Query psy5652
Match_columns 92
No_of_seqs 107 out of 1522
Neff 11.4
Searched_HMMs 46136
Date Fri Aug 16 23:11:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5652.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5652hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 3.4E-24 7.4E-29 119.3 3.6 89 1-92 131-243 (279)
2 KOG2462|consensus 99.9 9.7E-23 2.1E-27 113.6 3.9 76 1-83 188-263 (279)
3 KOG3576|consensus 99.7 2.1E-19 4.6E-24 97.0 -2.0 81 1-88 118-198 (267)
4 KOG3623|consensus 99.7 8.7E-18 1.9E-22 104.1 -0.7 76 1-83 895-970 (1007)
5 KOG3623|consensus 99.5 6.2E-15 1.4E-19 91.8 -0.6 83 1-83 241-329 (1007)
6 PHA00733 hypothetical protein 99.4 5.7E-13 1.2E-17 68.7 4.4 83 2-88 42-124 (128)
7 PHA02768 hypothetical protein; 99.3 2.2E-12 4.7E-17 56.6 1.9 43 35-79 5-47 (55)
8 KOG3576|consensus 99.2 6.3E-12 1.4E-16 68.5 2.7 79 2-87 147-236 (267)
9 KOG3608|consensus 99.2 2.5E-11 5.4E-16 70.9 3.3 83 2-91 265-349 (467)
10 KOG1074|consensus 99.2 2.2E-12 4.8E-17 81.5 -1.1 80 2-89 607-693 (958)
11 KOG3608|consensus 99.1 1.4E-11 3E-16 71.9 0.5 60 26-88 256-316 (467)
12 PF13465 zf-H2C2_2: Zinc-finge 99.0 2.4E-10 5.1E-15 43.3 2.2 26 50-75 1-26 (26)
13 KOG1074|consensus 99.0 2E-10 4.3E-15 73.0 2.3 54 36-90 880-933 (958)
14 PHA02768 hypothetical protein; 98.8 1.5E-10 3.3E-15 50.8 -1.5 42 1-51 6-47 (55)
15 KOG3993|consensus 98.8 1.2E-09 2.6E-14 65.2 -0.2 80 1-88 268-380 (500)
16 PHA00616 hypothetical protein 98.7 1.1E-08 2.3E-13 43.0 1.8 34 35-68 1-34 (44)
17 PLN03086 PRLI-interacting fact 98.7 1.9E-08 4.1E-13 62.7 3.5 61 2-74 455-515 (567)
18 PHA00616 hypothetical protein 98.7 1E-08 2.2E-13 43.1 1.6 29 63-92 1-29 (44)
19 PLN03086 PRLI-interacting fact 98.6 1.3E-07 2.8E-12 59.1 4.6 77 1-88 479-565 (567)
20 PHA00732 hypothetical protein 98.5 9.2E-08 2E-12 45.5 2.7 44 1-57 2-46 (79)
21 PHA00733 hypothetical protein 98.5 1.6E-07 3.5E-12 48.6 2.7 50 1-59 74-123 (128)
22 PF05605 zf-Di19: Drought indu 98.4 2.1E-06 4.5E-11 38.0 4.5 50 35-87 2-53 (54)
23 PF00096 zf-C2H2: Zinc finger, 98.3 1.3E-06 2.8E-11 31.8 2.4 20 37-56 2-21 (23)
24 PF00096 zf-C2H2: Zinc finger, 98.1 2.2E-06 4.8E-11 31.1 1.8 23 64-87 1-23 (23)
25 KOG3993|consensus 98.1 2.3E-06 4.9E-11 51.7 1.9 59 1-59 296-380 (500)
26 PF05605 zf-Di19: Drought indu 98.1 2E-06 4.3E-11 38.0 1.2 49 1-58 3-52 (54)
27 PF13465 zf-H2C2_2: Zinc-finge 98.1 8.5E-08 1.8E-12 36.2 -2.8 21 26-46 5-25 (26)
