3: zinc-finger
Probab=81.71 E-value=1.4 Score=20.62 Aligned_cols=8 Identities=25% Similarity=0.617 Sum_probs=4.4
Q ss_pred CCCCCCcc
Q psy3507 40 CKTCSTVS 47 (134)
Q Consensus 40 C~~C~~~f 47 (134)
|+.|+..|
T Consensus 24 CP~C~~gF 31 (35)
T PF14369_consen 24 CPRCHGGF 31 (35)
T ss_pred CcCCCCcE
Confidence 55555544
No 127
>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=81.56 E-value=1.2 Score=30.80 Aligned_cols=88 Identities=19% Similarity=0.336 Sum_probs=46.8
Q ss_pred cCCCCCCcccCCCCcceeeCCCCCccCChHHHHHHHHH--hcCCCceeccccCccccCchh-------HHHHhhh----c
Q psy3507 39 HCKTCSTVSHPNISYKYTCYACDYHTLMSEDMKKHMRK--HTGEKPYKCEYCAYSCTQSSA-------LKIHERK----H 105 (134)
Q Consensus 39 ~C~~C~~~f~~~~~~~~~C~~C~~~f~~~~~l~~H~~~--h~~~~~~~C~~C~~~f~~~~~-------l~~H~~~----h 105 (134)
.|-+|.+..-..+.+.|.|..|....-....+ .|+.. -.....|+|..|++. .+.+- -..|.+. .
T Consensus 127 ~C~EC~R~vw~hGGrif~CsfC~~flCEDDQF-EHQAsCQvLe~E~~KC~SCNrl-Gq~sCLRCK~cfCddHvrrKg~ky 204 (314)
T PF06524_consen 127 VCIECERGVWDHGGRIFKCSFCDNFLCEDDQF-EHQASCQVLESETFKCQSCNRL-GQYSCLRCKICFCDDHVRRKGFKY 204 (314)
T ss_pred EeeeeecccccCCCeEEEeecCCCeeeccchh-hhhhhhhhhhcccccccccccc-cchhhhheeeeehhhhhhhccccc
Confidence 45556555556667788888887654443333 34431 222344677666642 11111 2244432 2
Q ss_pred CCCCCeecCcChhhhcCHHHHHH
Q psy3507 106 TGDKPYICQQCRDTFSSLYLFRN 128 (134)
Q Consensus 106 ~~~~~~~C~~C~~~F~~~~~l~~ 128 (134)
...+++.|+.||..-.....|..
T Consensus 205 ~k~k~~PCPKCg~et~eTkdLSm 227 (314)
T PF06524_consen 205 EKGKPIPCPKCGYETQETKDLSM 227 (314)
T ss_pred ccCCCCCCCCCCCccccccccee
Confidence 23467889999876555444443
No 128
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=81.21 E-value=1.8 Score=34.55 Aligned_cols=8 Identities=25% Similarity=1.057 Sum_probs=4.4
Q ss_pred cCCCCCCc
Q psy3507 39 HCKTCSTV 46 (134)
Q Consensus 39 ~C~~C~~~ 46 (134)
.|..||..
T Consensus 437 ~C~~Cg~v 444 (730)
T COG1198 437 LCRDCGYI 444 (730)
T ss_pred ecccCCCc
Confidence 45556554
No 129
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=81.07 E-value=0.97 Score=27.28 Aligned_cols=27 Identities=19% Similarity=0.309 Sum_probs=16.2
Q ss_pred ccccCCCCCCcccCCCCcceeeCCCCC
Q psy3507 36 LMYHCKTCSTVSHPNISYKYTCYACDY 62 (134)
Q Consensus 36 ~~~~C~~C~~~f~~~~~~~~~C~~C~~ 62 (134)
-...|..||..|.......+.|+.||.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcCC
Confidence 346677777766544333356777774
No 130
>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=80.97 E-value=0.39 Score=22.69 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=5.0
Q ss_pred cCCCCCCccc
Q psy3507 39 HCKTCSTVSH 48 (134)
Q Consensus 39 ~C~~C~~~f~ 48 (134)
.|+.||++|.
T Consensus 3 ~C~~Cg~~Yh 12 (36)
T PF05191_consen 3 ICPKCGRIYH 12 (36)
T ss_dssp EETTTTEEEE
T ss_pred CcCCCCCccc
Confidence 3555555554
No 131
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=80.11 E-value=0.85 Score=28.26 Aligned_cols=20 Identities=30% Similarity=0.629 Sum_probs=17.1
Q ss_pred eecCcChhhhcCHHHHHHHHHhc
Q psy3507 111 YICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 111 ~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
..|-++|+.|.+ |++|+.+|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~ 96 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTH 96 (148)
T ss_pred EEEeccCcchHH---HHHHHhcc
Confidence 679999999875 89999886
No 132
>PRK04023 DNA polymerase II large subunit; Validated
Probab=80.09 E-value=2.5 Score=34.90 Aligned_cols=8 Identities=38% Similarity=0.899 Sum_probs=3.9
Q ss_pred eeccccCc
Q psy3507 83 YKCEYCAY 90 (134)
Q Consensus 83 ~~C~~C~~ 90 (134)
+.|+.|+.
T Consensus 664 y~CPKCG~ 671 (1121)
T PRK04023 664 DECEKCGR 671 (1121)
T ss_pred CcCCCCCC
Confidence 34555554
No 133
>PRK14873 primosome assembly protein PriA; Provisional
Probab=79.87 E-value=1.5 Score=34.71 Aligned_cols=39 Identities=23% Similarity=0.463 Sum_probs=29.1
Q ss_pred ecCcccccccccCCCCccccCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 20 ATCIHCRLLLVPTAEELMYHCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 20 ~~C~~C~~h~~~h~~~~~~~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
..|..|...+..|.......|..||.. . .+..|+.|+..
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~~----~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGRA----A-PDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcCC----C-cCccCCCCcCC
Confidence 356667777777877777889999974 1 36789999865
No 134
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=79.74 E-value=0.92 Score=28.01 Aligned_cols=26 Identities=19% Similarity=0.377 Sum_probs=16.6
Q ss_pred cccCCCCCCcccCCC-CcceeeCCCCC
Q psy3507 37 MYHCKTCSTVSHPNI-SYKYTCYACDY 62 (134)
Q Consensus 37 ~~~C~~C~~~f~~~~-~~~~~C~~C~~ 62 (134)
|++|..||+.|.... +..--|+.||-
T Consensus 1 PH~Ct~Cg~~f~dgs~eil~GCP~CGg 27 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEILSGCPECGG 27 (131)
T ss_pred CcccCcCCCCcCCCcHHHHccCcccCC
Confidence 467778888887433 34455777774
No 135
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=79.55 E-value=1.3 Score=25.49 Aligned_cols=26 Identities=23% Similarity=0.432 Sum_probs=17.1
Q ss_pred ccccCCCCCCcccC-CCCcceeeCCCC
Q psy3507 36 LMYHCKTCSTVSHP-NISYKYTCYACD 61 (134)
Q Consensus 36 ~~~~C~~C~~~f~~-~~~~~~~C~~C~ 61 (134)
.|-.|..||..|.. ....|..|+.|-
T Consensus 57 ~Pa~CkkCGfef~~~~ik~pSRCP~CK 83 (97)
T COG3357 57 RPARCKKCGFEFRDDKIKKPSRCPKCK 83 (97)
T ss_pred cChhhcccCccccccccCCcccCCcch
Confidence 45667777777774 344567777774
No 136
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=79.47 E-value=1.1 Score=20.76 Aligned_cols=27 Identities=19% Similarity=0.306 Sum_probs=12.0
Q ss_pred cCcccccccccCCCCccccCCCCCCcc
Q psy3507 21 TCIHCRLLLVPTAEELMYHCKTCSTVS 47 (134)
Q Consensus 21 ~C~~C~~h~~~h~~~~~~~C~~C~~~f 47 (134)
.|..|+.-...-+...-+.|..||.+|
T Consensus 5 ~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 5 KCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred EcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 444453333222333345566665554
No 137
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=79.47 E-value=1.2 Score=32.17 Aligned_cols=68 Identities=22% Similarity=0.444 Sum_probs=44.6
Q ss_pred eeeCCCCCccCChHHHHHHHHHhcCCCceeccccCc-------cccCchhHHHHhhhcCCCCCeecCc--Ch----hhhc
Q psy3507 55 YTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAY-------SCTQSSALKIHERKHTGDKPYICQQ--CR----DTFS 121 (134)
Q Consensus 55 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~-------~f~~~~~l~~H~~~h~~~~~~~C~~--C~----~~F~ 121 (134)
-.|..|...|.+...|..|++..+. .|-+|+. -|.+-..|..|.+. .-|.|.. |. ..|.
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~HE----~ChICD~v~p~~~QYFK~Y~~Le~HF~~----~hy~ct~qtc~~~k~~vf~ 292 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLRHE----ACHICDMVGPIRYQYFKSYEDLEAHFRN----AHYCCTFQTCRVGKCYVFP 292 (493)
T ss_pred chhhhccceecChHHHHHHHHhhhh----hhhhhhccCccchhhhhCHHHHHHHhhc----CceEEEEEEEecCcEEEec
Confidence 4688888888888888888875432 3555554 35555666666542 2355543 32 3688
Q ss_pred CHHHHHHHH
Q psy3507 122 SLYLFRNRL 130 (134)
Q Consensus 122 ~~~~l~~H~ 130 (134)
....|..|+
T Consensus 293 ~~~el~~h~ 301 (493)
T COG5236 293 YHTELLEHL 301 (493)
T ss_pred cHHHHHHHH
Confidence 888888886
No 138
>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=79.06 E-value=1.2 Score=22.16 Aligned_cols=25 Identities=24% Similarity=0.676 Sum_probs=12.6
Q ss_pred ccCCCCCCc--ccCCCCcceeeCCCCC
Q psy3507 38 YHCKTCSTV--SHPNISYKYTCYACDY 62 (134)
Q Consensus 38 ~~C~~C~~~--f~~~~~~~~~C~~C~~ 62 (134)
+.|+.||.. +.......|.|..|++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 556666643 1122334566666653
No 139
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=78.87 E-value=1.4 Score=20.80 Aligned_cols=25 Identities=20% Similarity=0.344 Sum_probs=16.2
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCC
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDY 62 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~ 62 (134)
..|++|+..+....+-.|-|..||.
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCce
Confidence 4577777776555666666766664
No 140
>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=78.47 E-value=1.5 Score=23.63 Aligned_cols=25 Identities=16% Similarity=0.404 Sum_probs=8.2
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
-.|..|++.|.. ..+.+.|..||..
T Consensus 10 ~~C~~C~~~F~~-~~rrhhCr~CG~~ 34 (69)
T PF01363_consen 10 SNCMICGKKFSL-FRRRHHCRNCGRV 34 (69)
T ss_dssp SB-TTT--B-BS-SS-EEE-TTT--E
T ss_pred CcCcCcCCcCCC-ceeeEccCCCCCE
Confidence 345566666632 2344555555543
No 141
>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=78.28 E-value=1.6 Score=23.50 Aligned_cols=27 Identities=19% Similarity=0.550 Sum_probs=14.3
Q ss_pred cCCCCCCcccC-CCCcceeeCCCCCccC
Q psy3507 39 HCKTCSTVSHP-NISYKYTCYACDYHTL 65 (134)
Q Consensus 39 ~C~~C~~~f~~-~~~~~~~C~~C~~~f~ 65 (134)
.|+.||..-.. .....|.|+.||....
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CccCcccccccccccceEEcCCCCCEEC
Confidence 45555555443 3344566666665543
No 142
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=77.85 E-value=1.4 Score=26.77 Aligned_cols=26 Identities=35% Similarity=0.586 Sum_probs=13.8
Q ss_pred cccCCCCCCcccCCCCcceeeCCCCC
Q psy3507 37 MYHCKTCSTVSHPNISYKYTCYACDY 62 (134)
Q Consensus 37 ~~~C~~C~~~f~~~~~~~~~C~~C~~ 62 (134)
...|..||..|.......+.|+.|+.
T Consensus 71 ~~~C~~Cg~~~~~~~~~~~~CP~Cgs 96 (117)
T PRK00564 71 ELECKDCSHVFKPNALDYGVCEKCHS 96 (117)
T ss_pred EEEhhhCCCccccCCccCCcCcCCCC
Confidence 35666666665543322234666664
No 143
>KOG1280|consensus
Probab=77.83 E-value=6.6 Score=28.47 Aligned_cols=42 Identities=19% Similarity=0.368 Sum_probs=27.9
Q ss_pred CCCCcceeeCCCCCccCChHHHHHHHHHhcCCCc--eeccccCc
Q psy3507 49 PNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKP--YKCEYCAY 90 (134)
Q Consensus 49 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~--~~C~~C~~ 90 (134)
+.....|.|++|+..-.+...|..|....+.+-+ ..|++|+.
T Consensus 74 ~y~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~ 117 (381)
T KOG1280|consen 74 HYDPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAA 117 (381)
T ss_pred ccccccccCCcccccccchhHHHHHhhhcCcccCcceeeecccc
Confidence 3344468999999888888888888775433322 45666653
No 144
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=77.28 E-value=2.5 Score=20.35 Aligned_cols=9 Identities=33% Similarity=0.999 Sum_probs=4.3
Q ss_pred eeeCCCCCc
Q psy3507 55 YTCYACDYH 63 (134)
Q Consensus 55 ~~C~~C~~~ 63 (134)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (40)
T smart00440 29 YVCTKCGHR 37 (40)
T ss_pred EEeCCCCCE
Confidence 445445443
No 145
>PRK14873 primosome assembly protein PriA; Provisional
Probab=76.32 E-value=2.5 Score=33.50 Aligned_cols=8 Identities=38% Similarity=0.920 Sum_probs=4.7
Q ss_pred cCCCCCCc
Q psy3507 39 HCKTCSTV 46 (134)
Q Consensus 39 ~C~~C~~~ 46 (134)
.|..||..
T Consensus 385 ~C~~Cg~~ 392 (665)
T PRK14873 385 ACARCRTP 392 (665)
T ss_pred EhhhCcCe
Confidence 56666654
No 146
>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=76.15 E-value=1.1 Score=25.85 Aligned_cols=29 Identities=21% Similarity=0.442 Sum_probs=15.5
Q ss_pred cccCCCCCCccc-CCCCcceeeCCCCCccC
Q psy3507 37 MYHCKTCSTVSH-PNISYKYTCYACDYHTL 65 (134)
Q Consensus 37 ~~~C~~C~~~f~-~~~~~~~~C~~C~~~f~ 65 (134)
.|.|+.||+.-- ....-.+.|..|++.|.
T Consensus 35 ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp -BEESSSSSSEEEEEETTEEEETTTTEEEE
T ss_pred CCcCCCCCCceeEEeeeEEeecCCCCCEEe
Confidence 366777776432 22223366777766654
No 147
>PRK05580 primosome assembly protein PriA; Validated
Probab=75.87 E-value=2.2 Score=33.80 Aligned_cols=39 Identities=21% Similarity=0.462 Sum_probs=28.5
Q ss_pred cCcccccccccCCCCccccCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 21 TCIHCRLLLVPTAEELMYHCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 21 ~C~~C~~h~~~h~~~~~~~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
.|..|...+..|.......|..||... ..+..|+.|+..
T Consensus 392 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~----~~~~~Cp~Cg~~ 430 (679)
T PRK05580 392 ECPHCDASLTLHRFQRRLRCHHCGYQE----PIPKACPECGST 430 (679)
T ss_pred CCCCCCCceeEECCCCeEECCCCcCCC----CCCCCCCCCcCC
Confidence 566676677777777778899999753 345679999765
No 148
>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=75.34 E-value=0.8 Score=27.57 Aligned_cols=25 Identities=20% Similarity=0.592 Sum_probs=12.7
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
..|..||..|...... +.|+.|+..
T Consensus 71 ~~C~~Cg~~~~~~~~~-~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFD-FSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EEECHHCC-HH-SSSSSS
T ss_pred EECCCCCCEEecCCCC-CCCcCCcCC
Confidence 5666666666533332 556666643
No 149
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=75.27 E-value=2.4 Score=21.34 Aligned_cols=10 Identities=30% Similarity=1.228 Sum_probs=4.9
Q ss_pred ceeeCCCCCc
Q psy3507 54 KYTCYACDYH 63 (134)
Q Consensus 54 ~~~C~~C~~~ 63 (134)
.+.|+.|+..
T Consensus 20 ~~vC~~Cg~~ 29 (52)
T smart00661 20 RFVCRKCGYE 29 (52)
T ss_pred EEECCcCCCe
Confidence 3455555543
No 150
>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=75.26 E-value=2 Score=19.10 Aligned_cols=9 Identities=44% Similarity=1.265 Sum_probs=2.9
Q ss_pred cceeeCCCC
Q psy3507 53 YKYTCYACD 61 (134)
Q Consensus 53 ~~~~C~~C~ 61 (134)
..|.|..|+
T Consensus 14 ~~Y~C~~Cd 22 (30)
T PF07649_consen 14 WFYRCSECD 22 (30)
T ss_dssp -EEE-TTT-
T ss_pred ceEECccCC
Confidence 344454443
No 151
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=75.16 E-value=2.5 Score=17.74 Aligned_cols=7 Identities=29% Similarity=1.046 Sum_probs=2.8
Q ss_pred CCCCCCc
Q psy3507 40 CKTCSTV 46 (134)
Q Consensus 40 C~~C~~~ 46 (134)
|+.||..
T Consensus 2 Cp~CG~~ 8 (23)
T PF13240_consen 2 CPNCGAE 8 (23)
T ss_pred CcccCCC
Confidence 3444443
No 152
>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=74.80 E-value=3.1 Score=18.54 Aligned_cols=21 Identities=24% Similarity=0.570 Sum_probs=9.0
Q ss_pred cCCCCCCcccCCCCcceeeCCCC
Q psy3507 39 HCKTCSTVSHPNISYKYTCYACD 61 (134)
Q Consensus 39 ~C~~C~~~f~~~~~~~~~C~~C~ 61 (134)
.|+.|++...... .|.|..|.
T Consensus 2 ~C~~C~~~~~~~~--~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY--FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE--eEEeCCCC
Confidence 4555554432211 45555544
No 153
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=74.67 E-value=0.19 Score=39.31 Aligned_cols=68 Identities=22% Similarity=0.379 Sum_probs=35.2
Q ss_pred ccceecCcccccccccCCCCccc-----cCCCCCCcccCCCC----------cc-eeeCCCCCccCChHHHHHHHHHhcC
Q psy3507 16 PFTLATCIHCRLLLVPTAEELMY-----HCKTCSTVSHPNIS----------YK-YTCYACDYHTLMSEDMKKHMRKHTG 79 (134)
Q Consensus 16 ~~~~~~C~~C~~h~~~h~~~~~~-----~C~~C~~~f~~~~~----------~~-~~C~~C~~~f~~~~~l~~H~~~h~~ 79 (134)
|-...+|..|..-+..-. ++.| .|..||-+|+--.. .. -.|+.|.+.|.++.+-+- |.
T Consensus 98 ~pD~a~C~~Cl~Ei~dp~-~rrY~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRf----HA- 171 (750)
T COG0068 98 PPDAATCEDCLEEIFDPN-SRRYLYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRF----HA- 171 (750)
T ss_pred CCchhhhHHHHHHhcCCC-CcceeccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCcccccc----cc-
Confidence 344567888855444332 2222 37778877771111 12 236666666655554332 22
Q ss_pred CCceeccccCc
Q psy3507 80 EKPYKCEYCAY 90 (134)
Q Consensus 80 ~~~~~C~~C~~ 90 (134)
+|..|+.||-
T Consensus 172 -Qp~aCp~CGP 181 (750)
T COG0068 172 -QPIACPKCGP 181 (750)
T ss_pred -ccccCcccCC
Confidence 4556666664
No 154
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=74.64 E-value=3.2 Score=19.91 Aligned_cols=7 Identities=29% Similarity=1.279 Sum_probs=2.5
Q ss_pred cCCCCCC
Q psy3507 39 HCKTCST 45 (134)
Q Consensus 39 ~C~~C~~ 45 (134)
+|..|+.
T Consensus 14 ~C~~C~~ 20 (39)
T smart00154 14 KCRHCGN 20 (39)
T ss_pred ECCccCC
Confidence 3333333
No 155
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=74.56 E-value=1.4 Score=25.39 Aligned_cols=30 Identities=17% Similarity=0.392 Sum_probs=19.1
Q ss_pred cccCCCCCCc-ccCCCCcceeeCCCCCccCC
Q psy3507 37 MYHCKTCSTV-SHPNISYKYTCYACDYHTLM 66 (134)
Q Consensus 37 ~~~C~~C~~~-f~~~~~~~~~C~~C~~~f~~ 66 (134)
.|.|+.||+. +.....-.+.|..|++.|..
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 36 KYFCPFCGKHAVKRQAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CccCCCCCCCceeeeeeEEEEcCCCCCEEeC
Confidence 4778888754 22334445778888877654
No 156
>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=73.25 E-value=1.4 Score=25.53 Aligned_cols=30 Identities=20% Similarity=0.419 Sum_probs=18.5
Q ss_pred cccCCCCCCcc-cCCCCcceeeCCCCCccCC
Q psy3507 37 MYHCKTCSTVS-HPNISYKYTCYACDYHTLM 66 (134)
Q Consensus 37 ~~~C~~C~~~f-~~~~~~~~~C~~C~~~f~~ 66 (134)
.|.|+.|++.- .....-.+.|..|++.|..
