Query psy12016
Match_columns 111
No_of_seqs 117 out of 2256
Neff 11.4
Searched_HMMs 46136
Date Fri Aug 16 16:30:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12016.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12016hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 4.7E-27 1E-31 137.5 4.9 101 2-111 141-244 (279)
2 KOG2462|consensus 99.9 1E-22 2.2E-27 119.5 4.2 93 3-104 173-265 (279)
3 KOG3623|consensus 99.7 5.2E-18 1.1E-22 110.9 1.6 82 15-103 890-971 (1007)
4 KOG1074|consensus 99.7 1.9E-17 4.2E-22 109.3 3.5 56 54-110 880-935 (958)
5 KOG3576|consensus 99.7 2.3E-17 4.9E-22 93.7 1.6 85 16-107 114-198 (267)
6 KOG1074|consensus 99.6 1.2E-16 2.7E-21 105.6 2.5 53 54-107 606-658 (958)
7 KOG3623|consensus 99.6 1.8E-15 3.8E-20 99.3 2.7 99 4-103 223-330 (1007)
8 KOG3608|consensus 99.5 3.1E-14 6.6E-19 87.0 5.7 104 3-106 191-316 (467)
9 KOG3576|consensus 99.5 5.7E-15 1.2E-19 84.1 2.4 101 4-110 130-240 (267)
10 PHA00733 hypothetical protein 99.3 1.5E-12 3.2E-17 70.6 3.9 84 15-107 36-124 (128)
11 KOG3608|consensus 99.2 3.3E-11 7.3E-16 74.0 6.0 91 3-103 249-342 (467)
12 PHA02768 hypothetical protein; 99.1 8.4E-11 1.8E-15 53.9 1.6 41 54-97 6-46 (55)
13 PHA02768 hypothetical protein; 99.1 1.2E-10 2.5E-15 53.5 2.0 44 19-70 5-48 (55)
14 PHA00733 hypothetical protein 99.0 1E-09 2.2E-14 59.6 5.0 64 6-78 61-124 (128)
15 PLN03086 PRLI-interacting fact 99.0 1.5E-09 3.2E-14 71.2 5.7 63 18-92 452-514 (567)
16 PLN03086 PRLI-interacting fact 98.9 4.1E-09 8.8E-14 69.2 6.5 90 5-107 466-565 (567)
17 PHA00616 hypothetical protein 98.9 7.5E-10 1.6E-14 48.5 1.6 29 82-110 1-29 (44)
18 KOG3993|consensus 98.8 4.3E-10 9.3E-15 70.5 -0.3 25 82-106 356-380 (500)
19 KOG3993|consensus 98.8 2.7E-09 5.8E-14 67.1 2.3 77 1-77 277-380 (500)
20 PF13465 zf-H2C2_2: Zinc-finge 98.8 4.9E-09 1.1E-13 41.3 2.1 24 7-30 2-25 (26)
21 PF13465 zf-H2C2_2: Zinc-finge 98.8 4.3E-09 9.3E-14 41.5 1.8 24 69-93 2-25 (26)
22 PHA00616 hypothetical protein 98.6 3.2E-08 7E-13 43.4 1.5 29 19-47 1-29 (44)
23 PHA00732 hypothetical protein 98.5 1.4E-07 2.9E-12 47.1 2.8 46 19-76 1-47 (79)
24 PHA00732 hypothetical protein 98.5 1.3E-07 2.8E-12 47.2 2.5 46 54-105 2-47 (79)
25 PF05605 zf-Di19: Drought indu 98.5 3.4E-07 7.4E-12 42.5 3.6 51 54-107 3-54 (54)
26 PF00096 zf-C2H2: Zinc finger, 98.4 3.7E-07 8.1E-12 34.8 1.9 23 83-105 1-23 (23)
27 PF13894 zf-C2H2_4: C2H2-type 98.3 9.3E-07 2E-11 33.8 2.0 24 83-106 1-24 (24)
28 PF00096 zf-C2H2: Zinc finger, 98.2 1.2E-06 2.6E-11 33.3 2.2 23 20-42 1-23 (23)
29 PF09237 GAGA: GAGA factor; I 98.2 1.8E-06 4E-11 38.7 2.5 31 80-110 22-52 (54)
30 PF13912 zf-C2H2_6: C2H2-type 98.2 9.4E-07 2E-11 35.0 1.1 26 82-107 1-26 (27)
31 PF05605 zf-Di19: Drought indu 98.0 1.5E-05 3.3E-10 36.9 4.1 51 19-77 2-53 (54)
32 PF13912 zf-C2H2_6: C2H2-type 98.0 4.2E-06 9.2E-11 33.0 1.9 25 19-43 1-25 (27)
33 PF13894 zf-C2H2_4: C2H2-type 97.9 1.6E-05 3.5E-10 30.1 2.5 23 20-42 1-23 (24)
34 PF12756 zf-C2H2_2: C2H2 type 97.8 1.4E-05 3.1E-10 41.4 2.3 73 21-105 1-73 (100)
35 COG5189 SFP1 Putative transcri 97.8 6.6E-06 1.4E-10 50.6 0.6 70 17-103 347-419 (423)
36 smart00355 ZnF_C2H2 zinc finge 97.7 5.7E-05 1.2E-09 29.0 2.2 24 83-106 1-24 (26)
37 PF13909 zf-H2C2_5: C2H2-type 97.5 0.00011 2.4E-09 28.0 2.2 24 83-107 1-24 (24)
38 PF09237 GAGA: GAGA factor; I 97.5 0.00023 4.9E-09 32.1 2.9 30 16-45 21-50 (54)
39 PF12874 zf-met: Zinc-finger o 97.4 0.00015 3.3E-09 27.9 1.9 23 20-42 1-23 (25)
40 smart00355 ZnF_C2H2 zinc finge 97.4 0.00019 4.2E-09 27.4 2.2 23 20-42 1-23 (26)
41 PF12874 zf-met: Zinc-finger o 97.3 0.00012 2.5E-09 28.2 1.2 23 83-105 1-23 (25)
42 PF12171 zf-C2H2_jaz: Zinc-fin 97.0 0.00033 7.2E-09 27.5 0.9 22 20-41 2-23 (27)
43 PF12171 zf-C2H2_jaz: Zinc-fin 97.0 0.00013 2.8E-09 28.7 -0.4 21 83-103 2-22 (27)
44 PF13909 zf-H2C2_5: C2H2-type 96.9 0.0016 3.6E-08 24.7 2.4 22 20-42 1-22 (24)
45 PRK04860 hypothetical protein; 96.8 0.0011 2.4E-08 37.6 2.3 38 53-95 119-156 (160)
46 PRK04860 hypothetical protein; 96.8 0.001 2.2E-08 37.7 1.9 26 82-111 119-144 (160)
47 PF13913 zf-C2HC_2: zinc-finge 96.5 0.0029 6.4E-08 24.4 1.8 22 83-105 3-24 (25)
48 smart00451 ZnF_U1 U1-like zinc 96.4 0.0043 9.4E-08 25.7 2.1 23 19-41 3-25 (35)
49 smart00451 ZnF_U1 U1-like zinc 96.2 0.0037 8E-08 25.9 1.4 22 82-103 3-24 (35)
50 KOG1146|consensus 95.6 0.0092 2E-07 43.7 2.0 78 17-105 463-541 (1406)
51 COG4049 Uncharacterized protei 94.9 0.017 3.6E-07 26.6 1.2 29 15-43 13-41 (65)
52 cd00350 rubredoxin_like Rubred 94.7 0.026 5.6E-07 23.2 1.4 24 54-90 2-25 (33)
53 COG4049 Uncharacterized protei 94.3 0.026 5.6E-07 26.0 1.1 25 82-106 17-41 (65)
54 PF12756 zf-C2H2_2: C2H2 type 94.0 0.095 2.1E-06 26.8 3.1 23 54-76 51-73 (100)
55 KOG4173|consensus 92.9 0.058 1.3E-06 31.8 1.2 79 19-106 79-170 (253)
56 COG1592 Rubrerythrin [Energy p 92.7 0.085 1.8E-06 30.2 1.7 23 53-89 134-156 (166)
57 KOG2893|consensus 92.6 0.045 9.8E-07 33.1 0.5 47 20-76 11-58 (341)
58 KOG2893|consensus 92.2 0.037 8E-07 33.4 -0.2 41 56-101 13-53 (341)
59 cd00729 rubredoxin_SM Rubredox 92.2 0.13 2.8E-06 21.3 1.5 24 54-90 3-26 (34)
60 KOG2231|consensus 91.9 0.52 1.1E-05 33.0 4.8 48 54-106 183-236 (669)
61 PF09986 DUF2225: Uncharacteri 91.8 0.056 1.2E-06 32.3 0.2 12 83-94 49-60 (214)
62 COG5048 FOG: Zn-finger [Genera 91.6 0.059 1.3E-06 34.8 0.2 54 54-108 290-349 (467)
63 PF12013 DUF3505: Protein of u 91.2 0.46 9.9E-06 25.2 3.3 26 82-107 80-109 (109)
64 TIGR00373 conserved hypothetic 91.1 0.3 6.5E-06 27.8 2.7 35 15-64 105-139 (158)
65 PF09538 FYDLN_acid: Protein o 90.8 0.21 4.5E-06 26.6 1.8 13 82-94 26-38 (108)
66 PF04959 ARS2: Arsenite-resist 90.8 0.11 2.4E-06 31.0 0.8 28 82-109 77-104 (214)
67 COG2888 Predicted Zn-ribbon RN 90.7 0.18 3.9E-06 23.6 1.3 31 54-90 28-58 (61)
68 PRK06266 transcription initiat 90.3 0.39 8.4E-06 28.0 2.7 35 16-65 114-148 (178)
69 smart00659 RPOLCX RNA polymera 90.0 0.36 7.8E-06 21.3 1.9 12 20-31 3-14 (44)
70 PF13719 zinc_ribbon_5: zinc-r 89.7 0.36 7.8E-06 20.3 1.7 33 54-92 3-35 (37)
71 TIGR02605 CxxC_CxxC_SSSS putat 89.7 0.15 3.3E-06 23.1 0.6 13 20-32 6-18 (52)
72 TIGR02098 MJ0042_CXXC MJ0042 f 89.4 0.4 8.7E-06 20.1 1.8 13 54-66 3-15 (38)
73 COG5048 FOG: Zn-finger [Genera 89.4 0.15 3.2E-06 33.0 0.6 62 18-86 288-355 (467)
74 smart00531 TFIIE Transcription 89.1 0.61 1.3E-05 26.2 2.8 13 54-66 100-112 (147)
75 KOG2482|consensus 89.0 0.63 1.4E-05 29.9 3.1 23 19-41 195-217 (423)
76 COG5236 Uncharacterized conser 89.0 0.4 8.7E-06 30.8 2.2 23 54-76 221-243 (493)
77 PF05443 ROS_MUCR: ROS/MUCR tr 88.9 0.27 5.8E-06 27.2 1.3 24 82-108 72-95 (132)
78 smart00834 CxxC_CXXC_SSSS Puta 88.7 0.22 4.8E-06 21.2 0.8 12 20-31 6-17 (41)
79 PF09723 Zn-ribbon_8: Zinc rib 88.4 0.12 2.5E-06 22.5 -0.3 14 20-33 6-19 (42)
80 PF13717 zinc_ribbon_4: zinc-r 88.1 0.65 1.4E-05 19.4 2.0 33 54-92 3-35 (36)
81 smart00614 ZnF_BED BED zinc fi 86.9 0.72 1.6E-05 20.7 1.9 23 82-104 18-45 (50)
82 COG1997 RPL43A Ribosomal prote 86.7 0.37 8.1E-06 24.5 0.9 31 54-95 36-66 (89)
83 TIGR00622 ssl1 transcription f 86.7 2 4.3E-05 23.1 3.7 86 17-105 13-104 (112)
84 KOG2186|consensus 86.2 0.59 1.3E-05 28.7 1.7 47 19-74 3-49 (276)
85 PRK00464 nrdR transcriptional 85.4 0.37 8.1E-06 27.4 0.6 15 54-68 29-43 (154)
86 KOG2186|consensus 85.2 0.47 1E-05 29.1 1.0 46 54-103 4-49 (276)
87 PF02892 zf-BED: BED zinc fing 84.9 1.2 2.7E-05 19.3 2.1 23 82-104 16-42 (45)
88 KOG4167|consensus 83.8 0.31 6.8E-06 34.3 -0.1 29 17-45 790-818 (907)
89 COG5189 SFP1 Putative transcri 83.6 0.64 1.4E-05 29.6 1.2 25 81-105 348-374 (423)
90 PRK00398 rpoP DNA-directed RNA 83.3 0.53 1.1E-05 20.8 0.5 14 19-32 3-16 (46)
91 KOG2482|consensus 83.1 2 4.4E-05 27.7 3.2 22 82-103 195-216 (423)
92 KOG2231|consensus 83.0 2.1 4.6E-05 30.2 3.5 69 20-103 183-260 (669)
93 PRK14890 putative Zn-ribbon RN 82.7 0.81 1.7E-05 21.5 1.0 30 54-90 26-56 (59)
94 PF12013 DUF3505: Protein of u 81.0 1.6 3.5E-05 23.1 2.0 27 52-78 79-109 (109)
95 PF00301 Rubredoxin: Rubredoxi 80.6 0.71 1.5E-05 20.7 0.4 12 20-31 2-13 (47)
96 PF03604 DNA_RNApol_7kD: DNA d 80.0 1.7 3.7E-05 17.7 1.4 11 20-30 1-11 (32)
97 PF08790 zf-LYAR: LYAR-type C2 80.0 0.49 1.1E-05 18.7 -0.1 17 84-101 2-18 (28)
98 TIGR02300 FYDLN_acid conserved 80.0 1.3 2.8E-05 24.3 1.4 33 20-69 10-42 (129)
99 COG4957 Predicted transcriptio 79.4 1.1 2.3E-05 24.9 0.9 22 83-107 77-98 (148)
100 COG4888 Uncharacterized Zn rib 79.3 0.66 1.4E-05 24.3 0.1 13 50-62 19-31 (104)
101 PRK03824 hypA hydrogenase nick 79.2 1.4 3.1E-05 24.4 1.5 15 18-32 69-83 (135)
102 smart00734 ZnF_Rad18 Rad18-lik 78.9 2.4 5.2E-05 16.3 1.6 19 21-40 3-21 (26)
103 KOG2785|consensus 78.6 4.1 9E-05 26.7 3.4 58 17-74 164-241 (390)
104 cd00730 rubredoxin Rubredoxin; 78.2 0.78 1.7E-05 20.8 0.2 8 82-89 34-41 (50)
105 PF04959 ARS2: Arsenite-resist 77.0 2.7 5.9E-05 25.3 2.2 26 16-41 74-99 (214)
106 PF14353 CpXC: CpXC protein 76.6 1.1 2.5E-05 24.4 0.6 21 54-74 39-59 (128)
107 KOG3408|consensus 75.8 1.6 3.6E-05 23.7 1.0 22 82-103 57-78 (129)
108 COG5151 SSL1 RNA polymerase II 75.6 4.2 9E-05 26.0 2.8 48 55-105 364-411 (421)
109 COG1996 RPC10 DNA-directed RNA 75.3 2.5 5.4E-05 19.1 1.4 10 20-29 7-16 (49)
110 PF01780 Ribosomal_L37ae: Ribo 74.8 1 2.2E-05 23.2 0.1 31 54-95 36-66 (90)
111 PHA00626 hypothetical protein 74.7 2.7 5.8E-05 19.6 1.4 17 17-33 21-37 (59)
112 PF10571 UPF0547: Uncharacteri 74.2 1.8 3.8E-05 16.7 0.7 10 21-30 16-25 (26)
113 TIGR00280 L37a ribosomal prote 73.5 1.4 2.9E-05 22.8 0.3 31 54-95 36-66 (91)
114 PTZ00255 60S ribosomal protein 73.5 1.5 3.2E-05 22.6 0.5 31 54-95 37-67 (90)
115 COG1198 PriA Primosomal protei 73.4 1.9 4.1E-05 30.8 1.1 10 82-91 475-484 (730)
116 smart00154 ZnF_AN1 AN1-like Zi 72.9 2.5 5.4E-05 18.0 1.1 15 19-33 12-26 (39)
117 PF09845 DUF2072: Zn-ribbon co 72.8 2.8 6.2E-05 23.2 1.5 15 19-33 1-15 (131)
118 KOG2785|consensus 72.7 4.6 0.0001 26.5 2.6 50 54-103 167-241 (390)
119 PF08274 PhnA_Zn_Ribbon: PhnA 72.3 2 4.3E-05 17.3 0.6 9 82-90 19-27 (30)
120 PF07975 C1_4: TFIIH C1-like d 72.1 1.6 3.4E-05 20.0 0.3 26 17-42 19-44 (51)
121 PF15135 UPF0515: Uncharacteri 71.8 7.1 0.00015 24.2 3.1 13 17-29 110-122 (278)
122 PRK12380 hydrogenase nickel in 71.2 3.6 7.9E-05 22.1 1.7 13 19-31 70-82 (113)
123 PF05191 ADK_lid: Adenylate ki 71.1 3.2 7E-05 17.4 1.2 33 54-95 2-34 (36)
124 PF13451 zf-trcl: Probable zin 70.7 1.8 4E-05 19.6 0.4 12 54-65 5-16 (49)
125 PRK03976 rpl37ae 50S ribosomal 70.4 1.7 3.7E-05 22.4 0.3 31 54-95 37-67 (90)
126 TIGR01206 lysW lysine biosynth 70.0 3.2 6.9E-05 19.2 1.1 11 54-64 3-13 (54)
127 KOG4727|consensus 69.9 3.1 6.7E-05 24.1 1.3 23 18-40 74-96 (193)
128 KOG2593|consensus 69.3 5.5 0.00012 26.6 2.4 14 54-67 129-142 (436)
129 COG5236 Uncharacterized conser 69.3 10 0.00022 24.8 3.5 76 20-107 221-306 (493)
130 KOG2593|consensus 69.0 5.3 0.00012 26.7 2.3 41 14-63 123-163 (436)
131 smart00440 ZnF_C2C2 C2C2 Zinc 68.1 1.4 3E-05 18.9 -0.3 10 83-92 29-38 (40)
132 TIGR00100 hypA hydrogenase nic 68.0 4 8.8E-05 22.0 1.4 13 19-31 70-82 (115)
133 COG3364 Zn-ribbon containing p 67.9 4.6 0.0001 21.3 1.5 14 19-32 2-15 (112)
134 PRK09678 DNA-binding transcrip 67.3 2.9 6.2E-05 20.6 0.7 16 54-69 28-45 (72)
135 PLN02294 cytochrome c oxidase 67.2 3.3 7.2E-05 24.0 1.0 17 16-32 138-154 (174)
136 PF07754 DUF1610: Domain of un 67.0 3.5 7.7E-05 15.6 0.8 10 18-27 15-24 (24)
137 PRK03681 hypA hydrogenase nick 66.6 3.3 7.1E-05 22.3 0.9 14 18-31 69-82 (114)
138 cd00924 Cyt_c_Oxidase_Vb Cytoc 65.9 4.2 9.1E-05 21.3 1.2 16 17-32 77-92 (97)
139 PF07295 DUF1451: Protein of u 65.5 3.9 8.5E-05 23.1 1.1 10 53-62 112-121 (146)
140 PF01428 zf-AN1: AN1-like Zinc 65.5 3.4 7.3E-05 17.9 0.7 16 18-33 12-27 (43)
141 KOG4167|consensus 65.3 1.5 3.3E-05 31.2 -0.6 25 82-106 792-816 (907)
142 PF06524 NOA36: NOA36 protein; 64.8 5.4 0.00012 24.9 1.7 27 13-40 136-162 (314)
143 PF13878 zf-C2H2_3: zinc-finge 64.0 9.8 0.00021 16.4 2.0 24 19-42 13-38 (41)
144 COG1675 TFA1 Transcription ini 62.9 12 0.00027 21.9 2.8 17 16-32 110-126 (176)
145 PF04780 DUF629: Protein of un 62.7 6.5 0.00014 26.7 1.9 22 83-104 58-79 (466)
146 PF10013 DUF2256: Uncharacteri 60.2 6.4 0.00014 17.2 1.0 15 84-98 10-24 (42)
147 COG2331 Uncharacterized protei 60.0 4.4 9.5E-05 20.2 0.6 10 20-29 13-22 (82)
148 PF09963 DUF2197: Uncharacteri 59.9 3.6 7.7E-05 19.2 0.3 8 82-89 31-38 (56)
149 PRK14873 primosome assembly pr 59.7 4 8.6E-05 29.0 0.6 10 82-91 422-431 (665)
150 COG4306 Uncharacterized protei 59.5 5.9 0.00013 21.8 1.1 42 54-95 40-81 (160)
151 KOG1146|consensus 59.5 2.9 6.3E-05 31.8 -0.1 48 58-105 441-488 (1406)
152 PF10083 DUF2321: Uncharacteri 59.1 4.6 0.0001 23.1 0.6 15 82-96 68-82 (158)
153 PRK04023 DNA polymerase II lar 58.9 9.6 0.00021 28.6 2.3 11 18-28 625-635 (1121)
154 PF02176 zf-TRAF: TRAF-type zi 58.6 6.6 0.00014 18.0 1.1 20 67-87 24-43 (60)
155 PF14787 zf-CCHC_5: GAG-polypr 58.1 6.2 0.00014 16.6 0.8 16 83-98 3-18 (36)
156 PLN03238 probable histone acet 58.0 11 0.00023 24.0 2.2 25 82-106 48-72 (290)
157 COG2879 Uncharacterized small 57.2 13 0.00027 17.8 1.8 17 95-111 25-41 (65)
158 PRK00564 hypA hydrogenase nick 57.2 5.8 0.00012 21.5 0.8 16 17-32 69-84 (117)
159 PF01155 HypA: Hydrogenase exp 56.8 11 0.00023 20.3 1.8 12 20-31 71-82 (113)
160 COG1655 Uncharacterized protei 56.6 2.1 4.5E-05 26.1 -1.0 20 16-35 16-35 (267)
161 TIGR00595 priA primosomal prot 56.0 5.6 0.00012 27.2 0.8 9 82-90 253-261 (505)
162 KOG0717|consensus 55.9 8.6 0.00019 26.1 1.6 22 20-41 293-314 (508)
163 KOG0717|consensus 55.6 7.1 0.00015 26.5 1.1 21 83-103 293-313 (508)
164 PF04423 Rad50_zn_hook: Rad50 54.9 16 0.00035 16.6 2.0 12 21-32 22-33 (54)
165 PF01096 TFIIS_C: Transcriptio 54.7 1 2.3E-05 19.2 -1.9 10 83-92 29-38 (39)
166 KOG0782|consensus 54.1 1 2.2E-05 31.2 -2.8 46 10-67 244-290 (1004)
167 PF12760 Zn_Tnp_IS1595: Transp 53.5 9.9 0.00021 16.7 1.2 8 82-89 37-44 (46)
168 COG4338 Uncharacterized protei 53.3 5.6 0.00012 17.9 0.3 14 84-97 14-27 (54)
169 COG3091 SprT Zn-dependent meta 52.0 8.7 0.00019 21.9 1.0 33 54-92 118-150 (156)
170 KOG2807|consensus 51.4 37 0.00081 22.2 3.7 22 18-39 289-310 (378)
171 PF15269 zf-C2H2_7: Zinc-finge 50.5 16 0.00035 16.1 1.5 22 20-41 21-42 (54)
172 COG1571 Predicted DNA-binding 49.7 14 0.00031 24.8 1.8 12 54-65 368-379 (421)
173 TIGR00515 accD acetyl-CoA carb 49.5 13 0.00029 23.5 1.6 33 20-67 27-59 (285)
174 TIGR00416 sms DNA repair prote 49.5 12 0.00027 25.3 1.6 13 18-30 6-18 (454)
175 KOG2071|consensus 48.6 13 0.00029 25.9 1.6 26 82-107 418-443 (579)
176 TIGR00627 tfb4 transcription f 48.2 17 0.00036 23.1 1.9 12 53-64 255-266 (279)
177 PF13824 zf-Mss51: Zinc-finger 48.0 18 0.00039 16.8 1.5 7 54-60 15-21 (55)
178 PRK05978 hypothetical protein; 48.0 9 0.0002 21.8 0.7 8 55-62 54-61 (148)
179 PRK11823 DNA repair protein Ra 47.8 14 0.0003 25.0 1.6 14 17-30 5-18 (446)
180 PF06220 zf-U1: U1 zinc finger 47.4 20 0.00043 15.2 1.6 14 82-95 3-16 (38)
181 KOG4124|consensus 46.9 3.7 8.1E-05 26.7 -1.0 51 51-101 347-417 (442)
182 PF12907 zf-met2: Zinc-binding 46.2 9 0.0002 16.5 0.4 22 54-75 2-26 (40)
183 PF01215 COX5B: Cytochrome c o 46.1 10 0.00022 21.3 0.7 17 17-33 110-126 (136)
184 PF07282 OrfB_Zn_ribbon: Putat 46.1 15 0.00033 17.4 1.3 11 82-92 46-56 (69)
185 PTZ00043 cytochrome c oxidase 45.5 13 0.00028 22.8 1.1 18 16-33 178-195 (268)
186 PF05290 Baculo_IE-1: Baculovi 45.2 20 0.00042 20.1 1.7 19 16-34 77-95 (140)
187 KOG1842|consensus 45.2 12 0.00027 25.3 1.1 27 54-80 16-42 (505)
188 KOG1842|consensus 44.5 11 0.00024 25.5 0.7 23 19-41 15-37 (505)
189 CHL00174 accD acetyl-CoA carbo 44.5 17 0.00038 23.2 1.6 33 20-67 39-71 (296)
190 COG0068 HypF Hydrogenase matur 44.0 4.8 0.0001 28.8 -0.9 59 21-92 125-183 (750)
191 PF10276 zf-CHCC: Zinc-finger 43.2 9.3 0.0002 16.5 0.2 11 82-92 29-39 (40)
192 PHA02998 RNA polymerase subuni 42.9 8 0.00017 22.7 -0.0 38 54-95 144-184 (195)
193 PRK04351 hypothetical protein; 42.8 13 0.00027 21.2 0.7 34 53-95 112-145 (149)
194 PLN00104 MYST -like histone ac 42.6 16 0.00035 24.8 1.3 25 82-106 198-222 (450)
195 COG3357 Predicted transcriptio 42.4 11 0.00025 19.5 0.5 14 18-31 57-70 (97)
196 PF03811 Zn_Tnp_IS1: InsA N-te 42.0 12 0.00026 15.7 0.5 7 82-88 29-35 (36)
197 PTZ00064 histone acetyltransfe 41.9 20 0.00043 24.8 1.6 25 82-106 280-304 (552)
198 PF10272 Tmpp129: Putative tra 40.8 5 0.00011 26.2 -1.1 11 54-64 341-351 (358)
199 PRK05580 primosome assembly pr 40.6 20 0.00043 25.7 1.6 9 82-90 421-429 (679)
200 PF14803 Nudix_N_2: Nudix N-te 39.6 5.5 0.00012 16.5 -0.7 6 55-60 24-29 (34)
201 COG1773 Rubredoxin [Energy pro 39.5 15 0.00033 17.1 0.6 14 19-32 3-16 (55)
202 PTZ00448 hypothetical protein; 39.3 24 0.00053 23.3 1.7 24 82-105 314-337 (373)
203 PRK05654 acetyl-CoA carboxylas 39.0 21 0.00045 22.8 1.4 33 20-67 28-60 (292)
204 PRK12496 hypothetical protein; 38.7 23 0.00049 20.5 1.4 28 52-92 126-153 (164)
205 COG2956 Predicted N-acetylgluc 38.7 17 0.00036 23.8 0.9 7 54-60 355-361 (389)
206 PF10263 SprT-like: SprT-like 38.5 19 0.0004 20.2 1.0 13 54-66 124-136 (157)
207 PF05129 Elf1: Transcription e 38.5 7.8 0.00017 19.5 -0.4 13 82-94 46-58 (81)
208 KOG3507|consensus 38.2 11 0.00025 17.7 0.1 11 54-64 38-48 (62)
209 COG5112 UFD2 U1-like Zn-finger 38.0 14 0.0003 19.7 0.4 22 82-103 55-76 (126)
210 PLN02748 tRNA dimethylallyltra 37.8 24 0.00053 24.1 1.6 23 82-104 418-441 (468)
211 COG1326 Uncharacterized archae 37.7 40 0.00088 20.2 2.3 12 54-65 31-42 (201)
212 PRK05452 anaerobic nitric oxid 37.1 17 0.00038 24.8 0.8 13 54-66 426-438 (479)
213 PRK11032 hypothetical protein; 37.0 22 0.00047 20.6 1.1 8 54-61 125-132 (160)
214 cd01121 Sms Sms (bacterial rad 36.9 21 0.00045 23.6 1.1 7 21-27 16-22 (372)
215 PRK00762 hypA hydrogenase nick 36.0 19 0.00041 19.7 0.7 12 19-31 70-81 (124)
216 PF01286 XPA_N: XPA protein N- 35.9 21 0.00046 14.8 0.7 12 21-32 5-16 (34)
217 PF13453 zf-TFIIB: Transcripti 35.8 42 0.0009 14.2 1.7 20 19-38 19-38 (41)