28 PHA00732 hypothetical protein 97.9 3.5E-06 7.7E-11 40.1 0.5 43 35-83 1-44 (79)
29 PF13894 zf-C2H2_4: C2H2-type 97.9 2.6E-05 5.7E-10 28.2 2.6 19 65-83 2-20 (24)
30 PF12756 zf-C2H2_2: C2H2 type 97.8 2.6E-05 5.7E-10 38.3 3.0 19 2-20 1-19 (100)
31 PF13912 zf-C2H2_6: C2H2-type 97.8 1.5E-05 3.3E-10 30.0 1.4 21 36-56 2-22 (27)
32 PF13894 zf-C2H2_4: C2H2-type 97.8 4.1E-05 8.9E-10 27.7 2.4 23 36-58 1-23 (24)
33 PF13912 zf-C2H2_6: C2H2-type 97.7 2.4E-05 5.2E-10 29.5 1.4 25 63-88 1-25 (27)
34 smart00355 ZnF_C2H2 zinc finge 97.5 0.00019 4.2E-09 26.2 2.6 19 65-83 2-20 (26)
35 PF09237 GAGA: GAGA factor; I 97.5 0.00018 3.8E-09 31.1 2.6 33 31-63 20-52 (54)
36 smart00355 ZnF_C2H2 zinc finge 97.5 0.0002 4.3E-09 26.1 2.6 24 36-59 1-24 (26)
37 PF09237 GAGA: GAGA factor; I 97.4 0.00082 1.8E-08 29.1 4.1 33 59-92 20-52 (54)
38 PRK04860 hypothetical protein; 97.4 0.00021 4.6E-09 38.4 2.6 39 34-76 118-156 (160)
39 PF12171 zf-C2H2_jaz: Zinc-fin 97.2 0.00015 3.2E-09 27.3 0.7 20 1-20 2-21 (27)
40 COG5189 SFP1 Putative transcri 97.1 0.00014 3E-09 43.0 0.4 20 1-20 350-371 (423)
41 PF12874 zf-met: Zinc-finger o 97.1 0.00051 1.1E-08 25.2 1.6 20 37-56 2-21 (25)
42 COG5189 SFP1 Putative transcri 97.0 0.00013 2.8E-09 43.0 -0.3 51 33-83 347-418 (423)
43 PF13909 zf-H2C2_5: C2H2-type 96.4 0.0058 1.3E-07 22.1 2.3 19 64-83 1-19 (24)
44 PF13913 zf-C2HC_2: zinc-finge 96.4 0.0052 1.1E-07 22.7 2.1 20 36-56 3-22 (25)
45 cd00350 rubredoxin_like Rubred 95.2 0.015 3.2E-07 22.9 1.3 24 36-71 2-25 (33)
46 KOG2186|consensus 95.1 0.012 2.5E-07 34.0 1.2 46 35-83 3-48 (276)
47 PRK04860 hypothetical protein; 95.0 0.0038 8.3E-08 33.7 -0.8 37 1-48 120-156 (160)
48 KOG2893|consensus 94.8 0.0078 1.7E-07 34.5 -0.1 39 40-82 15-53 (341)
49 COG2888 Predicted Zn-ribbon RN 94.5 0.039 8.4E-07 24.7 1.8 33 34-71 26-58 (61)
50 smart00451 ZnF_U1 U1-like zinc 94.5 0.051 1.1E-06 21.3 2.1 21 63-83 3-23 (35)
51 PF13717 zinc_ribbon_4: zinc-r 94.3 0.033 7.1E-07 22.4 1.3 32 2-45 4-35 (36)
52 PF09986 DUF2225: Uncharacteri 94.3 0.03 6.5E-07 31.7 1.5 48 1-48 6-61 (214)
53 PF12756 zf-C2H2_2: C2H2 type 93.9 0.084 1.8E-06 25.6 2.6 25 35-59 50-74 (100)
54 TIGR02098 MJ0042_CXXC MJ0042 f 93.8 0.035 7.5E-07 22.4 0.9 14 2-15 4-17 (38)
55 COG5048 FOG: Zn-finger [Genera 93.8 0.031 6.7E-07 34.0 1.1 59 2-67 291-355 (467)
56 COG4049 Uncharacterized protei 93.5 0.049 1.1E-06 24.1 1.2 26 31-56 13-38 (65)
57 PF13719 zinc_ribbon_5: zinc-r 93.5 0.047 1E-06 22.1 1.0 14 2-15 4-17 (37)