T Consensus 35 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 35 KYVCPFCGKKTVKRGSTGIWTCRKCGAKFAG 65 (91)
T ss_pred CccCCCCCCCceEEEeeEEEEcCCCCCEEeC
Confidence 47788887542 2333345778888777654
No 157
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=73.17 E-value=1.8 Score=19.65 Aligned_cols=24 Identities=21% Similarity=0.555 Sum_probs=9.5
Q ss_pred CcccccccccCCCCccccCCCCCC
Q psy3507 22 CIHCRLLLVPTAEELMYHCKTCST 45 (134)
Q Consensus 22 C~~C~~h~~~h~~~~~~~C~~C~~ 45 (134)
|+.|+..+....++..-.|+.|+.
T Consensus 6 C~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 6 CGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp -TTT--BEEE-SSSS-EEESSSS-
T ss_pred cCcCCccccCCCCcCEeECCCCcC
Confidence 555555555555555555555554
No 158
>KOG2785|consensus
Probab=73.03 E-value=6.5 Score=28.84 Aligned_cols=26 Identities=35% Similarity=0.507 Sum_probs=22.7
Q ss_pred ceeeCCCCCccCChHHHHHHHHHhcC
Q psy3507 54 KYTCYACDYHTLMSEDMKKHMRKHTG 79 (134)
Q Consensus 54 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 79 (134)
|-.|-.|++.+.+-..-..||..+++
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~Hg 191 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHG 191 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccC
Confidence 46799999999999999999998775
No 159
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=72.89 E-value=2.6 Score=31.36 Aligned_cols=31 Identities=13% Similarity=0.279 Sum_probs=22.8
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCccCChH
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYHTLMSE 68 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~f~~~~ 68 (134)
-.|+.||.+....+..-|+|+.|+..+....
T Consensus 351 p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 351 PVCPRCGGRMKSAGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCCccCCchhhcCCCCcccccccccCCccc
Confidence 4688888877766666788888887776644
No 160
>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=72.87 E-value=2.5 Score=28.56 Aligned_cols=24 Identities=17% Similarity=0.481 Sum_probs=18.2
Q ss_pred CCCeecCcChhhhcCHHHHHHHHH
Q psy3507 108 DKPYICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 108 ~~~~~C~~C~~~F~~~~~l~~H~~ 131 (134)
+..|.|..|+|.|.-..-+++|+.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~ 98 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIF 98 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHh
Confidence 445899999999999888888874
No 161
>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=72.84 E-value=1.9 Score=20.64 Aligned_cols=9 Identities=33% Similarity=1.054 Sum_probs=4.2
Q ss_pred eeeCCCCCc
Q psy3507 55 YTCYACDYH 63 (134)
Q Consensus 55 ~~C~~C~~~ 63 (134)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (39)
T PF01096_consen 29 YVCCNCGHR 37 (39)
T ss_dssp EEESSSTEE
T ss_pred EEeCCCCCe
Confidence 445555443
No 162
>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=72.29 E-value=2 Score=28.95 Aligned_cols=29 Identities=21% Similarity=0.254 Sum_probs=21.5
Q ss_pred CCCcceeeCCCCCccCChHHHHHHHHHhc
Q psy3507 50 NISYKYTCYACDYHTLMSEDMKKHMRKHT 78 (134)
Q Consensus 50 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 78 (134)
..+..|.|..|+|.|........|+..-+
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcC
Confidence 44557999999999999999999987543
No 163
>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=72.11 E-value=2.7 Score=20.57 Aligned_cols=15 Identities=27% Similarity=0.589 Sum_probs=8.3
Q ss_pred ecCcChhhhcCHHHH
Q psy3507 112 ICQQCRDTFSSLYLF 126 (134)
Q Consensus 112 ~C~~C~~~F~~~~~l 126 (134)
.|..||+.|+.+...
T Consensus 10 ~C~~C~rpf~WRKKW 24 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKW 24 (42)
T ss_pred cCcccCCcchHHHHH
Confidence 466666666555433
No 164
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=72.10 E-value=1.2 Score=26.27 Aligned_cols=26 Identities=19% Similarity=0.402 Sum_probs=15.9
Q ss_pred cccCCCCCCcccCC-CCcceeeCCCCC
Q psy3507 37 MYHCKTCSTVSHPN-ISYKYTCYACDY 62 (134)
Q Consensus 37 ~~~C~~C~~~f~~~-~~~~~~C~~C~~ 62 (134)
|+.|..||..|... .+...-|+.||-
T Consensus 2 pH~CtrCG~vf~~g~~~il~GCp~CG~ 28 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEILSGCPKCGC 28 (112)
T ss_pred CceecccccccccccHHHHccCccccc
Confidence 56777777777742 233445777764
No 165
>KOG4173|consensus
Probab=72.02 E-value=1.4 Score=29.47 Aligned_cols=53 Identities=25% Similarity=0.364 Sum_probs=41.2
Q ss_pred eeeCCCCCccCChHHHHHHHH-Hhc---------CCCceecc--ccCccccCchhHHHHh-hhcCC
Q psy3507 55 YTCYACDYHTLMSEDMKKHMR-KHT---------GEKPYKCE--YCAYSCTQSSALKIHE-RKHTG 107 (134)
Q Consensus 55 ~~C~~C~~~f~~~~~l~~H~~-~h~---------~~~~~~C~--~C~~~f~~~~~l~~H~-~~h~~ 107 (134)
-.|..|.+.|.+...|..|+. .|. |.-.|+|- .|+..|.+......|+ ++|.-
T Consensus 107 ~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk~ 172 (253)
T KOG4173|consen 107 NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMHKY 172 (253)
T ss_pred chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhccC
Confidence 389999999999999999976 332 44458884 4999999999999995 45643
No 166
>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=71.89 E-value=3.4 Score=24.52 Aligned_cols=23 Identities=22% Similarity=0.411 Sum_probs=21.0
Q ss_pred eec----CcChhhhcCHHHHHHHHHhc
Q psy3507 111 YIC----QQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 111 ~~C----~~C~~~F~~~~~l~~H~~~H 133 (134)
|.| ..|+....+...+++|++.+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~ 107 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKE 107 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHh
Confidence 899 99999999999999998754
No 167
>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=71.88 E-value=4.8 Score=23.87 Aligned_cols=26 Identities=42% Similarity=0.786 Sum_probs=21.6
Q ss_pred ceee----CCCCCccCChHHHHHHHHHhcC
Q psy3507 54 KYTC----YACDYHTLMSEDMKKHMRKHTG 79 (134)
Q Consensus 54 ~~~C----~~C~~~f~~~~~l~~H~~~h~~ 79 (134)
.|.| ..|+....+...|..|++.+++
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3889 9999999999999999886653
No 168
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=71.40 E-value=2.7 Score=26.11 Aligned_cols=58 Identities=22% Similarity=0.414 Sum_probs=30.8
Q ss_pred CCCccccCCCCCCcccCCC-CcceeeCCCCCccCC--hHHHHHHHHHhcCCCceeccccCccccCchh
Q psy3507 33 AEELMYHCKTCSTVSHPNI-SYKYTCYACDYHTLM--SEDMKKHMRKHTGEKPYKCEYCAYSCTQSSA 97 (134)
Q Consensus 33 ~~~~~~~C~~C~~~f~~~~-~~~~~C~~C~~~f~~--~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~ 97 (134)
.+.+.|+|++|..+..... -+|-+| ||...-. -..|-++-.+| -.||.|..+|.+.+.
T Consensus 76 ~d~~lYeCnIC~etS~ee~FLKPneC--CgY~iCn~Cya~LWK~~~~y-----pvCPvCkTSFKss~~ 136 (140)
T PF05290_consen 76 LDPKLYECNICKETSAEERFLKPNEC--CGYSICNACYANLWKFCNLY-----PVCPVCKTSFKSSSS 136 (140)
T ss_pred cCCCceeccCcccccchhhcCCcccc--cchHHHHHHHHHHHHHcccC-----CCCCccccccccccc
Confidence 3446788888887754111 122222 3432211 23344443333 378999888887653
No 169
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF15269 zf-C2H2_7: Zinc-finger
Probab=71.31 E-value=3.3 Score=20.51 Aligned_cols=21 Identities=29% Similarity=0.442 Sum_probs=14.7
Q ss_pred eecCcChhhhcCHHHHHHHHH
Q psy3507 111 YICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 111 ~~C~~C~~~F~~~~~l~~H~~ 131 (134)
|+|-+|..+....+.|-+||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 667777777777777777764
No 171
>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=70.96 E-value=3.6 Score=21.09 Aligned_cols=26 Identities=15% Similarity=0.300 Sum_probs=12.9
Q ss_pred CCCCCCcccCCCCcceeeCCCCCccCC
Q psy3507 40 CKTCSTVSHPNISYKYTCYACDYHTLM 66 (134)
Q Consensus 40 C~~C~~~f~~~~~~~~~C~~C~~~f~~ 66 (134)
|..|++.|.. ..+.+.|..||..|-.
T Consensus 5 C~~C~~~F~~-~~rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 5 CMGCGKPFTL-TRRRHHCRNCGRIFCS 30 (57)
T ss_pred CcccCccccC-CccccccCcCcCCcCh
Confidence 5555555553 2234555555555433
No 172
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=70.19 E-value=2.7 Score=25.28 Aligned_cols=25 Identities=24% Similarity=0.385 Sum_probs=14.0
Q ss_pred cccCCCCCCcccCCCCcceeeCCCCC
Q psy3507 37 MYHCKTCSTVSHPNISYKYTCYACDY 62 (134)
Q Consensus 37 ~~~C~~C~~~f~~~~~~~~~C~~C~~ 62 (134)
...|..||..|.... ..+.|+.||.
T Consensus 70 ~~~C~~Cg~~~~~~~-~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ-HDAQCPHCHG 94 (113)
T ss_pred EEEcccCCCEEecCC-cCccCcCCCC
Confidence 366777776665432 2345666663
No 173
>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=69.98 E-value=2.6 Score=29.24 Aligned_cols=96 Identities=21% Similarity=0.464 Sum_probs=57.2
Q ss_pred ccccccCCccceecCcccccccccCCCCccccCCCCCCcc------c------CCCCcceeeCCCCCccCChHHH-----
Q psy3507 8 TASIGLKNPFTLATCIHCRLLLVPTAEELMYHCKTCSTVS------H------PNISYKYTCYACDYHTLMSEDM----- 70 (134)
Q Consensus 8 ~~~~~~~~~~~~~~C~~C~~h~~~h~~~~~~~C~~C~~~f------~------~~~~~~~~C~~C~~~f~~~~~l----- 70 (134)
..+-.-.-|+....|..|.+-.-.| +.+.|+|..|..-. . .-....|+|..|++.-.. +-|
T Consensus 114 l~~HaC~Cpl~da~C~EC~R~vw~h-GGrif~CsfC~~flCEDDQFEHQAsCQvLe~E~~KC~SCNrlGq~-sCLRCK~c 191 (314)
T PF06524_consen 114 LSTHACTCPLQDAVCIECERGVWDH-GGRIFKCSFCDNFLCEDDQFEHQASCQVLESETFKCQSCNRLGQY-SCLRCKIC 191 (314)
T ss_pred cccccccCcCCCcEeeeeecccccC-CCeEEEeecCCCeeeccchhhhhhhhhhhhcccccccccccccch-hhhheeee
Confidence 3344444567777777775544444 45679999987532 2 122345777777764322 222
Q ss_pred --HHHHHH----hcCCCceeccccCccccCchhHHHHhhhc
Q psy3507 71 --KKHMRK----HTGEKPYKCEYCAYSCTQSSALKIHERKH 105 (134)
Q Consensus 71 --~~H~~~----h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 105 (134)
..|.+. -...+++.|+.|+........|..-.|+|
T Consensus 192 fCddHvrrKg~ky~k~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 192 FCDDHVRRKGFKYEKGKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred ehhhhhhhcccccccCCCCCCCCCCCcccccccceeeeecc
Confidence 334442 22347899999998777777776655555
No 174
>KOG2593|consensus
Probab=69.96 E-value=6.1 Score=29.44 Aligned_cols=35 Identities=23% Similarity=0.485 Sum_probs=19.6
Q ss_pred CCceeccccCccccCchhHHHHhhhcCCCCCeecCcCh
Q psy3507 80 EKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCR 117 (134)
Q Consensus 80 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~ 117 (134)
..-|.|+.|.+.|.....++ ..-...-.|.|..|+
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCG 160 (436)
T ss_pred cccccCCccccchhhhHHHH---hhcccCceEEEecCC
Confidence 34577777777776644332 222222357777775
No 175
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=69.78 E-value=5.4 Score=19.16 Aligned_cols=16 Identities=13% Similarity=0.281 Sum_probs=6.7
Q ss_pred eeeCCCCCccCChHHH
Q psy3507 55 YTCYACDYHTLMSEDM 70 (134)
Q Consensus 55 ~~C~~C~~~f~~~~~l 70 (134)
..|+.|+-.+.....|
T Consensus 20 d~C~~C~G~W~d~~el 35 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGEL 35 (41)
T ss_pred EECCCCCeEEccHHHH
Confidence 3344444444444333
No 176
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=69.20 E-value=1.8 Score=24.96 Aligned_cols=30 Identities=13% Similarity=0.213 Sum_probs=18.5
Q ss_pred cccCCCCCCc-ccCCCCcceeeCCCCCccCC
Q psy3507 37 MYHCKTCSTV-SHPNISYKYTCYACDYHTLM 66 (134)
Q Consensus 37 ~~~C~~C~~~-f~~~~~~~~~C~~C~~~f~~ 66 (134)
.|.|+.|++. +.....-.+.|..|++.|..
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 36 KHVCPVCGRPKVKRVGTGIWECRKCGAKFAG 66 (90)
T ss_pred CccCCCCCCCceEEEEEEEEEcCCCCCEEeC
Confidence 4778888654 22333445778888777654
No 177
>KOG4167|consensus
Probab=69.20 E-value=0.95 Score=35.77 Aligned_cols=27 Identities=19% Similarity=0.386 Sum_probs=24.0
Q ss_pred cceeeCCCCCccCChHHHHHHHHHhcC
Q psy3507 53 YKYTCYACDYHTLMSEDMKKHMRKHTG 79 (134)
Q Consensus 53 ~~~~C~~C~~~f~~~~~l~~H~~~h~~ 79 (134)
..|.|..|++.|.....+..||++|.-
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 359999999999999999999999863
No 178
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=68.60 E-value=6 Score=33.61 Aligned_cols=21 Identities=29% Similarity=0.738 Sum_probs=10.6
Q ss_pred cCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 39 HCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 39 ~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
.|+.||... +..|.|+.|+..
T Consensus 681 fCP~CGs~t----e~vy~CPsCGae 701 (1337)
T PRK14714 681 RCPDCGTHT----EPVYVCPDCGAE 701 (1337)
T ss_pred cCcccCCcC----CCceeCccCCCc
Confidence 466666542 123456666553
No 179
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=68.27 E-value=7.2 Score=18.85 Aligned_cols=24 Identities=33% Similarity=0.441 Sum_probs=15.7
Q ss_pred eeeCCCCCccCC--hHHHHHHHHHhc
Q psy3507 55 YTCYACDYHTLM--SEDMKKHMRKHT 78 (134)
Q Consensus 55 ~~C~~C~~~f~~--~~~l~~H~~~h~ 78 (134)
-.|+.||..|.. .++-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 467777776644 466677777663
No 180
>KOG2807|consensus
Probab=68.15 E-value=8 Score=27.87 Aligned_cols=25 Identities=32% Similarity=0.582 Sum_probs=18.6
Q ss_pred CceeccccCccccCchhHHHHhhhc
Q psy3507 81 KPYKCEYCAYSCTQSSALKIHERKH 105 (134)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~~h 105 (134)
..|.|..|...|...-+...|...|
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhh
Confidence 4488888888888877777775554
No 181
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=68.06 E-value=5.1 Score=20.79 Aligned_cols=25 Identities=16% Similarity=0.388 Sum_probs=12.6
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
-.|+.||+.|..... .-.|+.|+..
T Consensus 6 ~~C~~Cg~~~~~~dD-iVvCp~Cgap 30 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDD-IVVCPECGAP 30 (54)
T ss_pred ccChhhCCcccCCCC-EEECCCCCCc
Confidence 346666666543332 2456666544
No 182
>KOG2593|consensus
Probab=67.03 E-value=4.1 Score=30.30 Aligned_cols=31 Identities=19% Similarity=0.435 Sum_probs=20.5
Q ss_pred CCCccccCCCCCCccc--------CCCCcceeeCCCCCc
Q psy3507 33 AEELMYHCKTCSTVSH--------PNISYKYTCYACDYH 63 (134)
Q Consensus 33 ~~~~~~~C~~C~~~f~--------~~~~~~~~C~~C~~~ 63 (134)
+....|.|+.|++.|. ......|.|..|+-.
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGE 162 (436)
T ss_pred cccccccCCccccchhhhHHHHhhcccCceEEEecCCCc
Confidence 3445588888888877 333446788888744
No 183
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=66.75 E-value=5.3 Score=18.57 Aligned_cols=7 Identities=43% Similarity=1.065 Sum_probs=3.0
Q ss_pred eeeCCCC
Q psy3507 55 YTCYACD 61 (134)
Q Consensus 55 ~~C~~C~ 61 (134)
+.|+.|+
T Consensus 23 ~vC~~Cg 29 (34)
T PF14803_consen 23 LVCPACG 29 (34)
T ss_dssp EEETTTT
T ss_pred eECCCCC
Confidence 4444444
No 184
>PRK04023 DNA polymerase II large subunit; Validated
Probab=66.69 E-value=7 Score=32.46 Aligned_cols=9 Identities=22% Similarity=0.582 Sum_probs=5.3
Q ss_pred eeeCCCCCc
Q psy3507 55 YTCYACDYH 63 (134)
Q Consensus 55 ~~C~~C~~~ 63 (134)
+.|+.|+..
T Consensus 664 y~CPKCG~E 672 (1121)
T PRK04023 664 DECEKCGRE 672 (1121)
T ss_pred CcCCCCCCC
Confidence 556666644
No 185
>KOG3507|consensus
Probab=66.51 E-value=4.9 Score=21.16 Aligned_cols=27 Identities=22% Similarity=0.616 Sum_probs=13.4
Q ss_pred cccCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 37 MYHCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 37 ~~~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
.|.|.+||..-.-...-.+.|..||..
T Consensus 20 iYiCgdC~~en~lk~~D~irCReCG~R 46 (62)
T KOG3507|consen 20 IYICGDCGQENTLKRGDVIRCRECGYR 46 (62)
T ss_pred EEEeccccccccccCCCcEehhhcchH
Confidence 355555555443333334556666543
No 186
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=65.93 E-value=5.5 Score=20.04 Aligned_cols=26 Identities=19% Similarity=0.365 Sum_probs=11.1
Q ss_pred cccCCCCCCcccCCCCcceeeCCCCC
Q psy3507 37 MYHCKTCSTVSHPNISYKYTCYACDY 62 (134)
Q Consensus 37 ~~~C~~C~~~f~~~~~~~~~C~~C~~ 62 (134)
+-.|..|++.........+.|..|+.
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~~C~~ 36 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCSWCGL 36 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEETTTT-
T ss_pred CCCCcccCcccCCCCCCeEEECCCCC
Confidence 34455555544223333455555543
No 187
>KOG3408|consensus
Probab=65.63 E-value=6 Score=24.17 Aligned_cols=23 Identities=13% Similarity=0.525 Sum_probs=19.0
Q ss_pred CeecCcChhhhcCHHHHHHHHHh
Q psy3507 110 PYICQQCRDTFSSLYLFRNRLQS 132 (134)
Q Consensus 110 ~~~C~~C~~~F~~~~~l~~H~~~ 132 (134)
.|.|-.|.+-|.+...|..|.++
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhc
Confidence 48888888888888888888764
No 188
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=65.56 E-value=1.6 Score=34.52 Aligned_cols=75 Identities=17% Similarity=0.459 Sum_probs=50.0
Q ss_pred ccCCCCCCcccCCCCcc----e-eeCCCCCccCChHHHHHHHHHhcCCCce-eccccCccccCchhHHHHhhhcCCCCCe
Q psy3507 38 YHCKTCSTVSHPNISYK----Y-TCYACDYHTLMSEDMKKHMRKHTGEKPY-KCEYCAYSCTQSSALKIHERKHTGDKPY 111 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~----~-~C~~C~~~f~~~~~l~~H~~~h~~~~~~-~C~~C~~~f~~~~~l~~H~~~h~~~~~~ 111 (134)
=.|+.|-+.+..+.++. | .|..||-.|+....|-.-.. ++.-..| -|+.|.+.|..+.+-+-| ..|.
T Consensus 102 a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYDR~-nTsM~~F~lC~~C~~EY~dP~nRRfH------AQp~ 174 (750)
T COG0068 102 ATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYDRE-NTSMADFPLCPFCDKEYKDPLNRRFH------AQPI 174 (750)
T ss_pred hhhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCCcc-cCccccCcCCHHHHHHhcCccccccc------cccc
Confidence 46888876665444443 2 49999999988777654322 2222223 599999998888765544 3478
Q ss_pred ecCcChhh
Q psy3507 112 ICQQCRDT 119 (134)
Q Consensus 112 ~C~~C~~~ 119 (134)
.|+.||-.
T Consensus 175 aCp~CGP~ 182 (750)
T COG0068 175 ACPKCGPH 182 (750)
T ss_pred cCcccCCC
Confidence 99999863
No 189
>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=65.24 E-value=4.4 Score=25.63 Aligned_cols=14 Identities=21% Similarity=0.384 Sum_probs=7.3
Q ss_pred eeeCCCCCccCChH
Q psy3507 55 YTCYACDYHTLMSE 68 (134)
Q Consensus 55 ~~C~~C~~~f~~~~ 68 (134)
-.|..|++.|.+..