218 KOG3352|consensus 35.6 21 0.00047 20.3 0.9 15 79-94 131-145 (153)
219 PF14369 zf-RING_3: zinc-finge 35.6 19 0.00042 14.9 0.6 11 21-31 23-33 (35)
220 COG4896 Uncharacterized protei 35.4 23 0.00049 16.9 0.9 9 54-62 32-40 (68)
221 PF14311 DUF4379: Domain of un 35.2 50 0.0011 15.0 2.0 13 54-66 29-41 (55)
222 PF06397 Desulfoferrod_N: Desu 35.1 22 0.00047 15.0 0.7 12 18-29 5-16 (36)
223 KOG3214|consensus 34.8 14 0.00031 19.5 0.1 13 82-94 47-59 (109)
224 smart00731 SprT SprT homologue 34.7 24 0.00051 19.8 1.0 33 53-93 112-144 (146)
225 COG4391 Uncharacterized protei 34.5 26 0.00057 16.7 1.0 36 54-94 25-60 (62)
226 KOG2906|consensus 34.1 11 0.00023 19.9 -0.4 19 18-36 20-38 (105)
227 KOG0562|consensus 33.7 35 0.00075 20.0 1.6 26 82-107 153-178 (184)
228 smart00132 LIM Zinc-binding do 33.7 20 0.00044 14.2 0.5 10 83-92 28-37 (39)
229 COG3677 Transposase and inacti 33.2 24 0.00051 19.5 0.9 14 82-95 53-66 (129)
230 PF03966 Trm112p: Trm112p-like 33.0 24 0.00053 16.9 0.8 19 13-31 47-65 (68)
231 COG1594 RPB9 DNA-directed RNA 32.9 16 0.00034 19.7 0.1 17 17-33 20-36 (113)
232 PRK00420 hypothetical protein; 32.0 36 0.00079 18.4 1.4 11 82-92 40-50 (112)
233 PF04216 FdhE: Protein involve 31.7 10 0.00023 23.9 -0.7 13 82-94 238-250 (290)
234 KOG1088|consensus 31.7 22 0.00047 19.4 0.5 13 54-66 99-111 (124)
235 PF10537 WAC_Acf1_DNA_bd: ATP- 31.1 89 0.0019 16.6 3.1 38 18-62 2-39 (102)
236 KOG2907|consensus 30.2 31 0.00068 18.7 1.0 40 54-94 75-114 (116)
237 PRK12722 transcriptional activ 29.8 46 0.00099 19.9 1.7 28 54-90 135-162 (187)
238 KOG4317|consensus 29.5 27 0.00058 22.7 0.7 13 54-66 20-32 (383)
239 PF15616 TerY-C: TerY-C metal 29.4 24 0.00051 19.7 0.5 11 82-92 105-115 (131)
240 KOG1280|consensus 29.2 56 0.0012 21.6 2.1 27 54-80 80-106 (381)
241 PF04810 zf-Sec23_Sec24: Sec23 29.1 26 0.00057 14.8 0.5 11 82-92 24-34 (40)
242 PF04438 zf-HIT: HIT zinc fing 28.8 43 0.00093 13.3 1.1 16 17-32 11-26 (30)
243 PF00412 LIM: LIM domain; Int 28.6 23 0.0005 15.9 0.3 10 83-92 27-36 (58)
244 PRK12860 transcriptional activ 28.5 49 0.0011 19.8 1.7 27 54-89 135-161 (189)
245 COG1998 RPS31 Ribosomal protei 28.5 50 0.0011 15.0 1.3 10 82-91 37-46 (51)
246 PF05495 zf-CHY: CHY zinc fing 27.7 15 0.00032 17.9 -0.4 29 54-91 42-70 (71)
247 PF13821 DUF4187: Domain of un 27.5 47 0.001 15.4 1.2 18 82-99 27-44 (55)
248 TIGR00319 desulf_FeS4 desulfof 27.1 40 0.00088 13.5 0.9 12 18-29 6-17 (34)
249 COG1779 C4-type Zn-finger prot 27.1 10 0.00023 22.6 -1.2 7 21-27 16-22 (201)
250 COG4530 Uncharacterized protei 26.5 56 0.0012 17.7 1.5 27 55-93 11-37 (129)
251 KOG2747|consensus 26.5 34 0.00074 22.9 0.9 25 82-106 158-182 (396)
252 cd00974 DSRD Desulforedoxin (D 26.4 44 0.00095 13.4 0.9 11 19-29 4-14 (34)
253 TIGR03831 YgiT_finger YgiT-typ 26.4 33 0.00072 14.5 0.6 12 20-31 33-44 (46)
254 PRK14714 DNA polymerase II lar 26.3 77 0.0017 25.0 2.6 9 20-28 668-676 (1337)
255 KOG1994|consensus 26.0 31 0.00068 21.2 0.6 20 82-101 239-258 (268)
256 TIGR01384 TFS_arch transcripti 25.8 19 0.0004 18.8 -0.3 14 18-31 15-28 (104)
257 PRK14892 putative transcriptio 25.5 40 0.00087 17.8 0.9 11 54-64 43-53 (99)
258 COG1885 Uncharacterized protei 24.3 41 0.00089 17.9 0.8 12 19-30 49-60 (115)
259 PF11023 DUF2614: Protein of u 24.2 60 0.0013 17.6 1.4 9 54-62 70-78 (114)
260 COG5188 PRP9 Splicing factor 3 24.0 41 0.00088 22.3 0.8 22 19-40 238-259 (470)
261 PLN03239 histone acetyltransfe 23.9 61 0.0013 21.4 1.6 23 82-104 106-128 (351)
262 PF03107 C1_2: C1 domain; Int 23.8 51 0.0011 12.8 0.9 6 85-90 3-8 (30)
263 COG1066 Sms Predicted ATP-depe 23.5 55 0.0012 22.4 1.4 14 18-31 6-19 (456)
264 COG0675 Transposase and inacti 23.5 46 0.00099 21.1 1.0 9 82-90 322-330 (364)
265 PF08209 Sgf11: Sgf11 (transcr 23.4 74 0.0016 13.0 2.3 24 82-106 4-27 (33)
266 PF10071 DUF2310: Zn-ribbon-co 23.4 54 0.0012 20.7 1.3 28 54-89 221-248 (258)
267 PF11672 DUF3268: Protein of u 23.1 59 0.0013 17.3 1.2 10 19-28 2-11 (102)
268 TIGR01385 TFSII transcription 23.0 35 0.00076 21.9 0.4 37 53-93 258-297 (299)
269 PF02891 zf-MIZ: MIZ/SP-RING z 22.7 65 0.0014 14.4 1.2 8 54-61 42-49 (50)
270 COG5027 SAS2 Histone acetyltra 22.6 43 0.00092 22.2 0.7 26 82-107 158-183 (395)
271 PF02148 zf-UBP: Zn-finger in 22.4 49 0.0011 15.5 0.8 16 17-32 9-24 (63)
272 PF02748 PyrI_C: Aspartate car 22.3 54 0.0012 15.0 0.9 16 16-31 32-47 (52)
273 PF04328 DUF466: Protein of un 22.3 84 0.0018 15.1 1.6 13 98-110 28-40 (65)
274 PF14690 zf-ISL3: zinc-finger 22.3 48 0.001 14.2 0.7 7 20-26 3-9 (47)
275 smart00064 FYVE Protein presen 21.8 69 0.0015 15.0 1.3 12 20-31 11-22 (68)
276 PF14446 Prok-RING_1: Prokaryo 21.7 37 0.00081 15.7 0.3 8 85-92 8-15 (54)
277 TIGR03830 CxxCG_CxxCG_HTH puta 21.5 1.2E+02 0.0025 16.2 2.3 21 19-39 31-51 (127)
278 KOG2857|consensus 21.4 51 0.0011 18.7 0.8 22 19-40 17-38 (157)
279 COG5595 Zn-ribbon-containing, 21.2 35 0.00075 20.5 0.2 14 21-34 220-233 (256)
280 PF14255 Cys_rich_CPXG: Cystei 20.9 51 0.0011 15.1 0.6 9 84-92 2-10 (52)
281 PF08792 A2L_zn_ribbon: A2L zi 20.8 49 0.0011 13.5 0.5 11 54-64 22-32 (33)
282 TIGR00686 phnA alkylphosphonat 20.7 59 0.0013 17.5 0.9 11 20-30 20-30 (109)
283 PF08271 TF_Zn_Ribbon: TFIIB z 20.7 57 0.0012 13.9 0.8 9 54-62 20-28 (43)
284 PF12773 DZR: Double zinc ribb 20.6 89 0.0019 13.6 1.4 7 55-61 31-37 (50)
285 PF04606 Ogr_Delta: Ogr/Delta- 20.6 21 0.00045 15.8 -0.7 6 88-93 33-38 (47)
286 KOG3362|consensus 20.5 39 0.00085 19.2 0.3 20 82-101 129-148 (156)
287 KOG2636|consensus 20.3 94 0.002 21.4 1.9 23 17-39 399-422 (497)
No 1
>KOG2462|consensus
Probab=99.94 E-value=4.7e-27 Score=137.52 Aligned_cols=101 Identities=24% Similarity=0.394 Sum_probs=91.2
Q ss_pred hHHHHHHhhhhhcC---CCCceecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCchhhHhhhhhhcC
Q psy12016 2 FFLFFLEYLSVWQN---DSGMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYECG 78 (111)
Q Consensus 2 ~~~~~l~~~~~~~~---~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~ 78 (111)
.+...|..|.++|- ..+.+.|+.|++.+.+...|.-|+++|+. + ..|.+||+.|.+++.|+.|+++|+|
T Consensus 141 sT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l--~------c~C~iCGKaFSRPWLLQGHiRTHTG 212 (279)
T KOG2462|consen 141 STSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTL--P------CECGICGKAFSRPWLLQGHIRTHTG 212 (279)
T ss_pred ccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCC--C------cccccccccccchHHhhcccccccC
Confidence 45566778888883 36678999999999999999999999984 3 8999999999999999999999999
Q ss_pred CCCccccCCCCcccccchhHHHHHHHhhCCCCC
Q psy12016 79 QEPKYECDQCPHRTKHISSLKKHMALKHGVESQ 111 (111)
Q Consensus 79 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ek~~ 111 (111)
|+ ||.|..|+++|+.+++|+.|+++|.+.|+|
T Consensus 213 EK-PF~C~hC~kAFADRSNLRAHmQTHS~~K~~ 244 (279)
T KOG2462|consen 213 EK-PFSCPHCGKAFADRSNLRAHMQTHSDVKKH 244 (279)
T ss_pred CC-CccCCcccchhcchHHHHHHHHhhcCCccc
Confidence 88 999999999999999999999999999987
No 2
>KOG2462|consensus
Probab=99.87 E-value=1e-22 Score=119.50 Aligned_cols=93 Identities=25% Similarity=0.374 Sum_probs=86.8
Q ss_pred HHHHHHhhhhhcCCCCceecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCchhhHhhhhhhcCCCCc
Q psy12016 3 FLFFLEYLSVWQNDSGMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYECGQEPK 82 (111)
Q Consensus 3 ~~~~l~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~ 82 (111)
.+=.|+.|+++|+ -+..|.+||+.|...=.|+.|+++|+|++| |.|..|+++|...++|..|+++|.+.+ +
T Consensus 173 SmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKP------F~C~hC~kAFADRSNLRAHmQTHS~~K-~ 243 (279)
T KOG2462|consen 173 SMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKP------FSCPHCGKAFADRSNLRAHMQTHSDVK-K 243 (279)
T ss_pred ehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCC------ccCCcccchhcchHHHHHHHHhhcCCc-c
Confidence 3446899999987 789999999999999999999999999999 999999999999999999999998887 9
Q ss_pred cccCCCCcccccchhHHHHHHH
Q psy12016 83 YECDQCPHRTKHISSLKKHMAL 104 (111)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~ 104 (111)
|.|..|++.|...+.|.+|...
T Consensus 244 ~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 244 HQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred ccCcchhhHHHHHHHHHHhhhh
Confidence 9999999999999999999764
No 3
>KOG3623|consensus
Probab=99.69 E-value=5.2e-18 Score=110.85 Aligned_cols=82 Identities=37% Similarity=0.810 Sum_probs=78.4
Q ss_pred CCCCceecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCchhhHhhhhhhcCCCCccccCCCCccccc
Q psy12016 15 NDSGMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKH 94 (111)
Q Consensus 15 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~ 94 (111)
+.+++|.|+.|++.|...+.|.+|...|+|.++ |.|.+|.++|..+-.|..|++.|.|++ ||.|+.|++.|..
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRP------yqC~iCkKAFKHKHHLtEHkRLHSGEK-PfQCdKClKRFSH 962 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRP------YQCIICKKAFKHKHHLTEHKRLHSGEK-PFQCDKCLKRFSH 962 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCC------cccchhhHhhhhhhhhhhhhhhccCCC-cchhhhhhhhccc
Confidence 467899999999999999999999999999999 999999999999999999999999988 9999999999999
Q ss_pred chhHHHHHH
Q psy12016 95 ISSLKKHMA 103 (111)
Q Consensus 95 ~~~l~~H~~ 103 (111)
.+.+..||.
T Consensus 963 SGSYSQHMN 971 (1007)
T KOG3623|consen 963 SGSYSQHMN 971 (1007)
T ss_pred ccchHhhhc
Confidence 999999975
No 4
>KOG1074|consensus
Probab=99.68 E-value=1.9e-17 Score=109.28 Aligned_cols=56 Identities=29% Similarity=0.540 Sum_probs=52.7
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccchhHHHHHHHhhCCCC
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHISSLKKHMALKHGVES 110 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ek~ 110 (111)
..|.+|++.|.....|..|+++|++++ ||.|.+|++.|..+.+|+.||.+|+..+|
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~K-PF~C~fC~~aFttrgnLKvHMgtH~w~q~ 935 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPK-PFFCHFCEEAFTTRGNLKVHMGTHMWVQP 935 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCC-CccchhhhhhhhhhhhhhhhhccccccCC
Confidence 489999999999999999999999988 99999999999999999999999987655
No 5
>KOG3576|consensus
Probab=99.66 E-value=2.3e-17 Score=93.66 Aligned_cols=85 Identities=35% Similarity=0.630 Sum_probs=76.6
Q ss_pred CCCceecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccc
Q psy12016 16 DSGMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHI 95 (111)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~ 95 (111)
....|.|.+|++.|....-|.+|++.|...+. +.|..||+.|.....|..|.++|+|-+ ||+|..|+++|..+
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr------~lct~cgkgfndtfdlkrh~rthtgvr-pykc~~c~kaftqr 186 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKR------HLCTFCGKGFNDTFDLKRHTRTHTGVR-PYKCSLCEKAFTQR 186 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHH------HHHhhccCcccchhhhhhhhccccCcc-ccchhhhhHHHHhh
Confidence 34568999999999999999999999988877 999999999999999999999999977 99999999999999
Q ss_pred hhHHHHHHHhhC
Q psy12016 96 SSLKKHMALKHG 107 (111)
Q Consensus 96 ~~l~~H~~~~~~ 107 (111)
..|..|++.-||
T Consensus 187 csleshl~kvhg 198 (267)
T KOG3576|consen 187 CSLESHLKKVHG 198 (267)
T ss_pred ccHHHHHHHHcC
Confidence 999999875554
No 6
>KOG1074|consensus
Probab=99.63 E-value=1.2e-16 Score=105.58 Aligned_cols=53 Identities=23% Similarity=0.479 Sum_probs=50.2
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccchhHHHHHHHhhC
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHISSLKKHMALKHG 107 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 107 (111)
..|..|.+.....+.|+.|-++|+|++ ||+|.+|+++|..+.+|+.|+.+|..
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGER-PFkCKiCgRAFtTkGNLkaH~~vHka 658 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGER-PFKCKICGRAFTTKGNLKAHMSVHKA 658 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcC-ccccccccchhccccchhhccccccc
Confidence 389999999999999999999999988 99999999999999999999998875
No 7
>KOG3623|consensus
Probab=99.56 E-value=1.8e-15 Score=99.31 Aligned_cols=99 Identities=30% Similarity=0.573 Sum_probs=81.4
Q ss_pred HHHHHhhhhhcC--CCCceecCCCcccccchhHHHHHHhhhcCCCCC-------CCCCccccCccCcccCCchhhHhhhh
Q psy12016 4 LFFLEYLSVWQN--DSGMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQ-------NLDGLFSCDVCGKHYKYKKGLGRHKR 74 (111)
Q Consensus 4 ~~~l~~~~~~~~--~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~-------~~~~~~~c~~c~~~~~~~~~l~~h~~ 74 (111)
+..|++|+.-.. -+..|.|..|..+|.....|.+|+.+|...... ..-..|+|.+|+++|..+-.|+.|++
T Consensus 223 ltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlR 302 (1007)
T KOG3623|consen 223 LTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLR 302 (1007)
T ss_pred HHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhhe
Confidence 566777765442 244588999999999999999999988644332 11234899999999999999999999
Q ss_pred hhcCCCCccccCCCCcccccchhHHHHHH
Q psy12016 75 YECGQEPKYECDQCPHRTKHISSLKKHMA 103 (111)
Q Consensus 75 ~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 103 (111)
.|.|++ ||.|+.|.+.|...+.+..|+.
T Consensus 303 IHSGEK-PfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 303 IHSGEK-PFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred eecCCC-CcCCcccccccccCCccccccc
Confidence 999988 9999999999999999988874
No 8
>KOG3608|consensus
Probab=99.52 E-value=3.1e-14 Score=86.97 Aligned_cols=104 Identities=19% Similarity=0.411 Sum_probs=84.7
Q ss_pred HHHHHHhhhhhcCCCCceecCCCcccccchhHHHHHHhhhcCCCCCCC----------------------CCccccCccC
Q psy12016 3 FLFFLEYLSVWQNDSGMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNL----------------------DGLFSCDVCG 60 (111)
Q Consensus 3 ~~~~l~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~----------------------~~~~~c~~c~ 60 (111)
...-|++|.+.|+.++...|+.|+..|..+..|-.|.+..+.-..... .+-|+|+.|+
T Consensus 191 ~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCd 270 (467)
T KOG3608|consen 191 NKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCD 270 (467)
T ss_pred cHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccc
Confidence 456789999999999999999999999999999888765443322211 2347899999
Q ss_pred cccCCchhhHhhhhhhcCCCCccccCCCCcccccchhHHHHHHHhh
Q psy12016 61 KHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHISSLKKHMALKH 106 (111)
Q Consensus 61 ~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 106 (111)
.....++.|..|++..+.+-+||+|+.|+..+...++|.+|...|.
T Consensus 271 mtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 271 MTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred cCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 9999999999998887766669999999999999999999988776
No 9
>KOG3576|consensus
Probab=99.52 E-value=5.7e-15 Score=84.05 Aligned_cols=101 Identities=21% Similarity=0.408 Sum_probs=88.5
Q ss_pred HHHHHhhhhhcCCCCceecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCchhhHhhhhhhcCC----
Q psy12016 4 LFFLEYLSVWQNDSGMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYECGQ---- 79 (111)
Q Consensus 4 ~~~l~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~---- 79 (111)
-+.|..|..-|+..+.+.|..||+.|...-+|.+|+++|+|.++ |.|..|+++|...-.|..|.+.-++.
T Consensus 130 QRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrp------ykc~~c~kaftqrcsleshl~kvhgv~~~y 203 (267)
T KOG3576|consen 130 QRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRP------YKCSLCEKAFTQRCSLESHLKKVHGVQHQY 203 (267)
T ss_pred HHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccc------cchhhhhHHHHhhccHHHHHHHHcCchHHH
Confidence 46788899999999999999999999999999999999999999 99999999999999999998876653
Q ss_pred ------CCccccCCCCcccccchhHHHHHHHhhCCCC
Q psy12016 80 ------EPKYECDQCPHRTKHISSLKKHMALKHGVES 110 (111)
Q Consensus 80 ------~~~~~C~~C~~~f~~~~~l~~H~~~~~~ek~ 110 (111)
.+.|.|+.||.+-.....+-.|++.++...|
T Consensus 204 aykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 204 AYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred HHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 1268999999888888888889988876443
No 10
>PHA00733 hypothetical protein
Probab=99.34 E-value=1.5e-12 Score=70.65 Aligned_cols=84 Identities=19% Similarity=0.279 Sum_probs=67.8
Q ss_pred CCCCceecCCCcccccchhHHHHH--Hhh---hcCCCCCCCCCccccCccCcccCCchhhHhhhhhhcCCCCccccCCCC
Q psy12016 15 NDSGMFTCDVCFKEYKYKRGLVRH--KKN---SCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCP 89 (111)
Q Consensus 15 ~~~~~~~C~~C~~~f~~~~~l~~h--~~~---~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~ 89 (111)
...+++.|..|...|.....|..+ +.. +.+..+ |.|+.|++.|.....|..|++.+ .. ++.|..|+
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kP------y~C~~Cgk~Fss~s~L~~H~r~h--~~-~~~C~~Cg 106 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSP------YVCPLCLMPFSSSVSLKQHIRYT--EH-SKVCPVCG 106 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCC------ccCCCCCCcCCCHHHHHHHHhcC--Cc-CccCCCCC
Confidence 446778999999888887777665 222 122344 99999999999999999999875 34 79999999
Q ss_pred cccccchhHHHHHHHhhC
Q psy12016 90 HRTKHISSLKKHMALKHG 107 (111)
Q Consensus 90 ~~f~~~~~l~~H~~~~~~ 107 (111)
+.|.....|..|+...|+
T Consensus 107 K~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 107 KEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CccCCHHHHHHHHHHhcC
Confidence 999999999999987765
No 11
>KOG3608|consensus
Probab=99.23 E-value=3.3e-11 Score=73.98 Aligned_cols=91 Identities=21% Similarity=0.488 Sum_probs=47.3
Q ss_pred HHHHHHhhhhhcCCCCceecCCCcccccchhHHHHHHhh-hcCCCCCCCCCccccCccCcccCCchhhHhhhhhhcCCCC
Q psy12016 3 FLFFLEYLSVWQNDSGMFTCDVCFKEYKYKRGLVRHKKN-SCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYECGQEP 81 (111)
Q Consensus 3 ~~~~l~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~-~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~ 81 (111)
+-..|+.|.+.|. .-|.|+.|+.+....+.|.+|++. |...++ |+|+.|++.+.+...|..|..+|. +.