58 KOG2893|consensus 93.3 0.0077 1.7E-07 34.5 -1.9 43 3-56 13-55 (341)
59 COG5048 FOG: Zn-finger [Genera 93.2 0.0099 2.1E-07 36.1 -1.7 57 34-91 288-350 (467)
60 PF09538 FYDLN_acid: Protein o 93.2 0.14 3E-06 26.0 2.6 30 36-76 10-39 (108)
61 PRK14890 putative Zn-ribbon RN 93.1 0.22 4.7E-06 22.4 2.9 34 33-71 23-56 (59)
62 KOG1146|consensus 91.8 0.093 2E-06 37.0 1.3 22 1-22 466-487 (1406)
63 KOG1146|consensus 91.6 0.18 3.8E-06 35.7 2.4 54 31-84 461-539 (1406)
64 cd00729 rubredoxin_SM Rubredox 91.6 0.16 3.4E-06 20.2 1.4 25 35-71 2-26 (34)
65 smart00531 TFIIE Transcription 91.5 0.098 2.1E-06 27.9 0.9 38 32-73 96-133 (147)
66 COG1198 PriA Primosomal protei 91.4 0.21 4.6E-06 33.4 2.5 12 33-44 473-484 (730)
67 TIGR00373 conserved hypothetic 91.2 0.24 5.2E-06 26.8 2.3 34 31-73 105-138 (158)
68 COG1592 Rubrerythrin [Energy p 91.2 0.2 4.4E-06 27.4 2.0 25 34-71 133-157 (166)
69 PHA00626 hypothetical protein 91.1 0.31 6.8E-06 21.6 2.1 14 34-47 22-35 (59)
70 PRK00398 rpoP DNA-directed RNA 90.5 0.19 4E-06 21.3 1.2 11 35-45 21-31 (46)
71 PF09723 Zn-ribbon_8: Zinc rib 90.3 0.14 3E-06 21.3 0.7 15 1-15 6-20 (42)
72 PRK00464 nrdR transcriptional 90.2 0.29 6.3E-06 26.4 2.0 17 34-50 27-43 (154)
73 PRK06266 transcription initiat 89.4 0.38 8.2E-06 26.6 2.1 34 32-74 114-147 (178)
74 PRK09678 DNA-binding transcrip 89.3 0.26 5.6E-06 23.1 1.2 40 1-49 2-43 (72)
75 PF07754 DUF1610: Domain of un 88.4 0.8 1.7E-05 16.7 2.0 9 34-42 15-23 (24)
76 TIGR02300 FYDLN_acid conserved 88.3 0.41 8.9E-06 25.0 1.6 14 35-48 26-39 (129)
77 PF02892 zf-BED: BED zinc fing 88.3 0.68 1.5E-05 19.2 2.1 22 63-84 16-41 (45)
78 cd00730 rubredoxin Rubredoxin; 88.1 0.83 1.8E-05 19.8 2.3 13 1-13 2-14 (50)
79 KOG4173|consensus 87.8 0.15 3.3E-06 28.8 -0.1 51 37-87 108-170 (253)
80 TIGR02605 CxxC_CxxC_SSSS putat 87.8 0.27 5.9E-06 21.2 0.7 13 1-13 6-18 (52)
81 PF04959 ARS2: Arsenite-resist 86.9 0.5 1.1E-05 27.0 1.6 24 64-87 78-101 (214)
82 smart00614 ZnF_BED BED zinc fi 86.6 0.9 1.9E-05 19.5 2.0 10 36-45 19-28 (50)
83 smart00659 RPOLCX RNA polymera 85.7 0.76 1.6E-05 19.4 1.5 10 36-45 3-12 (44)
84 PF00301 Rubredoxin: Rubredoxi 85.0 0.55 1.2E-05 20.1 0.9 15 1-15 2-16 (47)
85 TIGR00595 priA primosomal prot 84.1 1.3 2.9E-05 28.5 2.7 10 34-43 252-261 (505)
86 KOG2593|consensus 84.1 0.5 1.1E-05 29.7 0.8 19 34-52 127-145 (436)
87 PF08790 zf-LYAR: LYAR-type C2 83.9 0.27 5.8E-06 18.7 -0.2 18 1-19 1-18 (28)