T Consensus 29 ReC~~C~~RFTTyE 42 (147)
T TIGR00244 29 RECLECHERFTTFE 42 (147)
T ss_pred ccCCccCCccceee
Confidence 45555555555543
No 190
>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=64.43 E-value=2.2 Score=18.97 Aligned_cols=10 Identities=20% Similarity=0.713 Sum_probs=5.9
Q ss_pred eeccccCccc
Q psy3507 83 YKCEYCAYSC 92 (134)
Q Consensus 83 ~~C~~C~~~f 92 (134)
|.|-.|++.|
T Consensus 1 ~sCiDC~~~F 10 (28)
T PF08790_consen 1 FSCIDCSKDF 10 (28)
T ss_dssp EEETTTTEEE
T ss_pred CeeecCCCCc
Confidence 3456666666
No 191
>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=63.94 E-value=6.3 Score=18.88 Aligned_cols=7 Identities=29% Similarity=1.089 Sum_probs=2.4
Q ss_pred eeeCCCC
Q psy3507 55 YTCYACD 61 (134)
Q Consensus 55 ~~C~~C~ 61 (134)
+.|..|+
T Consensus 25 w~C~~C~ 31 (40)
T PF04810_consen 25 WICNFCG 31 (40)
T ss_dssp EEETTT-
T ss_pred EECcCCC
Confidence 3444443
No 192
>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=63.23 E-value=4.8 Score=24.31 Aligned_cols=25 Identities=32% Similarity=0.696 Sum_probs=13.5
Q ss_pred cccCCCCCCcccCCCCcceeeCCCCC
Q psy3507 37 MYHCKTCSTVSHPNISYKYTCYACDY 62 (134)
Q Consensus 37 ~~~C~~C~~~f~~~~~~~~~C~~C~~ 62 (134)
...|..||..|.... ..+.|+.|+.
T Consensus 70 ~~~C~~Cg~~~~~~~-~~~~CP~Cgs 94 (115)
T TIGR00100 70 ECECEDCSEEVSPEI-DLYRCPKCHG 94 (115)
T ss_pred EEEcccCCCEEecCC-cCccCcCCcC
Confidence 356666666655332 2355666664
No 193
>PF15616 TerY-C: TerY-C metal binding domain
Probab=63.06 E-value=6.9 Score=24.31 Aligned_cols=15 Identities=20% Similarity=0.208 Sum_probs=7.3
Q ss_pred CCCCcceeeCCCCCc
Q psy3507 49 PNISYKYTCYACDYH 63 (134)
Q Consensus 49 ~~~~~~~~C~~C~~~ 63 (134)
..++....|+.|++.
T Consensus 100 i~g~~~~~CPwCg~~ 114 (131)
T PF15616_consen 100 IDGEGEVTCPWCGNE 114 (131)
T ss_pred eCCCCCEECCCCCCe
Confidence 334444555555543
No 194
>PRK00420 hypothetical protein; Validated
Probab=62.99 E-value=7.5 Score=23.47 Aligned_cols=28 Identities=14% Similarity=0.198 Sum_probs=17.5
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCccC
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYHTL 65 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~f~ 65 (134)
-.|+.||..+..-......|+.||....
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeee
Confidence 4578888665532334567888887544
No 195
>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=62.93 E-value=1.2 Score=22.78 Aligned_cols=15 Identities=33% Similarity=0.738 Sum_probs=4.1
Q ss_pred eeeCCCCCccCChHH
Q psy3507 55 YTCYACDYHTLMSED 69 (134)
Q Consensus 55 ~~C~~C~~~f~~~~~ 69 (134)
|.|+.|...|-..-+
T Consensus 22 y~C~~C~~~FC~dCD 36 (51)
T PF07975_consen 22 YRCPKCKNHFCIDCD 36 (51)
T ss_dssp E--TTTT--B-HHHH
T ss_pred EECCCCCCccccCcC
Confidence 444444444433333
No 196
>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=62.31 E-value=6.2 Score=18.38 Aligned_cols=10 Identities=20% Similarity=0.620 Sum_probs=4.0
Q ss_pred cCCCCCCccc
Q psy3507 39 HCKTCSTVSH 48 (134)
Q Consensus 39 ~C~~C~~~f~ 48 (134)
.|..|++.|.
T Consensus 5 ~C~eC~~~f~ 14 (34)
T PF01286_consen 5 KCDECGKPFM 14 (34)
T ss_dssp E-TTT--EES
T ss_pred hHhHhCCHHH
Confidence 4566666655
No 197
>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=61.59 E-value=7 Score=24.75 Aligned_cols=27 Identities=15% Similarity=0.347 Sum_probs=16.7
Q ss_pred cccCCCCCCccc--CCCCcceeeCCCCCcc
Q psy3507 37 MYHCKTCSTVSH--PNISYKYTCYACDYHT 64 (134)
Q Consensus 37 ~~~C~~C~~~f~--~~~~~~~~C~~C~~~f 64 (134)
.|.|..||.... ++ ...-+|+.|+...
T Consensus 112 ~l~C~~Cg~~~~~~~~-~~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 112 TLVCENCGHEVELTHP-ERLPPCPKCGHTE 140 (146)
T ss_pred eEecccCCCEEEecCC-CcCCCCCCCCCCe
Confidence 477888876544 33 3345688877643
No 198
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.37 E-value=1.9 Score=23.97 Aligned_cols=8 Identities=38% Similarity=1.144 Sum_probs=3.6
Q ss_pred eeeCCCCC
Q psy3507 55 YTCYACDY 62 (134)
Q Consensus 55 ~~C~~C~~ 62 (134)
|+|..|+.
T Consensus 13 Y~c~~cg~ 20 (82)
T COG2331 13 YECTECGN 20 (82)
T ss_pred Eeecccch
Confidence 44444443
No 199
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=61.25 E-value=5.9 Score=20.86 Aligned_cols=11 Identities=36% Similarity=0.875 Sum_probs=4.9
Q ss_pred CCCceeccccC
Q psy3507 79 GEKPYKCEYCA 89 (134)
Q Consensus 79 ~~~~~~C~~C~ 89 (134)
|+..-.|+.|.
T Consensus 41 GE~VArCPSCS 51 (67)
T COG5216 41 GEVVARCPSCS 51 (67)
T ss_pred CceEEEcCCce
Confidence 44444444443
No 200
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=61.06 E-value=6.2 Score=23.25 Aligned_cols=30 Identities=13% Similarity=0.265 Sum_probs=14.6
Q ss_pred CccccCCCCCCccc-------CCCCcceeeCCCCCcc
Q psy3507 35 ELMYHCKTCSTVSH-------PNISYKYTCYACDYHT 64 (134)
Q Consensus 35 ~~~~~C~~C~~~f~-------~~~~~~~~C~~C~~~f 64 (134)
++.|.|+.||..-. ....-.-.|..||.+|
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSF 56 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcceE
Confidence 34466666665432 1111234566666554
No 201
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=60.75 E-value=11 Score=19.56 Aligned_cols=30 Identities=23% Similarity=0.393 Sum_probs=16.6
Q ss_pred ccceecCcccccccc----cCCCCccccCCCCCC
Q psy3507 16 PFTLATCIHCRLLLV----PTAEELMYHCKTCST 45 (134)
Q Consensus 16 ~~~~~~C~~C~~h~~----~h~~~~~~~C~~C~~ 45 (134)
.....+|..|..|-= .-.....|.|..||.
T Consensus 19 ~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 19 NRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred CceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 344567888855422 222334577777764
No 202
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=60.73 E-value=5.4 Score=25.37 Aligned_cols=10 Identities=20% Similarity=0.547 Sum_probs=5.0
Q ss_pred cCCCCCCccc
Q psy3507 39 HCKTCSTVSH 48 (134)
Q Consensus 39 ~C~~C~~~f~ 48 (134)
.|+.||..|.
T Consensus 30 eC~~C~~RFT 39 (156)
T COG1327 30 ECLECGERFT 39 (156)
T ss_pred cccccccccc
Confidence 4555555554
No 203
>PF12773 DZR: Double zinc ribbon
Probab=59.76 E-value=15 Score=18.20 Aligned_cols=9 Identities=22% Similarity=0.656 Sum_probs=4.2
Q ss_pred ccCCCCCCc
Q psy3507 38 YHCKTCSTV 46 (134)
Q Consensus 38 ~~C~~C~~~ 46 (134)
..|+.||..
T Consensus 30 ~~C~~Cg~~ 38 (50)
T PF12773_consen 30 KICPNCGAE 38 (50)
T ss_pred CCCcCCcCC
Confidence 445555543
No 204
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=59.73 E-value=5.9 Score=29.53 Aligned_cols=28 Identities=21% Similarity=0.571 Sum_probs=24.1
Q ss_pred cCcccccccccCCCCccccCCCCCCcccC
Q psy3507 21 TCIHCRLLLVPTAEELMYHCKTCSTVSHP 49 (134)
Q Consensus 21 ~C~~C~~h~~~h~~~~~~~C~~C~~~f~~ 49 (134)
.|+.|+..|.+-... -|.|+.||..+..
T Consensus 352 ~Cp~Cg~~m~S~G~~-g~rC~kCg~~~~~ 379 (421)
T COG1571 352 VCPRCGGRMKSAGRN-GFRCKKCGTRARE 379 (421)
T ss_pred CCCccCCchhhcCCC-CcccccccccCCc
Confidence 799999988887665 8999999999873
No 205
>PF03563 Bunya_G2: Bunyavirus glycoprotein G2; InterPro: IPR005168 Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This entry represents the polyprotein region forming the G2 glycoprotein, which interacts with the IPR005167 from INTERPRO G1 glycoprotein [].
Probab=59.43 E-value=12 Score=26.15 Aligned_cols=36 Identities=31% Similarity=0.602 Sum_probs=23.8
Q ss_pred cCCCCCCcccCCCCcceeeCCCCCccCChHHHHHHHH
Q psy3507 39 HCKTCSTVSHPNISYKYTCYACDYHTLMSEDMKKHMR 75 (134)
Q Consensus 39 ~C~~C~~~f~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 75 (134)
+|.-||..+.+-..=+-.| +||..|.+.+.|+.|..
T Consensus 236 ~C~nC~La~HPFtnC~s~C-vCG~~f~~sd~mk~HR~ 271 (285)
T PF03563_consen 236 KCKNCGLAYHPFTNCGSHC-VCGMKFETSDRMKMHRE 271 (285)
T ss_pred hCcccCeeccCCCCCCCee-eccccccchHHHHHHHh
Confidence 4677777665433333344 68888888888887754
No 206
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=59.34 E-value=7.2 Score=24.12 Aligned_cols=11 Identities=36% Similarity=1.056 Sum_probs=5.3
Q ss_pred ccCCCCCCccc
Q psy3507 38 YHCKTCSTVSH 48 (134)
Q Consensus 38 ~~C~~C~~~f~ 48 (134)
|.|..|++.|.
T Consensus 54 yrC~~C~~tf~ 64 (129)
T COG3677 54 YKCKSCGSTFT 64 (129)
T ss_pred cccCCcCccee
Confidence 44444444444
No 207
>PRK12722 transcriptional activator FlhC; Provisional
Probab=59.04 E-value=7 Score=25.83 Aligned_cols=27 Identities=26% Similarity=0.607 Sum_probs=12.2
Q ss_pred ceecCcccccccccCCCCc--cccCCCCC
Q psy3507 18 TLATCIHCRLLLVPTAEEL--MYHCKTCS 44 (134)
Q Consensus 18 ~~~~C~~C~~h~~~h~~~~--~~~C~~C~ 44 (134)
+...|..|+-+..+|..+. .|.|+.|.
T Consensus 133 ~l~~C~~Cgg~fv~~~~e~~~~f~CplC~ 161 (187)
T PRK12722 133 QLSSCNCCGGHFVTHAHDPVGSFVCGLCQ 161 (187)
T ss_pred eeccCCCCCCCeeccccccCCCCcCCCCC
Confidence 3344555544444444332 34444444
No 208
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=58.83 E-value=6.4 Score=25.07 Aligned_cols=34 Identities=26% Similarity=0.763 Sum_probs=19.7
Q ss_pred CceeccccCccccCchhHHHHhhhcCCCCCeecCcChhh
Q psy3507 81 KPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDT 119 (134)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 119 (134)
-+|.|. |+..|.+. +.|-..-.|+ .|.|..|+..
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 357777 77765553 3333334444 6777777653
No 209
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=58.29 E-value=9.5 Score=26.40 Aligned_cols=49 Identities=12% Similarity=0.223 Sum_probs=28.8
Q ss_pred eecCcccccc--cccCCCCccccCCCCCCccc------CCCCcceeeCCCCCccCCh
Q psy3507 19 LATCIHCRLL--LVPTAEELMYHCKTCSTVSH------PNISYKYTCYACDYHTLMS 67 (134)
Q Consensus 19 ~~~C~~C~~h--~~~h~~~~~~~C~~C~~~f~------~~~~~~~~C~~C~~~f~~~ 67 (134)
.+-|..|..- .+.-..+..-.|..|.+.|. -.|.--|.|+.|+..|...
T Consensus 112 qFaC~~Cd~~WwRrvp~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 112 QFACSSCDHMWWRRVPQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred eeeccccchHHHhccCcccccccccccccccCCCccccccceeeeecccccccchhh
Confidence 3556666221 23333344466788888776 2222348888888888754
No 210
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=57.84 E-value=9.4 Score=19.39 Aligned_cols=9 Identities=33% Similarity=1.254 Sum_probs=4.0
Q ss_pred ceeeCCCCC
Q psy3507 54 KYTCYACDY 62 (134)
Q Consensus 54 ~~~C~~C~~ 62 (134)
.+.|..|+.
T Consensus 37 R~~CGkCgy 45 (51)
T COG1998 37 RWACGKCGY 45 (51)
T ss_pred eeEeccccc
Confidence 344444443
No 211
>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=57.80 E-value=3.2 Score=22.62 Aligned_cols=27 Identities=19% Similarity=0.470 Sum_probs=13.0
Q ss_pred ecCcccccccccCCCCccccCCCCCCccc
Q psy3507 20 ATCIHCRLLLVPTAEELMYHCKTCSTVSH 48 (134)
Q Consensus 20 ~~C~~C~~h~~~h~~~~~~~C~~C~~~f~ 48 (134)
+.| .|++++-...+.+.-+| .||+...
T Consensus 4 frC-~Cgr~lya~e~~kTkkC-~CG~~l~ 30 (68)
T PF09082_consen 4 FRC-DCGRYLYAKEGAKTKKC-VCGKTLK 30 (68)
T ss_dssp EEE-TTS--EEEETT-SEEEE-TTTEEEE
T ss_pred EEe-cCCCEEEecCCcceeEe-cCCCeee
Confidence 445 35555555555555556 6665543
No 212
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=57.75 E-value=9.2 Score=17.34 Aligned_cols=23 Identities=30% Similarity=0.626 Sum_probs=12.0
Q ss_pred CcccccccccCCCCccccCCCCC
Q psy3507 22 CIHCRLLLVPTAEELMYHCKTCS 44 (134)
Q Consensus 22 C~~C~~h~~~h~~~~~~~C~~C~ 44 (134)
|+.|+.-+..-.+...+.|..|.
T Consensus 4 C~~C~t~L~yP~gA~~vrCs~C~ 26 (31)
T TIGR01053 4 CGGCRTLLMYPRGASSVRCALCQ 26 (31)
T ss_pred cCCCCcEeecCCCCCeEECCCCC
Confidence 44554444444555555555554
No 213
>PRK12496 hypothetical protein; Provisional
Probab=56.73 E-value=8.4 Score=24.86 Aligned_cols=26 Identities=19% Similarity=0.414 Sum_probs=16.5
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCcc
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYHT 64 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~f 64 (134)
|.|.-|++.|....+ .-.|+.||...
T Consensus 128 ~~C~gC~~~~~~~~~-~~~C~~CG~~~ 153 (164)
T PRK12496 128 KVCKGCKKKYPEDYP-DDVCEICGSPV 153 (164)
T ss_pred EECCCCCccccCCCC-CCcCCCCCChh
Confidence 778888888753222 13588888543
No 214
>PRK04351 hypothetical protein; Provisional
Probab=56.64 E-value=9.4 Score=24.25 Aligned_cols=33 Identities=27% Similarity=0.596 Sum_probs=19.4
Q ss_pred ceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccC
Q psy3507 54 KYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQ 94 (134)
Q Consensus 54 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 94 (134)
.|.|..|+..+... +.+ +...|.|..|+..+..
T Consensus 112 ~Y~C~~Cg~~~~r~-------Rr~-n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 112 LYECQSCGQQYLRK-------RRI-NTKRYRCGKCRGKLKL 144 (149)
T ss_pred EEECCCCCCEeeee-------eec-CCCcEEeCCCCcEeee
Confidence 47787787655432 112 3355888888765543
No 215
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=56.15 E-value=10 Score=19.79 Aligned_cols=11 Identities=18% Similarity=0.685 Sum_probs=5.8
Q ss_pred cceeeCCCCCc
Q psy3507 53 YKYTCYACDYH 63 (134)
Q Consensus 53 ~~~~C~~C~~~ 63 (134)
..|.|+.||..
T Consensus 13 v~~~Cp~cGip 23 (55)
T PF13824_consen 13 VNFECPDCGIP 23 (55)
T ss_pred cCCcCCCCCCc
Confidence 34555555543
No 216
>KOG2071|consensus
Probab=56.09 E-value=6.9 Score=30.35 Aligned_cols=26 Identities=23% Similarity=0.448 Sum_probs=22.5
Q ss_pred CCCeecCcChhhhcCHHHHHHHHHhc
Q psy3507 108 DKPYICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 108 ~~~~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
..|-+|..||.+|........||..|
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhh
Confidence 56789999999999999888888877
No 217
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=55.95 E-value=13 Score=18.38 Aligned_cols=11 Identities=27% Similarity=0.788 Sum_probs=4.8
Q ss_pred cccCCCCCCcc
Q psy3507 37 MYHCKTCSTVS 47 (134)
Q Consensus 37 ~~~C~~C~~~f 47 (134)
...|+.|+..|
T Consensus 14 ~i~C~~C~~~~ 24 (51)
T PF00628_consen 14 MIQCDSCNRWY 24 (51)
T ss_dssp EEEBSTTSCEE
T ss_pred eEEcCCCChhh
Confidence 34444444443
No 218
>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 PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=54.86 E-value=7.2 Score=23.90 Aligned_cols=9 Identities=22% Similarity=0.726 Sum_probs=4.0
Q ss_pred ccCCCCCCcc
Q psy3507 38 YHCKTCSTVS 47 (134)
Q Consensus 38 ~~C~~C~~~f 47 (134)
..| .||..|
T Consensus 71 ~~C-~Cg~~~ 79 (124)
T PRK00762 71 IEC-ECGYEG 79 (124)
T ss_pred EEe-eCcCcc
Confidence 444 444443
No 220
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=54.43 E-value=19 Score=17.36 Aligned_cols=8 Identities=38% Similarity=0.986 Sum_probs=3.8
Q ss_pred ceeccccC
Q psy3507 82 PYKCEYCA 89 (134)
Q Consensus 82 ~~~C~~C~ 89 (134)
...|++|+
T Consensus 36 ~~~CP~C~ 43 (44)
T PF14634_consen 36 SVKCPICR 43 (44)
T ss_pred CCCCcCCC
Confidence 34555553
No 221
>KOG0717|consensus
Probab=53.71 E-value=8.1 Score=29.19 Aligned_cols=21 Identities=24% Similarity=0.499 Sum_probs=17.7
Q ss_pred eecCcChhhhcCHHHHHHHHH
Q psy3507 111 YICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 111 ~~C~~C~~~F~~~~~l~~H~~ 131 (134)
+.|..|.+.|.+...|.+|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 778889999999888888864
No 222
>PRK12860 transcriptional activator FlhC; Provisional
Probab=52.56 E-value=10 Score=25.09 Aligned_cols=28 Identities=32% Similarity=0.710 Sum_probs=14.4
Q ss_pred cceecCcccccccccCCCCc--cccCCCCC
Q psy3507 17 FTLATCIHCRLLLVPTAEEL--MYHCKTCS 44 (134)
Q Consensus 17 ~~~~~C~~C~~h~~~h~~~~--~~~C~~C~ 44 (134)
++...|..|+-+..+|..+. .|.|+.|.
T Consensus 132 L~l~~C~~Cgg~fv~~~~e~~~~f~CplC~ 161 (189)
T PRK12860 132 LQLARCCRCGGKFVTHAHDLRHNFVCGLCQ 161 (189)
T ss_pred eeeccCCCCCCCeeccccccCCCCcCCCCC
Confidence 44455555655555554432 45555554
No 223
>PRK11032 hypothetical protein; Provisional
Probab=52.44 E-value=10 Score=24.41 Aligned_cols=26 Identities=15% Similarity=0.285 Sum_probs=11.9
Q ss_pred ccCCCCCCccc-CCCCcceeeCCCCCc
Q psy3507 38 YHCKTCSTVSH-PNISYKYTCYACDYH 63 (134)
Q Consensus 38 ~~C~~C~~~f~-~~~~~~~~C~~C~~~ 63 (134)
..|..||.... ......-.|+.|+..