T Consensus 249 TeklL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkp------fKCd~Cd~~c~~esdL~kH~~~HS-~~- 318 (467)
T KOG3608|consen 249 TEKLLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKP------FKCDECDTRCVRESDLAKHVQVHS-KT- 318 (467)
T ss_pred HHHHHHHHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCC------ccccchhhhhccHHHHHHHHHhcc-cc-
Confidence 3344555555443 345566666666666666666543 333344 666666666666666666655543 22
Q ss_pred ccccCC--CCcccccchhHHHHHH
Q psy12016 82 KYECDQ--CPHRTKHISSLKKHMA 103 (111)
Q Consensus 82 ~~~C~~--C~~~f~~~~~l~~H~~ 103 (111)
.|.|.. |...+.+...+++|.+
T Consensus 319 ~y~C~h~~C~~s~r~~~q~~~H~~ 342 (467)
T KOG3608|consen 319 VYQCEHPDCHYSVRTYTQMRRHFL 342 (467)
T ss_pred ceecCCCCCcHHHHHHHHHHHHHH
Confidence 344443 4444444444444443
No 12
>PHA02768 hypothetical protein; Provisional
Probab=99.05 E-value=8.4e-11 Score=53.92 Aligned_cols=41 Identities=20% Similarity=0.489 Sum_probs=21.3
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccchh
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHISS 97 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~ 97 (111)
|.|+.||+.|.....|..|+++|. + +++|..|++.|...+.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k-~~kc~~C~k~f~~~s~ 46 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--T-NLKLSNCKRISLRTGE 46 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--C-cccCCcccceecccce
Confidence 455555555555555555555553 2 4555555555544443
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.05 E-value=1.2e-10 Score=53.45 Aligned_cols=44 Identities=11% Similarity=0.286 Sum_probs=39.0
Q ss_pred ceecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCchhhH
Q psy12016 19 MFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKKGLG 70 (111)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~ 70 (111)
-|.|+.||+.|.....|..|+++|+ .+ +.|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~------~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TN------LKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--Cc------ccCCcccceecccceeE
Confidence 3789999999999999999999998 45 89999999998776654
No 14
>PHA00733 hypothetical protein
Probab=99.01 E-value=1e-09 Score=59.62 Aligned_cols=64 Identities=19% Similarity=0.387 Sum_probs=52.1
Q ss_pred HHHhhhhhcCCCCceecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCchhhHhhhhhhcC
Q psy12016 6 FLEYLSVWQNDSGMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYECG 78 (111)
Q Consensus 6 ~l~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~ 78 (111)
+|..+...+ .++||.|+.|++.|.....|..|+..+. .+ +.|..|++.|.....|..|+...++
T Consensus 61 ~l~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~h~--~~------~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 61 YLYKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIRYTE--HS------KVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred HHHhhcccC-CCCCccCCCCCCcCCCHHHHHHHHhcCC--cC------ccCCCCCCccCCHHHHHHHHHHhcC
Confidence 345554444 4779999999999999999999988652 34 8999999999999999999886543
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.98 E-value=1.5e-09 Score=71.22 Aligned_cols=63 Identities=21% Similarity=0.511 Sum_probs=32.6
Q ss_pred CceecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCchhhHhhhhhhcCCCCccccCCCCccc
Q psy12016 18 GMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRT 92 (111)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f 92 (111)
..+.|+.|++.|. ...+..|+..+. .+ +.|+ |+..+ ....|..|+.++.+.+ ++.|..|+..+
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~~~H--kp------v~Cp-Cg~~~-~R~~L~~H~~thCp~K-pi~C~fC~~~v 514 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMKVFH--EP------LQCP-CGVVL-EKEQMVQHQASTCPLR-LITCRFCGDMV 514 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHHhcC--CC------ccCC-CCCCc-chhHHHhhhhccCCCC-ceeCCCCCCcc
Confidence 3345555655553 344555555542 33 5555 55433 3345555555555544 55566665555
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.93 E-value=4.1e-09 Score=69.21 Aligned_cols=90 Identities=20% Similarity=0.380 Sum_probs=72.4
Q ss_pred HHHHhhhhhcCCCCceecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCC----------chhhHhhhh
Q psy12016 5 FFLEYLSVWQNDSGMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKY----------KKGLGRHKR 74 (111)
Q Consensus 5 ~~l~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~----------~~~l~~h~~ 74 (111)
..|+.|...+. .++.|+ |+..+ .+..|..|+.++++.++ +.|..|+..+.. ...|..|..
T Consensus 466 s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kp------i~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~ 535 (567)
T PLN03086 466 GEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRL------ITCRFCGDMVQAGGSAMDVRDRLRGMSEHES 535 (567)
T ss_pred HHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCc------eeCCCCCCccccCccccchhhhhhhHHHHHH
Confidence 45788888874 689999 99755 66899999999999999 999999998852 346888888
Q ss_pred hhcCCCCccccCCCCcccccchhHHHHHHHhhC
Q psy12016 75 YECGQEPKYECDQCPHRTKHISSLKKHMALKHG 107 (111)
Q Consensus 75 ~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 107 (111)
.. +.+ ++.|..|++.+..+ .+..|+...|.
T Consensus 536 ~C-G~r-t~~C~~Cgk~Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 536 IC-GSR-TAPCDSCGRSVMLK-EMDIHQIAVHQ 565 (567)
T ss_pred hc-CCc-ceEccccCCeeeeh-hHHHHHHHhhc
Confidence 74 666 99999999888665 67778876654
No 17
>PHA00616 hypothetical protein
Probab=98.90 E-value=7.5e-10 Score=48.48 Aligned_cols=29 Identities=17% Similarity=0.364 Sum_probs=17.0
Q ss_pred ccccCCCCcccccchhHHHHHHHhhCCCC
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKHGVES 110 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~~ek~ 110 (111)
||.|..||+.|...+++..|++.+||++|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 35555666666666666666666665554
No 18
>KOG3993|consensus
Probab=98.84 E-value=4.3e-10 Score=70.51 Aligned_cols=25 Identities=20% Similarity=0.546 Sum_probs=21.3
Q ss_pred ccccCCCCcccccchhHHHHHHHhh
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKH 106 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~ 106 (111)
.|.|..|++.|.....|++|+.+|+
T Consensus 356 i~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 356 IFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred eeecHHhhhhhHHHHHHHHhHHhhh
Confidence 5788889999998889999987776
No 19
>KOG3993|consensus
Probab=98.80 E-value=2.7e-09 Score=67.07 Aligned_cols=77 Identities=21% Similarity=0.333 Sum_probs=61.6
Q ss_pred ChHHHHHHhhhhhcCCCCceecCCCcccccchhHHHHHHhhhcCCCC-----------C----------------CCCCc
Q psy12016 1 MFFLFFLEYLSVWQNDSGMFTCDVCFKEYKYKRGLVRHKKNSCKQKP-----------Q----------------NLDGL 53 (111)
Q Consensus 1 ~~~~~~l~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~-----------~----------------~~~~~ 53 (111)
|++.+.|-.|.-....-.-|.|++|+++|.-..+|..|.+.|-.... . +.+++
T Consensus 277 YeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi 356 (500)
T KOG3993|consen 277 YEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGI 356 (500)
T ss_pred hhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCce
Confidence 46677788887776666779999999999999999999987732211 0 23568
Q ss_pred cccCccCcccCCchhhHhhhhhhc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYEC 77 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~ 77 (111)
|.|..|++.|.+...|..|+.+|+
T Consensus 357 ~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 357 FSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred eecHHhhhhhHHHHHHHHhHHhhh
Confidence 999999999999999999977765
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.79 E-value=4.9e-09 Score=41.34 Aligned_cols=24 Identities=17% Similarity=0.308 Sum_probs=17.3
Q ss_pred HHhhhhhcCCCCceecCCCccccc
Q psy12016 7 LEYLSVWQNDSGMFTCDVCFKEYK 30 (111)
Q Consensus 7 l~~~~~~~~~~~~~~C~~C~~~f~ 30 (111)
|+.|+++|++++||.|+.|++.|.
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 566777777777777777777764
No 21
>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=98.78 E-value=4.3e-09 Score=41.51 Aligned_cols=24 Identities=33% Similarity=0.697 Sum_probs=16.5
Q ss_pred hHhhhhhhcCCCCccccCCCCcccc
Q psy12016 69 LGRHKRYECGQEPKYECDQCPHRTK 93 (111)
Q Consensus 69 l~~h~~~~~~~~~~~~C~~C~~~f~ 93 (111)
|..|+++|.+++ ||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k-~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEK-PYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSS-SEEESSSSEEES
T ss_pred HHHHhhhcCCCC-CCCCCCCcCeeC
Confidence 556777776665 777777777664
No 22
>PHA00616 hypothetical protein
Probab=98.57 E-value=3.2e-08 Score=43.36 Aligned_cols=29 Identities=24% Similarity=0.461 Sum_probs=19.4
Q ss_pred ceecCCCcccccchhHHHHHHhhhcCCCC
Q psy12016 19 MFTCDVCFKEYKYKRGLVRHKKNSCKQKP 47 (111)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~ 47 (111)
||.|+.||+.|..+.++..|++.|+++.+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 45666666666666666666666666655
No 23
>PHA00732 hypothetical protein
Probab=98.49 E-value=1.4e-07 Score=47.07 Aligned_cols=46 Identities=28% Similarity=0.511 Sum_probs=36.0
Q ss_pred ceecCCCcccccchhHHHHHHhh-hcCCCCCCCCCccccCccCcccCCchhhHhhhhhh
Q psy12016 19 MFTCDVCFKEYKYKRGLVRHKKN-SCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYE 76 (111)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~-~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~ 76 (111)
||.|..|++.|.....|..|++. |. + +.|+.|++.|. .+..|.++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~------~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---L------TKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---C------CccCCCCCEeC---Chhhhhccc
Confidence 57899999999999999999874 43 2 57999999887 356676554
No 24
>PHA00732 hypothetical protein
Probab=98.48 E-value=1.3e-07 Score=47.17 Aligned_cols=46 Identities=24% Similarity=0.477 Sum_probs=37.4
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccchhHHHHHHHh
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHISSLKKHMALK 105 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 105 (111)
|.|..|++.|.....|..|++.++. ++.|+.|++.|. .+..|..+.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhccc
Confidence 7899999999999999999985322 468999999997 467776543
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.47 E-value=3.4e-07 Score=42.46 Aligned_cols=51 Identities=27% Similarity=0.514 Sum_probs=32.8
Q ss_pred cccCccCcccCCchhhHhhhhhhcC-CCCccccCCCCcccccchhHHHHHHHhhC
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECG-QEPKYECDQCPHRTKHISSLKKHMALKHG 107 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~-~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 107 (111)
|.|+.|++ ......|..|....+. +.+.+.|+.|...+. .+|..|+...|+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 77888887 4445667777555443 333677888876543 377778777664
No 26
>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=98.35 E-value=3.7e-07 Score=34.75 Aligned_cols=23 Identities=35% Similarity=0.651 Sum_probs=18.5
Q ss_pred cccCCCCcccccchhHHHHHHHh
Q psy12016 83 YECDQCPHRTKHISSLKKHMALK 105 (111)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~ 105 (111)
|.|+.|++.|.....|..|++.|
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 56888888888888888888763
No 27
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.25 E-value=9.3e-07 Score=33.77 Aligned_cols=24 Identities=29% Similarity=0.692 Sum_probs=18.0
Q ss_pred cccCCCCcccccchhHHHHHHHhh
Q psy12016 83 YECDQCPHRTKHISSLKKHMALKH 106 (111)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~~ 106 (111)
|.|+.|+..|.....|..|+.++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 578888888888888888888764
No 28
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.25 E-value=1.2e-06 Score=33.31 Aligned_cols=23 Identities=30% Similarity=0.723 Sum_probs=17.5
Q ss_pred eecCCCcccccchhHHHHHHhhh
Q psy12016 20 FTCDVCFKEYKYKRGLVRHKKNS 42 (111)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~ 42 (111)
|.|+.|++.|..+..|..|++.|
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 56788888888888888887653
No 29
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=98.19 E-value=1.8e-06 Score=38.74 Aligned_cols=31 Identities=19% Similarity=0.464 Sum_probs=23.0
Q ss_pred CCccccCCCCcccccchhHHHHHHHhhCCCC
Q psy12016 80 EPKYECDQCPHRTKHISSLKKHMALKHGVES 110 (111)
Q Consensus 80 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~ek~ 110 (111)
.+|-.|++|+..+....+|++|+.+.|+-||
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 3388999999999999999999999998886
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=98.15 E-value=9.4e-07 Score=34.98 Aligned_cols=26 Identities=27% Similarity=0.636 Sum_probs=19.4
Q ss_pred ccccCCCCcccccchhHHHHHHHhhC
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKHG 107 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~~ 107 (111)
||.|..|++.|.....|..|++.|.+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 46788888888888888888776653
No 31
>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=98.04 E-value=1.5e-05 Score=36.89 Aligned_cols=51 Identities=25% Similarity=0.408 Sum_probs=36.3
Q ss_pred ceecCCCcccccchhHHHHHHhh-hcCCCCCCCCCccccCccCcccCCchhhHhhhhhhc
Q psy12016 19 MFTCDVCFKEYKYKRGLVRHKKN-SCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYEC 77 (111)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~-~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~ 77 (111)
.|.|+.|++ ..+...|..|... |..+.. .+.|+.|...+. ..+..|+...+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~-----~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESK-----NVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCC-----CccCCCchhhhh--hHHHHHHHHhc
Confidence 488999999 5566789999755 433221 289999997644 47888887654
No 32
>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=98.04 E-value=4.2e-06 Score=33.04 Aligned_cols=25 Identities=36% Similarity=0.749 Sum_probs=18.5
Q ss_pred ceecCCCcccccchhHHHHHHhhhc
Q psy12016 19 MFTCDVCFKEYKYKRGLVRHKKNSC 43 (111)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~~~ 43 (111)
||.|..|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 5677888888888877777776553
No 33
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.92 E-value=1.6e-05 Score=30.15 Aligned_cols=23 Identities=30% Similarity=0.722 Sum_probs=15.4
Q ss_pred eecCCCcccccchhHHHHHHhhh
Q psy12016 20 FTCDVCFKEYKYKRGLVRHKKNS 42 (111)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~ 42 (111)
|.|+.|+..|.....|..|+..+
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 56777777777777777777654
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.84 E-value=1.4e-05 Score=41.40 Aligned_cols=73 Identities=21% Similarity=0.277 Sum_probs=19.8
Q ss_pred ecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccchhHHH
Q psy12016 21 TCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHISSLKK 100 (111)
Q Consensus 21 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~ 100 (111)
.|..|+..|.....+..|+....+... +.. ..+.....+....+.... . .+.|..|++.|.+...|..
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~---------~~~-~~l~~~~~~~~~~~~~~~-~-~~~C~~C~~~f~s~~~l~~ 68 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDI---------PDQ-KYLVDPNRLLNYLRKKVK-E-SFRCPYCNKTFRSREALQE 68 (100)
T ss_dssp -----------------------------------------------------------S-SEEBSSSS-EESSHHHHHH
T ss_pred Ccccccccccccccccccccccccccc---------ccc-cccccccccccccccccC-C-CCCCCccCCCCcCHHHHHH
Confidence 488999999999999999865443211 110 111122222222222211 2 5889999999999999999
Q ss_pred HHHHh
Q psy12016 101 HMALK 105 (111)
Q Consensus 101 H~~~~ 105 (111)
|++.+
T Consensus 69 Hm~~~ 73 (100)
T PF12756_consen 69 HMRSK 73 (100)
T ss_dssp HHHHT
T ss_pred HHcCc
Confidence 98754
No 35
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.79 E-value=6.6e-06 Score=50.65 Aligned_cols=70 Identities=27% Similarity=0.511 Sum_probs=43.1
Q ss_pred CCceecCC--CcccccchhHHHHHHhh-hcCCCCCCCCCccccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccc
Q psy12016 17 SGMFTCDV--CFKEYKYKRGLVRHKKN-SCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTK 93 (111)
Q Consensus 17 ~~~~~C~~--C~~~f~~~~~l~~h~~~-~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~ 93 (111)
++||.|++ |++.+.....|+=|+.. |...+. .. .+ ....+.......+ ||+|++|++.++
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~------~~---------~p-~p~~~~~F~~~~K-PYrCevC~KRYK 409 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKL------HE---------NP-SPEKMNIFSAKDK-PYRCEVCDKRYK 409 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCccc------CC---------CC-CccccccccccCC-ceeccccchhhc
Confidence 47888887 88888888888777542 211111 00 00 0011111122334 999999999999
Q ss_pred cchhHHHHHH
Q psy12016 94 HISSLKKHMA 103 (111)
Q Consensus 94 ~~~~l~~H~~ 103 (111)
+...|+-|.+
T Consensus 410 NlNGLKYHr~ 419 (423)
T COG5189 410 NLNGLKYHRK 419 (423)
T ss_pred cCccceeccc
Confidence 9999988754
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.65 E-value=5.7e-05 Score=29.02 Aligned_cols=24 Identities=38% Similarity=0.664 Sum_probs=17.2
Q ss_pred cccCCCCcccccchhHHHHHHHhh
Q psy12016 83 YECDQCPHRTKHISSLKKHMALKH 106 (111)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~~ 106 (111)
+.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 457777777777777777777543
No 37
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.53 E-value=0.00011 Score=28.02 Aligned_cols=24 Identities=38% Similarity=0.766 Sum_probs=16.9
Q ss_pred cccCCCCcccccchhHHHHHHHhhC
Q psy12016 83 YECDQCPHRTKHISSLKKHMALKHG 107 (111)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~~~ 107 (111)
|.|..|+.... ...|.+|++.+++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 57888887776 7788888887764
No 38
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.45 E-value=0.00023 Score=32.12 Aligned_cols=30 Identities=23% Similarity=0.297 Sum_probs=14.9
Q ss_pred CCCceecCCCcccccchhHHHHHHhhhcCC
Q psy12016 16 DSGMFTCDVCFKEYKYKRGLVRHKKNSCKQ 45 (111)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~ 45 (111)
.+.|..|++|+..+....+|.+|+....+.
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 445566666666666666666666554443
No 39
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.41 E-value=0.00015 Score=27.85 Aligned_cols=23 Identities=30% Similarity=0.761 Sum_probs=17.9
Q ss_pred eecCCCcccccchhHHHHHHhhh
Q psy12016 20 FTCDVCFKEYKYKRGLVRHKKNS 42 (111)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~ 42 (111)
|.|..|+..|.....+..|++.+
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 56888888888888888887643
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.40 E-value=0.00019 Score=27.43 Aligned_cols=23 Identities=30% Similarity=0.603 Sum_probs=15.3
Q ss_pred eecCCCcccccchhHHHHHHhhh
Q psy12016 20 FTCDVCFKEYKYKRGLVRHKKNS 42 (111)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~ 42 (111)
|.|..|++.|.....+..|+..|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 35667777777777777776644
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.35 E-value=0.00012 Score=28.21 Aligned_cols=23 Identities=30% Similarity=0.628 Sum_probs=17.0
Q ss_pred cccCCCCcccccchhHHHHHHHh
Q psy12016 83 YECDQCPHRTKHISSLKKHMALK 105 (111)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~ 105 (111)
|.|..|+..|.+...+..|++.+
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 46778888888888888777543
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=97.00 E-value=0.00033 Score=27.51 Aligned_cols=22 Identities=36% Similarity=0.685 Sum_probs=16.7
Q ss_pred eecCCCcccccchhHHHHHHhh
Q psy12016 20 FTCDVCFKEYKYKRGLVRHKKN 41 (111)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~ 41 (111)
|.|..|++.|.....+..|+.+
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 5688888888888888777654
No 43
>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=96.99 E-value=0.00013 Score=28.73 Aligned_cols=21 Identities=33% Similarity=0.678 Sum_probs=13.8
Q ss_pred cccCCCCcccccchhHHHHHH
Q psy12016 83 YECDQCPHRTKHISSLKKHMA 103 (111)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~ 103 (111)
|.|..|++.|.+...|..|++
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 456777777777666666654
No 44
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.87 E-value=0.0016 Score=24.65 Aligned_cols=22 Identities=32% Similarity=0.555 Sum_probs=13.8
Q ss_pred eecCCCcccccchhHHHHHHhhh
Q psy12016 20 FTCDVCFKEYKYKRGLVRHKKNS 42 (111)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~ 42 (111)
|.|+.|+.... ...|.+|++.+
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 56777777666 66777776654
No 45
>PRK04860 hypothetical protein; Provisional
Probab=96.82 E-value=0.0011 Score=37.58 Aligned_cols=38 Identities=24% Similarity=0.585 Sum_probs=31.0
Q ss_pred ccccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccc
Q psy12016 53 LFSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHI 95 (111)
Q Consensus 53 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~ 95 (111)
.|.|. |+. ....+..|.+++.++. +|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~-~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEA-VYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCc-cEECCCCCceeEEe
Confidence 38997 887 5566788999998877 89999999888654
No 46
>PRK04860 hypothetical protein; Provisional
Probab=96.76 E-value=0.001 Score=37.74 Aligned_cols=26 Identities=23% Similarity=0.615 Sum_probs=16.5
Q ss_pred ccccCCCCcccccchhHHHHHHHhhCCCCC
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKHGVESQ 111 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~~ek~~ 111 (111)
+|.|. |+. ....+++|.+++.++++|
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~Y 144 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVY 144 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccE
Confidence 56666 665 445566677777776665
No 47
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.50 E-value=0.0029 Score=24.38 Aligned_cols=22 Identities=23% Similarity=0.443 Sum_probs=14.6
Q ss_pred cccCCCCcccccchhHHHHHHHh
Q psy12016 83 YECDQCPHRTKHISSLKKHMALK 105 (111)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~ 105 (111)
..|+.|++.| ....|..|+++.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~C 24 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKIC 24 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHhc
Confidence 4577788887 455667776653
No 48
>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=96.35 E-value=0.0043 Score=25.67 Aligned_cols=23 Identities=22% Similarity=0.442 Sum_probs=17.5
Q ss_pred ceecCCCcccccchhHHHHHHhh
Q psy12016 19 MFTCDVCFKEYKYKRGLVRHKKN 41 (111)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~ 41 (111)
+|.|..|+..|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57788888888877777777653
No 49
>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=96.18 E-value=0.0037 Score=25.89 Aligned_cols=22 Identities=18% Similarity=0.412 Sum_probs=17.6
Q ss_pred ccccCCCCcccccchhHHHHHH
Q psy12016 82 KYECDQCPHRTKHISSLKKHMA 103 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~ 103 (111)
+|.|..|+..|.....+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 5778888888888878877764
No 50
>KOG1146|consensus
Probab=95.55 E-value=0.0092 Score=43.70 Aligned_cols=78 Identities=19% Similarity=0.326 Sum_probs=43.0
Q ss_pred CCceecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCchhhHhhhhhh-cCCCCccccCCCCcccccc
Q psy12016 17 SGMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYE-CGQEPKYECDQCPHRTKHI 95 (111)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~-~~~~~~~~C~~C~~~f~~~ 95 (111)
.+.+.|+.|++.|.....|..|++.-+.+.. . ..|.. +.....+ ....+. .+.. +|.|..|...+...
T Consensus 463 ~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~------~--~~c~~-gq~~~~~-arg~~~~~~~~-p~~C~~C~~stttn 531 (1406)
T KOG1146|consen 463 FKTLKCPKCNWHYKLAQTLGVHMRSKHPESQ------S--AYCKA-GQNHPRL-ARGEVYRCPGK-PYPCRACNYSTTTN 531 (1406)
T ss_pred cccccCCccchhhhhHHHhhhcccccccccc------h--hHhHh-ccccccc-cccccccCCCC-cccceeeeeeeecc
Confidence 3556777777777777777777665332211 0 11110 0000000 001111 1223 88999999999999
Q ss_pred hhHHHHHHHh
Q psy12016 96 SSLKKHMALK 105 (111)
Q Consensus 96 ~~l~~H~~~~ 105 (111)
.+|..|+...
T Consensus 532 g~LsihlqS~ 541 (1406)
T KOG1146|consen 532 GNLSIHLQSD 541 (1406)
T ss_pred hHHHHHHHHH
Confidence 9999998643
No 51
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.90 E-value=0.017 Score=26.61 Aligned_cols=29 Identities=14% Similarity=0.482 Sum_probs=23.7
Q ss_pred CCCCceecCCCcccccchhHHHHHHhhhc
Q psy12016 15 NDSGMFTCDVCFKEYKYKRGLVRHKKNSC 43 (111)
Q Consensus 15 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~ 43 (111)
-++..+.|+.|+..|....++.+|.....
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 46777899999999999999999975433
No 52
>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=94.70 E-value=0.026 Score=23.23 Aligned_cols=24 Identities=29% Similarity=0.816 Sum_probs=13.6
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPH 90 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~ 90 (111)
|.|..||..+.... . ++.|+.|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~-~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------A-PWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------C-CCcCcCCCC
Confidence 56667765544321 2 667777763
No 53
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.32 E-value=0.026 Score=26.01 Aligned_cols=25 Identities=16% Similarity=0.357 Sum_probs=15.8
Q ss_pred ccccCCCCcccccchhHHHHHHHhh
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKH 106 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~ 106 (111)
-+.|+.|+..|...-++.+|..-.|
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhHHh
Confidence 5567777777766666666655443
No 54
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.04 E-value=0.095 Score=26.82 Aligned_cols=23 Identities=30% Similarity=0.777 Sum_probs=15.6
Q ss_pred cccCccCcccCCchhhHhhhhhh
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYE 76 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~ 76 (111)
+.|..|+..|.+...|..|++.+
T Consensus 51 ~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 51 FRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp EEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCccCCCCcCHHHHHHHHcCc
Confidence 67777777777777777777654
No 55
>KOG4173|consensus
Probab=92.87 E-value=0.058 Score=31.83 Aligned_cols=79 Identities=23% Similarity=0.391 Sum_probs=56.4
Q ss_pred ceecCC--CcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCchhhHhhhhhhc---------CCCCccccC-
Q psy12016 19 MFTCDV--CFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYEC---------GQEPKYECD- 86 (111)
Q Consensus 19 ~~~C~~--C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~---------~~~~~~~C~- 86 (111)
.+.|+. |.+.|.....+..|..+..+ ..|..|.+.|+....|..|..-.+ .+...|.|-
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~---------~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~Clv 149 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHG---------NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLV 149 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhccc---------chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHH
Confidence 356776 66777777777777544333 589999999999988888855433 223368884
Q ss_pred -CCCcccccchhHHHHHHHhh
Q psy12016 87 -QCPHRTKHISSLKKHMALKH 106 (111)
Q Consensus 87 -~C~~~f~~~~~l~~H~~~~~ 106 (111)
.|+..|......+.|+..-|
T Consensus 150 EgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 150 EGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred HhhhhhhhhhhhhhhHHHHhc
Confidence 59999999888888876544
No 56
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=92.73 E-value=0.085 Score=30.22 Aligned_cols=23 Identities=30% Similarity=0.777 Sum_probs=17.6
Q ss_pred ccccCccCcccCCchhhHhhhhhhcCCCCccccCCCC
Q psy12016 53 LFSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCP 89 (111)
Q Consensus 53 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~ 89 (111)
.|.|++||.. +.++. |..|+.||
T Consensus 134 ~~vC~vCGy~-------------~~ge~-P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEA-PEVCPICG 156 (166)
T ss_pred EEEcCCCCCc-------------ccCCC-CCcCCCCC
Confidence 3999999876 23433 89999998
No 57
>KOG2893|consensus
Probab=92.61 E-value=0.045 Score=33.06 Aligned_cols=47 Identities=30% Similarity=0.561 Sum_probs=34.4
Q ss_pred eecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCchhhHhh-hhhh
Q psy12016 20 FTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKKGLGRH-KRYE 76 (111)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h-~~~~ 76 (111)
.+|..|++.|....-|.+|++. +. |+|..|-+...+...|..| +++|
T Consensus 11 pwcwycnrefddekiliqhqka----kh------fkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQKA----KH------FKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred ceeeecccccchhhhhhhhhhh----cc------ceeeeehhhhccCCCceeehhhhh
Confidence 3688999999999988888764 34 8999998666665555444 4444
No 58
>KOG2893|consensus
Probab=92.17 E-value=0.037 Score=33.43 Aligned_cols=41 Identities=22% Similarity=0.515 Sum_probs=34.7
Q ss_pred cCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccchhHHHH
Q psy12016 56 CDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHISSLKKH 101 (111)
Q Consensus 56 c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H 101 (111)
|=.|++.|.....|.+|++. + .|+|..|-+.+.+.-.|..|
T Consensus 13 cwycnrefddekiliqhqka----k-hfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----K-HFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhh----c-cceeeeehhhhccCCCceee
Confidence 66799999999999988874 3 89999999888777777766
No 59
>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=92.17 E-value=0.13 Score=21.30 Aligned_cols=24 Identities=29% Similarity=0.648 Sum_probs=16.3
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPH 90 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~ 90 (111)
|.|..||..+... ..|..|+.|+.