88 PRK14873 primosome assembly pr 83.4 1.2 2.6E-05 29.8 2.3 10 35-44 422-431 (665)
89 COG1773 Rubredoxin [Energy pro 82.4 1.8 3.9E-05 19.2 2.0 15 1-15 4-18 (55)
90 smart00734 ZnF_Rad18 Rad18-lik 82.3 2 4.3E-05 15.8 1.9 18 37-55 3-20 (26)
91 KOG2186|consensus 79.8 0.48 1E-05 27.7 -0.3 50 1-60 4-53 (276)
92 PF10571 UPF0547: Uncharacteri 79.1 1.1 2.3E-05 16.6 0.7 8 3-10 17-24 (26)
93 PF01096 TFIIS_C: Transcriptio 77.9 1.8 3.8E-05 17.6 1.2 36 1-45 1-38 (39)
94 TIGR03831 YgiT_finger YgiT-typ 77.3 0.89 1.9E-05 18.8 0.2 14 34-47 31-44 (46)
95 PF14446 Prok-RING_1: Prokaryo 77.0 1.3 2.9E-05 19.6 0.7 16 2-17 7-22 (54)
96 smart00834 CxxC_CXXC_SSSS Puta 76.9 0.86 1.9E-05 18.4 0.1 13 1-13 6-18 (41)
97 COG0068 HypF Hydrogenase matur 76.6 0.91 2E-05 30.5 0.2 31 37-73 153-183 (750)
98 PF03811 Zn_Tnp_IS1: InsA N-te 76.6 3.6 7.8E-05 16.5 1.9 14 28-41 22-35 (36)
99 PF04959 ARS2: Arsenite-resist 76.4 3.1 6.6E-05 23.9 2.2 26 32-57 74-99 (214)
100 KOG3408|consensus 75.5 2.4 5.3E-05 22.0 1.5 25 33-57 55-79 (129)
101 PRK05580 primosome assembly pr 75.4 3.8 8.2E-05 27.6 2.7 11 34-44 420-430 (679)
102 PF13878 zf-C2H2_3: zinc-finge 75.3 1.4 3E-05 18.2 0.5 10 3-12 16-25 (41)
103 smart00661 RPOL9 RNA polymeras 75.2 4.3 9.4E-05 17.2 2.2 12 35-46 20-31 (52)
104 PF15269 zf-C2H2_7: Zinc-finge 75.2 2.9 6.4E-05 17.7 1.5 20 64-83 21-40 (54)
105 COG1997 RPL43A Ribosomal prote 75.0 2.9 6.3E-05 20.4 1.6 30 35-74 35-64 (89)
106 TIGR00622 ssl1 transcription f 75.0 5 0.00011 20.6 2.6 84 2-88 17-105 (112)
107 PF08274 PhnA_Zn_Ribbon: PhnA 74.7 1.6 3.5E-05 16.8 0.6 9 34-42 18-26 (30)
108 smart00440 ZnF_C2C2 C2C2 Zinc 74.4 5 0.00011 16.4 2.1 12 34-45 27-38 (40)
109 COG1198 PriA Primosomal protei 74.0 3.4 7.4E-05 28.1 2.3 47 3-72 438-484 (730)
110 PF05443 ROS_MUCR: ROS/MUCR tr 73.6 2.6 5.7E-05 22.3 1.4 24 35-61 72-95 (132)
111 COG4530 Uncharacterized protei 73.0 2.8 6E-05 21.4 1.4 14 34-47 25-38 (129)
112 PF01286 XPA_N: XPA protein N- 73.0 1.6 3.5E-05 17.3 0.4 16 2-17 5-20 (34)
113 smart00132 LIM Zinc-binding do 72.1 4.8 0.0001 15.5 1.8 12 2-13 1-12 (39)
114 PF10083 DUF2321: Uncharacteri 71.7 3.5 7.5E-05 22.5 1.6 17 34-50 67-83 (158)
115 PF04606 Ogr_Delta: Ogr/Delta- 71.4 1.4 3.1E-05 18.7 0.1 14 2-15 1-14 (47)
116 TIGR03830 CxxCG_CxxCG_HTH puta 71.1 3.5 7.5E-05 21.1 1.5 22 32-53 28-49 (127)
117 COG4306 Uncharacterized protei 70.4 5.1 0.00011 21.0 2.0 42 2-49 41-82 (160)