T Consensus 125 LvC~~Cg~~~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 125 LVCEKCHHHLAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred EEecCCCCEEEecCCCcCCCCCCCCCC
Confidence 55666664433 111223356666543
No 224
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=52.39 E-value=11 Score=18.45 Aligned_cols=22 Identities=18% Similarity=0.475 Sum_probs=8.6
Q ss_pred CCCCCCcccCCCCcceeeCCCC
Q psy3507 40 CKTCSTVSHPNISYKYTCYACD 61 (134)
Q Consensus 40 C~~C~~~f~~~~~~~~~C~~C~ 61 (134)
|..|++.+.......+.|..|+
T Consensus 14 C~~C~~~i~~~~~~~~~C~~C~ 35 (50)
T cd00029 14 CDVCRKSIWGLFKQGLRCSWCK 35 (50)
T ss_pred hhhcchhhhccccceeEcCCCC
Confidence 4444444332222334444443
No 225
>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=51.78 E-value=4.3 Score=19.77 Aligned_cols=13 Identities=31% Similarity=1.083 Sum_probs=7.4
Q ss_pred CCeecCcChhhhc
Q psy3507 109 KPYICQQCRDTFS 121 (134)
Q Consensus 109 ~~~~C~~C~~~F~ 121 (134)
.|+.|..|++.|=
T Consensus 12 ~~~~C~~C~~~FC 24 (43)
T PF01428_consen 12 LPFKCKHCGKSFC 24 (43)
T ss_dssp SHEE-TTTS-EE-
T ss_pred CCeECCCCCcccC
Confidence 3678888887774
No 226
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=51.78 E-value=3.7 Score=24.85 Aligned_cols=24 Identities=21% Similarity=0.467 Sum_probs=10.7
Q ss_pred ccCCCCCCcccCCCCcceeeCCCC
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACD 61 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~ 61 (134)
..|..|+..|..-....-.|..|.
T Consensus 55 ~~C~~C~~~fg~l~~~~~~C~~C~ 78 (118)
T PF02318_consen 55 RHCARCGKPFGFLFNRGRVCVDCK 78 (118)
T ss_dssp SB-TTTS-BCSCTSTTCEEETTTT
T ss_pred cchhhhCCcccccCCCCCcCCcCC
Confidence 345666655554333334455444
No 227
>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=51.50 E-value=18 Score=22.79 Aligned_cols=17 Identities=18% Similarity=0.333 Sum_probs=9.6
Q ss_pred ceeccccCccccCchhH
Q psy3507 82 PYKCEYCAYSCTQSSAL 98 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l 98 (134)
-+.|+.|++.|-..+..
T Consensus 124 f~~C~~C~kiyW~GsH~ 140 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGSHW 140 (147)
T ss_pred EEECCCCCCEecccccH
Confidence 35666666666554433
No 228
>KOG3408|consensus
Probab=51.19 E-value=9 Score=23.41 Aligned_cols=23 Identities=30% Similarity=0.489 Sum_probs=17.5
Q ss_pred ceeccccCccccCchhHHHHhhh
Q psy3507 82 PYKCEYCAYSCTQSSALKIHERK 104 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~ 104 (134)
.|-|-.|.+-|.+...|..|.++
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhc
Confidence 47788888888888888888664
No 229
>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=51.05 E-value=6.3 Score=21.55 Aligned_cols=27 Identities=22% Similarity=0.401 Sum_probs=13.0
Q ss_pred cccCCCCCCcccCCCC---cceeeCCCCCc
Q psy3507 37 MYHCKTCSTVSHPNIS---YKYTCYACDYH 63 (134)
Q Consensus 37 ~~~C~~C~~~f~~~~~---~~~~C~~C~~~ 63 (134)
...|..|+........ ..+.|+.|+..
T Consensus 41 ~v~Cg~C~~~~~~~~~~c~~~~~C~~C~~~ 70 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEYSCGADYFCPICGLY 70 (71)
T ss_dssp EEEETTT--EEES-SBTT--SEEETTTTEE
T ss_pred CeECCCCCCccChhhhhcCCCccCcCcCCC
Confidence 4566777666552211 34677777643
No 230
>KOG2906|consensus
Probab=50.96 E-value=11 Score=22.09 Aligned_cols=34 Identities=21% Similarity=0.574 Sum_probs=17.3
Q ss_pred eeccccCccccCchhHHHHhhhcCCCCC----eecCcChhhh
Q psy3507 83 YKCEYCAYSCTQSSALKIHERKHTGDKP----YICQQCRDTF 120 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~----~~C~~C~~~F 120 (134)
-.|+.||..-..-.. +++-..+.| |+|-.|+...
T Consensus 66 ~~Cp~Cgh~rayF~q----lQtRSADEPmT~FYkC~~C~~~W 103 (105)
T KOG2906|consen 66 ATCPTCGHERAYFMQ----LQTRSADEPMTTFYKCCKCKHRW 103 (105)
T ss_pred CcCCCCCCCceEEEE----eeeccCCCcHhHhhhhhcccccc
Confidence 368888743211111 223333444 8888887643
No 231
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=50.87 E-value=12 Score=15.93 Aligned_cols=6 Identities=33% Similarity=1.326 Sum_probs=2.8
Q ss_pred CCCCCC
Q psy3507 40 CKTCST 45 (134)
Q Consensus 40 C~~C~~ 45 (134)
|+.||.
T Consensus 5 Cp~Cg~ 10 (26)
T PF13248_consen 5 CPNCGA 10 (26)
T ss_pred CcccCC
Confidence 444444
No 232
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=49.77 E-value=28 Score=22.23 Aligned_cols=21 Identities=14% Similarity=0.395 Sum_probs=11.1
Q ss_pred eeeCCCCCccC------ChHHHHHHHH
Q psy3507 55 YTCYACDYHTL------MSEDMKKHMR 75 (134)
Q Consensus 55 ~~C~~C~~~f~------~~~~l~~H~~ 75 (134)
.+|..|++.|- ..+.+..|+.
T Consensus 15 v~C~~c~kWFCNg~~~~s~SHIv~HLv 41 (152)
T PF09416_consen 15 VKCNTCNKWFCNGRGNTSGSHIVNHLV 41 (152)
T ss_dssp EEETTTTEEEES--TTSSS-HHHHHHH
T ss_pred eEcCCCCcEeecCCCCCcccHHHHHHH
Confidence 45555555542 4466666754
No 233
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=49.76 E-value=11 Score=22.44 Aligned_cols=29 Identities=14% Similarity=0.245 Sum_probs=21.7
Q ss_pred cCCCCCCcccCCCCcceeeCCCCCccCCh
Q psy3507 39 HCKTCSTVSHPNISYKYTCYACDYHTLMS 67 (134)
Q Consensus 39 ~C~~C~~~f~~~~~~~~~C~~C~~~f~~~ 67 (134)
.|+.|+..|.......|.|+.|...+...
T Consensus 5 ~cp~c~sEytYed~~~~~cpec~~ew~~~ 33 (112)
T COG2824 5 PCPKCNSEYTYEDGGQLICPECAHEWNEN 33 (112)
T ss_pred CCCccCCceEEecCceEeCchhccccccc
Confidence 58888888776666688888888877643
No 234
>KOG2482|consensus
Probab=49.15 E-value=9.7 Score=27.67 Aligned_cols=51 Identities=18% Similarity=0.409 Sum_probs=35.8
Q ss_pred ceeccccCccc-cCchhHHHHhhh-cC---C------------------CCCeecCcChhhhcCHHHHHHHHHh
Q psy3507 82 PYKCEYCAYSC-TQSSALKIHERK-HT---G------------------DKPYICQQCRDTFSSLYLFRNRLQS 132 (134)
Q Consensus 82 ~~~C~~C~~~f-~~~~~l~~H~~~-h~---~------------------~~~~~C~~C~~~F~~~~~l~~H~~~ 132 (134)
..+|-.|...+ ..++....|+-. |. | -..+.|-.|.+.|..+..|+.||+.
T Consensus 144 slqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 144 SLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred eeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHh
Confidence 35788887644 345666667543 32 1 1237899999999999999999964
No 235
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=48.64 E-value=11 Score=28.67 Aligned_cols=13 Identities=15% Similarity=0.473 Sum_probs=8.1
Q ss_pred ccccCCCCCCccc
Q psy3507 36 LMYHCKTCSTVSH 48 (134)
Q Consensus 36 ~~~~C~~C~~~f~ 48 (134)
..|+|..||..|.
T Consensus 424 ~~~~c~~c~~~yd 436 (479)
T PRK05452 424 PRMQCSVCQWIYD 436 (479)
T ss_pred CeEEECCCCeEEC
Confidence 4466666666665
No 236
>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=48.39 E-value=12 Score=23.56 Aligned_cols=9 Identities=33% Similarity=1.028 Sum_probs=4.5
Q ss_pred eeccccCcc
Q psy3507 83 YKCEYCAYS 91 (134)
Q Consensus 83 ~~C~~C~~~ 91 (134)
|.|..|+..
T Consensus 144 ~~C~~C~~~ 152 (157)
T PF10263_consen 144 YRCGRCGGP 152 (157)
T ss_pred EECCCCCCE
Confidence 455555543
No 237
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=47.94 E-value=15 Score=19.98 Aligned_cols=8 Identities=38% Similarity=1.294 Sum_probs=3.1
Q ss_pred eccccCcc
Q psy3507 84 KCEYCAYS 91 (134)
Q Consensus 84 ~C~~C~~~ 91 (134)
.|+.|...
T Consensus 57 ~CP~C~~~ 64 (70)
T PF11793_consen 57 ECPYCSSP 64 (70)
T ss_dssp E-TTT-SE
T ss_pred CCcCCCCe
Confidence 46666543
No 238
>KOG0978|consensus
Probab=47.54 E-value=4.1 Score=32.34 Aligned_cols=16 Identities=19% Similarity=0.374 Sum_probs=9.9
Q ss_pred eeccccCccccCchhH
Q psy3507 83 YKCEYCAYSCTQSSAL 98 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l 98 (134)
-.||.|+.+|.....+
T Consensus 679 RKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 679 RKCPKCNAAFGANDVH 694 (698)
T ss_pred CCCCCCCCCCCccccc
Confidence 3677777777665443
No 239
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=47.50 E-value=20 Score=17.61 Aligned_cols=21 Identities=29% Similarity=0.834 Sum_probs=10.2
Q ss_pred ccCCCCCCcccCCCCcceeeCCCC
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACD 61 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~ 61 (134)
|.|+.|++.. .+ ..|.|..|.
T Consensus 1 ~~C~~C~~~i--~g-~r~~C~~C~ 21 (46)
T cd02249 1 YSCDGCLKPI--VG-VRYHCLVCE 21 (46)
T ss_pred CCCcCCCCCC--cC-CEEECCCCC
Confidence 3455555521 12 455565554
No 240
>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=47.12 E-value=12 Score=21.12 Aligned_cols=9 Identities=22% Similarity=0.966 Sum_probs=2.5
Q ss_pred ccccCCCCC
Q psy3507 36 LMYHCKTCS 44 (134)
Q Consensus 36 ~~~~C~~C~ 44 (134)
+.|.|+.|+
T Consensus 21 ~~F~CPfC~ 29 (81)
T PF05129_consen 21 KVFDCPFCN 29 (81)
T ss_dssp S----TTT-
T ss_pred ceEcCCcCC
Confidence 446666666
No 241
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=46.90 E-value=21 Score=17.22 Aligned_cols=9 Identities=22% Similarity=1.054 Sum_probs=4.6
Q ss_pred cceeeCCCC
Q psy3507 53 YKYTCYACD 61 (134)
Q Consensus 53 ~~~~C~~C~ 61 (134)
..|.|..|+
T Consensus 12 ~r~~C~~C~ 20 (41)
T cd02337 12 TRWHCTVCE 20 (41)
T ss_pred CceECCCCc
Confidence 445555554
No 242
>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=46.58 E-value=6.2 Score=28.69 Aligned_cols=27 Identities=19% Similarity=0.495 Sum_probs=10.3
Q ss_pred ccccCCCCCCcccCCCCcc-eeeCCCCC
Q psy3507 36 LMYHCKTCSTVSHPNISYK-YTCYACDY 62 (134)
Q Consensus 36 ~~~~C~~C~~~f~~~~~~~-~~C~~C~~ 62 (134)
+-|+|..|+.....-...| -.|..||.
T Consensus 284 RFFkC~~C~~Rt~sl~r~P~~~C~~Cg~ 311 (344)
T PF09332_consen 284 RFFKCKDCGNRTISLERLPKKHCSNCGS 311 (344)
T ss_dssp EEEE-T-TS-EEEESSSS--S--TTT-S
T ss_pred eeEECCCCCCeeeecccCCCCCCCcCCc
Confidence 3467777776654322223 34666664
No 243
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=46.34 E-value=4.6 Score=28.48 Aligned_cols=26 Identities=23% Similarity=0.490 Sum_probs=7.9
Q ss_pred CccccCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 35 ELMYHCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 35 ~~~~~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
.+-..|..|+..... ....|+.||..
T Consensus 195 ~R~L~Cs~C~t~W~~---~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 195 KRYLHCSLCGTEWRF---VRIKCPYCGNT 220 (290)
T ss_dssp EEEEEETTT--EEE-----TTS-TTT---
T ss_pred cEEEEcCCCCCeeee---cCCCCcCCCCC
Confidence 344445555543321 12345555543
No 244
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=46.33 E-value=7.7 Score=19.69 Aligned_cols=15 Identities=33% Similarity=0.769 Sum_probs=10.7
Q ss_pred CCCeecCcChhhhcC
Q psy3507 108 DKPYICQQCRDTFSS 122 (134)
Q Consensus 108 ~~~~~C~~C~~~F~~ 122 (134)
++++.|..||..|..
T Consensus 2 Dk~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVF 16 (49)
T ss_pred CeeEEcccCCCeEEE
Confidence 456778888877754
No 245
>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=46.01 E-value=15 Score=17.10 Aligned_cols=8 Identities=38% Similarity=1.277 Sum_probs=3.6
Q ss_pred eeCCCCCc
Q psy3507 56 TCYACDYH 63 (134)
Q Consensus 56 ~C~~C~~~ 63 (134)
.|..|+..
T Consensus 22 ~C~~C~Y~ 29 (35)
T PF02150_consen 22 ACRTCGYE 29 (35)
T ss_dssp EESSSS-E
T ss_pred CCCCCCCc
Confidence 45555543
No 246
>KOG2636|consensus
Probab=46.01 E-value=14 Score=27.77 Aligned_cols=28 Identities=21% Similarity=0.440 Sum_probs=22.1
Q ss_pred hhcCCCCCeecCcCh-hhhcCHHHHHHHH
Q psy3507 103 RKHTGDKPYICQQCR-DTFSSLYLFRNRL 130 (134)
Q Consensus 103 ~~h~~~~~~~C~~C~-~~F~~~~~l~~H~ 130 (134)
+.|.-...|.|.+|| +++.-+..+.+|.
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHh
Confidence 456666779999999 7888888888885
No 247
>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=45.98 E-value=20 Score=21.31 Aligned_cols=7 Identities=57% Similarity=1.611 Sum_probs=3.5
Q ss_pred eeeCCCC
Q psy3507 55 YTCYACD 61 (134)
Q Consensus 55 ~~C~~C~ 61 (134)
|.|..|+
T Consensus 32 y~C~~C~ 38 (102)
T PF11672_consen 32 YVCTPCD 38 (102)
T ss_pred EECCCCC
Confidence 4555554
No 248
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=45.65 E-value=19 Score=21.01 Aligned_cols=38 Identities=18% Similarity=0.432 Sum_probs=19.9
Q ss_pred ceeccccCccccCchhHHHHhhhc-CCC-CCeecCcChhhhc
Q psy3507 82 PYKCEYCAYSCTQSSALKIHERKH-TGD-KPYICQQCRDTFS 121 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~h-~~~-~~~~C~~C~~~F~ 121 (134)
...|+.||..-..-..++ ++.- .+. .-|.|..|+..++
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q--~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQ--TRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred cCCCCCCCCCeeEEEEec--cCCCCCCcEEEEEeCCCCCeeE
Confidence 368999985422211111 2221 111 2389999997764
No 249
>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=45.51 E-value=9.2 Score=18.50 Aligned_cols=12 Identities=25% Similarity=0.268 Sum_probs=7.8
Q ss_pred ccccCCCCCCcc
Q psy3507 36 LMYHCKTCSTVS 47 (134)
Q Consensus 36 ~~~~C~~C~~~f 47 (134)
++-.|++||..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 356677777665
No 250
>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=44.62 E-value=11 Score=22.15 Aligned_cols=12 Identities=25% Similarity=0.473 Sum_probs=6.2
Q ss_pred ccccCCCCCCcc
Q psy3507 36 LMYHCKTCSTVS 47 (134)
Q Consensus 36 ~~~~C~~C~~~f 47 (134)
+++.|+.||..|
T Consensus 78 ~~~rC~eCG~~f 89 (97)
T cd00924 78 KPKRCPECGHVF 89 (97)
T ss_pred CceeCCCCCcEE
Confidence 455555555544
No 251
>PF12907 zf-met2: Zinc-binding
Probab=44.46 E-value=9.5 Score=18.47 Aligned_cols=20 Identities=30% Similarity=0.572 Sum_probs=9.3
Q ss_pred eccccCccc---cCchhHHHHhh
Q psy3507 84 KCEYCAYSC---TQSSALKIHER 103 (134)
Q Consensus 84 ~C~~C~~~f---~~~~~l~~H~~ 103 (134)
.|.+|-..| .+...|..|..
T Consensus 3 ~C~iC~qtF~~t~~~~~L~eH~e 25 (40)
T PF12907_consen 3 ICKICRQTFMQTTNEPQLKEHAE 25 (40)
T ss_pred CcHHhhHHHHhcCCHHHHHHHHH
Confidence 455555322 22344666644
No 252
>PTZ00448 hypothetical protein; Provisional
Probab=44.35 E-value=17 Score=26.70 Aligned_cols=23 Identities=17% Similarity=0.496 Sum_probs=19.9
Q ss_pred CeecCcChhhhcCHHHHHHHHHh
Q psy3507 110 PYICQQCRDTFSSLYLFRNRLQS 132 (134)
Q Consensus 110 ~~~C~~C~~~F~~~~~l~~H~~~ 132 (134)
.|.|..|+-.|.+....+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999988888888864
No 253
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=44.26 E-value=16 Score=22.85 Aligned_cols=29 Identities=24% Similarity=0.522 Sum_probs=17.3
Q ss_pred ccccCCCCCCccc----CCCCcceeeCCCCCcc
Q psy3507 36 LMYHCKTCSTVSH----PNISYKYTCYACDYHT 64 (134)
Q Consensus 36 ~~~~C~~C~~~f~----~~~~~~~~C~~C~~~f 64 (134)
-.|.|..|+..+. +.....|.|..|+..+
T Consensus 111 ~~y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l 143 (146)
T smart00731 111 YPYRCTGCGQRYLRVRRSNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEEECCCCCCCCceEccccCcceEEcCCCCCEE
Confidence 3577777776655 1111457777777654
No 254
>KOG0957|consensus
Probab=43.94 E-value=20 Score=27.57 Aligned_cols=48 Identities=23% Similarity=0.484 Sum_probs=30.6
Q ss_pred ccceecCcccccccccCCCCccccCCCCCCccc-------------CCCCcceeeCCCCCccCC
Q psy3507 16 PFTLATCIHCRLLLVPTAEELMYHCKTCSTVSH-------------PNISYKYTCYACDYHTLM 66 (134)
Q Consensus 16 ~~~~~~C~~C~~h~~~h~~~~~~~C~~C~~~f~-------------~~~~~~~~C~~C~~~f~~ 66 (134)
+-..+.|++|++-.. ..+..+|+.|...|. ......+.|..|++.-.+
T Consensus 541 ~a~~ysCgiCkks~d---QHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk~esS 601 (707)
T KOG0957|consen 541 KAMNYSCGICKKSTD---QHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDKNESS 601 (707)
T ss_pred cccceeeeeeccchh---hHHHhhcchhhceeeccccCCccccCcccccCcceeecccccccCc
Confidence 344678999955333 334578999998887 122334789999665433
No 255
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=43.58 E-value=37 Score=22.27 Aligned_cols=32 Identities=19% Similarity=0.630 Sum_probs=17.1
Q ss_pred CCCceeccccCccccCchhHHHHhhhcCCCCCeecCcChhh
Q psy3507 79 GEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDT 119 (134)
Q Consensus 79 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 119 (134)
+..-|.|+.|.-.|+...+... -|.|+.||..
T Consensus 110 ~~~~y~C~~~~~r~sfdeA~~~---------~F~Cp~Cg~~ 141 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEAMEL---------GFTCPKCGED 141 (176)
T ss_pred cCCceeCCCCCCcccHHHHHHh---------CCCCCCCCch
Confidence 3344777666655544333221 2777777653
No 256
>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=43.31 E-value=24 Score=17.72 Aligned_cols=8 Identities=50% Similarity=1.497 Sum_probs=3.7
Q ss_pred ceeeCCCC
Q psy3507 54 KYTCYACD 61 (134)
Q Consensus 54 ~~~C~~C~ 61 (134)
.|.|..|.
T Consensus 15 R~~C~~C~ 22 (48)
T cd02341 15 RYHCSECD 22 (48)
T ss_pred eEECCCCC
Confidence 34444443
No 257
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=43.20 E-value=23 Score=25.43 Aligned_cols=26 Identities=23% Similarity=0.585 Sum_probs=13.0
Q ss_pred CCccccCCCCCCcccCCCCcceeeCCCCC
Q psy3507 34 EELMYHCKTCSTVSHPNISYKYTCYACDY 62 (134)
Q Consensus 34 ~~~~~~C~~C~~~f~~~~~~~~~C~~C~~ 62 (134)
|.+-..|..|+..-.. ..-.|+.||.
T Consensus 209 G~RyL~CslC~teW~~---~R~~C~~Cg~ 234 (309)
T PRK03564 209 GLRYLHCNLCESEWHV---VRVKCSNCEQ 234 (309)
T ss_pred CceEEEcCCCCCcccc---cCccCCCCCC
Confidence 3444556666654321 2345666664
No 258
>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=42.62 E-value=13 Score=17.55 Aligned_cols=12 Identities=25% Similarity=1.035 Sum_probs=5.0
Q ss_pred cccCCCCCCccc
Q psy3507 37 MYHCKTCSTVSH 48 (134)
Q Consensus 37 ~~~C~~C~~~f~ 48 (134)
.|+|+.||....