T Consensus 3 ~~C~~CG~i~~g~-------------~~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHEGE-------------EAPEKCPICGA 26 (34)
T ss_pred EECCCCCCEeECC-------------cCCCcCcCCCC
Confidence 7888888764321 22678888874
No 60
>KOG2231|consensus
Probab=91.95 E-value=0.52 Score=32.97 Aligned_cols=48 Identities=23% Similarity=0.472 Sum_probs=27.2
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCC------CcccccchhHHHHHHHhh
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQC------PHRTKHISSLKKHMALKH 106 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C------~~~f~~~~~l~~H~~~~~ 106 (111)
-.|..|...|.....+..|++.. .|-|..| +..|.....|..|-+..|
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~-----h~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFD-----HEFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccc-----eeheeecCcccccchhcccchHHHHHhhhcC
Confidence 35666666666666666666654 3333333 344555566666655444
No 61
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=91.79 E-value=0.056 Score=32.31 Aligned_cols=12 Identities=17% Similarity=0.528 Sum_probs=7.8
Q ss_pred cccCCCCccccc
Q psy12016 83 YECDQCPHRTKH 94 (111)
Q Consensus 83 ~~C~~C~~~f~~ 94 (111)
..|+.||.++..
T Consensus 49 ~vCP~CgyA~~~ 60 (214)
T PF09986_consen 49 WVCPHCGYAAFE 60 (214)
T ss_pred EECCCCCCcccc
Confidence 467778766543
No 62
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.61 E-value=0.059 Score=34.77 Aligned_cols=54 Identities=22% Similarity=0.501 Sum_probs=32.7
Q ss_pred cccCccCcccCCchhhHhhhh--hhcCC--CCccccC--CCCcccccchhHHHHHHHhhCC
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKR--YECGQ--EPKYECD--QCPHRTKHISSLKKHMALKHGV 108 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~--~~~~~--~~~~~C~--~C~~~f~~~~~l~~H~~~~~~e 108 (111)
+.|..|...+.....+..|.+ .|.++ + ++.|. .|++.|.....+..|..++.+-
T Consensus 290 ~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~-~~~~p~~~~~~~~~~~~~~~~~~~~~~~~ 349 (467)
T COG5048 290 IKSKQCNISFSRSSPLTRHLRSVNHSGESLK-PFSCPYSLCGKLFSRNDALKRHILLHTSI 349 (467)
T ss_pred CCCccccCCccccccccccccccccccccCC-ceeeeccCCCccccccccccCCcccccCC
Confidence 455666666666666666666 45555 4 66666 5666666666666665555543
No 63
>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=91.20 E-value=0.46 Score=25.17 Aligned_cols=26 Identities=31% Similarity=0.689 Sum_probs=22.8
Q ss_pred cccc----CCCCcccccchhHHHHHHHhhC
Q psy12016 82 KYEC----DQCPHRTKHISSLKKHMALKHG 107 (111)
Q Consensus 82 ~~~C----~~C~~~f~~~~~l~~H~~~~~~ 107 (111)
-|.| ..|+....+...+..|.+..||
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 4789 8999999999999999988875
No 64
>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=91.13 E-value=0.3 Score=27.81 Aligned_cols=35 Identities=17% Similarity=0.551 Sum_probs=23.6
Q ss_pred CCCCceecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccC
Q psy12016 15 NDSGMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYK 64 (111)
Q Consensus 15 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~ 64 (111)
.....|.|+.|+..|+....+. .. |.|+.||....
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~---------~~------F~Cp~Cg~~L~ 139 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME---------LN------FTCPRCGAMLD 139 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH---------cC------CcCCCCCCEee
Confidence 3455678888888777766553 13 88888886543
No 65
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=90.82 E-value=0.21 Score=26.60 Aligned_cols=13 Identities=15% Similarity=0.391 Sum_probs=6.7
Q ss_pred ccccCCCCccccc
Q psy12016 82 KYECDQCPHRTKH 94 (111)
Q Consensus 82 ~~~C~~C~~~f~~ 94 (111)
|..|+.||..|..
T Consensus 26 PivCP~CG~~~~~ 38 (108)
T PF09538_consen 26 PIVCPKCGTEFPP 38 (108)
T ss_pred CccCCCCCCccCc
Confidence 5555555555433
No 66
>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=90.77 E-value=0.11 Score=31.02 Aligned_cols=28 Identities=29% Similarity=0.446 Sum_probs=20.8
Q ss_pred ccccCCCCcccccchhHHHHHHHhhCCC
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKHGVE 109 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~~ek 109 (111)
.|.|..|++.|....-+++|+..-|.|+
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred EECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 6889999999998888899988777653
No 67
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.72 E-value=0.18 Score=23.65 Aligned_cols=31 Identities=26% Similarity=0.670 Sum_probs=18.7
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPH 90 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~ 90 (111)
|.|+.||...... -.+-...+. +|.|+.||.
T Consensus 28 F~CPnCGe~~I~R-----c~~CRk~g~-~Y~Cp~CGF 58 (61)
T COG2888 28 FPCPNCGEVEIYR-----CAKCRKLGN-PYRCPKCGF 58 (61)
T ss_pred eeCCCCCceeeeh-----hhhHHHcCC-ceECCCcCc
Confidence 8899999553322 112222235 899999973
No 68
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=90.30 E-value=0.39 Score=27.96 Aligned_cols=35 Identities=20% Similarity=0.627 Sum_probs=23.7
Q ss_pred CCCceecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCC
Q psy12016 16 DSGMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKY 65 (111)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~ 65 (111)
....|.|+.|+..|+....+. .. |.|+.||.....
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~------F~Cp~Cg~~L~~ 148 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YG------FRCPQCGEMLEE 148 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cC------CcCCCCCCCCee
Confidence 345688988988877765432 13 889999866544
No 69
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=90.00 E-value=0.36 Score=21.28 Aligned_cols=12 Identities=25% Similarity=0.719 Sum_probs=6.9
Q ss_pred eecCCCcccccc
Q psy12016 20 FTCDVCFKEYKY 31 (111)
Q Consensus 20 ~~C~~C~~~f~~ 31 (111)
|.|..|+..|..
T Consensus 3 Y~C~~Cg~~~~~ 14 (44)
T smart00659 3 YICGECGRENEI 14 (44)
T ss_pred EECCCCCCEeec
Confidence 556666665543
No 70
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.71 E-value=0.36 Score=20.34 Aligned_cols=33 Identities=21% Similarity=0.556 Sum_probs=16.5
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCccc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRT 92 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f 92 (111)
..|+.|+..|.....-. ..++. ..+|..|+..|
T Consensus 3 i~CP~C~~~f~v~~~~l-----~~~~~-~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKL-----PAGGR-KVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHc-----ccCCc-EEECCCCCcEe
Confidence 45666666655554311 11223 55666666555
No 71
>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=89.71 E-value=0.15 Score=23.07 Aligned_cols=13 Identities=15% Similarity=0.690 Sum_probs=8.4
Q ss_pred eecCCCcccccch
Q psy12016 20 FTCDVCFKEYKYK 32 (111)
Q Consensus 20 ~~C~~C~~~f~~~ 32 (111)
|.|..|+..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (52)
T TIGR02605 6 YRCTACGHRFEVL 18 (52)
T ss_pred EEeCCCCCEeEEE
Confidence 5677777766543
No 72
>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=89.42 E-value=0.4 Score=20.11 Aligned_cols=13 Identities=15% Similarity=0.644 Sum_probs=6.2
Q ss_pred cccCccCcccCCc
Q psy12016 54 FSCDVCGKHYKYK 66 (111)
Q Consensus 54 ~~c~~c~~~~~~~ 66 (111)
+.|+.|+..|...
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 3455555544444
No 73
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.38 E-value=0.15 Score=32.98 Aligned_cols=62 Identities=26% Similarity=0.443 Sum_probs=50.9
Q ss_pred CceecCCCcccccchhHHHHHHh--hhcCC--CCCCCCCccccC--ccCcccCCchhhHhhhhhhcCCCCccccC
Q psy12016 18 GMFTCDVCFKEYKYKRGLVRHKK--NSCKQ--KPQNLDGLFSCD--VCGKHYKYKKGLGRHKRYECGQEPKYECD 86 (111)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~--~~~~~--~~~~~~~~~~c~--~c~~~~~~~~~l~~h~~~~~~~~~~~~C~ 86 (111)
.++.|..|...|.....+..|.. .|.++ .+ +.|+ .|+..|.....+..|...+.+.. ++.+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~------~~~p~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ 355 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKP------FSCPYSLCGKLFSRNDALKRHILLHTSIS-PAKEK 355 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCc------eeeeccCCCccccccccccCCcccccCCC-ccccc
Confidence 36788899999999999999988 68887 67 8898 79999999999998988887755 55543
No 74
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=89.08 E-value=0.61 Score=26.21 Aligned_cols=13 Identities=23% Similarity=0.920 Sum_probs=7.1
Q ss_pred cccCccCcccCCc
Q psy12016 54 FSCDVCGKHYKYK 66 (111)
Q Consensus 54 ~~c~~c~~~~~~~ 66 (111)
|.|+.|+..|...
T Consensus 100 Y~Cp~C~~~y~~~ 112 (147)
T smart00531 100 YKCPNCQSKYTFL 112 (147)
T ss_pred EECcCCCCEeeHH
Confidence 5566665555543
No 75
>KOG2482|consensus
Probab=89.05 E-value=0.63 Score=29.87 Aligned_cols=23 Identities=26% Similarity=0.476 Sum_probs=20.8
Q ss_pred ceecCCCcccccchhHHHHHHhh
Q psy12016 19 MFTCDVCFKEYKYKRGLVRHKKN 41 (111)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~ 41 (111)
.+.|-.|.+.|..+..|..||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 46899999999999999999975
No 76
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=88.97 E-value=0.4 Score=30.80 Aligned_cols=23 Identities=26% Similarity=0.355 Sum_probs=14.9
Q ss_pred cccCccCcccCCchhhHhhhhhh
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYE 76 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~ 76 (111)
-.|..|...|.....|..|.+..
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~ 243 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLR 243 (493)
T ss_pred chhhhccceecChHHHHHHHHhh
Confidence 35666777777666676666643
No 77
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=88.93 E-value=0.27 Score=27.17 Aligned_cols=24 Identities=33% Similarity=0.686 Sum_probs=14.5
Q ss_pred ccccCCCCcccccchhHHHHHHHhhCC
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKHGV 108 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~~e 108 (111)
...|-+||+.|.. |++|+..|||-
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S
T ss_pred eeEEccCCcccch---HHHHHHHccCC
Confidence 4578889888765 58888888763
No 78
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=88.74 E-value=0.22 Score=21.20 Aligned_cols=12 Identities=17% Similarity=0.783 Sum_probs=6.5
Q ss_pred eecCCCcccccc
Q psy12016 20 FTCDVCFKEYKY 31 (111)
Q Consensus 20 ~~C~~C~~~f~~ 31 (111)
|.|..|+..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (41)
T smart00834 6 YRCEDCGHTFEV 17 (41)
T ss_pred EEcCCCCCEEEE
Confidence 456666655543
No 79
>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=88.36 E-value=0.12 Score=22.52 Aligned_cols=14 Identities=21% Similarity=0.769 Sum_probs=10.0
Q ss_pred eecCCCcccccchh
Q psy12016 20 FTCDVCFKEYKYKR 33 (111)
Q Consensus 20 ~~C~~C~~~f~~~~ 33 (111)
|.|..||..|....
T Consensus 6 y~C~~Cg~~fe~~~ 19 (42)
T PF09723_consen 6 YRCEECGHEFEVLQ 19 (42)
T ss_pred EEeCCCCCEEEEEE
Confidence 67888887776543
No 80
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=88.13 E-value=0.65 Score=19.44 Aligned_cols=33 Identities=21% Similarity=0.466 Sum_probs=15.1
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCccc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRT 92 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f 92 (111)
..|+.|+..|.-..... -..+. ..+|..|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~i-----p~~g~-~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKI-----PPKGR-KVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHC-----CCCCc-EEECCCCCCEe
Confidence 34555655555443321 11122 45566665544
No 81
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=86.89 E-value=0.72 Score=20.73 Aligned_cols=23 Identities=22% Similarity=0.599 Sum_probs=15.1
Q ss_pred ccccCCCCcccccc-----hhHHHHHHH
Q psy12016 82 KYECDQCPHRTKHI-----SSLKKHMAL 104 (111)
Q Consensus 82 ~~~C~~C~~~f~~~-----~~l~~H~~~ 104 (111)
...|..|++.+... +.|.+|++.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 35677777766544 577888773
No 82
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=86.69 E-value=0.37 Score=24.48 Aligned_cols=31 Identities=23% Similarity=0.576 Sum_probs=19.9
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHI 95 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~ 95 (111)
+.|+.|++. . ..+... . .|.|..|+..|+-.
T Consensus 36 ~~Cp~C~~~-~-------VkR~a~--G-IW~C~kCg~~fAGg 66 (89)
T COG1997 36 HVCPFCGRT-T-------VKRIAT--G-IWKCRKCGAKFAGG 66 (89)
T ss_pred CcCCCCCCc-c-------eeeecc--C-eEEcCCCCCeeccc
Confidence 788888865 1 122222 2 78888888887554
No 83
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=86.68 E-value=2 Score=23.09 Aligned_cols=86 Identities=16% Similarity=0.159 Sum_probs=48.8
Q ss_pred CCceecCCCcccccchhHHHHHHhhhcCCCCC---CCC---CccccCccCcccCCchhhHhhhhhhcCCCCccccCCCCc
Q psy12016 17 SGMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQ---NLD---GLFSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPH 90 (111)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~---~~~---~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~ 90 (111)
+-|..|+.|+-.......|.+.....-...+. .++ ..-.|--|...|........-. ..... .|.|..|..
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~--~~~~~-~y~C~~C~~ 89 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDE--LKDSH-RYVCAVCKN 89 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccccc--ccccc-ceeCCCCCC
Confidence 45778999998888888777653221111110 000 1124777887776543211000 11123 689999999
Q ss_pred ccccchhHHHHHHHh
Q psy12016 91 RTKHISSLKKHMALK 105 (111)
Q Consensus 91 ~f~~~~~l~~H~~~~ 105 (111)
.|-..-+.-.|...|
T Consensus 90 ~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 90 VFCVDCDVFVHESLH 104 (112)
T ss_pred ccccccchhhhhhcc
Confidence 998777666665544
No 84
>KOG2186|consensus
Probab=86.18 E-value=0.59 Score=28.67 Aligned_cols=47 Identities=30% Similarity=0.589 Sum_probs=31.9
Q ss_pred ceecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCchhhHhhhh
Q psy12016 19 MFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKR 74 (111)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~ 74 (111)
.|.|..||..... ..+.+|+..-.+ .. |.|..|+..|.. .....|..
T Consensus 3 ~FtCnvCgEsvKK-p~vekH~srCrn-~~------fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVKK-PQVEKHMSRCRN-AY------FSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhccc-cchHHHHHhccC-Ce------eEEeeccccccc-chhhhhhh
Confidence 4788899876544 456778655444 44 899999998887 44555644
No 85
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=85.39 E-value=0.37 Score=27.36 Aligned_cols=15 Identities=27% Similarity=0.594 Sum_probs=10.5
Q ss_pred cccCccCcccCCchh
Q psy12016 54 FSCDVCGKHYKYKKG 68 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~ 68 (111)
+.|+.||..|.....
T Consensus 29 ~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 29 RECLACGKRFTTFER 43 (154)
T ss_pred eeccccCCcceEeEe
Confidence 678888877766543
No 86
>KOG2186|consensus
Probab=85.18 E-value=0.47 Score=29.07 Aligned_cols=46 Identities=26% Similarity=0.555 Sum_probs=35.0
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccchhHHHHHH
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHISSLKKHMA 103 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 103 (111)
|.|..||....-+ .+..|+..-++ . .|.|..|+..|.. .++..|.+
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~-~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-A-YFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-C-eeEEeeccccccc-chhhhhhh
Confidence 7899999887655 45558776655 5 7999999999977 56666754
No 87
>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=84.92 E-value=1.2 Score=19.28 Aligned_cols=23 Identities=35% Similarity=0.564 Sum_probs=13.2
Q ss_pred ccccCCCCcccccc----hhHHHHHHH
Q psy12016 82 KYECDQCPHRTKHI----SSLKKHMAL 104 (111)
Q Consensus 82 ~~~C~~C~~~f~~~----~~l~~H~~~ 104 (111)
...|..|++.+... +.|..|++.
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHHHH
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 56788888777653 577777743
No 88
>KOG4167|consensus
Probab=83.76 E-value=0.31 Score=34.27 Aligned_cols=29 Identities=28% Similarity=0.465 Sum_probs=24.9
Q ss_pred CCceecCCCcccccchhHHHHHHhhhcCC
Q psy12016 17 SGMFTCDVCFKEYKYKRGLVRHKKNSCKQ 45 (111)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~ 45 (111)
...|.|.+|++.|.....+..||++|...
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHHHH
Confidence 45689999999999999999999988643
No 89
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=83.61 E-value=0.64 Score=29.58 Aligned_cols=25 Identities=32% Similarity=0.588 Sum_probs=21.4
Q ss_pred CccccCC--CCcccccchhHHHHHHHh
Q psy12016 81 PKYECDQ--CPHRTKHISSLKKHMALK 105 (111)
Q Consensus 81 ~~~~C~~--C~~~f~~~~~l~~H~~~~ 105 (111)
+||+|++ |++.+++...|+-|+.--
T Consensus 348 KpykCpV~gC~K~YknqnGLKYH~lhG 374 (423)
T COG5189 348 KPYKCPVEGCNKKYKNQNGLKYHMLHG 374 (423)
T ss_pred ceecCCCCCchhhhccccchhhhhhcc
Confidence 3999986 999999999999997533
No 90
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=83.29 E-value=0.53 Score=20.79 Aligned_cols=14 Identities=21% Similarity=0.610 Sum_probs=9.5
Q ss_pred ceecCCCcccccch
Q psy12016 19 MFTCDVCFKEYKYK 32 (111)
Q Consensus 19 ~~~C~~C~~~f~~~ 32 (111)
.|.|+.|+..|...
T Consensus 3 ~y~C~~CG~~~~~~ 16 (46)
T PRK00398 3 EYKCARCGREVELD 16 (46)
T ss_pred EEECCCCCCEEEEC
Confidence 47788888766553
No 91
>KOG2482|consensus
Probab=83.09 E-value=2 Score=27.71 Aligned_cols=22 Identities=27% Similarity=0.567 Sum_probs=20.0
Q ss_pred ccccCCCCcccccchhHHHHHH
Q psy12016 82 KYECDQCPHRTKHISSLKKHMA 103 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~ 103 (111)
.+.|-.|.+.|..+..|+.||+
T Consensus 195 r~~CLyCekifrdkntLkeHMr 216 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMR 216 (423)
T ss_pred hheeeeeccccCCcHHHHHHHH
Confidence 4689999999999999999986
No 92
>KOG2231|consensus
Probab=83.04 E-value=2.1 Score=30.15 Aligned_cols=69 Identities=20% Similarity=0.401 Sum_probs=43.4
Q ss_pred eecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccC------cccCCchhhHhhhhhhcCCCCccccC--CCC-c
Q psy12016 20 FTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCG------KHYKYKKGLGRHKRYECGQEPKYECD--QCP-H 90 (111)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~------~~~~~~~~l~~h~~~~~~~~~~~~C~--~C~-~ 90 (111)
..|..|...|.....+.+|++.+. +.|..|. ..|.....|..|-+.. .|.|. .|. +
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h----------~~chfC~~~~~~neyy~~~~dLe~HfR~~-----HflCE~~~C~~~ 247 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDH----------EFCHFCDYKTGQNEYYNDYDDLEEHFRKG-----HFLCEEEFCRTK 247 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccce----------eheeecCcccccchhcccchHHHHHhhhc-----Cccccccccccc
Confidence 468889999999999998887654 5566553 3444456677776643 77776 454 2
Q ss_pred ccccchhHHHHHH
Q psy12016 91 RTKHISSLKKHMA 103 (111)
Q Consensus 91 ~f~~~~~l~~H~~ 103 (111)
.|.....+..+++
T Consensus 248 ~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 248 KFYVAFELEIELK 260 (669)
T ss_pred eeeehhHHHHHHH
Confidence 3333334444444
No 93
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=82.67 E-value=0.81 Score=21.52 Aligned_cols=30 Identities=23% Similarity=0.555 Sum_probs=18.1
Q ss_pred cccCccCcc-cCCchhhHhhhhhhcCCCCccccCCCCc
Q psy12016 54 FSCDVCGKH-YKYKKGLGRHKRYECGQEPKYECDQCPH 90 (111)
Q Consensus 54 ~~c~~c~~~-~~~~~~l~~h~~~~~~~~~~~~C~~C~~ 90 (111)
|.|+.||.. ..+-.. -..... +|.|+.||.
T Consensus 26 F~CPnCG~~~I~RC~~------CRk~~~-~Y~CP~CGF 56 (59)
T PRK14890 26 FLCPNCGEVIIYRCEK------CRKQSN-PYTCPKCGF 56 (59)
T ss_pred eeCCCCCCeeEeechh------HHhcCC-ceECCCCCC
Confidence 889999876 222211 111224 899999974
No 94
>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=81.01 E-value=1.6 Score=23.09 Aligned_cols=27 Identities=33% Similarity=0.567 Sum_probs=22.8
Q ss_pred Ccccc----CccCcccCCchhhHhhhhhhcC
Q psy12016 52 GLFSC----DVCGKHYKYKKGLGRHKRYECG 78 (111)
Q Consensus 52 ~~~~c----~~c~~~~~~~~~l~~h~~~~~~ 78 (111)
.+|.| ..|+....+...+..|.+.+++
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 45899 8899999999999999887654
No 95
>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=80.63 E-value=0.71 Score=20.68 Aligned_cols=12 Identities=33% Similarity=0.744 Sum_probs=6.2
Q ss_pred eecCCCcccccc
Q psy12016 20 FTCDVCFKEYKY 31 (111)
Q Consensus 20 ~~C~~C~~~f~~ 31 (111)
|.|..|+..+..
T Consensus 2 y~C~~CgyvYd~ 13 (47)
T PF00301_consen 2 YQCPVCGYVYDP 13 (47)
T ss_dssp EEETTTSBEEET
T ss_pred cCCCCCCEEEcC
Confidence 455555555443
No 96
>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=80.03 E-value=1.7 Score=17.73 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=6.0
Q ss_pred eecCCCccccc
Q psy12016 20 FTCDVCFKEYK 30 (111)
Q Consensus 20 ~~C~~C~~~f~ 30 (111)
|.|..|+..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 45666666554
No 97
>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=79.97 E-value=0.49 Score=18.70 Aligned_cols=17 Identities=29% Similarity=0.524 Sum_probs=7.6
Q ss_pred ccCCCCcccccchhHHHH
Q psy12016 84 ECDQCPHRTKHISSLKKH 101 (111)
Q Consensus 84 ~C~~C~~~f~~~~~l~~H 101 (111)
.|..|++.| .....+.|
T Consensus 2 sCiDC~~~F-~~~~y~~H 18 (28)
T PF08790_consen 2 SCIDCSKDF-DGDSYKSH 18 (28)
T ss_dssp EETTTTEEE-EGGGTTT-
T ss_pred eeecCCCCc-CcCCcCCC
Confidence 455555555 33333444
No 98
>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=79.97 E-value=1.3 Score=24.30 Aligned_cols=33 Identities=12% Similarity=0.228 Sum_probs=21.5
Q ss_pred eecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCchhh
Q psy12016 20 FTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKKGL 69 (111)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l 69 (111)
..|+.|++.|.... ..+ ..|+.||..+.....+
T Consensus 10 r~Cp~cg~kFYDLn-----------k~p------~vcP~cg~~~~~~~~~ 42 (129)
T TIGR02300 10 RICPNTGSKFYDLN-----------RRP------AVSPYTGEQFPPEEAL 42 (129)
T ss_pred ccCCCcCccccccC-----------CCC------ccCCCcCCccCcchhh
Confidence 46888888775532 234 6888888877665443
No 99
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=79.39 E-value=1.1 Score=24.88 Aligned_cols=22 Identities=27% Similarity=0.427 Sum_probs=17.6
Q ss_pred cccCCCCcccccchhHHHHHHHhhC
Q psy12016 83 YECDQCPHRTKHISSLKKHMALKHG 107 (111)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~~~ 107 (111)
..|-++|+.|.+ |++|+.+|+|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccC
Confidence 468888888854 7999988876
No 100
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=79.33 E-value=0.66 Score=24.26 Aligned_cols=13 Identities=38% Similarity=0.956 Sum_probs=7.3
Q ss_pred CCCccccCccCcc
Q psy12016 50 LDGLFSCDVCGKH 62 (111)
Q Consensus 50 ~~~~~~c~~c~~~ 62 (111)
+++.|.|+.|+..