118 COG1996 RPC10 DNA-directed RNA 70.1 2.1 4.7E-05 18.5 0.5 10 1-10 7-16 (49)
119 PF12013 DUF3505: Protein of u 70.0 7 0.00015 19.6 2.5 23 36-58 81-107 (109)
120 KOG1842|consensus 69.6 3.4 7.3E-05 26.4 1.5 26 34-59 14-39 (505)
121 PF04423 Rad50_zn_hook: Rad50 68.7 1.7 3.6E-05 19.0 0.0 9 38-46 23-31 (54)
122 PF06524 NOA36: NOA36 protein; 68.7 1.2 2.6E-05 26.3 -0.5 23 61-83 207-229 (314)
123 COG1779 C4-type Zn-finger prot 68.3 2.4 5.1E-05 24.0 0.6 35 2-46 16-54 (201)
124 COG3677 Transposase and inacti 67.9 2.4 5.3E-05 22.3 0.6 17 1-17 54-70 (129)
125 PTZ00255 60S ribosomal protein 67.5 3.2 7E-05 20.4 0.9 12 63-74 54-65 (90)
126 PF14353 CpXC: CpXC protein 67.5 2.3 4.9E-05 22.1 0.4 18 1-18 39-56 (128)
127 PF09963 DUF2197: Uncharacteri 67.4 1.1 2.4E-05 19.9 -0.6 36 2-43 4-39 (56)
128 TIGR01206 lysW lysine biosynth 67.3 3.1 6.8E-05 18.4 0.8 30 1-45 3-32 (54)
129 PF04780 DUF629: Protein of un 67.1 6.4 0.00014 25.4 2.3 25 64-88 58-82 (466)
130 PF13824 zf-Mss51: Zinc-finger 66.8 6 0.00013 17.6 1.6 10 34-43 13-22 (55)
131 PF07800 DUF1644: Protein of u 65.8 17 0.00037 20.0 3.5 56 35-92 80-137 (162)
132 KOG2907|consensus 65.3 6 0.00013 20.3 1.6 39 34-74 73-113 (116)
133 COG4896 Uncharacterized protei 64.6 2 4.2E-05 19.5 -0.1 37 2-45 4-41 (68)
134 PF03604 DNA_RNApol_7kD: DNA d 64.3 3 6.5E-05 16.3 0.4 11 1-11 1-11 (32)
135 KOG2785|consensus 64.2 16 0.00035 23.0 3.5 50 35-84 166-241 (390)
136 PRK03824 hypA hydrogenase nick 63.4 2.5 5.5E-05 22.3 0.1 15 34-48 69-83 (135)
137 TIGR00280 L37a ribosomal prote 62.4 3.3 7.3E-05 20.4 0.4 12 63-74 53-64 (91)
138 PF13451 zf-trcl: Probable zin 62.4 2.7 6E-05 18.2 0.1 17 62-78 3-19 (49)
139 PRK12380 hydrogenase nickel in 61.7 4.3 9.4E-05 20.7 0.8 14 35-48 70-83 (113)
140 PF15135 UPF0515: Uncharacteri 61.7 2.9 6.2E-05 24.6 0.1 12 35-46 155-166 (278)
141 COG3091 SprT Zn-dependent meta 61.0 4.5 9.8E-05 22.0 0.8 34 34-72 116-149 (156)
142 TIGR00340 zpr1_rel ZPR1-relate 59.4 4.8 0.00011 22.1 0.8 11 34-44 27-37 (163)
143 PF14369 zf-RING_3: zinc-finge 58.9 4.4 9.6E-05 16.1 0.4 10 3-12 24-33 (35)
144 PF10013 DUF2256: Uncharacteri 58.9 8.6 0.00019 16.1 1.3 12 65-76 10-21 (42)
145 KOG4167|consensus 58.0 2 4.4E-05 29.1 -0.9 26 35-60 792-817 (907)
146 smart00154 ZnF_AN1 AN1-like Zi 57.9 4.3 9.4E-05 16.5 0.3 13 1-13 13-25 (39)
147 PF04810 zf-Sec23_Sec24: Sec23 57.7 13 0.00029 15.1 1.8 14 31-44 20-33 (40)