T Consensus 6 ~YkC~~CGniVe 17 (36)
T PF06397_consen 6 FYKCEHCGNIVE 17 (36)
T ss_dssp EEE-TTT--EEE
T ss_pred EEEccCCCCEEE
Confidence 466666665543
No 259
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=42.37 E-value=21 Score=22.78 Aligned_cols=12 Identities=25% Similarity=0.742 Sum_probs=6.2
Q ss_pred ccccCCCCCCcc
Q psy3507 36 LMYHCKTCSTVS 47 (134)
Q Consensus 36 ~~~~C~~C~~~f 47 (134)
..|.|+.|+..+
T Consensus 50 ~~~~C~~C~~~~ 61 (166)
T cd04476 50 GTYRCEKCNKSV 61 (166)
T ss_pred CcEECCCCCCcC
Confidence 345555555543
No 260
>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=42.08 E-value=19 Score=27.34 Aligned_cols=21 Identities=24% Similarity=0.627 Sum_probs=17.9
Q ss_pred eecCcChhhhcCHHHHHHHHH
Q psy3507 111 YICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 111 ~~C~~C~~~F~~~~~l~~H~~ 131 (134)
+.|+.|.+.|.....+..|+.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~ 78 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHME 78 (466)
T ss_pred eeCCcccceeCCHHHHHHHHH
Confidence 678889999999988888874
No 261
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=41.85 E-value=28 Score=22.53 Aligned_cols=13 Identities=23% Similarity=0.652 Sum_probs=5.7
Q ss_pred eeccccCccccCc
Q psy3507 83 YKCEYCAYSCTQS 95 (134)
Q Consensus 83 ~~C~~C~~~f~~~ 95 (134)
+.|+.|++.|-..
T Consensus 131 ~~C~~CgkiYW~G 143 (165)
T COG1656 131 YRCPKCGKIYWKG 143 (165)
T ss_pred eECCCCcccccCc
Confidence 3344444444333
No 262
>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=41.53 E-value=19 Score=27.42 Aligned_cols=26 Identities=15% Similarity=0.374 Sum_probs=19.4
Q ss_pred ceeccccCccccCchhHHHHhhh-cCC
Q psy3507 82 PYKCEYCAYSCTQSSALKIHERK-HTG 107 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~-h~~ 107 (134)
-+.|+.|++.|.....+..|+.. |.+
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 36788888888888888888764 544
No 263
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=41.19 E-value=22 Score=18.04 Aligned_cols=20 Identities=30% Similarity=0.884 Sum_probs=11.9
Q ss_pred CCCeecCcChhhhcCHHHHHHHH
Q psy3507 108 DKPYICQQCRDTFSSLYLFRNRL 130 (134)
Q Consensus 108 ~~~~~C~~C~~~F~~~~~l~~H~ 130 (134)
.+|--|+.|...|.. |..|+
T Consensus 3 ~k~GYCE~Cr~kfd~---l~~Hi 22 (49)
T smart00586 3 KKPGYCENCREKYDD---LETHL 22 (49)
T ss_pred CCCcccccHhHHHhh---HHHHh
Confidence 345567777766653 55554
No 264
>KOG2272|consensus
Probab=41.09 E-value=36 Score=23.81 Aligned_cols=14 Identities=14% Similarity=0.468 Sum_probs=8.7
Q ss_pred CceeccccCccccC
Q psy3507 81 KPYKCEYCAYSCTQ 94 (134)
Q Consensus 81 ~~~~C~~C~~~f~~ 94 (134)
..|.|..|.+.|.-
T Consensus 220 eHFvCa~CekPFlG 233 (332)
T KOG2272|consen 220 EHFVCAKCEKPFLG 233 (332)
T ss_pred hheeehhcCCcccc
Confidence 34677777666654
No 265
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=40.95 E-value=17 Score=24.59 Aligned_cols=41 Identities=17% Similarity=0.267 Sum_probs=24.1
Q ss_pred ccccccccCCccceecCcccccccc-cCCCCcc---ccCCCCCCc
Q psy3507 6 VCTASIGLKNPFTLATCIHCRLLLV-PTAEELM---YHCKTCSTV 46 (134)
Q Consensus 6 ~~~~~~~~~~~~~~~~C~~C~~h~~-~h~~~~~---~~C~~C~~~ 46 (134)
+.++.....+|+...+|..|..|-- .+.++++ |.|+.|...
T Consensus 179 l~G~ne~~~~~~~alIC~~C~hhngl~~~~ek~~~efiC~~Cn~~ 223 (251)
T COG5415 179 LAGGNELDLSPFKALICPQCHHHNGLYRLAEKPIIEFICPHCNHK 223 (251)
T ss_pred HhCCCccccCchhhhccccccccccccccccccchheecccchhh
Confidence 3445555668888888998855432 2333333 556666543
No 266
>PRK11823 DNA repair protein RadA; Provisional
Probab=40.94 E-value=22 Score=26.86 Aligned_cols=25 Identities=24% Similarity=0.582 Sum_probs=15.0
Q ss_pred cccCCCCCCcccCCCCcceeeCCCCCcc
Q psy3507 37 MYHCKTCSTVSHPNISYKYTCYACDYHT 64 (134)
Q Consensus 37 ~~~C~~C~~~f~~~~~~~~~C~~C~~~f 64 (134)
.|.|..||..+ .....+|+.|+.+-
T Consensus 7 ~y~C~~Cg~~~---~~~~g~Cp~C~~w~ 31 (446)
T PRK11823 7 AYVCQECGAES---PKWLGRCPECGAWN 31 (446)
T ss_pred eEECCcCCCCC---cccCeeCcCCCCcc
Confidence 47777777654 33445677776543
No 267
>KOG2636|consensus
Probab=40.76 E-value=22 Score=26.86 Aligned_cols=28 Identities=29% Similarity=0.521 Sum_probs=21.2
Q ss_pred HhcCCCceeccccC-ccccCchhHHHHhh
Q psy3507 76 KHTGEKPYKCEYCA-YSCTQSSALKIHER 103 (134)
Q Consensus 76 ~h~~~~~~~C~~C~-~~f~~~~~l~~H~~ 103 (134)
.|--...|.|.+|| .++.-+..+.+|-.
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHHhH
Confidence 45556678888888 78888888888854
No 268
>PF04641 Rtf2: Rtf2 RING-finger
Probab=40.63 E-value=39 Score=23.47 Aligned_cols=53 Identities=17% Similarity=0.236 Sum_probs=31.5
Q ss_pred CCccccCCCCCCcccCCCCcceeeC-CCCCccCChHHHHHHHHHhcCCCceeccccCccccCc
Q psy3507 34 EELMYHCKTCSTVSHPNISYKYTCY-ACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQS 95 (134)
Q Consensus 34 ~~~~~~C~~C~~~f~~~~~~~~~C~-~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 95 (134)
....|.|++.+..|. +..+|..- .||-+|.....-.. . ....|++|+..|...
T Consensus 110 ~~~~~~CPvt~~~~~--~~~~fv~l~~cG~V~s~~alke~--k-----~~~~Cp~c~~~f~~~ 163 (260)
T PF04641_consen 110 SEGRFICPVTGKEFN--GKHKFVYLRPCGCVFSEKALKEL--K-----KSKKCPVCGKPFTEE 163 (260)
T ss_pred CCceeECCCCCcccC--CceeEEEEcCCCCEeeHHHHHhh--c-----ccccccccCCccccC
Confidence 345688888888873 33344433 57777765432221 1 234588888887743
No 269
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.07 E-value=9.3 Score=26.18 Aligned_cols=23 Identities=17% Similarity=0.287 Sum_probs=12.9
Q ss_pred CceeccccCccccCchhHHHHhh
Q psy3507 81 KPYKCEYCAYSCTQSSALKIHER 103 (134)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~ 103 (134)
+.+.||+|+..|....-+..-.|
T Consensus 18 k~ieCPvC~tkFkkeev~tgsiR 40 (267)
T COG1655 18 KTIECPVCNTKFKKEEVKTGSIR 40 (267)
T ss_pred ceeccCcccchhhhhheecccee
Confidence 44667777776666544433333
No 270
>PRK05978 hypothetical protein; Provisional
Probab=39.52 E-value=23 Score=22.49 Aligned_cols=6 Identities=50% Similarity=1.143 Sum_probs=2.4
Q ss_pred eCCCCC
Q psy3507 57 CYACDY 62 (134)
Q Consensus 57 C~~C~~ 62 (134)
|+.||.
T Consensus 55 C~~CG~ 60 (148)
T PRK05978 55 CAACGE 60 (148)
T ss_pred ccccCC
Confidence 444443
No 271
>KOG1280|consensus
Probab=39.47 E-value=33 Score=25.08 Aligned_cols=38 Identities=21% Similarity=0.544 Sum_probs=27.1
Q ss_pred CCceeccccCccccCchhHHHHhhh-cCCCCC-eecCcCh
Q psy3507 80 EKPYKCEYCAYSCTQSSALKIHERK-HTGDKP-YICQQCR 117 (134)
Q Consensus 80 ~~~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~-~~C~~C~ 117 (134)
...|.|+.|+..-.+...|..|... |....+ ..|++|+
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 3469999999998889999999665 543322 3556554
No 272
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=39.46 E-value=19 Score=21.71 Aligned_cols=28 Identities=14% Similarity=0.344 Sum_probs=12.5
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCccCC
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYHTLM 66 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~f~~ 66 (134)
.+|+.|++...--+.. ..|..|+....-
T Consensus 70 V~CP~C~K~TKmLGr~-D~CM~C~~pLTL 97 (114)
T PF11023_consen 70 VECPNCGKQTKMLGRV-DACMHCKEPLTL 97 (114)
T ss_pred eECCCCCChHhhhchh-hccCcCCCcCcc
Confidence 4455555554322222 245555544333
No 273
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=39.43 E-value=48 Score=17.24 Aligned_cols=45 Identities=7% Similarity=0.101 Sum_probs=18.3
Q ss_pred CccccCCCCCCcccCCCCcceeeCCCCCccCChHHHHHHHHHhcCCCceeccc
Q psy3507 35 ELMYHCKTCSTVSHPNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEY 87 (134)
Q Consensus 35 ~~~~~C~~C~~~f~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~ 87 (134)
...+.|++-...|. .|.....|+..|...+ +...+ .......|++
T Consensus 9 ~~~~~CPiT~~~~~----~PV~s~~C~H~fek~a-I~~~i---~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQPFE----DPVKSKKCGHTFEKEA-ILQYI---QRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB-S----SEEEESSS--EEEHHH-HHHHC---TTTS-EE-SC
T ss_pred EeccCCCCcCChhh----CCcCcCCCCCeecHHH-HHHHH---HhcCCCCCCC
Confidence 34466666665543 3555666666664433 33332 2234456665
No 274
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=39.32 E-value=31 Score=14.79 Aligned_cols=21 Identities=29% Similarity=0.578 Sum_probs=8.7
Q ss_pred ccccccccCCCCccccCCCCC
Q psy3507 24 HCRLLLVPTAEELMYHCKTCS 44 (134)
Q Consensus 24 ~C~~h~~~h~~~~~~~C~~C~ 44 (134)
.|+.-+.--.+-....|..|.
T Consensus 3 ~Cr~~L~yp~GA~sVrCa~C~ 23 (25)
T PF06943_consen 3 GCRTLLMYPRGAPSVRCACCH 23 (25)
T ss_pred CCCceEEcCCCCCCeECCccC
Confidence 333333333344444444443
No 275
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.28 E-value=12 Score=18.85 Aligned_cols=16 Identities=31% Similarity=0.607 Sum_probs=10.5
Q ss_pred ecCcChhhhcCHHHHH
Q psy3507 112 ICQQCRDTFSSLYLFR 127 (134)
Q Consensus 112 ~C~~C~~~F~~~~~l~ 127 (134)
.|+.|++.|..+....
T Consensus 14 ICpvCqRPFsWRkKW~ 29 (54)
T COG4338 14 ICPVCQRPFSWRKKWA 29 (54)
T ss_pred hhhhhcCchHHHHHHH
Confidence 5777777777655443
No 276
>KOG3002|consensus
Probab=39.19 E-value=29 Score=24.79 Aligned_cols=91 Identities=20% Similarity=0.296 Sum_probs=49.4
Q ss_pred ccceecCcccccccccCCCCc---cccCCCCCCcccCCCCcceeeCCCCCccCChHHHHHHHHHhcCCCceeccc----c
Q psy3507 16 PFTLATCIHCRLLLVPTAEEL---MYHCKTCSTVSHPNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEY----C 88 (134)
Q Consensus 16 ~~~~~~C~~C~~h~~~h~~~~---~~~C~~C~~~f~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~----C 88 (134)
-+....|++|..-+..+.-+- -..|..|-. ++...|+.|...+.....+.. ..-.....+.|+. |
T Consensus 45 ~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~------~~~~~CP~Cr~~~g~~R~~am--EkV~e~~~vpC~~~~~GC 116 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSPPIFQCDNGHLACSSCRT------KVSNKCPTCRLPIGNIRCRAM--EKVAEAVLVPCKNAKLGC 116 (299)
T ss_pred chhhccCchhhccCcccceecCCCcEehhhhhh------hhcccCCccccccccHHHHHH--HHHHHhceecccccccCC
Confidence 445566777754444332111 022223321 456789999888886655443 3223334566663 7
Q ss_pred CccccCchhHHHHhhhcCCCCCeecCcC
Q psy3507 89 AYSCTQSSALKIHERKHTGDKPYICQQC 116 (134)
Q Consensus 89 ~~~f~~~~~l~~H~~~h~~~~~~~C~~C 116 (134)
.+.|.-... ..|.+.-.. +|+.|+.=
T Consensus 117 ~~~~~Y~~~-~~HE~~C~f-~~~~CP~p 142 (299)
T KOG3002|consen 117 TKSFPYGEK-SKHEKVCEF-RPCSCPVP 142 (299)
T ss_pred ceeeccccc-ccccccccc-CCcCCCCC
Confidence 777766655 556555443 67777654
No 277
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=39.15 E-value=27 Score=16.72 Aligned_cols=23 Identities=17% Similarity=0.443 Sum_probs=9.9
Q ss_pred ccCCCCCCcccCCCCcceeeCCCC
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACD 61 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~ 61 (134)
..|..|++.+.... ..+.|..|+
T Consensus 12 ~~C~~C~~~i~~~~-~~~~C~~C~ 34 (49)
T smart00109 12 TKCCVCRKSIWGSF-QGLRCSWCK 34 (49)
T ss_pred CCccccccccCcCC-CCcCCCCCC
Confidence 34555555443211 234455553
No 278
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=39.06 E-value=25 Score=23.48 Aligned_cols=29 Identities=17% Similarity=0.400 Sum_probs=18.4
Q ss_pred ccccCCCCCC---cccCCCCcceeeCCCCCcc
Q psy3507 36 LMYHCKTCST---VSHPNISYKYTCYACDYHT 64 (134)
Q Consensus 36 ~~~~C~~C~~---~f~~~~~~~~~C~~C~~~f 64 (134)
+.|.|+.|+. .|.........|+.|+..|
T Consensus 151 kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~ 182 (202)
T PF13901_consen 151 KGFICEICNSDDIIFPFQIDTTVRCPKCKSVF 182 (202)
T ss_pred CCCCCccCCCCCCCCCCCCCCeeeCCcCcccc
Confidence 4577777764 3334444567788887765
No 279
>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=38.88 E-value=24 Score=26.71 Aligned_cols=26 Identities=23% Similarity=0.568 Sum_probs=15.9
Q ss_pred cccCCCCCCcccCCCCcceeeCCCCCccC
Q psy3507 37 MYHCKTCSTVSHPNISYKYTCYACDYHTL 65 (134)
Q Consensus 37 ~~~C~~C~~~f~~~~~~~~~C~~C~~~f~ 65 (134)
.|.|..||..+ .....+|+.|+.+-.
T Consensus 7 ~y~C~~Cg~~~---~~~~g~Cp~C~~w~t 32 (454)
T TIGR00416 7 KFVCQHCGADS---PKWQGKCPACHAWNT 32 (454)
T ss_pred eEECCcCCCCC---ccccEECcCCCCccc
Confidence 47777777754 334566777765433
No 280
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=38.82 E-value=17 Score=17.78 Aligned_cols=9 Identities=22% Similarity=0.678 Sum_probs=3.9
Q ss_pred CCCCCCccc
Q psy3507 40 CKTCSTVSH 48 (134)
Q Consensus 40 C~~C~~~f~ 48 (134)
|+.||..+.
T Consensus 5 C~~Cg~~l~ 13 (47)
T PF13005_consen 5 CPDCGGELK 13 (47)
T ss_pred CCCCCceee
Confidence 444444433
No 281
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.66 E-value=30 Score=21.34 Aligned_cols=32 Identities=19% Similarity=0.370 Sum_probs=20.7
Q ss_pred cccCCCCCCccc------------CCCCcceeeCCCCCccCChH
Q psy3507 37 MYHCKTCSTVSH------------PNISYKYTCYACDYHTLMSE 68 (134)
Q Consensus 37 ~~~C~~C~~~f~------------~~~~~~~~C~~C~~~f~~~~ 68 (134)
..+|+.|+.... ..-+.|--|..||+.|....
T Consensus 39 i~qcp~csasirgd~~vegvlglg~dye~psfchncgs~fpwte 82 (160)
T COG4306 39 ITQCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPWTE 82 (160)
T ss_pred HhcCCccCCcccccceeeeeeccCCCCCCcchhhcCCCCCCcHH
Confidence 356777776544 33345666888888887754
No 282
>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=38.52 E-value=27 Score=25.74 Aligned_cols=24 Identities=29% Similarity=0.632 Sum_probs=14.3
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCcc
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYHT 64 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~f 64 (134)
|.|..||..+ .....+|+.|+.+-
T Consensus 1 ~~c~~cg~~~---~~~~g~cp~c~~w~ 24 (372)
T cd01121 1 YVCSECGYVS---PKWLGKCPECGEWN 24 (372)
T ss_pred CCCCCCCCCC---CCccEECcCCCCce
Confidence 5677777654 23445677776543
No 283
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=38.30 E-value=42 Score=16.36 Aligned_cols=27 Identities=11% Similarity=0.117 Sum_probs=9.5
Q ss_pred CCCCCCcccCCCCcceeeCCCCCccCChH
Q psy3507 40 CKTCSTVSHPNISYKYTCYACDYHTLMSE 68 (134)
Q Consensus 40 C~~C~~~f~~~~~~~~~C~~C~~~f~~~~ 68 (134)
|++|-. |......|..=+ ||.+|....
T Consensus 1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~c 27 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLP-CGHVFCKDC 27 (43)
T ss_dssp -TTT-----TTSS-EEE-S-SS-EEEHHH
T ss_pred CCcccc-ccCCCCCCEEEe-CccHHHHHH
Confidence 455555 544444444433 666665443
No 284
>KOG0696|consensus
Probab=38.22 E-value=12 Score=28.43 Aligned_cols=59 Identities=20% Similarity=0.368 Sum_probs=37.4
Q ss_pred CCcceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccCchhHHHH-hhhcCCCCCeecCcChh
Q psy3507 51 ISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIH-ERKHTGDKPYICQQCRD 118 (134)
Q Consensus 51 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H-~~~h~~~~~~~C~~C~~ 118 (134)
+...|+|.+|. +..|.+.|. -..|.|+--++.+.+...-..| .+.|+-..|--|.+||.
T Consensus 70 gKQGfQCqvC~--------fvvHkrChe-fVtF~CPGadkg~dtDdpr~kHkf~~~tYssPTFCDhCGs 129 (683)
T KOG0696|consen 70 GKQGFQCQVCC--------FVVHKRCHE-FVTFSCPGADKGPDTDDPRSKHKFKIHTYSSPTFCDHCGS 129 (683)
T ss_pred ccCceeeeEEe--------ehhhhhhcc-eEEEECCCCCCCCCCCCcccccceeeeecCCCchhhhHHH
Confidence 44567777774 355666663 2347777777777776666666 34566556666777764
No 285
>PRK07591 threonine synthase; Validated
Probab=37.52 E-value=23 Score=26.53 Aligned_cols=22 Identities=18% Similarity=0.511 Sum_probs=9.5
Q ss_pred ccCCCCCCcccCCCCcceeeCCCC
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACD 61 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~ 61 (134)
++|..||+.|... .. +.|+.|+
T Consensus 19 l~C~~Cg~~~~~~-~~-~~C~~cg 40 (421)
T PRK07591 19 LKCRECGAEYPLG-PI-HVCEECF 40 (421)
T ss_pred EEeCCCCCcCCCC-CC-ccCCCCC
Confidence 4444455444432 11 4444444
No 286
>PRK11827 hypothetical protein; Provisional
Probab=37.51 E-value=25 Score=18.68 Aligned_cols=28 Identities=21% Similarity=0.197 Sum_probs=11.6
Q ss_pred cCcccccccccCCCCccccCCCCCCccc
Q psy3507 21 TCIHCRLLLVPTAEELMYHCKTCSTVSH 48 (134)
Q Consensus 21 ~C~~C~~h~~~h~~~~~~~C~~C~~~f~ 48 (134)
.|..|+.-.+.........|..|+..|.
T Consensus 10 aCP~ckg~L~~~~~~~~Lic~~~~laYP 37 (60)
T PRK11827 10 ACPVCNGKLWYNQEKQELICKLDNLAFP 37 (60)
T ss_pred ECCCCCCcCeEcCCCCeEECCccCeecc
Confidence 4555533333322223344555555444
No 287
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=37.37 E-value=14 Score=24.63 Aligned_cols=11 Identities=27% Similarity=0.498 Sum_probs=5.1
Q ss_pred ccCCCCCCccc
Q psy3507 38 YHCKTCSTVSH 48 (134)
Q Consensus 38 ~~C~~C~~~f~ 48 (134)
+.|+.||.++.