T Consensus 19 L~k~FtCp~Cghe 31 (104)
T COG4888 19 LPKTFTCPRCGHE 31 (104)
T ss_pred CCceEecCccCCe
Confidence 4455666666544
No 101
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=79.16 E-value=1.4 Score=24.40 Aligned_cols=15 Identities=27% Similarity=0.696 Sum_probs=9.5
Q ss_pred CceecCCCcccccch
Q psy12016 18 GMFTCDVCFKEYKYK 32 (111)
Q Consensus 18 ~~~~C~~C~~~f~~~ 32 (111)
..+.|..|+..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 446777777666553
No 102
>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=78.87 E-value=2.4 Score=16.31 Aligned_cols=19 Identities=32% Similarity=0.644 Sum_probs=11.4
Q ss_pred ecCCCcccccchhHHHHHHh
Q psy12016 21 TCDVCFKEYKYKRGLVRHKK 40 (111)
Q Consensus 21 ~C~~C~~~f~~~~~l~~h~~ 40 (111)
.|+.|++.+ ....+..|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 477777776 3345555543
No 103
>KOG2785|consensus
Probab=78.63 E-value=4.1 Score=26.70 Aligned_cols=58 Identities=17% Similarity=0.159 Sum_probs=35.4
Q ss_pred CCceecCCCcccccchhHHHHHHhhhcCCCCCCC-----------------CCccccCccC---cccCCchhhHhhhh
Q psy12016 17 SGMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNL-----------------DGLFSCDVCG---KHYKYKKGLGRHKR 74 (111)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~-----------------~~~~~c~~c~---~~~~~~~~l~~h~~ 74 (111)
..|-.|-.|+..+.....-..||..+++-..... ...+.|..|+ ..|.+...++.||.
T Consensus 164 ~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 164 LIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred cCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 3456688899988888888888876655322111 1234555555 55555555666655
No 104
>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=78.23 E-value=0.78 Score=20.83 Aligned_cols=8 Identities=25% Similarity=0.912 Sum_probs=4.2
Q ss_pred ccccCCCC
Q psy12016 82 KYECDQCP 89 (111)
Q Consensus 82 ~~~C~~C~ 89 (111)
.|.|+.|+
T Consensus 34 ~w~CP~C~ 41 (50)
T cd00730 34 DWVCPVCG 41 (50)
T ss_pred CCCCCCCC
Confidence 34555554
No 105
>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=77.01 E-value=2.7 Score=25.34 Aligned_cols=26 Identities=27% Similarity=0.413 Sum_probs=20.6
Q ss_pred CCCceecCCCcccccchhHHHHHHhh
Q psy12016 16 DSGMFTCDVCFKEYKYKRGLVRHKKN 41 (111)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~ 41 (111)
.+.-|.|+.|++.|.....+..|+..
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhh
Confidence 44569999999999999999999865
No 106
>PF14353 CpXC: CpXC protein
Probab=76.59 E-value=1.1 Score=24.38 Aligned_cols=21 Identities=29% Similarity=0.735 Sum_probs=14.3
Q ss_pred cccCccCcccCCchhhHhhhh
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKR 74 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~ 74 (111)
+.|+.||..+.....+.-|..
T Consensus 39 ~~CP~Cg~~~~~~~p~lY~D~ 59 (128)
T PF14353_consen 39 FTCPSCGHKFRLEYPLLYHDP 59 (128)
T ss_pred EECCCCCCceecCCCEEEEcC
Confidence 688888888776665554443
No 107
>KOG3408|consensus
Probab=75.80 E-value=1.6 Score=23.67 Aligned_cols=22 Identities=23% Similarity=0.529 Sum_probs=19.0
Q ss_pred ccccCCCCcccccchhHHHHHH
Q psy12016 82 KYECDQCPHRTKHISSLKKHMA 103 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~ 103 (111)
.|.|..|.+.|.+...|..|.+
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHh
Confidence 6889999999999988888865
No 108
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=75.62 E-value=4.2 Score=26.04 Aligned_cols=48 Identities=17% Similarity=0.298 Sum_probs=27.0
Q ss_pred ccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccchhHHHHHHHh
Q psy12016 55 SCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHISSLKKHMALK 105 (111)
Q Consensus 55 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 105 (111)
.|-.|-..|+-...-..-.. .... .|.|+.|...|....+.-.|...|
T Consensus 364 ~Cf~CQ~~fp~~~~~~~~~~--~ss~-rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 364 HCFVCQGPFPKPPVSPFDES--TSSG-RYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred cceeccCCCCCCCCCccccc--cccc-ceechhhhhhhhhhhHHHHHHHHh
Confidence 35666655554432111111 1123 689999998888777766665443
No 109
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=75.27 E-value=2.5 Score=19.15 Aligned_cols=10 Identities=30% Similarity=0.863 Sum_probs=5.1
Q ss_pred eecCCCcccc
Q psy12016 20 FTCDVCFKEY 29 (111)
Q Consensus 20 ~~C~~C~~~f 29 (111)
|.|..|++.|
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 4455555544
No 110
>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=74.77 E-value=1 Score=23.20 Aligned_cols=31 Identities=29% Similarity=0.744 Sum_probs=20.2
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHI 95 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~ 95 (111)
|.|+.|++.-. .+...| .|.|..|+..|+-.
T Consensus 36 y~Cp~Cgk~~v--------kR~a~G---IW~C~~C~~~~AGG 66 (90)
T PF01780_consen 36 YTCPFCGKTSV--------KRVATG---IWKCKKCGKKFAGG 66 (90)
T ss_dssp BEESSSSSSEE--------EEEETT---EEEETTTTEEEE-B
T ss_pred CcCCCCCCcee--------EEeeeE---EeecCCCCCEEeCC
Confidence 89999987621 122222 78999999888543
No 111
>PHA00626 hypothetical protein
Probab=74.66 E-value=2.7 Score=19.57 Aligned_cols=17 Identities=18% Similarity=0.198 Sum_probs=10.6
Q ss_pred CCceecCCCcccccchh
Q psy12016 17 SGMFTCDVCFKEYKYKR 33 (111)
Q Consensus 17 ~~~~~C~~C~~~f~~~~ 33 (111)
...|.|+.|+..|+...
T Consensus 21 snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 21 SDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CcceEcCCCCCeechhh
Confidence 34577777777665543
No 112
>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=74.23 E-value=1.8 Score=16.74 Aligned_cols=10 Identities=20% Similarity=0.660 Sum_probs=7.4
Q ss_pred ecCCCccccc
Q psy12016 21 TCDVCFKEYK 30 (111)
Q Consensus 21 ~C~~C~~~f~ 30 (111)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5788887774
No 113
>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=73.49 E-value=1.4 Score=22.77 Aligned_cols=31 Identities=26% Similarity=0.581 Sum_probs=19.9
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHI 95 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~ 95 (111)
|.|+.|++.-. .+... . .|.|..|++.|+-.
T Consensus 36 y~CpfCgk~~v--------kR~a~--G-IW~C~~C~~~~AGG 66 (91)
T TIGR00280 36 YVCPFCGKKTV--------KRGST--G-IWTCRKCGAKFAGG 66 (91)
T ss_pred ccCCCCCCCce--------EEEee--E-EEEcCCCCCEEeCC
Confidence 88999985411 11221 2 78899999887544
No 114
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=73.46 E-value=1.5 Score=22.59 Aligned_cols=31 Identities=29% Similarity=0.641 Sum_probs=20.0
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHI 95 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~ 95 (111)
|.|+.|++.-. .+... ..|.|..|++.|+-.
T Consensus 37 y~CpfCgk~~v--------kR~a~---GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 37 YFCPFCGKHAV--------KRQAV---GIWRCKGCKKTVAGG 67 (90)
T ss_pred ccCCCCCCCce--------eeeee---EEEEcCCCCCEEeCC
Confidence 89999985421 11111 278999999888654
No 115
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=73.37 E-value=1.9 Score=30.80 Aligned_cols=10 Identities=20% Similarity=0.683 Sum_probs=7.6
Q ss_pred ccccCCCCcc
Q psy12016 82 KYECDQCPHR 91 (111)
Q Consensus 82 ~~~C~~C~~~ 91 (111)
|..|+.||..
T Consensus 475 p~~Cp~Cgs~ 484 (730)
T COG1198 475 PQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCC
Confidence 7788888854
No 116
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=72.90 E-value=2.5 Score=18.03 Aligned_cols=15 Identities=20% Similarity=0.383 Sum_probs=12.5
Q ss_pred ceecCCCcccccchh
Q psy12016 19 MFTCDVCFKEYKYKR 33 (111)
Q Consensus 19 ~~~C~~C~~~f~~~~ 33 (111)
|+.|..|+..|..+.
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 788999999988763
No 117
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=72.80 E-value=2.8 Score=23.15 Aligned_cols=15 Identities=13% Similarity=0.370 Sum_probs=11.5
Q ss_pred ceecCCCcccccchh
Q psy12016 19 MFTCDVCFKEYKYKR 33 (111)
Q Consensus 19 ~~~C~~C~~~f~~~~ 33 (111)
|..|..|++.|..-+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 567888998887654
No 118
>KOG2785|consensus
Probab=72.67 E-value=4.6 Score=26.50 Aligned_cols=50 Identities=22% Similarity=0.305 Sum_probs=39.8
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCC----------------------CccccCCCC---cccccchhHHHHHH
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQE----------------------PKYECDQCP---HRTKHISSLKKHMA 103 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~----------------------~~~~C~~C~---~~f~~~~~l~~H~~ 103 (111)
-.|..|+..+.....-..||..+++-. ..+.|-.|+ +.|.+....+.||.
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 468889999998888888988887631 146888899 88888888888875
No 119
>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=72.29 E-value=2 Score=17.28 Aligned_cols=9 Identities=33% Similarity=0.903 Sum_probs=4.9
Q ss_pred ccccCCCCc
Q psy12016 82 KYECDQCPH 90 (111)
Q Consensus 82 ~~~C~~C~~ 90 (111)
.+.|+.|+.
T Consensus 19 ~~vCp~C~~ 27 (30)
T PF08274_consen 19 LLVCPECGH 27 (30)
T ss_dssp SEEETTTTE
T ss_pred EEeCCcccc
Confidence 455655553
No 120
>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=72.08 E-value=1.6 Score=19.98 Aligned_cols=26 Identities=15% Similarity=0.359 Sum_probs=15.4
Q ss_pred CCceecCCCcccccchhHHHHHHhhh
Q psy12016 17 SGMFTCDVCFKEYKYKRGLVRHKKNS 42 (111)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~ 42 (111)
...|.|+.|...|...=++-.|...|
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CCeEECCCCCCccccCcChhhhcccc
Confidence 35699999999999988887776554
No 121
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=71.82 E-value=7.1 Score=24.19 Aligned_cols=13 Identities=23% Similarity=0.687 Sum_probs=9.5
Q ss_pred CCceecCCCcccc
Q psy12016 17 SGMFTCDVCFKEY 29 (111)
Q Consensus 17 ~~~~~C~~C~~~f 29 (111)
...|.|..|+..+
T Consensus 110 drqFaC~~Cd~~W 122 (278)
T PF15135_consen 110 DRQFACSSCDHMW 122 (278)
T ss_pred ceeeeccccchHH
Confidence 3678999997543
No 122
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=71.23 E-value=3.6 Score=22.08 Aligned_cols=13 Identities=15% Similarity=0.112 Sum_probs=6.9
Q ss_pred ceecCCCcccccc
Q psy12016 19 MFTCDVCFKEYKY 31 (111)
Q Consensus 19 ~~~C~~C~~~f~~ 31 (111)
...|..|+..|..
T Consensus 70 ~~~C~~Cg~~~~~ 82 (113)
T PRK12380 70 QAWCWDCSQVVEI 82 (113)
T ss_pred EEEcccCCCEEec
Confidence 3556666655433
No 123
>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=71.06 E-value=3.2 Score=17.38 Aligned_cols=33 Identities=21% Similarity=0.415 Sum_probs=18.4
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHI 95 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~ 95 (111)
..|..||..|-... ..... +-.|+.||..+..+
T Consensus 2 r~C~~Cg~~Yh~~~--------~pP~~-~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 2 RICPKCGRIYHIEF--------NPPKV-EGVCDNCGGELVQR 34 (36)
T ss_dssp EEETTTTEEEETTT--------B--SS-TTBCTTTTEBEBEE
T ss_pred cCcCCCCCcccccc--------CCCCC-CCccCCCCCeeEeC
Confidence 46777877754322 22223 56788888665443
No 124
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=70.69 E-value=1.8 Score=19.57 Aligned_cols=12 Identities=25% Similarity=1.088 Sum_probs=5.4
Q ss_pred cccCccCcccCC
Q psy12016 54 FSCDVCGKHYKY 65 (111)
Q Consensus 54 ~~c~~c~~~~~~ 65 (111)
+.|..||..|..
T Consensus 5 l~C~dCg~~Fvf 16 (49)
T PF13451_consen 5 LTCKDCGAEFVF 16 (49)
T ss_pred EEcccCCCeEEE
Confidence 444445444433
No 125
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=70.36 E-value=1.7 Score=22.36 Aligned_cols=31 Identities=32% Similarity=0.674 Sum_probs=19.9
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHI 95 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~ 95 (111)
|.|+.|++.-. .+...| .|.|..|+..|+-.
T Consensus 37 y~CpfCgk~~v--------kR~a~G---IW~C~~C~~~~AGG 67 (90)
T PRK03976 37 HVCPVCGRPKV--------KRVGTG---IWECRKCGAKFAGG 67 (90)
T ss_pred ccCCCCCCCce--------EEEEEE---EEEcCCCCCEEeCC
Confidence 88999975411 112222 78899999887553
No 126
>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=69.99 E-value=3.2 Score=19.20 Aligned_cols=11 Identities=36% Similarity=1.020 Sum_probs=5.9
Q ss_pred cccCccCcccC
Q psy12016 54 FSCDVCGKHYK 64 (111)
Q Consensus 54 ~~c~~c~~~~~ 64 (111)
+.|+.|+..+.
T Consensus 3 ~~CP~CG~~ie 13 (54)
T TIGR01206 3 FECPDCGAEIE 13 (54)
T ss_pred cCCCCCCCEEe
Confidence 45666665443
No 127
>KOG4727|consensus
Probab=69.93 E-value=3.1 Score=24.12 Aligned_cols=23 Identities=30% Similarity=0.491 Sum_probs=20.0
Q ss_pred CceecCCCcccccchhHHHHHHh
Q psy12016 18 GMFTCDVCFKEYKYKRGLVRHKK 40 (111)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~ 40 (111)
.-|.|.+|+-+|....++..|+.
T Consensus 74 ~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 74 GGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred CceeeeecceeehhhHHHHHHhc
Confidence 34899999999999999998864
No 128
>KOG2593|consensus
Probab=69.28 E-value=5.5 Score=26.64 Aligned_cols=14 Identities=29% Similarity=0.764 Sum_probs=7.3
Q ss_pred cccCccCcccCCch
Q psy12016 54 FSCDVCGKHYKYKK 67 (111)
Q Consensus 54 ~~c~~c~~~~~~~~ 67 (111)
|.|+.|.+.|....
T Consensus 129 Y~Cp~C~kkyt~Le 142 (436)
T KOG2593|consen 129 YVCPNCQKKYTSLE 142 (436)
T ss_pred ccCCccccchhhhH
Confidence 55555555554443
No 129
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=69.28 E-value=10 Score=24.81 Aligned_cols=76 Identities=24% Similarity=0.329 Sum_probs=49.0
Q ss_pred eecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccC----cccCCchhhHhhhhhhcCCCCccccCC--CC----
Q psy12016 20 FTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCG----KHYKYKKGLGRHKRYECGQEPKYECDQ--CP---- 89 (111)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~----~~~~~~~~l~~h~~~~~~~~~~~~C~~--C~---- 89 (111)
..|..|...|.....|..|++..... - +.|+.-+ +.|.+...|..|.+. - .|.|.+ |.
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~HE~-C------hICD~v~p~~~QYFK~Y~~Le~HF~~----~-hy~ct~qtc~~~k~ 288 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLRHEA-C------HICDMVGPIRYQYFKSYEDLEAHFRN----A-HYCCTFQTCRVGKC 288 (493)
T ss_pred chhhhccceecChHHHHHHHHhhhhh-h------hhhhccCccchhhhhCHHHHHHHhhc----C-ceEEEEEEEecCcE
Confidence 46999999999999999998865432 2 4555433 234444556555543 2 566532 22
Q ss_pred cccccchhHHHHHHHhhC
Q psy12016 90 HRTKHISSLKKHMALKHG 107 (111)
Q Consensus 90 ~~f~~~~~l~~H~~~~~~ 107 (111)
..|.....|..|+-..|+
T Consensus 289 ~vf~~~~el~~h~~~~h~ 306 (493)
T COG5236 289 YVFPYHTELLEHLTRFHK 306 (493)
T ss_pred EEeccHHHHHHHHHHHhh
Confidence 357778888888766654
No 130
>KOG2593|consensus
Probab=69.02 E-value=5.3 Score=26.67 Aligned_cols=41 Identities=22% Similarity=0.515 Sum_probs=26.1
Q ss_pred cCCCCceecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCccc
Q psy12016 14 QNDSGMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHY 63 (111)
Q Consensus 14 ~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~ 63 (111)
.+...-|.|+.|.+.|.....++ ......-. |.|..|+...
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~------F~C~~C~gel 163 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQ---LLDNETGE------FHCENCGGEL 163 (436)
T ss_pred ccccccccCCccccchhhhHHHH---hhcccCce------EEEecCCCch
Confidence 34456699999999988765443 22221122 8999998653
No 131
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=68.08 E-value=1.4 Score=18.91 Aligned_cols=10 Identities=50% Similarity=1.198 Sum_probs=5.6
Q ss_pred cccCCCCccc
Q psy12016 83 YECDQCPHRT 92 (111)
Q Consensus 83 ~~C~~C~~~f 92 (111)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 5566666544
No 132
>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=68.02 E-value=4 Score=21.97 Aligned_cols=13 Identities=23% Similarity=0.457 Sum_probs=7.8
Q ss_pred ceecCCCcccccc
Q psy12016 19 MFTCDVCFKEYKY 31 (111)
Q Consensus 19 ~~~C~~C~~~f~~ 31 (111)
...|..|+..|..
T Consensus 70 ~~~C~~Cg~~~~~ 82 (115)
T TIGR00100 70 ECECEDCSEEVSP 82 (115)
T ss_pred EEEcccCCCEEec
Confidence 3567777765544
No 133
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=67.85 E-value=4.6 Score=21.31 Aligned_cols=14 Identities=14% Similarity=0.342 Sum_probs=11.0
Q ss_pred ceecCCCcccccch
Q psy12016 19 MFTCDVCFKEYKYK 32 (111)
Q Consensus 19 ~~~C~~C~~~f~~~ 32 (111)
|..|..||..|..-
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 56788888888774
No 134
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=67.33 E-value=2.9 Score=20.61 Aligned_cols=16 Identities=13% Similarity=0.499 Sum_probs=10.1
Q ss_pred cccC--ccCcccCCchhh
Q psy12016 54 FSCD--VCGKHYKYKKGL 69 (111)
Q Consensus 54 ~~c~--~c~~~~~~~~~l 69 (111)
+.|. .||..|.....+
T Consensus 28 ~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 28 HQCQNVNCSATFITYESV 45 (72)
T ss_pred eecCCCCCCCEEEEEEEE
Confidence 5676 677776665443
No 135
>PLN02294 cytochrome c oxidase subunit Vb
Probab=67.18 E-value=3.3 Score=23.98 Aligned_cols=17 Identities=24% Similarity=0.688 Sum_probs=11.9
Q ss_pred CCCceecCCCcccccch
Q psy12016 16 DSGMFTCDVCFKEYKYK 32 (111)
Q Consensus 16 ~~~~~~C~~C~~~f~~~ 32 (111)
..+|.+|++||..|..+
T Consensus 138 kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 138 KGKSFECPVCTQYFELE 154 (174)
T ss_pred CCCceeCCCCCCEEEEE
Confidence 34577788888877654
No 136
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=66.96 E-value=3.5 Score=15.63 Aligned_cols=10 Identities=30% Similarity=0.434 Sum_probs=7.4
Q ss_pred CceecCCCcc
Q psy12016 18 GMFTCDVCFK 27 (111)
Q Consensus 18 ~~~~C~~C~~ 27 (111)
.+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4688888874
No 137
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=66.60 E-value=3.3 Score=22.29 Aligned_cols=14 Identities=14% Similarity=0.361 Sum_probs=8.5
Q ss_pred CceecCCCcccccc
Q psy12016 18 GMFTCDVCFKEYKY 31 (111)
Q Consensus 18 ~~~~C~~C~~~f~~ 31 (111)
....|..|+..|..
T Consensus 69 ~~~~C~~Cg~~~~~ 82 (114)
T PRK03681 69 AECWCETCQQYVTL 82 (114)
T ss_pred cEEEcccCCCeeec
Confidence 34667777765533
No 138
>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=65.94 E-value=4.2 Score=21.30 Aligned_cols=16 Identities=19% Similarity=0.291 Sum_probs=11.8
Q ss_pred CCceecCCCcccccch
Q psy12016 17 SGMFTCDVCFKEYKYK 32 (111)
Q Consensus 17 ~~~~~C~~C~~~f~~~ 32 (111)
.+|.+|..||..|...
T Consensus 77 g~~~rC~eCG~~fkL~ 92 (97)
T cd00924 77 GKPKRCPECGHVFKLV 92 (97)
T ss_pred CCceeCCCCCcEEEEE
Confidence 3678888888887653
No 139
>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=65.55 E-value=3.9 Score=23.11 Aligned_cols=10 Identities=30% Similarity=1.026 Sum_probs=5.6
Q ss_pred ccccCccCcc
Q psy12016 53 LFSCDVCGKH 62 (111)
Q Consensus 53 ~~~c~~c~~~ 62 (111)
.+.|..||..
T Consensus 112 ~l~C~~Cg~~ 121 (146)
T PF07295_consen 112 TLVCENCGHE 121 (146)
T ss_pred eEecccCCCE
Confidence 3566666644
No 140
>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=65.52 E-value=3.4 Score=17.93 Aligned_cols=16 Identities=31% Similarity=0.544 Sum_probs=10.6
Q ss_pred CceecCCCcccccchh
Q psy12016 18 GMFTCDVCFKEYKYKR 33 (111)
Q Consensus 18 ~~~~C~~C~~~f~~~~ 33 (111)
.|+.|..|+..|....
T Consensus 12 ~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKH 27 (43)
T ss_dssp SHEE-TTTS-EE-TTT
T ss_pred CCeECCCCCcccCccc
Confidence 5789999999998764
No 141
>KOG4167|consensus
Probab=65.29 E-value=1.5 Score=31.17 Aligned_cols=25 Identities=24% Similarity=0.445 Sum_probs=21.8
Q ss_pred ccccCCCCcccccchhHHHHHHHhh
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKH 106 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~ 106 (111)
.|.|.+|++.|.---++..||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 5889999999988888888998886
No 142
>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=64.83 E-value=5.4 Score=24.89 Aligned_cols=27 Identities=19% Similarity=0.523 Sum_probs=18.5
Q ss_pred hcCCCCceecCCCcccccchhHHHHHHh
Q psy12016 13 WQNDSGMFTCDVCFKEYKYKRGLVRHKK 40 (111)
Q Consensus 13 ~~~~~~~~~C~~C~~~f~~~~~l~~h~~ 40 (111)
|..+.+.|.|..|......-..+. |++
T Consensus 136 w~hGGrif~CsfC~~flCEDDQFE-HQA 162 (314)
T PF06524_consen 136 WDHGGRIFKCSFCDNFLCEDDQFE-HQA 162 (314)
T ss_pred ccCCCeEEEeecCCCeeeccchhh-hhh
Confidence 445677899999987766665544 444
No 143
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=63.96 E-value=9.8 Score=16.36 Aligned_cols=24 Identities=29% Similarity=0.290 Sum_probs=15.8
Q ss_pred ceecCCCcccccch--hHHHHHHhhh
Q psy12016 19 MFTCDVCFKEYKYK--RGLVRHKKNS 42 (111)
Q Consensus 19 ~~~C~~C~~~f~~~--~~l~~h~~~~ 42 (111)
.-.|+.|+..+... .+-..|.+.|
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHHHH
Confidence 35799999776654 5556665554
No 144
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=62.87 E-value=12 Score=21.88 Aligned_cols=17 Identities=18% Similarity=0.821 Sum_probs=9.7
Q ss_pred CCCceecCCCcccccch
Q psy12016 16 DSGMFTCDVCFKEYKYK 32 (111)
Q Consensus 16 ~~~~~~C~~C~~~f~~~ 32 (111)
....|.|+.|...++..
T Consensus 110 ~~~~y~C~~~~~r~sfd 126 (176)
T COG1675 110 ENNYYVCPNCHVKYSFD 126 (176)
T ss_pred cCCceeCCCCCCcccHH
Confidence 44456776666555443
No 145
>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=62.65 E-value=6.5 Score=26.68 Aligned_cols=22 Identities=23% Similarity=0.516 Sum_probs=11.8
Q ss_pred cccCCCCcccccchhHHHHHHH
Q psy12016 83 YECDQCPHRTKHISSLKKHMAL 104 (111)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~ 104 (111)
+.|+.|.+.|.....+..|+..
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHH
Confidence 3455555555555555555543
No 146
>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=60.16 E-value=6.4 Score=17.18 Aligned_cols=15 Identities=13% Similarity=0.233 Sum_probs=10.3
Q ss_pred ccCCCCcccccchhH
Q psy12016 84 ECDQCPHRTKHISSL 98 (111)
Q Consensus 84 ~C~~C~~~f~~~~~l 98 (111)
.|..|++.|.+.--+
T Consensus 10 ~C~~C~rpf~WRKKW 24 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKW 24 (42)
T ss_pred cCcccCCcchHHHHH
Confidence 578888888765443
No 147
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.99 E-value=4.4 Score=20.16 Aligned_cols=10 Identities=20% Similarity=0.906 Sum_probs=7.4
Q ss_pred eecCCCcccc
Q psy12016 20 FTCDVCFKEY 29 (111)
Q Consensus 20 ~~C~~C~~~f 29 (111)
|.|..|+..|
T Consensus 13 Y~c~~cg~~~ 22 (82)
T COG2331 13 YECTECGNRF 22 (82)
T ss_pred EeecccchHH
Confidence 6788887765
No 148
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=59.92 E-value=3.6 Score=19.21 Aligned_cols=8 Identities=50% Similarity=1.443 Sum_probs=4.7
Q ss_pred ccccCCCC
Q psy12016 82 KYECDQCP 89 (111)
Q Consensus 82 ~~~C~~C~ 89 (111)
.|.|+.|.