148 smart00709 Zpr1 Duplicated dom 57.0 5.6 0.00012 21.8 0.8 11 35-45 29-39 (160)
149 COG4957 Predicted transcriptio 56.4 8.5 0.00018 20.5 1.3 26 36-64 77-102 (148)
150 PF12156 ATPase-cat_bd: Putati 56.1 5.7 0.00012 19.3 0.6 33 2-43 2-34 (88)
151 PF04780 DUF629: Protein of un 55.7 13 0.00028 24.1 2.2 26 35-60 57-83 (466)
152 PRK12496 hypothetical protein; 55.6 8.6 0.00019 21.1 1.3 10 36-45 128-137 (164)
153 PF14311 DUF4379: Domain of un 55.6 14 0.00031 16.0 1.8 14 35-48 28-41 (55)
154 PF05876 Terminase_GpA: Phage 55.4 17 0.00037 24.1 2.8 40 2-48 202-242 (557)
155 KOG1280|consensus 55.3 21 0.00046 22.3 2.9 38 33-70 77-116 (381)
156 COG4888 Uncharacterized Zn rib 54.8 6.7 0.00015 19.8 0.8 11 34-44 21-31 (104)
157 COG4847 Uncharacterized protei 53.7 2.8 6E-05 20.8 -0.7 17 1-17 7-23 (103)
158 COG5236 Uncharacterized conser 53.4 8 0.00017 24.1 1.1 17 3-19 223-239 (493)
159 PF13821 DUF4187: Domain of un 53.3 3.8 8.2E-05 18.2 -0.2 16 3-18 30-45 (55)
160 TIGR00100 hypA hydrogenase nic 53.1 6.5 0.00014 20.2 0.6 26 34-71 69-94 (115)
161 PF07975 C1_4: TFIIH C1-like d 52.3 8 0.00017 16.9 0.7 20 33-52 19-38 (51)
162 COG1571 Predicted DNA-binding 51.3 13 0.00029 23.7 1.8 12 35-46 367-378 (421)
163 COG5151 SSL1 RNA polymerase II 51.0 28 0.0006 21.6 2.9 22 62-83 387-408 (421)
164 KOG2482|consensus 50.6 14 0.0003 23.1 1.7 21 64-84 196-216 (423)
165 PF02176 zf-TRAF: TRAF-type zi 50.4 5.4 0.00012 17.5 0.0 38 35-73 9-52 (60)
166 PRK05452 anaerobic nitric oxid 50.2 14 0.0003 24.0 1.8 40 31-71 421-466 (479)
167 PF03107 C1_2: C1 domain; Int 49.9 10 0.00023 14.2 0.8 8 35-42 15-22 (30)
168 PF01428 zf-AN1: AN1-like Zinc 49.8 4.6 0.0001 16.7 -0.2 12 2-13 15-26 (43)
169 TIGR00310 ZPR1_znf ZPR1 zinc f 48.5 21 0.00045 20.3 2.1 36 1-45 1-40 (192)
170 KOG2231|consensus 47.8 23 0.00051 24.2 2.5 16 3-18 185-200 (669)
171 PF06397 Desulfoferrod_N: Desu 47.5 5.1 0.00011 16.1 -0.2 9 1-9 7-15 (36)
172 PF09943 DUF2175: Uncharacteri 46.3 4 8.6E-05 20.6 -0.8 17 1-17 3-19 (101)
173 KOG0402|consensus 46.1 6.7 0.00014 19.0 -0.0 9 1-9 37-45 (92)
174 PF13240 zinc_ribbon_2: zinc-r 46.0 14 0.00031 13.0 0.9 7 3-9 2-8 (23)
175 PF13696 zf-CCHC_2: Zinc knuck 45.9 8.7 0.00019 15.0 0.3 6 2-7 10-15 (32)
176 KOG0801|consensus 45.6 12 0.00025 20.7 0.8 13 1-13 139-151 (205)
177 PF08792 A2L_zn_ribbon: A2L zi 45.2 8.1 0.00018 15.1 0.2 8 3-10 24-31 (33)
178 PF00412 LIM: LIM domain; Int 45.0 14 0.00031 15.8 1.0 14 1-14 27-40 (58)