T Consensus 44 ~~C~~CgYR~~ 54 (201)
T COG1779 44 GVCERCGYRST 54 (201)
T ss_pred EEccccCCccc
Confidence 34444554443
No 288
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=37.36 E-value=18 Score=22.51 Aligned_cols=27 Identities=19% Similarity=0.600 Sum_probs=12.1
Q ss_pred ecCc--ccccccccCCCCccccCCCCCCcc
Q psy3507 20 ATCI--HCRLLLVPTAEELMYHCKTCSTVS 47 (134)
Q Consensus 20 ~~C~--~C~~h~~~h~~~~~~~C~~C~~~f 47 (134)
.-|. .|++-...- +...|.|+.|++..
T Consensus 19 ~aC~~~~C~kKv~~~-~~~~y~C~~C~~~~ 47 (146)
T PF08646_consen 19 PACPNEKCNKKVTEN-GDGSYRCEKCNKTV 47 (146)
T ss_dssp EE-TSTTTS-B-EEE-TTTEEEETTTTEEE
T ss_pred CCCCCccCCCEeecC-CCcEEECCCCCCcC
Confidence 3466 664433322 33446666666554
No 289
>KOG0717|consensus
Probab=37.16 E-value=21 Score=27.11 Aligned_cols=22 Identities=32% Similarity=0.481 Sum_probs=18.5
Q ss_pred eeccccCccccCchhHHHHhhh
Q psy3507 83 YKCEYCAYSCTQSSALKIHERK 104 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~ 104 (134)
+-|.+|++.|.+...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6799999999999999888654
No 290
>PRK06450 threonine synthase; Validated
Probab=36.99 E-value=22 Score=25.80 Aligned_cols=23 Identities=22% Similarity=0.567 Sum_probs=12.1
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCC
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDY 62 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~ 62 (134)
++|..||+.|.. ...+.|+.|+.
T Consensus 4 ~~C~~Cg~~~~~--~~~~~C~~cg~ 26 (338)
T PRK06450 4 EVCMKCGKERES--IYEIRCKKCGG 26 (338)
T ss_pred eEECCcCCcCCC--cccccCCcCCC
Confidence 456666666532 22355666653
No 291
>PHA02942 putative transposase; Provisional
Probab=36.95 E-value=39 Score=25.00 Aligned_cols=11 Identities=27% Similarity=0.905 Sum_probs=5.9
Q ss_pred ceeccccCccc
Q psy3507 82 PYKCEYCAYSC 92 (134)
Q Consensus 82 ~~~C~~C~~~f 92 (134)
.|.|+.||...
T Consensus 342 ~f~C~~CG~~~ 352 (383)
T PHA02942 342 YFHCPSCGYEN 352 (383)
T ss_pred EEECCCCCCEe
Confidence 45565555543
No 292
>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=36.95 E-value=13 Score=19.00 Aligned_cols=11 Identities=18% Similarity=0.655 Sum_probs=5.7
Q ss_pred ecCcChhhhcC
Q psy3507 112 ICQQCRDTFSS 122 (134)
Q Consensus 112 ~C~~C~~~F~~ 122 (134)
.|++|++.|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 88899888864
No 293
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=36.80 E-value=28 Score=20.76 Aligned_cols=21 Identities=14% Similarity=0.301 Sum_probs=17.1
Q ss_pred eecCcChhhhcCHHHHHHHHH
Q psy3507 111 YICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 111 ~~C~~C~~~F~~~~~l~~H~~ 131 (134)
+-|-.|.+-|.+...|..|.+
T Consensus 56 hYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 56 HYCIECARYFITEKALMEHKK 76 (126)
T ss_pred eeeehhHHHHHHHHHHHHHhc
Confidence 678888888888888888864
No 294
>PLN02294 cytochrome c oxidase subunit Vb
Probab=36.75 E-value=17 Score=23.64 Aligned_cols=19 Identities=26% Similarity=0.576 Sum_probs=14.1
Q ss_pred hhhcCCCCCeecCcChhhhc
Q psy3507 102 ERKHTGDKPYICQQCRDTFS 121 (134)
Q Consensus 102 ~~~h~~~~~~~C~~C~~~F~ 121 (134)
+..+.| +|..|+.||..|.
T Consensus 134 f~L~kG-kp~RCpeCG~~fk 152 (174)
T PLN02294 134 FWLEKG-KSFECPVCTQYFE 152 (174)
T ss_pred EEecCC-CceeCCCCCCEEE
Confidence 344444 6899999999886
No 295
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=36.33 E-value=28 Score=24.63 Aligned_cols=24 Identities=25% Similarity=0.649 Sum_probs=12.0
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCcc
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYHT 64 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~f 64 (134)
|.|+.|...|-. .+-.|+.|+-.|
T Consensus 256 yvCs~Clsi~C~---~p~~C~~Cgt~f 279 (279)
T TIGR00627 256 FVCSVCLSVLCQ---YTPICKTCKTAF 279 (279)
T ss_pred EECCCccCCcCC---CCCCCCCCCCCC
Confidence 666666555532 223555555443
No 296
>KOG3799|consensus
Probab=36.27 E-value=17 Score=22.69 Aligned_cols=42 Identities=24% Similarity=0.343 Sum_probs=22.3
Q ss_pred eecCcccccccccCCCCccccCCCCCCccc---------CCCCcceeeCCCCC
Q psy3507 19 LATCIHCRLLLVPTAEELMYHCKTCSTVSH---------PNISYKYTCYACDY 62 (134)
Q Consensus 19 ~~~C~~C~~h~~~h~~~~~~~C~~C~~~f~---------~~~~~~~~C~~C~~ 62 (134)
..+|++|.+-. -...--+.|.+|.-.|- .+....+.|..|.+
T Consensus 65 datC~IC~KTK--FADG~GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k 115 (169)
T KOG3799|consen 65 DATCGICHKTK--FADGCGHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCRK 115 (169)
T ss_pred Ccchhhhhhcc--cccccCcccchhhhhHHHhcCCeeeeccCceEEeccCCcH
Confidence 35677873322 12222355666655543 34445677777765
No 297
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=36.19 E-value=34 Score=17.42 Aligned_cols=12 Identities=25% Similarity=0.697 Sum_probs=6.3
Q ss_pred eeccccCccccC
Q psy3507 83 YKCEYCAYSCTQ 94 (134)
Q Consensus 83 ~~C~~C~~~f~~ 94 (134)
+.|+.|+..|..
T Consensus 29 W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 29 WKCPKCGHEWKA 40 (55)
T ss_pred EECCCCCCeeEc
Confidence 555555554444
No 298
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=36.09 E-value=30 Score=20.72 Aligned_cols=31 Identities=19% Similarity=0.159 Sum_probs=19.0
Q ss_pred CCCCcccCCCCcceeeCCCCCccCChHHHHHH
Q psy3507 42 TCSTVSHPNISYKYTCYACDYHTLMSEDMKKH 73 (134)
Q Consensus 42 ~C~~~f~~~~~~~~~C~~C~~~f~~~~~l~~H 73 (134)
++|..+.. ...-+.|+.||..+.+......-
T Consensus 20 ~~G~~~~v-~~~~~~C~~CGe~~~~~e~~~~~ 50 (127)
T TIGR03830 20 YKGESITI-GVPGWYCPACGEELLDPEESKRN 50 (127)
T ss_pred EcCEEEEE-eeeeeECCCCCCEEEcHHHHHHH
Confidence 34444444 33457788898888777655443
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=35.63 E-value=3.5 Score=19.32 Aligned_cols=11 Identities=18% Similarity=0.625 Sum_probs=4.8
Q ss_pred CeecCcChhhh
Q psy3507 110 PYICQQCRDTF 120 (134)
Q Consensus 110 ~~~C~~C~~~F 120 (134)
+..|..||-.+
T Consensus 21 ~isC~~CGPr~ 31 (35)
T PF07503_consen 21 FISCTNCGPRY 31 (35)
T ss_dssp T--BTTCC-SC
T ss_pred CccCCCCCCCE
Confidence 45666666544
No 300
>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=35.47 E-value=41 Score=16.77 Aligned_cols=8 Identities=25% Similarity=0.924 Sum_probs=3.9
Q ss_pred cceeeCCC
Q psy3507 53 YKYTCYAC 60 (134)
Q Consensus 53 ~~~~C~~C 60 (134)
..|.|..|
T Consensus 14 ~r~~C~~C 21 (49)
T cd02335 14 IRIKCAEC 21 (49)
T ss_pred cEEECCCC
Confidence 34555554
No 301
>PLN02748 tRNA dimethylallyltransferase
Probab=35.31 E-value=27 Score=26.64 Aligned_cols=24 Identities=17% Similarity=0.540 Sum_probs=20.6
Q ss_pred CCeecCcChh-hhcCHHHHHHHHHh
Q psy3507 109 KPYICQQCRD-TFSSLYLFRNRLQS 132 (134)
Q Consensus 109 ~~~~C~~C~~-~F~~~~~l~~H~~~ 132 (134)
+.|.|..|++ .+....++..|++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 4588999997 89999999999854
No 302
>PHA02998 RNA polymerase subunit; Provisional
Probab=35.26 E-value=35 Score=22.46 Aligned_cols=11 Identities=18% Similarity=0.443 Sum_probs=5.0
Q ss_pred eeccccCcccc
Q psy3507 83 YKCEYCAYSCT 93 (134)
Q Consensus 83 ~~C~~C~~~f~ 93 (134)
|.|..|+..|.
T Consensus 172 YkC~~CG~~wk 182 (195)
T PHA02998 172 HACRDCKKHFK 182 (195)
T ss_pred EEcCCCCCccC
Confidence 44444444443
No 303
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=35.26 E-value=37 Score=24.14 Aligned_cols=24 Identities=25% Similarity=0.443 Sum_probs=18.2
Q ss_pred CCCeecCcChhhhcCHHHHHHHHH
Q psy3507 108 DKPYICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 108 ~~~~~C~~C~~~F~~~~~l~~H~~ 131 (134)
..-|.|+.|-+-|.+...|.+|+.
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHH
Confidence 345788888888888888888865
No 304
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=35.22 E-value=56 Score=26.15 Aligned_cols=52 Identities=23% Similarity=0.365 Sum_probs=30.7
Q ss_pred cccccccccccCCccceecCcccccccccCCCCccccCCCCCCcccCCCCcceeeCCCCCccCCh
Q psy3507 3 NYLVCTASIGLKNPFTLATCIHCRLLLVPTAEELMYHCKTCSTVSHPNISYKYTCYACDYHTLMS 67 (134)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~C~~C~~h~~~h~~~~~~~C~~C~~~f~~~~~~~~~C~~C~~~f~~~ 67 (134)
.++.| +..+|-....|..|+..+.. -.|+.||....... --|+.||......
T Consensus 3 ~Cp~C----g~~n~~~akFC~~CG~~l~~------~~Cp~CG~~~~~~~---~fC~~CG~~~~~~ 54 (645)
T PRK14559 3 ICPQC----QFENPNNNRFCQKCGTSLTH------KPCPQCGTEVPVDE---AHCPNCGAETGTI 54 (645)
T ss_pred cCCCC----CCcCCCCCccccccCCCCCC------CcCCCCCCCCCccc---ccccccCCcccch
Confidence 34555 33455556678888665421 25888888743222 2488888765554
No 305
>KOG2923|consensus
Probab=34.98 E-value=25 Score=18.92 Aligned_cols=11 Identities=36% Similarity=0.942 Sum_probs=5.4
Q ss_pred CCCceeccccC
Q psy3507 79 GEKPYKCEYCA 89 (134)
Q Consensus 79 ~~~~~~C~~C~ 89 (134)
|+..-.|+-|+
T Consensus 41 ge~Va~CpsCS 51 (67)
T KOG2923|consen 41 GEDVARCPSCS 51 (67)
T ss_pred CCeeecCCCce
Confidence 44444555554
No 306
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=34.92 E-value=39 Score=19.93 Aligned_cols=12 Identities=33% Similarity=0.445 Sum_probs=6.1
Q ss_pred ceeeCCCCCccC
Q psy3507 54 KYTCYACDYHTL 65 (134)
Q Consensus 54 ~~~C~~C~~~f~ 65 (134)
...|+.||..+.
T Consensus 42 h~~C~~CG~y~~ 53 (99)
T PRK14892 42 IITCGNCGLYTE 53 (99)
T ss_pred eEECCCCCCccC
Confidence 345666655443
No 307
>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=34.65 E-value=35 Score=16.15 Aligned_cols=11 Identities=27% Similarity=0.652 Sum_probs=3.4
Q ss_pred ceeeCCCCCcc
Q psy3507 54 KYTCYACDYHT 64 (134)
Q Consensus 54 ~~~C~~C~~~f 64 (134)
.|-|+.|...+
T Consensus 3 ryyCdyC~~~~ 13 (38)
T PF06220_consen 3 RYYCDYCKKYL 13 (38)
T ss_dssp S-B-TTT--B-
T ss_pred Ceeccccccee
Confidence 35566666655
No 308
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=34.24 E-value=22 Score=19.51 Aligned_cols=12 Identities=33% Similarity=0.927 Sum_probs=5.4
Q ss_pred cccCCCCCCccc
Q psy3507 37 MYHCKTCSTVSH 48 (134)
Q Consensus 37 ~~~C~~C~~~f~ 48 (134)
.|.|+.|++.|.
T Consensus 17 ~~~C~~C~~~~~ 28 (70)
T PF07191_consen 17 HYHCEACQKDYK 28 (70)
T ss_dssp EEEETTT--EEE
T ss_pred EEECccccccce
Confidence 355666665543
No 309
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=34.22 E-value=16 Score=19.12 Aligned_cols=10 Identities=30% Similarity=0.899 Sum_probs=6.1
Q ss_pred CceeccccCc
Q psy3507 81 KPYKCEYCAY 90 (134)
Q Consensus 81 ~~~~C~~C~~ 90 (134)
..|-|+.|..
T Consensus 30 ~tYmC~eC~~ 39 (56)
T PF09963_consen 30 HTYMCDECKE 39 (56)
T ss_pred cceeChhHHH
Confidence 3477777654
No 310
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=33.06 E-value=34 Score=17.90 Aligned_cols=20 Identities=20% Similarity=0.592 Sum_probs=10.2
Q ss_pred ccCCCCCCcccCCCCcceeeCCCC
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACD 61 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~ 61 (134)
..|+.||..- .....|+.||
T Consensus 28 ~~C~~CG~~~----~~H~vC~~CG 47 (57)
T PRK12286 28 VECPNCGEPK----LPHRVCPSCG 47 (57)
T ss_pred eECCCCCCcc----CCeEECCCCC
Confidence 4566666532 1234566665
No 311
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=32.64 E-value=34 Score=17.51 Aligned_cols=27 Identities=19% Similarity=0.418 Sum_probs=9.9
Q ss_pred cCcc--cccccccCCCCcc--ccCCCCCCcc
Q psy3507 21 TCIH--CRLLLVPTAEELM--YHCKTCSTVS 47 (134)
Q Consensus 21 ~C~~--C~~h~~~h~~~~~--~~C~~C~~~f 47 (134)
.|.. |..-+....+... ..|+.|+..|
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSEE
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCcC
Confidence 4544 5444444333333 5565555544
No 312
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=32.49 E-value=34 Score=20.62 Aligned_cols=9 Identities=22% Similarity=0.626 Sum_probs=6.1
Q ss_pred eecCccccc
Q psy3507 19 LATCIHCRL 27 (134)
Q Consensus 19 ~~~C~~C~~ 27 (134)
.+.|..|+.
T Consensus 22 ~l~C~kCgy 30 (113)
T COG1594 22 KLVCRKCGY 30 (113)
T ss_pred EEECCCCCc
Confidence 677888833
No 313
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=32.48 E-value=28 Score=29.23 Aligned_cols=45 Identities=31% Similarity=0.493 Sum_probs=26.4
Q ss_pred eecCcccccccc-------cCCCCccccCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 19 LATCIHCRLLLV-------PTAEELMYHCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 19 ~~~C~~C~~h~~-------~h~~~~~~~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
...|+.|.+... --..+..|.|+.||+.+.-..-.--.|+.||-.
T Consensus 796 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 847 (1006)
T PRK12775 796 VATCPKCHRPLEGDEEYVCCATSELQWRCDDCGKVSEGFAFPYGMCPACGGK 847 (1006)
T ss_pred CccCcccCCCCCCCceeEEecCcceeeehhhhccccccccCCcCcCcccccc
Confidence 357888822211 123456799999998865322222358888854
No 314
>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=32.28 E-value=25 Score=18.00 Aligned_cols=30 Identities=37% Similarity=0.711 Sum_probs=15.3
Q ss_pred eecCccccccccc--CCCCccccCCCCCCccc
Q psy3507 19 LATCIHCRLLLVP--TAEELMYHCKTCSTVSH 48 (134)
Q Consensus 19 ~~~C~~C~~h~~~--h~~~~~~~C~~C~~~f~ 48 (134)
...|+.|++-+-. ...+...+|+-|+....
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~ 35 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINH 35 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccce
Confidence 3456666443222 22234566777776544
No 315
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=31.83 E-value=36 Score=17.25 Aligned_cols=19 Identities=26% Similarity=0.810 Sum_probs=10.6
Q ss_pred CCeecCcChhhhcCHHHHHHHH
Q psy3507 109 KPYICQQCRDTFSSLYLFRNRL 130 (134)
Q Consensus 109 ~~~~C~~C~~~F~~~~~l~~H~ 130 (134)
++--|+.|...|.. |..|+
T Consensus 4 k~GYCE~C~~ky~~---l~~Hi 22 (49)
T PF07535_consen 4 KPGYCENCRVKYDD---LEEHI 22 (49)
T ss_pred CCccCccccchhhh---HHHHh
Confidence 34456666666543 55555
No 316
>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=31.37 E-value=40 Score=24.23 Aligned_cols=26 Identities=23% Similarity=0.485 Sum_probs=12.8
Q ss_pred CCccccCCCCCCcccCCCCcceeeCCCCC
Q psy3507 34 EELMYHCKTCSTVSHPNISYKYTCYACDY 62 (134)
Q Consensus 34 ~~~~~~C~~C~~~f~~~~~~~~~C~~C~~ 62 (134)
|.+-..|..|+..... ..-.|+.||.
T Consensus 207 G~RyL~CslC~teW~~---~R~~C~~Cg~ 232 (305)
T TIGR01562 207 GLRYLSCSLCATEWHY---VRVKCSHCEE 232 (305)
T ss_pred CceEEEcCCCCCcccc---cCccCCCCCC
Confidence 3444556666654321 2345666664
No 317
>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=30.91 E-value=45 Score=21.44 Aligned_cols=20 Identities=15% Similarity=0.165 Sum_probs=13.8
Q ss_pred CCCCcceeeCCCCCccCChH
Q psy3507 49 PNISYKYTCYACDYHTLMSE 68 (134)
Q Consensus 49 ~~~~~~~~C~~C~~~f~~~~ 68 (134)
...+.|.-|..||+.|+.-.
T Consensus 63 ~~~~~PsYC~~CGkpyPWt~ 82 (158)
T PF10083_consen 63 GHYEAPSYCHNCGKPYPWTE 82 (158)
T ss_pred CCCCCChhHHhCCCCCchHH
Confidence 34446777888888887754
No 318
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=30.88 E-value=37 Score=24.96 Aligned_cols=28 Identities=18% Similarity=0.365 Sum_probs=21.4
Q ss_pred hhcCCCCCeecCcCh-hhhcCHHHHHHHH
Q psy3507 103 RKHTGDKPYICQQCR-DTFSSLYLFRNRL 130 (134)
Q Consensus 103 ~~h~~~~~~~C~~C~-~~F~~~~~l~~H~ 130 (134)
+.|.-.+.|.|.+|| +.+.-+..+.+|.
T Consensus 367 klhgLd~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 367 KLHGLDIEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred HhcCCCcceeeeecccccccchHHHHhhh
Confidence 456667789999999 7777777777774
No 319
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=30.75 E-value=36 Score=17.61 Aligned_cols=8 Identities=25% Similarity=0.837 Sum_probs=4.4
Q ss_pred ccCCCCCC
Q psy3507 38 YHCKTCST 45 (134)
Q Consensus 38 ~~C~~C~~ 45 (134)
..|+.||.
T Consensus 27 ~~C~~cG~ 34 (55)
T TIGR01031 27 VVCPNCGE 34 (55)
T ss_pred eECCCCCC
Confidence 44555655
No 320
>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=30.40 E-value=50 Score=15.18 Aligned_cols=21 Identities=19% Similarity=0.347 Sum_probs=11.5
Q ss_pred ceeccccCccccCchhHHHHhh
Q psy3507 82 PYKCEYCAYSCTQSSALKIHER 103 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~ 103 (134)
.+.|+.|++.... +-+..|+.
T Consensus 4 ~~~C~nC~R~v~a-~RfA~HLe 24 (33)
T PF08209_consen 4 YVECPNCGRPVAA-SRFAPHLE 24 (33)
T ss_dssp EEE-TTTSSEEEG-GGHHHHHH
T ss_pred eEECCCCcCCcch-hhhHHHHH
Confidence 3667777765443 34566654
No 321
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=29.99 E-value=30 Score=21.51 Aligned_cols=23 Identities=26% Similarity=0.603 Sum_probs=9.3
Q ss_pred cCcccccccccCCCCccccCCCCCC
Q psy3507 21 TCIHCRLLLVPTAEELMYHCKTCST 45 (134)
Q Consensus 21 ~C~~C~~h~~~h~~~~~~~C~~C~~ 45 (134)
.|..|+.-+..+.|+ ..|+.|+.