T Consensus 31 tYmC~eC~ 38 (56)
T PF09963_consen 31 TYMCDECK 38 (56)
T ss_pred ceeChhHH
Confidence 56666664
No 149
>PRK14873 primosome assembly protein PriA; Provisional
Probab=59.68 E-value=4 Score=28.99 Aligned_cols=10 Identities=20% Similarity=0.889 Sum_probs=6.8
Q ss_pred ccccCCCCcc
Q psy12016 82 KYECDQCPHR 91 (111)
Q Consensus 82 ~~~C~~C~~~ 91 (111)
|+.|+.|+..
T Consensus 422 p~~Cp~Cgs~ 431 (665)
T PRK14873 422 DWRCPRCGSD 431 (665)
T ss_pred CccCCCCcCC
Confidence 6677777754
No 150
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.52 E-value=5.9 Score=21.77 Aligned_cols=42 Identities=17% Similarity=0.269 Sum_probs=21.6
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHI 95 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~ 95 (111)
..|+.|.....-...+..=+.....-++|--|.-||+.|.+.
T Consensus 40 ~qcp~csasirgd~~vegvlglg~dye~psfchncgs~fpwt 81 (160)
T COG4306 40 TQCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPWT 81 (160)
T ss_pred hcCCccCCcccccceeeeeeccCCCCCCcchhhcCCCCCCcH
Confidence 367777655443333322222222223356688888888764
No 151
>KOG1146|consensus
Probab=59.45 E-value=2.9 Score=31.82 Aligned_cols=48 Identities=19% Similarity=0.189 Sum_probs=28.5
Q ss_pred ccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccchhHHHHHHHh
Q psy12016 58 VCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHISSLKKHMALK 105 (111)
Q Consensus 58 ~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 105 (111)
.++..+.+...+..++.+.....+.+.|+.|+..|.....|..|++.-
T Consensus 441 ~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRsk 488 (1406)
T KOG1146|consen 441 KAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSK 488 (1406)
T ss_pred chhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhccccc
Confidence 344444444444444444333233777888887777777777777763
No 152
>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=59.06 E-value=4.6 Score=23.05 Aligned_cols=15 Identities=13% Similarity=0.297 Sum_probs=12.8
Q ss_pred ccccCCCCcccccch
Q psy12016 82 KYECDQCPHRTKHIS 96 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~ 96 (111)
|..|..||+.|+|-.
T Consensus 68 PsYC~~CGkpyPWt~ 82 (158)
T PF10083_consen 68 PSYCHNCGKPYPWTE 82 (158)
T ss_pred ChhHHhCCCCCchHH
Confidence 788999999998864
No 153
>PRK04023 DNA polymerase II large subunit; Validated
Probab=58.89 E-value=9.6 Score=28.60 Aligned_cols=11 Identities=45% Similarity=0.748 Sum_probs=7.5
Q ss_pred CceecCCCccc
Q psy12016 18 GMFTCDVCFKE 28 (111)
Q Consensus 18 ~~~~C~~C~~~ 28 (111)
....|+.||..
T Consensus 625 g~RfCpsCG~~ 635 (1121)
T PRK04023 625 GRRKCPSCGKE 635 (1121)
T ss_pred cCccCCCCCCc
Confidence 34568888866
No 154
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=58.59 E-value=6.6 Score=18.02 Aligned_cols=20 Identities=30% Similarity=0.524 Sum_probs=9.6
Q ss_pred hhhHhhhhhhcCCCCccccCC
Q psy12016 67 KGLGRHKRYECGQEPKYECDQ 87 (111)
Q Consensus 67 ~~l~~h~~~~~~~~~~~~C~~ 87 (111)
..|..|........ +..|..
T Consensus 24 ~~l~~H~~~~C~~~-~v~C~~ 43 (60)
T PF02176_consen 24 KELDDHLENECPKR-PVPCPY 43 (60)
T ss_dssp CCHHHHHHTTSTTS-EEE-SS
T ss_pred HHHHHHHHccCCCC-cEECCC
Confidence 34555555444434 555665
No 155
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=58.08 E-value=6.2 Score=16.57 Aligned_cols=16 Identities=19% Similarity=0.266 Sum_probs=8.3
Q ss_pred cccCCCCcccccchhH
Q psy12016 83 YECDQCPHRTKHISSL 98 (111)
Q Consensus 83 ~~C~~C~~~f~~~~~l 98 (111)
-.|..|++.|.+.++.
T Consensus 3 ~~CprC~kg~Hwa~~C 18 (36)
T PF14787_consen 3 GLCPRCGKGFHWASEC 18 (36)
T ss_dssp -C-TTTSSSCS-TTT-
T ss_pred ccCcccCCCcchhhhh
Confidence 3577777777766554
No 156
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=58.05 E-value=11 Score=23.96 Aligned_cols=25 Identities=28% Similarity=0.503 Sum_probs=17.5
Q ss_pred ccccCCCCcccccchhHHHHHHHhh
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKH 106 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~ 106 (111)
-|.|+.|-+.|.....+.+|+..+.
T Consensus 48 lyiCe~Clky~~~~~~l~~H~~~C~ 72 (290)
T PLN03238 48 LYICEYCLKYMRKKKSLLRHLAKCD 72 (290)
T ss_pred EEEcCCCcchhCCHHHHHHHHHhCC
Confidence 6777777777777777777766443
No 157
>COG2879 Uncharacterized small protein [Function unknown]
Probab=57.19 E-value=13 Score=17.82 Aligned_cols=17 Identities=24% Similarity=0.274 Sum_probs=12.5
Q ss_pred chhHHHHHHHhhCCCCC
Q psy12016 95 ISSLKKHMALKHGVESQ 111 (111)
Q Consensus 95 ~~~l~~H~~~~~~ek~~ 111 (111)
-.+..+|++.+|.++|.
T Consensus 25 YdnYVehmr~~hPd~p~ 41 (65)
T COG2879 25 YDNYVEHMRKKHPDKPP 41 (65)
T ss_pred HHHHHHHHHHhCcCCCc
Confidence 45677788888888773
No 158
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=57.18 E-value=5.8 Score=21.46 Aligned_cols=16 Identities=19% Similarity=0.401 Sum_probs=10.2
Q ss_pred CCceecCCCcccccch
Q psy12016 17 SGMFTCDVCFKEYKYK 32 (111)
Q Consensus 17 ~~~~~C~~C~~~f~~~ 32 (111)
+..+.|..|+..|...
T Consensus 69 p~~~~C~~Cg~~~~~~ 84 (117)
T PRK00564 69 KVELECKDCSHVFKPN 84 (117)
T ss_pred CCEEEhhhCCCccccC
Confidence 3446788888666543
No 159
>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=56.76 E-value=11 Score=20.26 Aligned_cols=12 Identities=25% Similarity=0.542 Sum_probs=6.1
Q ss_pred eecCCCcccccc
Q psy12016 20 FTCDVCFKEYKY 31 (111)
Q Consensus 20 ~~C~~C~~~f~~ 31 (111)
..|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 456666655544
No 160
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.62 E-value=2.1 Score=26.12 Aligned_cols=20 Identities=20% Similarity=0.381 Sum_probs=14.7
Q ss_pred CCCceecCCCcccccchhHH
Q psy12016 16 DSGMFTCDVCFKEYKYKRGL 35 (111)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l 35 (111)
.++...|++|+..|......
T Consensus 16 ~kk~ieCPvC~tkFkkeev~ 35 (267)
T COG1655 16 YKKTIECPVCNTKFKKEEVK 35 (267)
T ss_pred hhceeccCcccchhhhhhee
Confidence 45568899999988766543
No 161
>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=55.96 E-value=5.6 Score=27.24 Aligned_cols=9 Identities=33% Similarity=0.755 Sum_probs=5.5
Q ss_pred ccccCCCCc
Q psy12016 82 KYECDQCPH 90 (111)
Q Consensus 82 ~~~C~~C~~ 90 (111)
|..|+.|+.
T Consensus 253 ~~~Cp~C~s 261 (505)
T TIGR00595 253 PKTCPQCGS 261 (505)
T ss_pred CCCCCCCCC
Confidence 556666664
No 162
>KOG0717|consensus
Probab=55.91 E-value=8.6 Score=26.10 Aligned_cols=22 Identities=32% Similarity=0.677 Sum_probs=19.7
Q ss_pred eecCCCcccccchhHHHHHHhh
Q psy12016 20 FTCDVCFKEYKYKRGLVRHKKN 41 (111)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~ 41 (111)
+.|.+|++.|.+...+..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999988753
No 163
>KOG0717|consensus
Probab=55.60 E-value=7.1 Score=26.49 Aligned_cols=21 Identities=29% Similarity=0.406 Sum_probs=18.2
Q ss_pred cccCCCCcccccchhHHHHHH
Q psy12016 83 YECDQCPHRTKHISSLKKHMA 103 (111)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~ 103 (111)
+.|.+|++.|.+...|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 789999999999988888854
No 164
>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=54.92 E-value=16 Score=16.56 Aligned_cols=12 Identities=17% Similarity=0.545 Sum_probs=5.2
Q ss_pred ecCCCcccccch
Q psy12016 21 TCDVCFKEYKYK 32 (111)
Q Consensus 21 ~C~~C~~~f~~~ 32 (111)
.|++|+..|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 677777766554
No 165
>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=54.65 E-value=1 Score=19.16 Aligned_cols=10 Identities=50% Similarity=1.066 Sum_probs=5.9
Q ss_pred cccCCCCccc
Q psy12016 83 YECDQCPHRT 92 (111)
Q Consensus 83 ~~C~~C~~~f 92 (111)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 5566666544
No 166
>KOG0782|consensus
Probab=54.13 E-value=1 Score=31.17 Aligned_cols=46 Identities=22% Similarity=0.327 Sum_probs=26.8
Q ss_pred hhhhcCCCCceecCCCcccccchhHHHHHHhhhcCC-CCCCCCCccccCccCcccCCch
Q psy12016 10 LSVWQNDSGMFTCDVCFKEYKYKRGLVRHKKNSCKQ-KPQNLDGLFSCDVCGKHYKYKK 67 (111)
Q Consensus 10 ~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~-~~~~~~~~~~c~~c~~~~~~~~ 67 (111)
|.+.|.+...-.|..|++.|.++-.+. ..+ .. ..|.+|..+|-.+.
T Consensus 244 HHWVHrrRqeGkC~~CgKgFQQKf~Fh------sKEivA------isCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 244 HHWVHRRRQEGKCNTCGKGFQQKFFFH------SKEIVA------ISCSWCKQAYHLKV 290 (1004)
T ss_pred HhHhhHhhhccccchhhhhhhhheeec------cccEEE------EEehHHHHHhhcch
Confidence 445554444456888888876654332 222 12 57788877766554
No 167
>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=53.51 E-value=9.9 Score=16.66 Aligned_cols=8 Identities=38% Similarity=1.385 Sum_probs=4.1
Q ss_pred ccccCCCC
Q psy12016 82 KYECDQCP 89 (111)
Q Consensus 82 ~~~C~~C~ 89 (111)
.|.|..|.
T Consensus 37 ~~~C~~C~ 44 (46)
T PF12760_consen 37 RYRCKACR 44 (46)
T ss_pred eEECCCCC
Confidence 45555554
No 168
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.32 E-value=5.6 Score=17.87 Aligned_cols=14 Identities=14% Similarity=0.299 Sum_probs=10.2
Q ss_pred ccCCCCcccccchh
Q psy12016 84 ECDQCPHRTKHISS 97 (111)
Q Consensus 84 ~C~~C~~~f~~~~~ 97 (111)
.|++|++.|.+..-
T Consensus 14 ICpvCqRPFsWRkK 27 (54)
T COG4338 14 ICPVCQRPFSWRKK 27 (54)
T ss_pred hhhhhcCchHHHHH
Confidence 58888888876543
No 169
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=52.04 E-value=8.7 Score=21.92 Aligned_cols=33 Identities=33% Similarity=0.887 Sum_probs=21.4
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCccc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRT 92 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f 92 (111)
|.|. |+..+.... .|..+..| + .|.|..|+...
T Consensus 118 Y~C~-C~q~~l~~R---Rhn~~~~g-~-~YrC~~C~gkL 150 (156)
T COG3091 118 YRCQ-CQQHYLRIR---RHNTVRRG-E-VYRCGKCGGKL 150 (156)
T ss_pred EEee-cCCccchhh---hccccccc-c-eEEeccCCceE
Confidence 8888 888876654 33333323 4 68898887554
No 170
>KOG2807|consensus
Probab=51.40 E-value=37 Score=22.17 Aligned_cols=22 Identities=18% Similarity=0.232 Sum_probs=13.8
Q ss_pred CceecCCCcccccchhHHHHHH
Q psy12016 18 GMFTCDVCFKEYKYKRGLVRHK 39 (111)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~ 39 (111)
-|-.|+.|+-.......|.+..
T Consensus 289 LP~eCpiC~ltLVss~hLARSy 310 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLARSY 310 (378)
T ss_pred CCccCCccceeEecchHHHHHH
Confidence 4556777777666666665543
No 171
>PF15269 zf-C2H2_7: Zinc-finger
Probab=50.47 E-value=16 Score=16.15 Aligned_cols=22 Identities=27% Similarity=0.380 Sum_probs=16.8
Q ss_pred eecCCCcccccchhHHHHHHhh
Q psy12016 20 FTCDVCFKEYKYKRGLVRHKKN 41 (111)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~ 41 (111)
|.|-.|......++.|-.||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 5677888777778888888764
No 172
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=49.71 E-value=14 Score=24.79 Aligned_cols=12 Identities=33% Similarity=0.935 Sum_probs=6.1
Q ss_pred cccCccCcccCC
Q psy12016 54 FSCDVCGKHYKY 65 (111)
Q Consensus 54 ~~c~~c~~~~~~ 65 (111)
|.|..|+..+..
T Consensus 368 ~rC~kCg~~~~~ 379 (421)
T COG1571 368 FRCKKCGTRARE 379 (421)
T ss_pred cccccccccCCc
Confidence 555555544443
No 173
>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=49.50 E-value=13 Score=23.53 Aligned_cols=33 Identities=24% Similarity=0.431 Sum_probs=21.1
Q ss_pred eecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCch
Q psy12016 20 FTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKK 67 (111)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~ 67 (111)
..|+.|+.....+. |.. .- +.|+.|+..+....
T Consensus 27 ~~c~~c~~~~~~~~-l~~--------~~------~vc~~c~~h~rl~a 59 (285)
T TIGR00515 27 TKCPKCGQVLYTKE-LER--------NL------EVCPKCDHHMRMDA 59 (285)
T ss_pred eECCCCcchhhHHH-HHh--------hC------CCCCCCCCcCcCCH
Confidence 46999987765443 211 11 68999998877553
No 174
>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=49.47 E-value=12 Score=25.31 Aligned_cols=13 Identities=23% Similarity=0.577 Sum_probs=9.4
Q ss_pred CceecCCCccccc
Q psy12016 18 GMFTCDVCFKEYK 30 (111)
Q Consensus 18 ~~~~C~~C~~~f~ 30 (111)
..|.|..||....
T Consensus 6 ~~y~C~~Cg~~~~ 18 (454)
T TIGR00416 6 SKFVCQHCGADSP 18 (454)
T ss_pred CeEECCcCCCCCc
Confidence 3588999986643
No 175
>KOG2071|consensus
Probab=48.61 E-value=13 Score=25.95 Aligned_cols=26 Identities=23% Similarity=0.474 Sum_probs=22.8
Q ss_pred ccccCCCCcccccchhHHHHHHHhhC
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKHG 107 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~~ 107 (111)
|-.|..||..|........||.+|-.
T Consensus 418 pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 418 PNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred cchhcccccccccchhhhhHhhhhhh
Confidence 77899999999999999888887754
No 176
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=48.20 E-value=17 Score=23.06 Aligned_cols=12 Identities=33% Similarity=0.539 Sum_probs=6.2
Q ss_pred ccccCccCcccC
Q psy12016 53 LFSCDVCGKHYK 64 (111)
Q Consensus 53 ~~~c~~c~~~~~ 64 (111)
+|.|+.|...|.
T Consensus 255 GyvCs~Clsi~C 266 (279)
T TIGR00627 255 GFVCSVCLSVLC 266 (279)
T ss_pred eEECCCccCCcC
Confidence 356666554443
No 177
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=48.00 E-value=18 Score=16.84 Aligned_cols=7 Identities=57% Similarity=1.578 Sum_probs=3.9
Q ss_pred cccCccC
Q psy12016 54 FSCDVCG 60 (111)
Q Consensus 54 ~~c~~c~ 60 (111)
|.|+.||
T Consensus 15 ~~Cp~cG 21 (55)
T PF13824_consen 15 FECPDCG 21 (55)
T ss_pred CcCCCCC
Confidence 5555555
No 178
>PRK05978 hypothetical protein; Provisional
Probab=47.97 E-value=9 Score=21.77 Aligned_cols=8 Identities=38% Similarity=1.282 Sum_probs=3.7
Q ss_pred ccCccCcc
Q psy12016 55 SCDVCGKH 62 (111)
Q Consensus 55 ~c~~c~~~ 62 (111)
.|+.||..
T Consensus 54 ~C~~CG~~ 61 (148)
T PRK05978 54 HCAACGED 61 (148)
T ss_pred CccccCCc
Confidence 44555443
No 179
>PRK11823 DNA repair protein RadA; Provisional
Probab=47.81 E-value=14 Score=25.00 Aligned_cols=14 Identities=21% Similarity=0.498 Sum_probs=9.7
Q ss_pred CCceecCCCccccc
Q psy12016 17 SGMFTCDVCFKEYK 30 (111)
Q Consensus 17 ~~~~~C~~C~~~f~ 30 (111)
...|.|..||....
T Consensus 5 ~~~y~C~~Cg~~~~ 18 (446)
T PRK11823 5 KTAYVCQECGAESP 18 (446)
T ss_pred CCeEECCcCCCCCc
Confidence 34588998886643
No 180
>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=47.44 E-value=20 Score=15.15 Aligned_cols=14 Identities=36% Similarity=0.785 Sum_probs=5.5
Q ss_pred ccccCCCCcccccc
Q psy12016 82 KYECDQCPHRTKHI 95 (111)
Q Consensus 82 ~~~C~~C~~~f~~~ 95 (111)
.|-|+.|+..+...
T Consensus 3 ryyCdyC~~~~~~d 16 (38)
T PF06220_consen 3 RYYCDYCKKYLTHD 16 (38)
T ss_dssp S-B-TTT--B-S--
T ss_pred CeecccccceecCC
Confidence 57799999888443
No 181
>KOG4124|consensus
Probab=46.89 E-value=3.7 Score=26.67 Aligned_cols=51 Identities=37% Similarity=0.725 Sum_probs=31.3
Q ss_pred CCccccCc--cCcccCCchhhHhhhhhhc------------------CCCCccccCCCCcccccchhHHHH
Q psy12016 51 DGLFSCDV--CGKHYKYKKGLGRHKRYEC------------------GQEPKYECDQCPHRTKHISSLKKH 101 (111)
Q Consensus 51 ~~~~~c~~--c~~~~~~~~~l~~h~~~~~------------------~~~~~~~C~~C~~~f~~~~~l~~H 101 (111)
++.+.|.+ |.+.......|..|....+ .+.++++|++|.+.++....|+-|
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCce
Confidence 34566665 6666666655554433211 123489999999888777666544
No 182
>PF12907 zf-met2: Zinc-binding
Probab=46.16 E-value=9 Score=16.53 Aligned_cols=22 Identities=18% Similarity=0.543 Sum_probs=10.2
Q ss_pred cccCccCcccC---CchhhHhhhhh
Q psy12016 54 FSCDVCGKHYK---YKKGLGRHKRY 75 (111)
Q Consensus 54 ~~c~~c~~~~~---~~~~l~~h~~~ 75 (111)
+.|.+|...|. +...|..|-..
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~en 26 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAEN 26 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHc
Confidence 45666663332 22345555443
No 183
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=46.12 E-value=10 Score=21.26 Aligned_cols=17 Identities=24% Similarity=0.366 Sum_probs=13.3
Q ss_pred CCceecCCCcccccchh
Q psy12016 17 SGMFTCDVCFKEYKYKR 33 (111)
Q Consensus 17 ~~~~~C~~C~~~f~~~~ 33 (111)
.++.+|+.||..|....
T Consensus 110 g~~~RCpeCG~~fkL~~ 126 (136)
T PF01215_consen 110 GKPQRCPECGQVFKLKY 126 (136)
T ss_dssp TSEEEETTTEEEEEEEE
T ss_pred CCccCCCCCCeEEEEEE
Confidence 45789999999887653
No 184
>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=46.10 E-value=15 Score=17.44 Aligned_cols=11 Identities=18% Similarity=0.739 Sum_probs=7.0
Q ss_pred ccccCCCCccc
Q psy12016 82 KYECDQCPHRT 92 (111)
Q Consensus 82 ~~~C~~C~~~f 92 (111)
.|.|+.||..+
T Consensus 46 ~~~C~~Cg~~~ 56 (69)
T PF07282_consen 46 VFTCPNCGFEM 56 (69)
T ss_pred eEEcCCCCCEE
Confidence 66777776553
No 185
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=45.46 E-value=13 Score=22.80 Aligned_cols=18 Identities=17% Similarity=0.515 Sum_probs=14.2
Q ss_pred CCCceecCCCcccccchh
Q psy12016 16 DSGMFTCDVCFKEYKYKR 33 (111)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~ 33 (111)
..++.+|.+||..|....
T Consensus 178 EGkpqRCpECGqVFKLVr 195 (268)
T PTZ00043 178 EGFLYRCGECDQIFMLVR 195 (268)
T ss_pred CCCCccCCCCCcEEEEEE
Confidence 456789999999997643
No 186
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=45.22 E-value=20 Score=20.09 Aligned_cols=19 Identities=21% Similarity=0.590 Sum_probs=13.9
Q ss_pred CCCceecCCCcccccchhH
Q psy12016 16 DSGMFTCDVCFKEYKYKRG 34 (111)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~ 34 (111)
..+.|+|..|..+......
T Consensus 77 d~~lYeCnIC~etS~ee~F 95 (140)
T PF05290_consen 77 DPKLYECNICKETSAEERF 95 (140)
T ss_pred CCCceeccCcccccchhhc
Confidence 4577999999877655544
No 187
>KOG1842|consensus
Probab=45.20 E-value=12 Score=25.26 Aligned_cols=27 Identities=26% Similarity=0.368 Sum_probs=21.5
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCC
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQE 80 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~ 80 (111)
|.|+.|...|.+...|..|..+.|.++
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 788888888888888888887766544
No 188
>KOG1842|consensus
Probab=44.54 E-value=11 Score=25.52 Aligned_cols=23 Identities=22% Similarity=0.437 Sum_probs=20.3
Q ss_pred ceecCCCcccccchhHHHHHHhh
Q psy12016 19 MFTCDVCFKEYKYKRGLVRHKKN 41 (111)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~ 41 (111)
-|.|+.|...|.....|..|...
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~ 37 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDV 37 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhh
Confidence 48999999999999999999754
No 189
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=44.50 E-value=17 Score=23.21 Aligned_cols=33 Identities=30% Similarity=0.557 Sum_probs=21.1
Q ss_pred eecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCch
Q psy12016 20 FTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKK 67 (111)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~ 67 (111)
..|+.|+.....+. |.. .. +.|+.|+..|....
T Consensus 39 ~kc~~C~~~~~~~~-l~~--------~~------~vcp~c~~h~rltA 71 (296)
T CHL00174 39 VQCENCYGLNYKKF-LKS--------KM------NICEQCGYHLKMSS 71 (296)
T ss_pred eECCCccchhhHHH-HHH--------cC------CCCCCCCCCcCCCH
Confidence 46888887654443 211 12 68999998877653
No 190
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=43.96 E-value=4.8 Score=28.77 Aligned_cols=59 Identities=19% Similarity=0.475 Sum_probs=33.0
Q ss_pred ecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCchhhHhhhhhhcCCCCccccCCCCccc
Q psy12016 21 TCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRT 92 (111)
Q Consensus 21 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f 92 (111)
.|..||-.|+....|- ..+.++.-.. .-.|+.|.+.+..+.+ .+-| . + |..|+.||-..
T Consensus 125 ~CT~CGPRfTIi~alP-YDR~nTsM~~-----F~lC~~C~~EY~dP~n----RRfH-A-Q-p~aCp~CGP~~ 183 (750)
T COG0068 125 NCTNCGPRFTIIEALP-YDRENTSMAD-----FPLCPFCDKEYKDPLN----RRFH-A-Q-PIACPKCGPHL 183 (750)
T ss_pred ccCCCCcceeeeccCC-CCcccCcccc-----CcCCHHHHHHhcCccc----cccc-c-c-cccCcccCCCe
Confidence 4777887776654432 1111111111 1378888887776643 2333 2 3 88999999643
No 191
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=43.24 E-value=9.3 Score=16.46 Aligned_cols=11 Identities=27% Similarity=0.543 Sum_probs=8.5
Q ss_pred ccccCCCCccc
Q psy12016 82 KYECDQCPHRT 92 (111)
Q Consensus 82 ~~~C~~C~~~f 92 (111)
+..|++|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 57888888766
No 192
>PHA02998 RNA polymerase subunit; Provisional
Probab=42.94 E-value=8 Score=22.69 Aligned_cols=38 Identities=18% Similarity=0.414 Sum_probs=21.3
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCC---ccccCCCCcccccc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEP---KYECDQCPHRTKHI 95 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~---~~~C~~C~~~f~~~ 95 (111)
..|+.|+..-.....+ ++....++ -|.|..|+..|...
T Consensus 144 v~CPkCg~~~A~f~ql----QTRSADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 144 TPCPNCKSKNTTPMMI----QTRAADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCceEEEEE----eeccCCCCceEEEEcCCCCCccCCc
Confidence 5788888543332222 22223332 36899999887543
No 193
>PRK04351 hypothetical protein; Provisional
Probab=42.81 E-value=13 Score=21.18 Aligned_cols=34 Identities=35% Similarity=0.929 Sum_probs=21.9
Q ss_pred ccccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccccc
Q psy12016 53 LFSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKHI 95 (111)
Q Consensus 53 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~ 95 (111)
.|.|..|+..+.+.. + + ... .|.|..|+..+...
T Consensus 112 ~Y~C~~Cg~~~~r~R------r-~-n~~-~yrCg~C~g~L~~~ 145 (149)
T PRK04351 112 LYECQSCGQQYLRKR------R-I-NTK-RYRCGKCRGKLKLI 145 (149)
T ss_pred EEECCCCCCEeeeee------e-c-CCC-cEEeCCCCcEeeec
Confidence 489988987665432 1 1 224 79999998766443
No 194
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=42.59 E-value=16 Score=24.79 Aligned_cols=25 Identities=28% Similarity=0.469 Sum_probs=21.6
Q ss_pred ccccCCCCcccccchhHHHHHHHhh
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKH 106 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~ 106 (111)
.|.|+.|-+.|.....|.+|+..+.