179 PF07503 zf-HYPF: HypF finger; 44.5 12 0.00027 14.9 0.6 10 36-45 22-31 (35)
180 PRK00564 hypA hydrogenase nick 43.2 12 0.00026 19.3 0.7 14 34-47 70-83 (117)
181 TIGR00515 accD acetyl-CoA carb 42.9 8.8 0.00019 23.1 0.1 11 35-45 26-36 (285)
182 COG1675 TFA1 Transcription ini 42.5 31 0.00068 19.3 2.2 33 32-73 110-142 (176)
183 COG1594 RPB9 DNA-directed RNA 42.5 22 0.00047 18.3 1.5 38 35-74 72-111 (113)
184 PF11494 Ta0938: Ta0938; Inte 42.4 15 0.00033 18.4 0.9 35 2-48 16-50 (105)
185 PF08271 TF_Zn_Ribbon: TFIIB z 42.4 10 0.00022 15.6 0.3 9 1-9 1-9 (43)
186 PLN02294 cytochrome c oxidase 42.2 17 0.00036 20.3 1.1 15 33-47 139-153 (174)
187 PF05741 zf-nanos: Nanos RNA b 42.0 5 0.00011 17.8 -0.7 10 34-43 32-41 (55)
188 PF14803 Nudix_N_2: Nudix N-te 41.7 17 0.00036 14.4 0.8 13 32-44 19-31 (34)
189 PF06689 zf-C4_ClpX: ClpX C4-t 41.2 17 0.00038 14.9 0.9 16 2-17 3-18 (41)
190 PF07282 OrfB_Zn_ribbon: Putat 41.1 38 0.00083 15.3 2.7 14 61-74 44-57 (69)
191 COG4338 Uncharacterized protei 40.8 12 0.00026 16.1 0.4 13 65-77 14-26 (54)
192 TIGR00319 desulf_FeS4 desulfof 40.7 9.1 0.0002 14.8 -0.0 10 1-10 8-17 (34)
193 cd00974 DSRD Desulforedoxin (D 40.7 9.3 0.0002 14.8 0.0 10 1-10 5-14 (34)
194 CHL00174 accD acetyl-CoA carbo 40.7 10 0.00022 23.0 0.2 11 36-46 58-68 (296)
195 KOG2231|consensus 40.5 31 0.00067 23.6 2.3 21 37-57 184-204 (669)
196 KOG3507|consensus 40.1 27 0.00057 15.8 1.4 30 33-73 18-47 (62)
197 PF01780 Ribosomal_L37ae: Ribo 40.1 10 0.00023 18.7 0.1 11 35-45 53-63 (90)
198 PF13248 zf-ribbon_3: zinc-rib 39.5 20 0.00044 12.9 0.9 7 2-8 4-10 (26)
199 PF03119 DNA_ligase_ZBD: NAD-d 39.1 12 0.00027 13.9 0.3 13 2-14 1-13 (28)
200 PRK05654 acetyl-CoA carboxylas 38.6 21 0.00045 21.7 1.2 11 64-74 47-57 (292)
201 PRK01343 zinc-binding protein; 37.8 17 0.00036 16.3 0.6 9 2-10 11-19 (57)
202 PF05129 Elf1: Transcription e 37.8 12 0.00026 18.0 0.2 13 35-47 46-58 (81)
203 PF10276 zf-CHCC: Zinc-finger 37.7 24 0.00051 14.6 1.0 12 34-45 28-39 (40)
204 KOG3214|consensus 37.6 18 0.00038 18.3 0.7 14 63-76 47-60 (109)
205 cd00924 Cyt_c_Oxidase_Vb Cytoc 37.5 22 0.00047 17.8 1.0 13 34-46 78-90 (97)
206 TIGR00244 transcriptional regu 37.5 15 0.00033 19.9 0.5 16 2-17 30-45 (147)
207 PF11781 RRN7: RNA polymerase 37.4 18 0.00039 14.4 0.6 7 3-9 11-17 (36)
208 KOG4602|consensus 36.8 17 0.00036 21.7 0.6 9 35-43 268-276 (318)
209 COG3364 Zn-ribbon containing p 35.6 26 0.00057 17.8 1.1 26 35-70 2-27 (112)