T Consensus 30 hCp~Cg~PLF~KdG~--v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPLFRKDGE--VFCPVCGY 52 (131)
T ss_pred hCcccCCcceeeCCe--EECCCCCc
Confidence 344444433333332 33444543
No 322
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=29.88 E-value=28 Score=22.82 Aligned_cols=23 Identities=22% Similarity=0.489 Sum_probs=13.6
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
+.|.-|++.|. ...-.|+.||..
T Consensus 140 ~rC~GC~~~f~---~~~~~Cp~CG~~ 162 (177)
T COG1439 140 LRCHGCKRIFP---EPKDFCPICGSP 162 (177)
T ss_pred EEEecCceecC---CCCCcCCCCCCc
Confidence 66777777776 222347777654
No 323
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=29.68 E-value=36 Score=18.31 Aligned_cols=7 Identities=43% Similarity=1.488 Sum_probs=3.2
Q ss_pred ccCCCCC
Q psy3507 38 YHCKTCS 44 (134)
Q Consensus 38 ~~C~~C~ 44 (134)
|.|+.||
T Consensus 1 y~C~KCg 7 (64)
T PF09855_consen 1 YKCPKCG 7 (64)
T ss_pred CCCCCCC
Confidence 3444444
No 324
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=29.68 E-value=49 Score=17.51 Aligned_cols=9 Identities=22% Similarity=0.722 Sum_probs=3.9
Q ss_pred eeeCCCCCc
Q psy3507 55 YTCYACDYH 63 (134)
Q Consensus 55 ~~C~~C~~~ 63 (134)
-.|..|+..
T Consensus 31 V~C~~Cg~~ 39 (59)
T PRK00415 31 VRCLVCGKT 39 (59)
T ss_pred EECcccCCC
Confidence 344444443
No 325
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=29.46 E-value=68 Score=23.23 Aligned_cols=25 Identities=32% Similarity=0.642 Sum_probs=17.2
Q ss_pred CceeccccCccccCchhHHHHhhhc
Q psy3507 81 KPYKCEYCAYSCTQSSALKIHERKH 105 (134)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~~h 105 (134)
..|+|+.|...|...-+...|...|
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHHh
Confidence 3477887777777777777775544
No 326
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=29.36 E-value=74 Score=15.05 Aligned_cols=8 Identities=25% Similarity=0.621 Sum_probs=3.7
Q ss_pred CCCCCCcc
Q psy3507 40 CKTCSTVS 47 (134)
Q Consensus 40 C~~C~~~f 47 (134)
|.+|-..|
T Consensus 3 C~IC~~~~ 10 (44)
T PF13639_consen 3 CPICLEEF 10 (44)
T ss_dssp ETTTTCBH
T ss_pred CcCCChhh
Confidence 44444444
No 327
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=29.19 E-value=25 Score=16.74 Aligned_cols=12 Identities=17% Similarity=0.387 Sum_probs=9.0
Q ss_pred ccccCCCCCCcc
Q psy3507 36 LMYHCKTCSTVS 47 (134)
Q Consensus 36 ~~~~C~~C~~~f 47 (134)
..+.|+.||..+
T Consensus 31 p~~~C~~CGE~~ 42 (46)
T TIGR03831 31 PALVCPQCGEEY 42 (46)
T ss_pred CccccccCCCEe
Confidence 447799999865
No 328
>KOG1842|consensus
Probab=29.00 E-value=26 Score=26.47 Aligned_cols=24 Identities=13% Similarity=0.300 Sum_probs=17.7
Q ss_pred ceeeCCCCCccCChHHHHHHHHHh
Q psy3507 54 KYTCYACDYHTLMSEDMKKHMRKH 77 (134)
Q Consensus 54 ~~~C~~C~~~f~~~~~l~~H~~~h 77 (134)
.|.|++|...|.+.+.|..|...-
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~e 38 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVE 38 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhh
Confidence 477888887777777777776643
No 329
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=28.87 E-value=7.8 Score=21.02 Aligned_cols=12 Identities=25% Similarity=0.528 Sum_probs=4.5
Q ss_pred cCCCceeccccC
Q psy3507 78 TGEKPYKCEYCA 89 (134)
Q Consensus 78 ~~~~~~~C~~C~ 89 (134)
.|.-..+|+-|.
T Consensus 25 ~GvViv~C~gC~ 36 (66)
T PF05180_consen 25 KGVVIVQCPGCK 36 (66)
T ss_dssp TSEEEEE-TTS-
T ss_pred CCeEEEECCCCc
Confidence 343344555554
No 330
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=28.81 E-value=45 Score=17.85 Aligned_cols=11 Identities=27% Similarity=0.700 Sum_probs=6.8
Q ss_pred ccCCCCCCccc
Q psy3507 38 YHCKTCSTVSH 48 (134)
Q Consensus 38 ~~C~~C~~~f~ 48 (134)
..|++|++...
T Consensus 7 v~CP~C~k~~~ 17 (62)
T PRK00418 7 VNCPTCGKPVE 17 (62)
T ss_pred ccCCCCCCccc
Confidence 55677776544
No 331
>KOG2071|consensus
Probab=28.76 E-value=42 Score=26.32 Aligned_cols=26 Identities=31% Similarity=0.432 Sum_probs=20.3
Q ss_pred cceeeCCCCCccCChHHHHHHHHHhc
Q psy3507 53 YKYTCYACDYHTLMSEDMKKHMRKHT 78 (134)
Q Consensus 53 ~~~~C~~C~~~f~~~~~l~~H~~~h~ 78 (134)
.+..|..||..|........||..|.
T Consensus 417 ~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 417 SPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CcchhcccccccccchhhhhHhhhhh
Confidence 35789999999998888777776654
No 332
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=28.74 E-value=21 Score=18.31 Aligned_cols=12 Identities=17% Similarity=0.653 Sum_probs=7.2
Q ss_pred CCccccCCCCCC
Q psy3507 34 EELMYHCKTCST 45 (134)
Q Consensus 34 ~~~~~~C~~C~~ 45 (134)
++....|+.||+
T Consensus 43 ~~~i~~Cp~CgR 54 (56)
T PF02591_consen 43 GDEIVFCPNCGR 54 (56)
T ss_pred CCCeEECcCCCc
Confidence 345566676665
No 333
>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=28.29 E-value=26 Score=17.98 Aligned_cols=16 Identities=19% Similarity=0.571 Sum_probs=8.8
Q ss_pred CCCccccCCCCCCccc
Q psy3507 33 AEELMYHCKTCSTVSH 48 (134)
Q Consensus 33 ~~~~~~~C~~C~~~f~ 48 (134)
.+...|.|.+|++.+.
T Consensus 31 ~~~~~~rC~YCe~~~~ 46 (52)
T PF02748_consen 31 KEPIKLRCHYCERIIT 46 (52)
T ss_dssp TTTCEEEETTT--EEE
T ss_pred CCCCEEEeeCCCCEec
Confidence 3455677888877653
No 334
>PRK06260 threonine synthase; Validated
Probab=28.28 E-value=40 Score=24.92 Aligned_cols=25 Identities=28% Similarity=0.668 Sum_probs=13.8
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
++|..||+.|... ...+.|+.|+..
T Consensus 4 ~~C~~cg~~~~~~-~~~~~Cp~cg~~ 28 (397)
T PRK06260 4 LKCIECGKEYDPD-EIIYTCPECGGL 28 (397)
T ss_pred EEECCCCCCCCCC-CccccCCCCCCe
Confidence 5566666666432 224566666543
No 335
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=28.24 E-value=52 Score=17.15 Aligned_cols=10 Identities=30% Similarity=0.906 Sum_probs=2.4
Q ss_pred cccCCCCCCc
Q psy3507 37 MYHCKTCSTV 46 (134)
Q Consensus 37 ~~~C~~C~~~ 46 (134)
.|.|++||.+
T Consensus 33 ~y~Cp~CgAt 42 (55)
T PF05741_consen 33 KYVCPICGAT 42 (55)
T ss_dssp G---TTT---
T ss_pred cCcCCCCcCc
Confidence 3666666654
No 336
>KOG0402|consensus
Probab=28.19 E-value=21 Score=20.32 Aligned_cols=29 Identities=17% Similarity=0.400 Sum_probs=19.0
Q ss_pred ccCCCCCCccc-CCCCcceeeCCCCCccCC
Q psy3507 38 YHCKTCSTVSH-PNISYKYTCYACDYHTLM 66 (134)
Q Consensus 38 ~~C~~C~~~f~-~~~~~~~~C~~C~~~f~~ 66 (134)
|.|+.||+.-- ....-.+.|..|.+.+..
T Consensus 37 y~CsfCGK~~vKR~AvGiW~C~~C~kv~ag 66 (92)
T KOG0402|consen 37 YTCSFCGKKTVKRKAVGIWKCGSCKKVVAG 66 (92)
T ss_pred hhhhhcchhhhhhhceeEEecCCccceecc
Confidence 88888887543 333345778888777643
No 337
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=27.97 E-value=39 Score=25.15 Aligned_cols=22 Identities=23% Similarity=0.434 Sum_probs=10.3
Q ss_pred ccCCCCCCcccCCCCcceeeCCCC
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACD 61 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~ 61 (134)
+.|..||+.|. ....+.|+.|+
T Consensus 3 l~C~~Cg~~~~--~~~~~~C~~c~ 24 (398)
T TIGR03844 3 LRCPGCGEVLP--DHYTLSCPLDC 24 (398)
T ss_pred EEeCCCCCccC--CccccCCCCCC
Confidence 34555555553 22235555444
No 338
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=27.77 E-value=34 Score=25.85 Aligned_cols=53 Identities=17% Similarity=0.366 Sum_probs=32.0
Q ss_pred ccCCCCCCccc--CCCCcceeeCCCCCccCChHHHHHHHHH----h-----cCCCceeccccCcc
Q psy3507 38 YHCKTCSTVSH--PNISYKYTCYACDYHTLMSEDMKKHMRK----H-----TGEKPYKCEYCAYS 91 (134)
Q Consensus 38 ~~C~~C~~~f~--~~~~~~~~C~~C~~~f~~~~~l~~H~~~----h-----~~~~~~~C~~C~~~ 91 (134)
-.|-+|.+ |. ..+-.+..|+.|+.+.-..-.|...+.. - ..+..|.|.-||+.
T Consensus 129 C~C~iC~k-fD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~ 192 (446)
T PF07227_consen 129 CMCCICSK-FDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKT 192 (446)
T ss_pred CCccccCC-cccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCCh
Confidence 45677766 54 4444567788888877666666655321 0 11345888888763
No 339
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=27.69 E-value=30 Score=17.75 Aligned_cols=10 Identities=20% Similarity=0.627 Sum_probs=6.9
Q ss_pred cCCCCCCccc
Q psy3507 39 HCKTCSTVSH 48 (134)
Q Consensus 39 ~C~~C~~~f~ 48 (134)
.|++||..+.
T Consensus 2 ~CPyCge~~~ 11 (52)
T PF14255_consen 2 QCPYCGEPIE 11 (52)
T ss_pred CCCCCCCeeE
Confidence 5777777665
No 340
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=27.21 E-value=42 Score=21.06 Aligned_cols=21 Identities=19% Similarity=0.295 Sum_probs=10.7
Q ss_pred CcccccccccccCCccceecCccc
Q psy3507 2 HNYLVCTASIGLKNPFTLATCIHC 25 (134)
Q Consensus 2 h~~~~~~~~~~~~~~~~~~~C~~C 25 (134)
.|+..|++-|... ....|+.|
T Consensus 4 ~nC~~CgklF~~~---~~~iCp~C 24 (137)
T TIGR03826 4 ANCPKCGRLFVKT---GRDVCPSC 24 (137)
T ss_pred ccccccchhhhhc---CCccCHHH
Confidence 4555666655542 12346666
No 341
>KOG3362|consensus
Probab=27.10 E-value=20 Score=22.65 Aligned_cols=20 Identities=30% Similarity=0.607 Sum_probs=11.3
Q ss_pred ceeeCCCCCccCChHHHHHH
Q psy3507 54 KYTCYACDYHTLMSEDMKKH 73 (134)
Q Consensus 54 ~~~C~~C~~~f~~~~~l~~H 73 (134)
+|.|..||..+-+..-+..|
T Consensus 129 ~ysC~~CG~kyCsv~C~~~H 148 (156)
T KOG3362|consen 129 KYSCVNCGTKYCSVRCLKTH 148 (156)
T ss_pred hhHHHhcCCceeechhhhhc
Confidence 45566666655555555544
No 342
>KOG4727|consensus
Probab=27.08 E-value=57 Score=21.36 Aligned_cols=27 Identities=22% Similarity=0.333 Sum_probs=21.5
Q ss_pred CCCCcceeeCCCCCccCChHHHHHHHH
Q psy3507 49 PNISYKYTCYACDYHTLMSEDMKKHMR 75 (134)
Q Consensus 49 ~~~~~~~~C~~C~~~f~~~~~l~~H~~ 75 (134)
......|-|++|+-++....++..|+.
T Consensus 70 ~sq~~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 70 RSQKGGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ccccCceeeeecceeehhhHHHHHHhc
Confidence 344456899999999999999888875
No 343
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=26.92 E-value=51 Score=25.06 Aligned_cols=23 Identities=17% Similarity=0.460 Sum_probs=20.7
Q ss_pred CCeecCcChhhhcCHHHHHHHHH
Q psy3507 109 KPYICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 109 ~~~~C~~C~~~F~~~~~l~~H~~ 131 (134)
..|.|+.|-+-|.+...|.+|+.
T Consensus 197 ~lyiCe~Cl~y~~~~~~~~~H~~ 219 (450)
T PLN00104 197 KLYFCEFCLKFMKRKEQLQRHMK 219 (450)
T ss_pred eEEEchhhhhhhcCHHHHHHHHh
Confidence 45899999999999999999985
No 344
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=26.74 E-value=77 Score=15.27 Aligned_cols=21 Identities=33% Similarity=1.039 Sum_probs=9.4
Q ss_pred ccCCCCCCcccCCCCcceeeCCCC
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACD 61 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~ 61 (134)
+.|..|+..+ ....|.|..|.
T Consensus 5 ~~C~~C~~~i---~g~ry~C~~C~ 25 (44)
T smart00291 5 YSCDTCGKPI---VGVRYHCLVCP 25 (44)
T ss_pred cCCCCCCCCC---cCCEEECCCCC
Confidence 4455555521 12345555553
No 345
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=26.74 E-value=67 Score=16.58 Aligned_cols=15 Identities=27% Similarity=0.605 Sum_probs=7.4
Q ss_pred ceecCcccccccccC
Q psy3507 18 TLATCIHCRLLLVPT 32 (134)
Q Consensus 18 ~~~~C~~C~~h~~~h 32 (134)
....|..|+.....|
T Consensus 25 ~l~~c~~cg~~~~~H 39 (56)
T PF01783_consen 25 NLVKCPNCGEPKLPH 39 (56)
T ss_dssp SEEESSSSSSEESTT
T ss_pred ceeeeccCCCEeccc
Confidence 445555555444444
No 346
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=26.73 E-value=19 Score=21.04 Aligned_cols=33 Identities=12% Similarity=0.061 Sum_probs=15.2
Q ss_pred ccccCCCCCCcccCCCCc-ceeeCCCCCccCChH
Q psy3507 36 LMYHCKTCSTVSHPNISY-KYTCYACDYHTLMSE 68 (134)
Q Consensus 36 ~~~~C~~C~~~f~~~~~~-~~~C~~C~~~f~~~~ 68 (134)
++..|..|.+......-. .-.|+.|...|...-
T Consensus 61 ~~iiCGvC~~~LT~~EY~~~~~Cp~C~spFNp~C 94 (105)
T COG4357 61 KAIICGVCRKLLTRAEYGMCGSCPYCQSPFNPGC 94 (105)
T ss_pred ccEEhhhhhhhhhHHHHhhcCCCCCcCCCCCccc
Confidence 334455555544311100 123777776666543
No 347
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=26.73 E-value=31 Score=15.61 Aligned_cols=13 Identities=23% Similarity=0.922 Sum_probs=9.8
Q ss_pred ccccCCCCCCccc
Q psy3507 36 LMYHCKTCSTVSH 48 (134)
Q Consensus 36 ~~~~C~~C~~~f~ 48 (134)
+-|+|+.||....
T Consensus 6 ~~ykC~~Cgniv~ 18 (34)
T TIGR00319 6 QVYKCEVCGNIVE 18 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 4588888887765
No 348
>PLN03239 histone acetyltransferase; Provisional
Probab=26.67 E-value=57 Score=23.95 Aligned_cols=24 Identities=17% Similarity=0.185 Sum_probs=20.4
Q ss_pred CCCeecCcChhhhcCHHHHHHHHH
Q psy3507 108 DKPYICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 108 ~~~~~C~~C~~~F~~~~~l~~H~~ 131 (134)
+.-|.|+.|-+-|.+...|.+|+.
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHH
Confidence 346999999999999999999874
No 349
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=26.51 E-value=32 Score=15.59 Aligned_cols=13 Identities=23% Similarity=0.876 Sum_probs=9.3
Q ss_pred ccccCCCCCCccc
Q psy3507 36 LMYHCKTCSTVSH 48 (134)
Q Consensus 36 ~~~~C~~C~~~f~ 48 (134)
+-|+|+.||....
T Consensus 3 ~~ykC~~CGniv~ 15 (34)
T cd00974 3 EVYKCEICGNIVE 15 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 3578888887664
No 350
>COG4640 Predicted membrane protein [Function unknown]
Probab=26.46 E-value=61 Score=24.29 Aligned_cols=16 Identities=13% Similarity=0.316 Sum_probs=9.5
Q ss_pred eeCCCCCccCChHHHH
Q psy3507 56 TCYACDYHTLMSEDMK 71 (134)
Q Consensus 56 ~C~~C~~~f~~~~~l~ 71 (134)
.|+.||..|.....+.
T Consensus 17 qC~qCG~~~t~~~sqa 32 (465)
T COG4640 17 QCTQCGHKFTSRQSQA 32 (465)
T ss_pred cccccCCcCCchhhhh
Confidence 3666666666655443
No 351
>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=26.25 E-value=24 Score=25.02 Aligned_cols=30 Identities=27% Similarity=0.473 Sum_probs=15.4
Q ss_pred ccCCCCCCcccCC--CCcceeeCCCCCccCCh
Q psy3507 38 YHCKTCSTVSHPN--ISYKYTCYACDYHTLMS 67 (134)
Q Consensus 38 ~~C~~C~~~f~~~--~~~~~~C~~C~~~f~~~ 67 (134)
.+|+.|+...... ....+.|+.|+..|...
T Consensus 27 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~ 58 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERNLEVCPKCDHHMRMD 58 (285)
T ss_pred eECCCCcchhhHHHHHhhCCCCCCCCCcCcCC
Confidence 4566666654421 11235666666665543
No 352
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=26.23 E-value=52 Score=16.12 Aligned_cols=23 Identities=35% Similarity=0.868 Sum_probs=11.2
Q ss_pred cccCCCCCCcccCCCCcceeeCCCC
Q psy3507 37 MYHCKTCSTVSHPNISYKYTCYACD 61 (134)
Q Consensus 37 ~~~C~~C~~~f~~~~~~~~~C~~C~ 61 (134)
.+.|+.|+... .....|.|..|.
T Consensus 4 ~~~C~~C~~~~--i~g~Ry~C~~C~ 26 (46)
T PF00569_consen 4 GYTCDGCGTDP--IIGVRYHCLVCP 26 (46)
T ss_dssp SCE-SSS-SSS--EESSEEEESSSS
T ss_pred CeECcCCCCCc--CcCCeEECCCCC
Confidence 36677776631 122456777664
No 353
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.17 E-value=92 Score=17.57 Aligned_cols=38 Identities=16% Similarity=0.192 Sum_probs=25.1
Q ss_pred cCCCCCCccc---CCCCcceeeCCCCCccCChHHHHHHHHH
Q psy3507 39 HCKTCSTVSH---PNISYKYTCYACDYHTLMSEDMKKHMRK 76 (134)
Q Consensus 39 ~C~~C~~~f~---~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 76 (134)
.|+.|+.... ..+...=.|+.|+-.+.....|..-+..
T Consensus 3 lCP~C~v~l~~~~rs~vEiD~CPrCrGVWLDrGELdKli~r 43 (88)
T COG3809 3 LCPICGVELVMSVRSGVEIDYCPRCRGVWLDRGELDKLIER 43 (88)
T ss_pred ccCcCCceeeeeeecCceeeeCCccccEeecchhHHHHHHH
Confidence 4777776554 2333334588888888888888776553
No 354
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=26.14 E-value=75 Score=15.38 Aligned_cols=7 Identities=43% Similarity=1.602 Sum_probs=3.2
Q ss_pred ceeeCCC
Q psy3507 54 KYTCYAC 60 (134)
Q Consensus 54 ~~~C~~C 60 (134)
.|+|..|
T Consensus 14 ry~C~~C 20 (43)
T cd02340 14 RYKCLVC 20 (43)
T ss_pred eEECCCC
Confidence 3444444
No 355
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=25.82 E-value=71 Score=21.38 Aligned_cols=11 Identities=27% Similarity=0.591 Sum_probs=7.4
Q ss_pred ceeccccCccc
Q psy3507 82 PYKCEYCAYSC 92 (134)
Q Consensus 82 ~~~C~~C~~~f 92 (134)
...|..||..+
T Consensus 30 lvrC~eCG~V~ 40 (201)
T COG1326 30 LVRCEECGTVH 40 (201)
T ss_pred EEEccCCCcEe
Confidence 46777777665
No 356
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=25.66 E-value=33 Score=22.46 Aligned_cols=28 Identities=29% Similarity=0.635 Sum_probs=7.6
Q ss_pred cceecCcccccccccCCCC--ccccCCCCC
Q psy3507 17 FTLATCIHCRLLLVPTAEE--LMYHCKTCS 44 (134)
Q Consensus 17 ~~~~~C~~C~~h~~~h~~~--~~~~C~~C~ 44 (134)
.....|..|+-+..++..+ ..|.|+.|.