T Consensus 198 lyiCe~Cl~y~~~~~~~~~H~~~C~ 222 (450)
T PLN00104 198 LYFCEFCLKFMKRKEQLQRHMKKCD 222 (450)
T ss_pred EEEchhhhhhhcCHHHHHHHHhcCC
Confidence 6889999999999999999987554
No 195
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=42.41 E-value=11 Score=19.45 Aligned_cols=14 Identities=21% Similarity=0.382 Sum_probs=11.2
Q ss_pred CceecCCCcccccc
Q psy12016 18 GMFTCDVCFKEYKY 31 (111)
Q Consensus 18 ~~~~C~~C~~~f~~ 31 (111)
.|..|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 56789999988865
No 196
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=41.98 E-value=12 Score=15.67 Aligned_cols=7 Identities=43% Similarity=1.678 Sum_probs=4.3
Q ss_pred ccccCCC
Q psy12016 82 KYECDQC 88 (111)
Q Consensus 82 ~~~C~~C 88 (111)
.|.|..|
T Consensus 29 ryrC~~C 35 (36)
T PF03811_consen 29 RYRCKDC 35 (36)
T ss_pred eEecCcC
Confidence 5666655
No 197
>PTZ00064 histone acetyltransferase; Provisional
Probab=41.95 E-value=20 Score=24.85 Aligned_cols=25 Identities=16% Similarity=0.192 Sum_probs=21.6
Q ss_pred ccccCCCCcccccchhHHHHHHHhh
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKH 106 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~ 106 (111)
.|.|+.|-+.|.....|.+|+..+.
T Consensus 280 LYICEfCLkY~~s~~~l~rH~~~C~ 304 (552)
T PTZ00064 280 LHFCEYCLDFFCFEDELIRHLSRCQ 304 (552)
T ss_pred EEEccchhhhhCCHHHHHHHHhcCC
Confidence 6889999999999999999987654
No 198
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=40.83 E-value=5 Score=26.22 Aligned_cols=11 Identities=18% Similarity=0.709 Sum_probs=6.4
Q ss_pred cccCccCcccC
Q psy12016 54 FSCDVCGKHYK 64 (111)
Q Consensus 54 ~~c~~c~~~~~ 64 (111)
..|+.|...|.
T Consensus 341 ~~CPtCRa~FC 351 (358)
T PF10272_consen 341 CPCPTCRAKFC 351 (358)
T ss_pred CCCCCCcccce
Confidence 45666665554
No 199
>PRK05580 primosome assembly protein PriA; Validated
Probab=40.65 E-value=20 Score=25.72 Aligned_cols=9 Identities=22% Similarity=0.722 Sum_probs=5.3
Q ss_pred ccccCCCCc
Q psy12016 82 KYECDQCPH 90 (111)
Q Consensus 82 ~~~C~~C~~ 90 (111)
|..|+.|+.
T Consensus 421 ~~~Cp~Cg~ 429 (679)
T PRK05580 421 PKACPECGS 429 (679)
T ss_pred CCCCCCCcC
Confidence 556666654
No 200
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=39.56 E-value=5.5 Score=16.46 Aligned_cols=6 Identities=50% Similarity=1.553 Sum_probs=2.5
Q ss_pred ccCccC
Q psy12016 55 SCDVCG 60 (111)
Q Consensus 55 ~c~~c~ 60 (111)
.|+.|+
T Consensus 24 vC~~Cg 29 (34)
T PF14803_consen 24 VCPACG 29 (34)
T ss_dssp EETTTT
T ss_pred ECCCCC
Confidence 444443
No 201
>COG1773 Rubredoxin [Energy production and conversion]
Probab=39.52 E-value=15 Score=17.08 Aligned_cols=14 Identities=29% Similarity=0.615 Sum_probs=9.7
Q ss_pred ceecCCCcccccch
Q psy12016 19 MFTCDVCFKEYKYK 32 (111)
Q Consensus 19 ~~~C~~C~~~f~~~ 32 (111)
.|.|..|+..|.-.
T Consensus 3 ~~~C~~CG~vYd~e 16 (55)
T COG1773 3 RWRCSVCGYVYDPE 16 (55)
T ss_pred ceEecCCceEeccc
Confidence 47788888776543
No 202
>PTZ00448 hypothetical protein; Provisional
Probab=39.28 E-value=24 Score=23.32 Aligned_cols=24 Identities=17% Similarity=0.375 Sum_probs=19.7
Q ss_pred ccccCCCCcccccchhHHHHHHHh
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALK 105 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~ 105 (111)
.|.|..|+-.|.+....+.|.++.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSD 337 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSE 337 (373)
T ss_pred CccccccccccCCHHHHHHHhhhh
Confidence 477999999998888888887753
No 203
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=39.04 E-value=21 Score=22.79 Aligned_cols=33 Identities=24% Similarity=0.450 Sum_probs=20.8
Q ss_pred eecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcccCCch
Q psy12016 20 FTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKHYKYKK 67 (111)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~ 67 (111)
..|+.|+.....+. |.. .. +.|+.|+..+....
T Consensus 28 ~~c~~c~~~~~~~~-l~~--------~~------~vc~~c~~h~rl~a 60 (292)
T PRK05654 28 TKCPSCGQVLYRKE-LEA--------NL------NVCPKCGHHMRISA 60 (292)
T ss_pred eECCCccchhhHHH-HHh--------cC------CCCCCCCCCeeCCH
Confidence 46999987654443 221 11 68999998876553
No 204
>PRK12496 hypothetical protein; Provisional
Probab=38.74 E-value=23 Score=20.48 Aligned_cols=28 Identities=21% Similarity=0.379 Sum_probs=17.7
Q ss_pred CccccCccCcccCCchhhHhhhhhhcCCCCccccCCCCccc
Q psy12016 52 GLFSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRT 92 (111)
Q Consensus 52 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f 92 (111)
+.+.|.-|++.|.... . .-.|+.||...
T Consensus 126 w~~~C~gC~~~~~~~~------------~-~~~C~~CG~~~ 153 (164)
T PRK12496 126 WRKVCKGCKKKYPEDY------------P-DDVCEICGSPV 153 (164)
T ss_pred eeEECCCCCccccCCC------------C-CCcCCCCCChh
Confidence 4478888988775321 1 23588888554
No 205
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=38.65 E-value=17 Score=23.84 Aligned_cols=7 Identities=43% Similarity=1.578 Sum_probs=3.6
Q ss_pred cccCccC
Q psy12016 54 FSCDVCG 60 (111)
Q Consensus 54 ~~c~~c~ 60 (111)
|.|..||
T Consensus 355 YRC~~CG 361 (389)
T COG2956 355 YRCQNCG 361 (389)
T ss_pred ceecccC
Confidence 4555554
No 206
>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=38.50 E-value=19 Score=20.22 Aligned_cols=13 Identities=38% Similarity=1.170 Sum_probs=7.7
Q ss_pred cccCccCcccCCc
Q psy12016 54 FSCDVCGKHYKYK 66 (111)
Q Consensus 54 ~~c~~c~~~~~~~ 66 (111)
|.|..|+..+...
T Consensus 124 ~~C~~C~~~~~r~ 136 (157)
T PF10263_consen 124 YRCPSCGREYKRH 136 (157)
T ss_pred EEcCCCCCEeeee
Confidence 6666676555443
No 207
>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=38.47 E-value=7.8 Score=19.52 Aligned_cols=13 Identities=15% Similarity=0.434 Sum_probs=7.0
Q ss_pred ccccCCCCccccc
Q psy12016 82 KYECDQCPHRTKH 94 (111)
Q Consensus 82 ~~~C~~C~~~f~~ 94 (111)
...|..|+..|..
T Consensus 46 ~~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 46 ILSCRVCGESFQT 58 (81)
T ss_dssp EEEESSS--EEEE
T ss_pred EEEecCCCCeEEE
Confidence 4567777766643
No 208
>KOG3507|consensus
Probab=38.18 E-value=11 Score=17.71 Aligned_cols=11 Identities=27% Similarity=0.724 Sum_probs=7.7
Q ss_pred cccCccCcccC
Q psy12016 54 FSCDVCGKHYK 64 (111)
Q Consensus 54 ~~c~~c~~~~~ 64 (111)
+.|.+||....
T Consensus 38 irCReCG~RIl 48 (62)
T KOG3507|consen 38 IRCRECGYRIL 48 (62)
T ss_pred EehhhcchHHH
Confidence 78888886533
No 209
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=38.00 E-value=14 Score=19.74 Aligned_cols=22 Identities=18% Similarity=0.282 Sum_probs=16.7
Q ss_pred ccccCCCCcccccchhHHHHHH
Q psy12016 82 KYECDQCPHRTKHISSLKKHMA 103 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~ 103 (111)
.+.|..|.+.|.....|..|.+
T Consensus 55 qhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhc
Confidence 5678888888888777777754
No 210
>PLN02748 tRNA dimethylallyltransferase
Probab=37.85 E-value=24 Score=24.15 Aligned_cols=23 Identities=17% Similarity=0.460 Sum_probs=19.0
Q ss_pred ccccCCCCc-ccccchhHHHHHHH
Q psy12016 82 KYECDQCPH-RTKHISSLKKHMAL 104 (111)
Q Consensus 82 ~~~C~~C~~-~f~~~~~l~~H~~~ 104 (111)
.|.|+.|+. .+.....|..|++.
T Consensus 418 ~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 418 QYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred cccccCCCCcccCCHHHHHHHhcc
Confidence 678999997 78888888888753
No 211
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=37.68 E-value=40 Score=20.20 Aligned_cols=12 Identities=25% Similarity=0.650 Sum_probs=9.1
Q ss_pred cccCccCcccCC
Q psy12016 54 FSCDVCGKHYKY 65 (111)
Q Consensus 54 ~~c~~c~~~~~~ 65 (111)
..|..||..++.
T Consensus 31 vrC~eCG~V~~~ 42 (201)
T COG1326 31 VRCEECGTVHPA 42 (201)
T ss_pred EEccCCCcEeec
Confidence 788889877643
No 212
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=37.05 E-value=17 Score=24.80 Aligned_cols=13 Identities=31% Similarity=0.687 Sum_probs=9.5
Q ss_pred cccCccCcccCCc
Q psy12016 54 FSCDVCGKHYKYK 66 (111)
Q Consensus 54 ~~c~~c~~~~~~~ 66 (111)
|.|..|+..+...
T Consensus 426 ~~c~~c~~~yd~~ 438 (479)
T PRK05452 426 MQCSVCQWIYDPA 438 (479)
T ss_pred EEECCCCeEECCC
Confidence 7888888776654
No 213
>PRK11032 hypothetical protein; Provisional
Probab=36.97 E-value=22 Score=20.56 Aligned_cols=8 Identities=25% Similarity=1.007 Sum_probs=3.9
Q ss_pred cccCccCc
Q psy12016 54 FSCDVCGK 61 (111)
Q Consensus 54 ~~c~~c~~ 61 (111)
..|..||.
T Consensus 125 LvC~~Cg~ 132 (160)
T PRK11032 125 LVCEKCHH 132 (160)
T ss_pred EEecCCCC
Confidence 44555553
No 214
>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=36.87 E-value=21 Score=23.60 Aligned_cols=7 Identities=29% Similarity=0.785 Sum_probs=3.2
Q ss_pred ecCCCcc
Q psy12016 21 TCDVCFK 27 (111)
Q Consensus 21 ~C~~C~~ 27 (111)
.|+.|+.
T Consensus 16 ~cp~c~~ 22 (372)
T cd01121 16 KCPECGE 22 (372)
T ss_pred ECcCCCC
Confidence 3555543
No 215
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.03 E-value=19 Score=19.73 Aligned_cols=12 Identities=25% Similarity=0.265 Sum_probs=6.8
Q ss_pred ceecCCCcccccc
Q psy12016 19 MFTCDVCFKEYKY 31 (111)
Q Consensus 19 ~~~C~~C~~~f~~ 31 (111)
...| .|+..|..
T Consensus 70 ~~~C-~Cg~~~~~ 81 (124)
T PRK00762 70 EIEC-ECGYEGVV 81 (124)
T ss_pred eEEe-eCcCcccc
Confidence 3566 66655543
No 216
>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=35.87 E-value=21 Score=14.79 Aligned_cols=12 Identities=33% Similarity=0.678 Sum_probs=4.1
Q ss_pred ecCCCcccccch
Q psy12016 21 TCDVCFKEYKYK 32 (111)
Q Consensus 21 ~C~~C~~~f~~~ 32 (111)
.|..|++.|..+
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 455555555443
No 217
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=35.80 E-value=42 Score=14.18 Aligned_cols=20 Identities=15% Similarity=0.152 Sum_probs=14.8
Q ss_pred ceecCCCcccccchhHHHHH
Q psy12016 19 MFTCDVCFKEYKYKRGLVRH 38 (111)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h 38 (111)
...|+.|+..+.....|.+-
T Consensus 19 id~C~~C~G~W~d~~el~~~ 38 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELEKL 38 (41)
T ss_pred EEECCCCCeEEccHHHHHHH
Confidence 45788898888887776643
No 218
>KOG3352|consensus
Probab=35.56 E-value=21 Score=20.34 Aligned_cols=15 Identities=33% Similarity=0.603 Sum_probs=11.8
Q ss_pred CCCccccCCCCccccc
Q psy12016 79 QEPKYECDQCPHRTKH 94 (111)
Q Consensus 79 ~~~~~~C~~C~~~f~~ 94 (111)
++ ..+|.+|+..|..
T Consensus 131 ge-~~rc~eCG~~fkL 145 (153)
T KOG3352|consen 131 GE-TQRCPECGHYFKL 145 (153)
T ss_pred CC-cccCCcccceEEe
Confidence 35 6789999998864
No 219
>PF14369 zf-RING_3: zinc-finger
Probab=35.55 E-value=19 Score=14.86 Aligned_cols=11 Identities=18% Similarity=0.594 Sum_probs=8.9
Q ss_pred ecCCCcccccc
Q psy12016 21 TCDVCFKEYKY 31 (111)
Q Consensus 21 ~C~~C~~~f~~ 31 (111)
.|+.|+..|..
T Consensus 23 ~CP~C~~gFvE 33 (35)
T PF14369_consen 23 ACPRCHGGFVE 33 (35)
T ss_pred CCcCCCCcEeE
Confidence 59999988854
No 220
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.39 E-value=23 Score=16.88 Aligned_cols=9 Identities=22% Similarity=0.907 Sum_probs=5.4
Q ss_pred cccCccCcc
Q psy12016 54 FSCDVCGKH 62 (111)
Q Consensus 54 ~~c~~c~~~ 62 (111)
|-|++|...
T Consensus 32 ymC~eC~~R 40 (68)
T COG4896 32 YMCPECEHR 40 (68)
T ss_pred EechhhHhh
Confidence 666666543
No 221
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=35.16 E-value=50 Score=14.95 Aligned_cols=13 Identities=31% Similarity=0.951 Sum_probs=7.0
Q ss_pred cccCccCcccCCc
Q psy12016 54 FSCDVCGKHYKYK 66 (111)
Q Consensus 54 ~~c~~c~~~~~~~ 66 (111)
+.|..|+..+...
T Consensus 29 W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 29 WKCPKCGHEWKAS 41 (55)
T ss_pred EECCCCCCeeEcc
Confidence 5666665544443
No 222
>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=35.12 E-value=22 Score=14.96 Aligned_cols=12 Identities=17% Similarity=0.598 Sum_probs=6.2
Q ss_pred CceecCCCcccc
Q psy12016 18 GMFTCDVCFKEY 29 (111)
Q Consensus 18 ~~~~C~~C~~~f 29 (111)
..|.|..|+...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 457888888654
No 223
>KOG3214|consensus
Probab=34.77 E-value=14 Score=19.46 Aligned_cols=13 Identities=23% Similarity=0.531 Sum_probs=7.7
Q ss_pred ccccCCCCccccc
Q psy12016 82 KYECDQCPHRTKH 94 (111)
Q Consensus 82 ~~~C~~C~~~f~~ 94 (111)
...|.+|+..|..
T Consensus 47 ~~sC~iC~esFqt 59 (109)
T KOG3214|consen 47 KASCRICEESFQT 59 (109)
T ss_pred eeeeeehhhhhcc
Confidence 4456666666643
No 224
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=34.66 E-value=24 Score=19.77 Aligned_cols=33 Identities=24% Similarity=0.706 Sum_probs=19.6
Q ss_pred ccccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccc
Q psy12016 53 LFSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTK 93 (111)
Q Consensus 53 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~ 93 (111)
.|.|..|+..+.... + +..-. .+.|..|+..+.
T Consensus 112 ~y~C~~C~~~~~~~r------r-~~~~~-~y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRYLRVR------R-SNNVS-RYRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCCceEc------c-ccCcc-eEEcCCCCCEEE
Confidence 478888887654321 1 11113 688988886653
No 225
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.55 E-value=26 Score=16.69 Aligned_cols=36 Identities=17% Similarity=0.254 Sum_probs=19.3
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCccccc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKH 94 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~ 94 (111)
+.|+--+..+..+.... .. ++++-..|++|+..|..
T Consensus 25 l~C~g~~~p~~HPrV~L---~m--g~~gev~CPYC~t~y~l 60 (62)
T COG4391 25 LMCPGPEPPNDHPRVFL---DM--GDEGEVVCPYCSTRYRL 60 (62)
T ss_pred EEcCCCCCCCCCCEEEE---Ec--CCCCcEecCccccEEEe
Confidence 67765444433332211 11 33335679999988753
No 226
>KOG2906|consensus
Probab=34.10 E-value=11 Score=19.85 Aligned_cols=19 Identities=21% Similarity=0.557 Sum_probs=13.7
Q ss_pred CceecCCCcccccchhHHH
Q psy12016 18 GMFTCDVCFKEYKYKRGLV 36 (111)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~ 36 (111)
..|.|..|.+.|.....+.
T Consensus 20 ~rf~C~tCpY~~~I~~ei~ 38 (105)
T KOG2906|consen 20 NRFSCRTCPYVFPISREIS 38 (105)
T ss_pred eeEEcCCCCceeeEeeeee
Confidence 3578999998887765443
No 227
>KOG0562|consensus
Probab=33.67 E-value=35 Score=19.96 Aligned_cols=26 Identities=23% Similarity=0.432 Sum_probs=20.5
Q ss_pred ccccCCCCcccccchhHHHHHHHhhC
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKHG 107 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~~ 107 (111)
+..|..|+..-....-|+.|++.+..
T Consensus 153 dLrC~~Cq~~~~~~~kLK~Hl~~~~~ 178 (184)
T KOG0562|consen 153 DLRCWRCQTFGPHFPKLKAHLREEYD 178 (184)
T ss_pred ceeehhhhhcccccHHHHHHHHHHHh
Confidence 67899999555667889999887764
No 228
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=33.65 E-value=20 Score=14.24 Aligned_cols=10 Identities=20% Similarity=0.936 Sum_probs=5.6
Q ss_pred cccCCCCccc
Q psy12016 83 YECDQCPHRT 92 (111)
Q Consensus 83 ~~C~~C~~~f 92 (111)
|.|..|+..+
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 5566665544
No 229
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.18 E-value=24 Score=19.55 Aligned_cols=14 Identities=21% Similarity=0.634 Sum_probs=10.4
Q ss_pred ccccCCCCcccccc
Q psy12016 82 KYECDQCPHRTKHI 95 (111)
Q Consensus 82 ~~~C~~C~~~f~~~ 95 (111)
.|.|..|++.|...
T Consensus 53 RyrC~~C~~tf~~~ 66 (129)
T COG3677 53 RYKCKSCGSTFTVE 66 (129)
T ss_pred ccccCCcCcceeee
Confidence 68888888887543
No 230
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=32.96 E-value=24 Score=16.88 Aligned_cols=19 Identities=26% Similarity=0.485 Sum_probs=13.0
Q ss_pred hcCCCCceecCCCcccccc
Q psy12016 13 WQNDSGMFTCDVCFKEYKY 31 (111)
Q Consensus 13 ~~~~~~~~~C~~C~~~f~~ 31 (111)
.+..++...|+.|+..|..
T Consensus 47 ~~i~eg~L~Cp~c~r~YPI 65 (68)
T PF03966_consen 47 VEIVEGELICPECGREYPI 65 (68)
T ss_dssp EETTTTEEEETTTTEEEEE
T ss_pred ccccCCEEEcCCCCCEEeC
Confidence 4455667788888877754
No 231
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=32.93 E-value=16 Score=19.74 Aligned_cols=17 Identities=24% Similarity=0.425 Sum_probs=12.1
Q ss_pred CCceecCCCcccccchh
Q psy12016 17 SGMFTCDVCFKEYKYKR 33 (111)
Q Consensus 17 ~~~~~C~~C~~~f~~~~ 33 (111)
..-+.|..|+.......
T Consensus 20 ~~~l~C~kCgye~~~~~ 36 (113)
T COG1594 20 GGKLVCRKCGYEEEASN 36 (113)
T ss_pred CcEEECCCCCcchhccc
Confidence 44688999987766553
No 232
>PRK00420 hypothetical protein; Validated
Probab=32.02 E-value=36 Score=18.41 Aligned_cols=11 Identities=9% Similarity=0.042 Sum_probs=6.9
Q ss_pred ccccCCCCccc
Q psy12016 82 KYECDQCPHRT 92 (111)
Q Consensus 82 ~~~C~~C~~~f 92 (111)
...|+.|+...
T Consensus 40 ~~~Cp~Cg~~~ 50 (112)
T PRK00420 40 EVVCPVHGKVY 50 (112)
T ss_pred ceECCCCCCee
Confidence 45677777644
No 233
>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=31.74 E-value=10 Score=23.87 Aligned_cols=13 Identities=23% Similarity=0.452 Sum_probs=8.8
Q ss_pred ccccCCCCccccc
Q psy12016 82 KYECDQCPHRTKH 94 (111)
Q Consensus 82 ~~~C~~C~~~f~~ 94 (111)
...|..|+..++.
T Consensus 238 ve~C~~C~~YlK~ 250 (290)
T PF04216_consen 238 VEVCESCGSYLKT 250 (290)
T ss_dssp EEEETTTTEEEEE
T ss_pred EEECCcccchHHH
Confidence 5678888865543
No 234
>KOG1088|consensus
Probab=31.71 E-value=22 Score=19.39 Aligned_cols=13 Identities=15% Similarity=0.529 Sum_probs=6.5
Q ss_pred cccCccCcccCCc
Q psy12016 54 FSCDVCGKHYKYK 66 (111)
Q Consensus 54 ~~c~~c~~~~~~~ 66 (111)
..|++||..|+-.
T Consensus 99 l~CpetG~vfpI~ 111 (124)
T KOG1088|consen 99 LVCPETGRVFPIS 111 (124)
T ss_pred EecCCCCcEeecc
Confidence 4555555555443
No 235
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=31.15 E-value=89 Score=16.57 Aligned_cols=38 Identities=11% Similarity=0.250 Sum_probs=26.3
Q ss_pred CceecCCCcccccchhHHHHHHhhhcCCCCCCCCCccccCccCcc
Q psy12016 18 GMFTCDVCFKEYKYKRGLVRHKKNSCKQKPQNLDGLFSCDVCGKH 62 (111)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~ 62 (111)
..|.|+.=+..|.....+...+..-.. .. |.|...|+.
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~~y~~-~v------wtC~~TGk~ 39 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMILYNQ-RV------WTCEITGKS 39 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHHHHhC-Ce------eEEecCCCC
Confidence 356778888888888777766654333 33 888887764
No 236
>KOG2907|consensus
Probab=30.19 E-value=31 Score=18.67 Aligned_cols=40 Identities=23% Similarity=0.453 Sum_probs=20.5
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCccccc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTKH 94 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~ 94 (111)
-.|+.||..=-....++. .....|.---|.|..|+..|..
T Consensus 75 ~kCpkCghe~m~Y~T~Ql-RSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQL-RSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCchhhhhhhhc-ccccCCceEEEEcCccceeeec
Confidence 478888854333222221 1112222214779889877754
No 237
>PRK12722 transcriptional activator FlhC; Provisional
Probab=29.80 E-value=46 Score=19.85 Aligned_cols=28 Identities=25% Similarity=0.629 Sum_probs=18.6
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPH 90 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~ 90 (111)
..|..|+..|..... .... .|.|+.|..
T Consensus 135 ~~C~~Cgg~fv~~~~--------e~~~-~f~CplC~~ 162 (187)
T PRK12722 135 SSCNCCGGHFVTHAH--------DPVG-SFVCGLCQP 162 (187)
T ss_pred ccCCCCCCCeecccc--------ccCC-CCcCCCCCC
Confidence 478889888774432 1123 789999874
No 238
>KOG4317|consensus
Probab=29.53 E-value=27 Score=22.66 Aligned_cols=13 Identities=23% Similarity=0.623 Sum_probs=6.3
Q ss_pred cccCccCcccCCc
Q psy12016 54 FSCDVCGKHYKYK 66 (111)
Q Consensus 54 ~~c~~c~~~~~~~ 66 (111)
|+|+.|+..+.+.
T Consensus 20 YtCPRCn~~YCsl 32 (383)
T KOG4317|consen 20 YTCPRCNLLYCSL 32 (383)
T ss_pred ccCCCCCccceee
Confidence 4555555444433
No 239
>PF15616 TerY-C: TerY-C metal binding domain
Probab=29.38 E-value=24 Score=19.69 Aligned_cols=11 Identities=18% Similarity=0.561 Sum_probs=8.3
Q ss_pred ccccCCCCccc
Q psy12016 82 KYECDQCPHRT 92 (111)
Q Consensus 82 ~~~C~~C~~~f 92 (111)
...|++|+..-
T Consensus 105 ~~~CPwCg~~g 115 (131)
T PF15616_consen 105 EVTCPWCGNEG 115 (131)
T ss_pred CEECCCCCCee
Confidence 67899998653
No 240
>KOG1280|consensus
Probab=29.24 E-value=56 Score=21.58 Aligned_cols=27 Identities=22% Similarity=0.442 Sum_probs=15.9
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCC
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQE 80 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~ 80 (111)
|.|++|+..=.....+..|....+.+-
T Consensus 80 ftCPyC~~~Gfte~~f~~Hv~s~Hpda 106 (381)
T KOG1280|consen 80 FTCPYCGIMGFTERQFGTHVLSQHPEA 106 (381)
T ss_pred ccCCcccccccchhHHHHHhhhcCccc
Confidence 566666666555666666655544443
No 241
>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=29.07 E-value=26 Score=14.84 Aligned_cols=11 Identities=18% Similarity=0.770 Sum_probs=6.4
Q ss_pred ccccCCCCccc
Q psy12016 82 KYECDQCPHRT 92 (111)
Q Consensus 82 ~~~C~~C~~~f 92 (111)
.|.|..|+...