T Consensus 132 l~l~~C~~C~~~fv~~~~~~~~~~~Cp~C~ 161 (175)
T PF05280_consen 132 LQLAPCRRCGGHFVTHAHDPRHSFVCPFCQ 161 (175)
T ss_dssp EEEEE-TTT--EEEEESS--SS----TT--
T ss_pred ccccCCCCCCCCeECcCCCCCcCcCCCCCC
Confidence 3344555554444443222 234444444
No 357
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=25.52 E-value=48 Score=21.71 Aligned_cols=19 Identities=16% Similarity=0.389 Sum_probs=13.1
Q ss_pred CCeecCcChhhhcCHHHHH
Q psy3507 109 KPYICQQCRDTFSSLYLFR 127 (134)
Q Consensus 109 ~~~~C~~C~~~F~~~~~l~ 127 (134)
....|..||+.|.....+.
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVA 131 (181)
T ss_pred ccCcCcccCCccCcHhHHH
Confidence 4677888888887655443
No 358
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=25.51 E-value=25 Score=25.09 Aligned_cols=30 Identities=30% Similarity=0.603 Sum_probs=13.6
Q ss_pred ccCCCCCCcccCC--CCcceeeCCCCCccCCh
Q psy3507 38 YHCKTCSTVSHPN--ISYKYTCYACDYHTLMS 67 (134)
Q Consensus 38 ~~C~~C~~~f~~~--~~~~~~C~~C~~~f~~~ 67 (134)
.+|+.|+...... .+..+.|+.|+..|...
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICEQCGYHLKMS 70 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCCCCCCCcCCC
Confidence 4455555544311 11234555555555443
No 359
>PTZ00448 hypothetical protein; Provisional
Probab=25.32 E-value=56 Score=24.13 Aligned_cols=23 Identities=22% Similarity=0.531 Sum_probs=20.1
Q ss_pred ceeeCCCCCccCChHHHHHHHHH
Q psy3507 54 KYTCYACDYHTLMSEDMKKHMRK 76 (134)
Q Consensus 54 ~~~C~~C~~~f~~~~~l~~H~~~ 76 (134)
.|.|..|+..|.+....+.|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 47899999999988899999874
No 360
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=25.11 E-value=67 Score=18.05 Aligned_cols=9 Identities=33% Similarity=0.962 Sum_probs=5.0
Q ss_pred ccCCCCCCc
Q psy3507 38 YHCKTCSTV 46 (134)
Q Consensus 38 ~~C~~C~~~ 46 (134)
|.|+-||..
T Consensus 2 ~~CPCCg~~ 10 (78)
T PF14206_consen 2 YPCPCCGYY 10 (78)
T ss_pred ccCCCCCcE
Confidence 456666643
No 361
>PTZ00064 histone acetyltransferase; Provisional
Probab=25.06 E-value=63 Score=25.04 Aligned_cols=24 Identities=25% Similarity=0.351 Sum_probs=21.0
Q ss_pred CCCeecCcChhhhcCHHHHHHHHH
Q psy3507 108 DKPYICQQCRDTFSSLYLFRNRLQ 131 (134)
Q Consensus 108 ~~~~~C~~C~~~F~~~~~l~~H~~ 131 (134)
..-|.|+.|-+-|.+...|.+|+.
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~ 301 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLS 301 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHh
Confidence 345899999999999999999985
No 362
>KOG0782|consensus
Probab=24.86 E-value=14 Score=29.01 Aligned_cols=51 Identities=18% Similarity=0.386 Sum_probs=32.7
Q ss_pred HHHHHHHHHhcCCCceeccccCccccCchhHHHHhhhcCCC-CCeecCcChhhhcCHH
Q psy3507 68 EDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHTGD-KPYICQQCRDTFSSLY 124 (134)
Q Consensus 68 ~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~~C~~C~~~F~~~~ 124 (134)
+.+.+|--+|.....-+|..|++.|.++..+ |..+ ....|..|...|-.+-
T Consensus 239 ~~fvrHHWVHrrRqeGkC~~CgKgFQQKf~F------hsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 239 SGFVRHHWVHRRRQEGKCNTCGKGFQQKFFF------HSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred ccchHHhHhhHhhhccccchhhhhhhhheee------ccccEEEEEehHHHHHhhcch
Confidence 3666666666555556799999888765433 2222 2367888888776543
No 363
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=24.76 E-value=24 Score=23.54 Aligned_cols=21 Identities=38% Similarity=0.698 Sum_probs=0.0
Q ss_pred CceeccccCc-cccCchhHHHH
Q psy3507 81 KPYKCEYCAY-SCTQSSALKIH 101 (134)
Q Consensus 81 ~~~~C~~C~~-~f~~~~~l~~H 101 (134)
+.|.|.+||. +|.-+..+..|
T Consensus 100 ~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 100 VEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp ----------------------
T ss_pred CeeeeEeCCCcceecHHHHHHh
Confidence 4466666663 44455555555
No 364
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=24.55 E-value=52 Score=23.34 Aligned_cols=28 Identities=18% Similarity=0.371 Sum_probs=20.2
Q ss_pred cCcccccccccCCCCccccCCCCCCccc
Q psy3507 21 TCIHCRLLLVPTAEELMYHCKTCSTVSH 48 (134)
Q Consensus 21 ~C~~C~~h~~~h~~~~~~~C~~C~~~f~ 48 (134)
.|+.|+.-+..-.++....|+.||..+-
T Consensus 113 FCg~CG~~~~~~~~g~~~~C~~cg~~~f 140 (279)
T COG2816 113 FCGRCGTKTYPREGGWARVCPKCGHEHF 140 (279)
T ss_pred CCCCCCCcCccccCceeeeCCCCCCccC
Confidence 5778877776666677777888886654
No 365
>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=24.07 E-value=1.1e+02 Score=15.46 Aligned_cols=45 Identities=9% Similarity=0.004 Sum_probs=23.9
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCcccc
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCT 93 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 93 (134)
+.|++|+..+... ....||..|.. ..+...++. ...|+.|+..+.
T Consensus 2 ~~Cpi~~~~~~~P-----v~~~~G~v~~~-~~i~~~~~~-----~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKDP-----VILPSGQTYER-RAIEKWLLS-----HGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCCC-----EECCCCCEEeH-HHHHHHHHH-----CCCCCCCcCCCC
Confidence 4577777765432 22345655533 444444443 136777776653
No 366
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.82 E-value=58 Score=17.38 Aligned_cols=39 Identities=18% Similarity=0.429 Sum_probs=18.6
Q ss_pred eeCCCCCc-cCChHHHHHHHHHhcCCCceeccccCccccC
Q psy3507 56 TCYACDYH-TLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQ 94 (134)
Q Consensus 56 ~C~~C~~~-f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 94 (134)
+|-+|++. +.....+..-......-..|-|++|......
T Consensus 4 kCiiCd~v~~iD~rt~~tKrLrN~PIrtymC~eC~~Rva~ 43 (68)
T COG4896 4 KCIICDRVDEIDNRTFKTKRLRNKPIRTYMCPECEHRVAI 43 (68)
T ss_pred eEEEecceeeecchhHHHHHhhCCCceeEechhhHhhhch
Confidence 46666643 3333333333223333344777777654433
No 367
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=23.59 E-value=55 Score=17.77 Aligned_cols=8 Identities=38% Similarity=0.941 Sum_probs=3.4
Q ss_pred eeCCCCCc
Q psy3507 56 TCYACDYH 63 (134)
Q Consensus 56 ~C~~C~~~ 63 (134)
.|..||..
T Consensus 40 ~C~~CG~~ 47 (67)
T COG2051 40 TCLICGTT 47 (67)
T ss_pred EecccccE
Confidence 34444433
No 368
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.24 E-value=86 Score=16.74 Aligned_cols=20 Identities=10% Similarity=0.004 Sum_probs=10.0
Q ss_pred ccccCCCCccccCCCCCCcc
Q psy3507 28 LLVPTAEELMYHCKTCSTVS 47 (134)
Q Consensus 28 h~~~h~~~~~~~C~~C~~~f 47 (134)
+..++.+.+++.|+-=+-.|
T Consensus 15 ~~~I~~~~~~l~C~g~~~p~ 34 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPPN 34 (62)
T ss_pred ceEEEeCCeeEEcCCCCCCC
Confidence 34445555666665444333
No 369
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=23.22 E-value=77 Score=18.64 Aligned_cols=34 Identities=12% Similarity=0.189 Sum_probs=12.2
Q ss_pred CCccccCCCCCCccc------CCCCcceeeCCCCCccCCh
Q psy3507 34 EELMYHCKTCSTVSH------PNISYKYTCYACDYHTLMS 67 (134)
Q Consensus 34 ~~~~~~C~~C~~~f~------~~~~~~~~C~~C~~~f~~~ 67 (134)
+.+.-.|..||.... .....-|-|+.|-+.|...
T Consensus 11 g~ke~~CalCG~tWg~~y~Ev~G~rLfFCCd~ca~EF~nm 50 (105)
T PF11494_consen 11 GTKEMGCALCGATWGDYYEEVDGERLFFCCDDCAKEFKNM 50 (105)
T ss_dssp -SGGGS-SS---S---SS-B-TT--BSSS--SSSS-TTS-
T ss_pred ccccccccccCCcHHHHHHhhcCCEEEEEcHHHHHHHHHH
Confidence 345566777776654 2222345677777766654
No 370
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=22.79 E-value=59 Score=20.34 Aligned_cols=23 Identities=30% Similarity=0.699 Sum_probs=13.4
Q ss_pred ccCCCCCCcccCCCCcceeeCCCCCc
Q psy3507 38 YHCKTCSTVSHPNISYKYTCYACDYH 63 (134)
Q Consensus 38 ~~C~~C~~~f~~~~~~~~~C~~C~~~ 63 (134)
-+|..||..|-.... .|+.|+..
T Consensus 30 ~kC~~CG~v~~PPr~---~Cp~C~~~ 52 (140)
T COG1545 30 TKCKKCGRVYFPPRA---YCPKCGSE 52 (140)
T ss_pred EEcCCCCeEEcCCcc---cCCCCCCC
Confidence 457777777654332 36666544
No 371
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=22.70 E-value=29 Score=24.70 Aligned_cols=30 Identities=23% Similarity=0.454 Sum_probs=14.4
Q ss_pred ccCCCCCCcccCC--CCcceeeCCCCCccCCh
Q psy3507 38 YHCKTCSTVSHPN--ISYKYTCYACDYHTLMS 67 (134)
Q Consensus 38 ~~C~~C~~~f~~~--~~~~~~C~~C~~~f~~~ 67 (134)
.+|+.|+...... ....+.|+.|+..|.-.
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCPKCGHHMRIS 59 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCCCCCCCeeCC
Confidence 4566666554411 11124566666655443
No 372
>KOG2747|consensus
Probab=22.40 E-value=59 Score=24.28 Aligned_cols=25 Identities=32% Similarity=0.582 Sum_probs=21.3
Q ss_pred CCCeecCcChhhhcCHHHHHHHHHh
Q psy3507 108 DKPYICQQCRDTFSSLYLFRNRLQS 132 (134)
Q Consensus 108 ~~~~~C~~C~~~F~~~~~l~~H~~~ 132 (134)
...|.|+.|-+.+.++..|.+|+..
T Consensus 156 ~~lYiCEfCLkY~~s~~~l~rH~~k 180 (396)
T KOG2747|consen 156 DKLYICEFCLKYMKSRTSLQRHLKK 180 (396)
T ss_pred CeEEEehHHHhHhchHHHHHHHHHh
Confidence 3458999999999999999999864
No 373
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=22.30 E-value=74 Score=16.21 Aligned_cols=8 Identities=25% Similarity=0.804 Sum_probs=3.1
Q ss_pred ccCCCCCC
Q psy3507 38 YHCKTCST 45 (134)
Q Consensus 38 ~~C~~C~~ 45 (134)
..|+.|+.
T Consensus 41 v~C~~C~~ 48 (64)
T smart00647 41 VTCPKCGF 48 (64)
T ss_pred eECCCCCC
Confidence 33433433
No 374
>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=22.30 E-value=38 Score=15.11 Aligned_cols=11 Identities=27% Similarity=0.818 Sum_probs=5.1
Q ss_pred ccccCCCCCCc
Q psy3507 36 LMYHCKTCSTV 46 (134)
Q Consensus 36 ~~~~C~~C~~~ 46 (134)
-.|.|+.|+..
T Consensus 12 ~kY~Cp~C~~~ 22 (30)
T PF04438_consen 12 AKYRCPRCGAR 22 (30)
T ss_dssp ESEE-TTT--E
T ss_pred CEEECCCcCCc
Confidence 34777777764
No 375
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins 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. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
Probab=21.46 E-value=90 Score=16.34 Aligned_cols=23 Identities=17% Similarity=0.251 Sum_probs=16.0
Q ss_pred eecCcChhhhcCHHHHHHHHHhc
Q psy3507 111 YICQQCRDTFSSLYLFRNRLQSH 133 (134)
Q Consensus 111 ~~C~~C~~~F~~~~~l~~H~~~H 133 (134)
|--.-||+.|.+..++.+.+..+
T Consensus 28 ~Y~sP~Gk~~Rs~~ev~~yL~~~ 50 (62)
T cd00122 28 YYYSPCGKKLRSKPEVARYLEKT 50 (62)
T ss_pred EEECCCCceecCHHHHHHHHHhC
Confidence 33455788888888888777643
No 376
>PRK08359 transcription factor; Validated
Probab=21.17 E-value=32 Score=22.56 Aligned_cols=27 Identities=15% Similarity=0.253 Sum_probs=13.4
Q ss_pred ccCCCCCCccc-------CCCCcceeeCCCCCcc
Q psy3507 38 YHCKTCSTVSH-------PNISYKYTCYACDYHT 64 (134)
Q Consensus 38 ~~C~~C~~~f~-------~~~~~~~~C~~C~~~f 64 (134)
-.|++||.... -.+.....|..|...|
T Consensus 7 ~~CEiCG~~i~g~~~~v~ieGael~VC~~Ca~k~ 40 (176)
T PRK08359 7 RYCEICGAEIRGPGHRIRIEGAELLVCDRCYEKY 40 (176)
T ss_pred ceeecCCCccCCCCeEEEEcCeEEehHHHHHHHh
Confidence 34666665544 2233345566665333
No 377
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.04 E-value=60 Score=22.85 Aligned_cols=24 Identities=17% Similarity=0.488 Sum_probs=13.8
Q ss_pred cCCCCCCcccCCCCcceeeCCCCCccCC
Q psy3507 39 HCKTCSTVSHPNISYKYTCYACDYHTLM 66 (134)
Q Consensus 39 ~C~~C~~~f~~~~~~~~~C~~C~~~f~~ 66 (134)
.|+.||. .....+.|+.||..+..
T Consensus 311 ~C~~cg~----~~~r~~~C~~cg~~~~r 334 (364)
T COG0675 311 TCPCCGH----LSGRLFKCPRCGFVHDR 334 (364)
T ss_pred cccccCC----ccceeEECCCCCCeehh
Confidence 4666666 22345677777765443
No 378
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.85 E-value=74 Score=22.29 Aligned_cols=26 Identities=19% Similarity=0.281 Sum_probs=14.4
Q ss_pred cCCCCCCccc---CCCCcceeeCCCCCcc
Q psy3507 39 HCKTCSTVSH---PNISYKYTCYACDYHT 64 (134)
Q Consensus 39 ~C~~C~~~f~---~~~~~~~~C~~C~~~f 64 (134)
.|+.||.... ..+...|-|+.|...+
T Consensus 237 pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~~~ 265 (269)
T PRK14811 237 PCPRCGTPIEKIVVGGRGTHFCPQCQPLR 265 (269)
T ss_pred CCCcCCCeeEEEEECCCCcEECCCCcCCC
Confidence 4666665444 3344456666665543
No 379
>KOG4124|consensus
Probab=20.77 E-value=14 Score=26.93 Aligned_cols=47 Identities=34% Similarity=0.793 Sum_probs=31.6
Q ss_pred Cceeccc--cCccccCchhHHHHhhh-c------------------CCCCCeecCcChhhhcCHHHHH
Q psy3507 81 KPYKCEY--CAYSCTQSSALKIHERK-H------------------TGDKPYICQQCRDTFSSLYLFR 127 (134)
Q Consensus 81 ~~~~C~~--C~~~f~~~~~l~~H~~~-h------------------~~~~~~~C~~C~~~F~~~~~l~ 127 (134)
+++.|++ |++.+.....|..|... | ...|+|.|++|.+.++....|.
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~ 415 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLK 415 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCC
Confidence 5567755 77777777777776442 2 1247899999998877654443
No 380
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=20.72 E-value=57 Score=16.38 Aligned_cols=8 Identities=38% Similarity=1.111 Sum_probs=3.5
Q ss_pred eeccccCc
Q psy3507 83 YKCEYCAY 90 (134)
Q Consensus 83 ~~C~~C~~ 90 (134)
|.|++|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 88888875
No 381
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=20.59 E-value=97 Score=18.52 Aligned_cols=62 Identities=16% Similarity=0.230 Sum_probs=29.3
Q ss_pred CCccccCCCCCCccc-CCCCcceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccCchhHHHH
Q psy3507 34 EELMYHCKTCSTVSH-PNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIH 101 (134)
Q Consensus 34 ~~~~~~C~~C~~~f~-~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H 101 (134)
|...|.|+.||.... ...=+.--|+.|+......- +. .++. ....++.=--+|+-+..|..-
T Consensus 39 G~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~~~~~~W-~~-~~~~----~ll~~~y~HvVFTlP~~L~~~ 101 (111)
T PF14319_consen 39 GFHRYRCEDCGHEKIVYNSCKNRHCPSCQAKATEQW-IE-KQRE----DLLPVPYFHVVFTLPHELRPL 101 (111)
T ss_pred CcceeecCCCCceEEecCcccCcCCCCCCChHHHHH-HH-HHHh----hCCCCCeEEEEEcCcHHHHHH
Confidence 445578888886544 11112235788876432221 11 1111 112333333456666666543
No 382
>KOG1729|consensus
Probab=20.24 E-value=12 Score=26.55 Aligned_cols=28 Identities=14% Similarity=0.279 Sum_probs=13.1
Q ss_pred ccCCCCCC-cccCCCCcceeeCCCCCccCC
Q psy3507 38 YHCKTCST-VSHPNISYKYTCYACDYHTLM 66 (134)
Q Consensus 38 ~~C~~C~~-~f~~~~~~~~~C~~C~~~f~~ 66 (134)
-.|..|++ .|.- ..+..-|..||..|-.
T Consensus 169 ~~C~~C~~~~Ftl-~~RRHHCR~CG~ivC~ 197 (288)
T KOG1729|consen 169 TECMVCGCTEFTL-SERRHHCRNCGDIVCA 197 (288)
T ss_pred eecccCCCccccH-HHHHHHHHhcchHhhh
Confidence 45666666 3332 2222335555555544
No 383
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=20.09 E-value=1.1e+02 Score=21.89 Aligned_cols=25 Identities=16% Similarity=0.300 Sum_probs=22.4
Q ss_pred CCcceeeCCCCCccCChHHHHHHHH
Q psy3507 51 ISYKYTCYACDYHTLMSEDMKKHMR 75 (134)
Q Consensus 51 ~~~~~~C~~C~~~f~~~~~l~~H~~ 75 (134)
....|.|+.|-+-|.+...|.+|+.
T Consensus 45 ~~~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 45 CTKLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred CCeEEEcCCCcchhCCHHHHHHHHH
Confidence 3457999999999999999999987
No 384
>KOG0320|consensus
Probab=20.05 E-value=22 Score=23.34 Aligned_cols=51 Identities=20% Similarity=0.369 Sum_probs=28.1
Q ss_pred CccccCCCCCCcccCCCCcceeeCCCCCccCChHHHHHHHHHhcCCCceeccccCccccC
Q psy3507 35 ELMYHCKTCSTVSHPNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQ 94 (134)
Q Consensus 35 ~~~~~C~~C~~~f~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 94 (134)
+.-|.|++|--.+.... -.-..||..|-..- ++.-++ ....|+.|++....
T Consensus 129 ~~~~~CPiCl~~~sek~---~vsTkCGHvFC~~C-ik~alk-----~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKV---PVSTKCGHVFCSQC-IKDALK-----NTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhhcc---ccccccchhHHHHH-HHHHHH-----hCCCCCCcccccch
Confidence 34488888887764222 13446777775432 222222 22478998875443
No 385
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=20.02 E-value=69 Score=22.28 Aligned_cols=28 Identities=21% Similarity=0.407 Sum_probs=17.0
Q ss_pred cCcccccccccCCCCccccCCCCCCccc
Q psy3507 21 TCIHCRLLLVPTAEELMYHCKTCSTVSH 48 (134)
Q Consensus 21 ~C~~C~~h~~~h~~~~~~~C~~C~~~f~ 48 (134)
.|+.|+.-+....+.....|+.|+...-
T Consensus 101 fC~~CG~~~~~~~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 101 FCGYCGHPMHPSKTEWAMLCPHCRERYY 128 (256)
T ss_pred cccccCCCCeecCCceeEECCCCCCEEC
Confidence 5777766555555555566777775543
Done!