T Consensus 24 ~w~C~~C~~~N 34 (40)
T PF04810_consen 24 TWICNFCGTKN 34 (40)
T ss_dssp EEEETTT--EE
T ss_pred EEECcCCCCcC
Confidence 77888887543
No 242
>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=28.78 E-value=43 Score=13.28 Aligned_cols=16 Identities=19% Similarity=0.428 Sum_probs=8.2
Q ss_pred CCceecCCCcccccch
Q psy12016 17 SGMFTCDVCFKEYKYK 32 (111)
Q Consensus 17 ~~~~~C~~C~~~f~~~ 32 (111)
...|.|+.|+..+.+.
T Consensus 11 ~~kY~Cp~C~~~~CSl 26 (30)
T PF04438_consen 11 PAKYRCPRCGARYCSL 26 (30)
T ss_dssp EESEE-TTT--EESSH
T ss_pred CCEEECCCcCCceeCc
Confidence 3457788887766554
No 243
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=28.58 E-value=23 Score=15.87 Aligned_cols=10 Identities=20% Similarity=0.936 Sum_probs=4.4
Q ss_pred cccCCCCccc
Q psy12016 83 YECDQCPHRT 92 (111)
Q Consensus 83 ~~C~~C~~~f 92 (111)
|.|..|++.+
T Consensus 27 f~C~~C~~~l 36 (58)
T PF00412_consen 27 FKCSKCGKPL 36 (58)
T ss_dssp SBETTTTCBT
T ss_pred cccCCCCCcc
Confidence 4444444433
No 244
>PRK12860 transcriptional activator FlhC; Provisional
Probab=28.51 E-value=49 Score=19.75 Aligned_cols=27 Identities=19% Similarity=0.511 Sum_probs=18.0
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCC
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCP 89 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~ 89 (111)
..|..|+..|..... .... .|.|+.|.
T Consensus 135 ~~C~~Cgg~fv~~~~--------e~~~-~f~CplC~ 161 (189)
T PRK12860 135 ARCCRCGGKFVTHAH--------DLRH-NFVCGLCQ 161 (189)
T ss_pred ccCCCCCCCeecccc--------ccCC-CCcCCCCC
Confidence 478889888774422 1123 78899887
No 245
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=28.46 E-value=50 Score=15.04 Aligned_cols=10 Identities=20% Similarity=0.913 Sum_probs=6.7
Q ss_pred ccccCCCCcc
Q psy12016 82 KYECDQCPHR 91 (111)
Q Consensus 82 ~~~C~~C~~~ 91 (111)
.+.|..|+.+
T Consensus 37 R~~CGkCgyT 46 (51)
T COG1998 37 RWACGKCGYT 46 (51)
T ss_pred eeEeccccce
Confidence 4677777743
No 246
>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=27.75 E-value=15 Score=17.90 Aligned_cols=29 Identities=24% Similarity=0.595 Sum_probs=14.3
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcc
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHR 91 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~ 91 (111)
..|..|+........ ..+ . .+.|+.|+..
T Consensus 42 v~Cg~C~~~~~~~~~-------~c~-~-~~~C~~C~~~ 70 (71)
T PF05495_consen 42 VICGKCRTEQPIDEY-------SCG-A-DYFCPICGLY 70 (71)
T ss_dssp EEETTT--EEES-SB-------TT----SEEETTTTEE
T ss_pred eECCCCCCccChhhh-------hcC-C-CccCcCcCCC
Confidence 677777766554432 111 2 5778877644
No 247
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=27.46 E-value=47 Score=15.37 Aligned_cols=18 Identities=17% Similarity=0.285 Sum_probs=10.9
Q ss_pred ccccCCCCcccccchhHH
Q psy12016 82 KYECDQCPHRTKHISSLK 99 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~ 99 (111)
.+-|-+|+..|.+...|.
T Consensus 27 ~~YC~~Cg~~Y~d~~dL~ 44 (55)
T PF13821_consen 27 HNYCFWCGTKYDDEEDLE 44 (55)
T ss_pred CceeeeeCCccCCHHHHH
Confidence 455666666666655554
No 248
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=27.09 E-value=40 Score=13.52 Aligned_cols=12 Identities=25% Similarity=0.742 Sum_probs=7.8
Q ss_pred CceecCCCcccc
Q psy12016 18 GMFTCDVCFKEY 29 (111)
Q Consensus 18 ~~~~C~~C~~~f 29 (111)
+.|.|..|+...
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 357777777654
No 249
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=27.05 E-value=10 Score=22.61 Aligned_cols=7 Identities=43% Similarity=0.923 Sum_probs=4.1
Q ss_pred ecCCCcc
Q psy12016 21 TCDVCFK 27 (111)
Q Consensus 21 ~C~~C~~ 27 (111)
.|+.|+.
T Consensus 16 ~CPvCg~ 22 (201)
T COG1779 16 DCPVCGG 22 (201)
T ss_pred cCCcccc
Confidence 4666665
No 250
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.54 E-value=56 Score=17.68 Aligned_cols=27 Identities=7% Similarity=-0.107 Sum_probs=18.5
Q ss_pred ccCccCcccCCchhhHhhhhhhcCCCCccccCCCCcccc
Q psy12016 55 SCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCPHRTK 93 (111)
Q Consensus 55 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~ 93 (111)
.|+.|++.|.-. ++.|..|++||+.|.
T Consensus 11 idPetg~KFYDL------------NrdPiVsPytG~s~P 37 (129)
T COG4530 11 IDPETGKKFYDL------------NRDPIVSPYTGKSYP 37 (129)
T ss_pred cCccccchhhcc------------CCCccccCcccccch
Confidence 577777776532 123888889998883
No 251
>KOG2747|consensus
Probab=26.52 E-value=34 Score=22.91 Aligned_cols=25 Identities=28% Similarity=0.515 Sum_probs=21.9
Q ss_pred ccccCCCCcccccchhHHHHHHHhh
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKH 106 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~ 106 (111)
.|.|+.|-+.+.+...|.+|+..+.
T Consensus 158 lYiCEfCLkY~~s~~~l~rH~~kC~ 182 (396)
T KOG2747|consen 158 LYICEFCLKYMKSRTSLQRHLKKCK 182 (396)
T ss_pred EEEehHHHhHhchHHHHHHHHHhcC
Confidence 6889999999999999999988765
No 252
>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=26.44 E-value=44 Score=13.44 Aligned_cols=11 Identities=18% Similarity=0.830 Sum_probs=5.9
Q ss_pred ceecCCCcccc
Q psy12016 19 MFTCDVCFKEY 29 (111)
Q Consensus 19 ~~~C~~C~~~f 29 (111)
.|.|..|+...
T Consensus 4 ~ykC~~CGniv 14 (34)
T cd00974 4 VYKCEICGNIV 14 (34)
T ss_pred EEEcCCCCcEE
Confidence 35566665543
No 253
>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=26.41 E-value=33 Score=14.49 Aligned_cols=12 Identities=33% Similarity=0.703 Sum_probs=8.5
Q ss_pred eecCCCcccccc
Q psy12016 20 FTCDVCFKEYKY 31 (111)
Q Consensus 20 ~~C~~C~~~f~~ 31 (111)
+.|+.||..+..
T Consensus 33 ~~C~~CGE~~~~ 44 (46)
T TIGR03831 33 LVCPQCGEEYLD 44 (46)
T ss_pred cccccCCCEeeC
Confidence 568889876643
No 254
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.26 E-value=77 Score=24.99 Aligned_cols=9 Identities=33% Similarity=0.608 Sum_probs=6.9
Q ss_pred eecCCCccc
Q psy12016 20 FTCDVCFKE 28 (111)
Q Consensus 20 ~~C~~C~~~ 28 (111)
+.|+.|+..
T Consensus 668 rkCPkCG~~ 676 (1337)
T PRK14714 668 RRCPSCGTE 676 (1337)
T ss_pred EECCCCCCc
Confidence 678888864
No 255
>KOG1994|consensus
Probab=26.02 E-value=31 Score=21.23 Aligned_cols=20 Identities=30% Similarity=0.489 Sum_probs=17.8
Q ss_pred ccccCCCCcccccchhHHHH
Q psy12016 82 KYECDQCPHRTKHISSLKKH 101 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H 101 (111)
.|.|-+||-.|.....|-.|
T Consensus 239 h~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 239 HYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred ceEEEEeccccCCHHHHHHh
Confidence 79999999999998888776
No 256
>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=25.77 E-value=19 Score=18.83 Aligned_cols=14 Identities=29% Similarity=0.664 Sum_probs=11.0
Q ss_pred CceecCCCcccccc
Q psy12016 18 GMFTCDVCFKEYKY 31 (111)
Q Consensus 18 ~~~~C~~C~~~f~~ 31 (111)
..+.|+.|+..+..
T Consensus 15 ~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 15 GVYVCPSCGYEKEK 28 (104)
T ss_pred CeEECcCCCCcccc
Confidence 46889999977665
No 257
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=25.46 E-value=40 Score=17.79 Aligned_cols=11 Identities=27% Similarity=0.757 Sum_probs=6.2
Q ss_pred cccCccCcccC
Q psy12016 54 FSCDVCGKHYK 64 (111)
Q Consensus 54 ~~c~~c~~~~~ 64 (111)
..|..||..+.
T Consensus 43 ~~C~~CG~y~~ 53 (99)
T PRK14892 43 ITCGNCGLYTE 53 (99)
T ss_pred EECCCCCCccC
Confidence 46666665443
No 258
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.28 E-value=41 Score=17.94 Aligned_cols=12 Identities=17% Similarity=0.564 Sum_probs=7.7
Q ss_pred ceecCCCccccc
Q psy12016 19 MFTCDVCFKEYK 30 (111)
Q Consensus 19 ~~~C~~C~~~f~ 30 (111)
...|+.||..|.
T Consensus 49 ~t~CP~Cg~~~e 60 (115)
T COG1885 49 STSCPKCGEPFE 60 (115)
T ss_pred cccCCCCCCccc
Confidence 456777776654
No 259
>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=24.19 E-value=60 Score=17.63 Aligned_cols=9 Identities=44% Similarity=1.161 Sum_probs=5.8
Q ss_pred cccCccCcc
Q psy12016 54 FSCDVCGKH 62 (111)
Q Consensus 54 ~~c~~c~~~ 62 (111)
..|+.|++.
T Consensus 70 V~CP~C~K~ 78 (114)
T PF11023_consen 70 VECPNCGKQ 78 (114)
T ss_pred eECCCCCCh
Confidence 567777654
No 260
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=23.96 E-value=41 Score=22.28 Aligned_cols=22 Identities=18% Similarity=0.344 Sum_probs=19.1
Q ss_pred ceecCCCcccccchhHHHHHHh
Q psy12016 19 MFTCDVCFKEYKYKRGLVRHKK 40 (111)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~ 40 (111)
-+.|..|++.|.....+..|..
T Consensus 238 ~~YC~~C~r~f~~~~VFe~Hl~ 259 (470)
T COG5188 238 KVYCVKCGREFSRSKVFEYHLE 259 (470)
T ss_pred ceeeHhhhhHhhhhHHHHHHHh
Confidence 4679999999999999988874
No 261
>PLN03239 histone acetyltransferase; Provisional
Probab=23.94 E-value=61 Score=21.41 Aligned_cols=23 Identities=22% Similarity=0.135 Sum_probs=19.3
Q ss_pred ccccCCCCcccccchhHHHHHHH
Q psy12016 82 KYECDQCPHRTKHISSLKKHMAL 104 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~ 104 (111)
-|.|+.|-+.|.....|.+|+..
T Consensus 106 lYiCE~Clky~~~~~~l~~H~~~ 128 (351)
T PLN03239 106 LYVCEFSFGFFARKSELLRFQAK 128 (351)
T ss_pred EEEeccchhhhcCHHHHHHHHHh
Confidence 78899999888888888888753
No 262
>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=23.80 E-value=51 Score=12.85 Aligned_cols=6 Identities=50% Similarity=1.437 Sum_probs=2.6
Q ss_pred cCCCCc
Q psy12016 85 CDQCPH 90 (111)
Q Consensus 85 C~~C~~ 90 (111)
|..|++
T Consensus 3 C~~C~~ 8 (30)
T PF03107_consen 3 CDVCRR 8 (30)
T ss_pred CCCCCC
Confidence 444443
No 263
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=23.50 E-value=55 Score=22.35 Aligned_cols=14 Identities=21% Similarity=0.320 Sum_probs=10.2
Q ss_pred CceecCCCcccccc
Q psy12016 18 GMFTCDVCFKEYKY 31 (111)
Q Consensus 18 ~~~~C~~C~~~f~~ 31 (111)
..|.|..||.....
T Consensus 6 t~f~C~~CG~~s~K 19 (456)
T COG1066 6 TAFVCQECGYVSPK 19 (456)
T ss_pred cEEEcccCCCCCcc
Confidence 46889999976543
No 264
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.45 E-value=46 Score=21.07 Aligned_cols=9 Identities=22% Similarity=0.973 Sum_probs=4.5
Q ss_pred ccccCCCCc
Q psy12016 82 KYECDQCPH 90 (111)
Q Consensus 82 ~~~C~~C~~ 90 (111)
.+.|+.||.
T Consensus 322 ~~~C~~cg~ 330 (364)
T COG0675 322 LFKCPRCGF 330 (364)
T ss_pred eEECCCCCC
Confidence 445555553
No 265
>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=23.45 E-value=74 Score=13.04 Aligned_cols=24 Identities=21% Similarity=0.361 Sum_probs=12.1
Q ss_pred ccccCCCCcccccchhHHHHHHHhh
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKH 106 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~ 106 (111)
.+.|+.|++.... +-+..|+....
T Consensus 4 ~~~C~nC~R~v~a-~RfA~HLekCm 27 (33)
T PF08209_consen 4 YVECPNCGRPVAA-SRFAPHLEKCM 27 (33)
T ss_dssp EEE-TTTSSEEEG-GGHHHHHHHHT
T ss_pred eEECCCCcCCcch-hhhHHHHHHHH
Confidence 4567777765433 34455655443
No 266
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=23.45 E-value=54 Score=20.67 Aligned_cols=28 Identities=29% Similarity=0.763 Sum_probs=18.7
Q ss_pred cccCccCcccCCchhhHhhhhhhcCCCCccccCCCC
Q psy12016 54 FSCDVCGKHYKYKKGLGRHKRYECGQEPKYECDQCP 89 (111)
Q Consensus 54 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~ 89 (111)
-.|+.||..-.....+ ++-- .|+|+.|.
T Consensus 221 r~CP~Cg~~W~L~~pl-------h~iF-dFKCD~CR 248 (258)
T PF10071_consen 221 RKCPSCGGDWRLKEPL-------HDIF-DFKCDPCR 248 (258)
T ss_pred CCCCCCCCccccCCch-------hhce-eccCCcce
Confidence 4789998876655444 1223 78898885
No 267
>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=23.08 E-value=59 Score=17.30 Aligned_cols=10 Identities=20% Similarity=0.414 Sum_probs=6.0
Q ss_pred ceecCCCccc
Q psy12016 19 MFTCDVCFKE 28 (111)
Q Consensus 19 ~~~C~~C~~~ 28 (111)
|-.|+.|+..
T Consensus 2 p~~CpYCg~~ 11 (102)
T PF11672_consen 2 PIICPYCGGP 11 (102)
T ss_pred CcccCCCCCe
Confidence 4557777653
No 268
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=23.03 E-value=35 Score=21.91 Aligned_cols=37 Identities=30% Similarity=0.577 Sum_probs=20.3
Q ss_pred ccccCccCcccCCchhhHhhhhhhcCCCC---ccccCCCCcccc
Q psy12016 53 LFSCDVCGKHYKYKKGLGRHKRYECGQEP---KYECDQCPHRTK 93 (111)
Q Consensus 53 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~---~~~C~~C~~~f~ 93 (111)
.+.|+.|+..=.....++ +...+++ -|.|..|+..|.
T Consensus 258 ~~~C~~C~~~~~~~~q~Q----trsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQ----TRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccCCCCCCccceEEEec----ccCCCCCCeEEEEcCCCCCeee
Confidence 379999985433332222 2222231 367988987654
No 269
>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=22.71 E-value=65 Score=14.42 Aligned_cols=8 Identities=38% Similarity=1.360 Sum_probs=2.6
Q ss_pred cccCccCc
Q psy12016 54 FSCDVCGK 61 (111)
Q Consensus 54 ~~c~~c~~ 61 (111)
|.|+.|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 66666653
No 270
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=22.56 E-value=43 Score=22.16 Aligned_cols=26 Identities=23% Similarity=0.271 Sum_probs=22.0
Q ss_pred ccccCCCCcccccchhHHHHHHHhhC
Q psy12016 82 KYECDQCPHRTKHISSLKKHMALKHG 107 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~~~ 107 (111)
.|.|+.|-+.|.+...|.+|.+.+.-
T Consensus 158 vyICefClkY~~s~~~~~rH~~kC~~ 183 (395)
T COG5027 158 VYICEFCLKYYGSQTSLVRHRKKCSL 183 (395)
T ss_pred EEEhhhhHHHhcchhHHHHHHhcCcC
Confidence 67899999999999999999887653
No 271
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=22.40 E-value=49 Score=15.48 Aligned_cols=16 Identities=19% Similarity=0.198 Sum_probs=9.3
Q ss_pred CCceecCCCcccccch
Q psy12016 17 SGMFTCDVCFKEYKYK 32 (111)
Q Consensus 17 ~~~~~C~~C~~~f~~~ 32 (111)
+..+.|-.|+..+...
T Consensus 9 ~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 9 SNLWLCLTCGYVGCGR 24 (63)
T ss_dssp SSEEEETTTS-EEETT
T ss_pred CceEEeCCCCcccccC
Confidence 4456677777666654
No 272
>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=22.30 E-value=54 Score=14.96 Aligned_cols=16 Identities=13% Similarity=0.295 Sum_probs=9.1
Q ss_pred CCCceecCCCcccccc
Q psy12016 16 DSGMFTCDVCFKEYKY 31 (111)
Q Consensus 16 ~~~~~~C~~C~~~f~~ 31 (111)
....+.|..|++.+..
T Consensus 32 ~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 32 EPIKLRCHYCERIITE 47 (52)
T ss_dssp TTCEEEETTT--EEEH
T ss_pred CCCEEEeeCCCCEecc
Confidence 4455778888776654
No 273
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=22.27 E-value=84 Score=15.12 Aligned_cols=13 Identities=31% Similarity=0.337 Sum_probs=8.2
Q ss_pred HHHHHHHhhCCCC
Q psy12016 98 LKKHMALKHGVES 110 (111)
Q Consensus 98 l~~H~~~~~~ek~ 110 (111)
+..|++.+|.++|
T Consensus 28 Yv~H~~~~HP~~p 40 (65)
T PF04328_consen 28 YVEHMRRHHPDEP 40 (65)
T ss_pred HHHHHHHHCcCCC
Confidence 3457777776655
No 274
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=22.25 E-value=48 Score=14.19 Aligned_cols=7 Identities=29% Similarity=0.529 Sum_probs=3.7
Q ss_pred eecCCCc
Q psy12016 20 FTCDVCF 26 (111)
Q Consensus 20 ~~C~~C~ 26 (111)
..|+.|+
T Consensus 3 ~~Cp~Cg 9 (47)
T PF14690_consen 3 PRCPHCG 9 (47)
T ss_pred ccCCCcC
Confidence 4455555
No 275
>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 PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=21.73 E-value=37 Score=15.75 Aligned_cols=8 Identities=25% Similarity=0.845 Sum_probs=3.6
Q ss_pred cCCCCccc
Q psy12016 85 CDQCPHRT 92 (111)
Q Consensus 85 C~~C~~~f 92 (111)
|..|+..|
T Consensus 8 C~~Cg~~~ 15 (54)
T PF14446_consen 8 CPVCGKKF 15 (54)
T ss_pred ChhhCCcc
Confidence 44444444
No 277
>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=21.54 E-value=1.2e+02 Score=16.21 Aligned_cols=21 Identities=19% Similarity=0.263 Sum_probs=15.7
Q ss_pred ceecCCCcccccchhHHHHHH
Q psy12016 19 MFTCDVCFKEYKYKRGLVRHK 39 (111)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~ 39 (111)
-+.|+.||..+........-.
T Consensus 31 ~~~C~~CGe~~~~~e~~~~~~ 51 (127)
T TIGR03830 31 GWYCPACGEELLDPEESKRNS 51 (127)
T ss_pred eeECCCCCCEEEcHHHHHHHH
Confidence 367999999888877665443
No 278
>KOG2857|consensus
Probab=21.43 E-value=51 Score=18.71 Aligned_cols=22 Identities=23% Similarity=0.375 Sum_probs=19.9
Q ss_pred ceecCCCcccccchhHHHHHHh
Q psy12016 19 MFTCDVCFKEYKYKRGLVRHKK 40 (111)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~ 40 (111)
-|.|+.|.-.+++-.-++.|..
T Consensus 17 KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 17 KYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hccCCCCCCccccchhhhhccC
Confidence 5999999999999999998865
No 279
>COG5595 Zn-ribbon-containing, possibly nucleic-acid-binding protein [General function prediction only]
Probab=21.25 E-value=35 Score=20.54 Aligned_cols=14 Identities=29% Similarity=0.691 Sum_probs=7.3
Q ss_pred ecCCCcccccchhH
Q psy12016 21 TCDVCFKEYKYKRG 34 (111)
Q Consensus 21 ~C~~C~~~f~~~~~ 34 (111)
.|+.|++.+..+..
T Consensus 220 ~CPsC~k~Wqlk~~ 233 (256)
T COG5595 220 CCPSCGKDWQLKNP 233 (256)
T ss_pred CCCcccccceeccc
Confidence 45666655544443
No 280
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=20.88 E-value=51 Score=15.10 Aligned_cols=9 Identities=22% Similarity=0.726 Sum_probs=5.4
Q ss_pred ccCCCCccc
Q psy12016 84 ECDQCPHRT 92 (111)
Q Consensus 84 ~C~~C~~~f 92 (111)
.|+.||..+
T Consensus 2 ~CPyCge~~ 10 (52)
T PF14255_consen 2 QCPYCGEPI 10 (52)
T ss_pred CCCCCCCee
Confidence 466666554
No 281
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=20.83 E-value=49 Score=13.48 Aligned_cols=11 Identities=27% Similarity=0.770 Sum_probs=7.2
Q ss_pred cccCccCcccC
Q psy12016 54 FSCDVCGKHYK 64 (111)
Q Consensus 54 ~~c~~c~~~~~ 64 (111)
+.|..|+..|+
T Consensus 22 ~~C~~Cg~~~~ 32 (33)
T PF08792_consen 22 EVCIFCGSSFP 32 (33)
T ss_pred EEcccCCcEee
Confidence 56777776653
No 282
>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=20.69 E-value=59 Score=17.51 Aligned_cols=11 Identities=27% Similarity=0.942 Sum_probs=4.9
Q ss_pred eecCCCccccc
Q psy12016 20 FTCDVCFKEYK 30 (111)
Q Consensus 20 ~~C~~C~~~f~ 30 (111)
|.|++|+..+.
T Consensus 20 ~iCpeC~~EW~ 30 (109)
T TIGR00686 20 LICPSCLYEWN 30 (109)
T ss_pred eECcccccccc
Confidence 44444444443
No 283
>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=20.65 E-value=57 Score=13.91 Aligned_cols=9 Identities=33% Similarity=0.874 Sum_probs=4.3
Q ss_pred cccCccCcc
Q psy12016 54 FSCDVCGKH 62 (111)
Q Consensus 54 ~~c~~c~~~ 62 (111)
+.|..||..
T Consensus 20 ~vC~~CG~V 28 (43)
T PF08271_consen 20 LVCPNCGLV 28 (43)
T ss_dssp EEETTT-BB
T ss_pred EECCCCCCE
Confidence 455555543
No 284
>PF12773 DZR: Double zinc ribbon
Probab=20.63 E-value=89 Score=13.60 Aligned_cols=7 Identities=43% Similarity=1.165 Sum_probs=3.2
Q ss_pred ccCccCc
Q psy12016 55 SCDVCGK 61 (111)
Q Consensus 55 ~c~~c~~ 61 (111)
.|+.|+.
T Consensus 31 ~C~~Cg~ 37 (50)
T PF12773_consen 31 ICPNCGA 37 (50)
T ss_pred CCcCCcC
Confidence 4444443
No 285
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=20.57 E-value=21 Score=15.76 Aligned_cols=6 Identities=33% Similarity=0.656 Sum_probs=2.8
Q ss_pred CCcccc
Q psy12016 88 CPHRTK 93 (111)
Q Consensus 88 C~~~f~ 93 (111)
||..|.
T Consensus 33 Cg~tfv 38 (47)
T PF04606_consen 33 CGHTFV 38 (47)
T ss_pred CCCEEE
Confidence 554443
No 286
>KOG3362|consensus
Probab=20.51 E-value=39 Score=19.21 Aligned_cols=20 Identities=35% Similarity=0.737 Sum_probs=9.4
Q ss_pred ccccCCCCcccccchhHHHH
Q psy12016 82 KYECDQCPHRTKHISSLKKH 101 (111)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H 101 (111)
+|.|.-||-.+.+..-+..|
T Consensus 129 ~ysC~~CG~kyCsv~C~~~H 148 (156)
T KOG3362|consen 129 KYSCVNCGTKYCSVRCLKTH 148 (156)
T ss_pred hhHHHhcCCceeechhhhhc
Confidence 34454555444444444444
No 287
>KOG2636|consensus
Probab=20.31 E-value=94 Score=21.42 Aligned_cols=23 Identities=26% Similarity=0.560 Sum_probs=13.7
Q ss_pred CCceecCCCc-ccccchhHHHHHH
Q psy12016 17 SGMFTCDVCF-KEYKYKRGLVRHK 39 (111)
Q Consensus 17 ~~~~~C~~C~-~~f~~~~~l~~h~ 39 (111)
...|.|.+|| +++.-...+.+|-
T Consensus 399 ~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 399 DIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred CcccceeeccCccccCcHHHHHHh
Confidence 3446677776 5555556666664
Done!