210 PF01844 HNH: HNH endonuclease 35.6 17 0.00036 14.8 0.4 16 3-18 1-16 (47)
211 PRK03976 rpl37ae 50S ribosomal 35.4 18 0.00038 17.9 0.5 12 35-46 54-65 (90)
212 PHA02998 RNA polymerase subuni 34.9 50 0.0011 18.7 2.2 12 64-75 172-183 (195)
213 PF14255 Cys_rich_CPXG: Cystei 34.7 20 0.00044 15.7 0.6 15 1-15 1-15 (52)
214 TIGR03829 YokU_near_AblA uncha 34.1 14 0.00031 18.2 0.1 15 38-52 38-52 (89)
215 PF10367 Vps39_2: Vacuolar sor 34.0 23 0.00049 17.4 0.8 12 2-13 80-91 (109)
216 smart00504 Ubox Modified RING 33.1 28 0.00061 15.1 1.0 12 1-12 2-13 (63)
217 PRK05978 hypothetical protein; 33.1 37 0.00081 18.5 1.5 16 37-52 35-50 (148)
218 PF03367 zf-ZPR1: ZPR1 zinc-fi 32.7 5.6 0.00012 21.8 -1.6 10 35-44 30-39 (161)
219 PF10272 Tmpp129: Putative tra 32.6 16 0.00034 22.9 0.1 10 36-45 341-350 (358)
220 TIGR01384 TFS_arch transcripti 32.5 54 0.0012 16.2 2.0 38 35-74 62-101 (104)
221 PRK00420 hypothetical protein; 32.0 50 0.0011 17.1 1.8 12 35-46 40-51 (112)
222 smart00507 HNHc HNH nucleases. 32.0 42 0.00091 13.5 1.4 11 2-12 12-22 (52)
223 smart00064 FYVE Protein presen 31.8 58 0.0013 14.6 2.0 9 37-45 12-20 (68)
224 TIGR00143 hypF [NiFe] hydrogen 31.5 12 0.00026 25.6 -0.5 31 37-73 120-150 (711)
225 PF04981 NMD3: NMD3 family ; 31.2 52 0.0011 19.2 2.0 13 34-46 34-46 (236)
226 KOG0978|consensus 31.0 17 0.00037 24.9 0.1 21 58-78 673-693 (698)
227 PF05191 ADK_lid: Adenylate ki 30.9 20 0.00042 14.3 0.2 13 2-14 3-15 (36)
228 KOG2906|consensus 30.6 29 0.00062 17.5 0.8 13 34-46 20-32 (105)
229 PF14375 Cys_rich_CWC: Cystein 30.4 27 0.00058 14.9 0.6 11 3-13 1-11 (50)
230 COG1326 Uncharacterized archae 30.3 74 0.0016 18.3 2.4 10 63-72 30-39 (201)
231 PF06170 DUF983: Protein of un 30.2 29 0.00063 16.9 0.8 12 2-13 10-21 (86)
232 PF14787 zf-CCHC_5: GAG-polypr 30.2 18 0.00038 14.6 0.0 13 65-77 4-16 (36)
233 cd01410 SIRT7 SIRT7: Eukaryoti 30.0 1.1E+02 0.0025 17.4 3.6 43 27-72 87-129 (206)
234 KOG2636|consensus 29.8 47 0.001 21.7 1.8 28 30-57 396-424 (497)
235 KOG2272|consensus 29.8 20 0.00044 21.4 0.2 21 27-47 213-233 (332)
236 PF05766 NinG: Bacteriophage L 29.7 30 0.00065 19.7 0.9 16 2-17 8-23 (189)
237 COG1327 Predicted transcriptio 29.6 25 0.00054 19.2 0.5 17 2-18 30-46 (156)
238 COG5112 UFD2 U1-like Zn-finger 29.5 29 0.00063 17.8 0.7 25 32-56 52-76 (126)
239 PRK14138 NAD-dependent deacety 29.4 1.3E+02 0.0027 17.8 3.5 42 27-72 111-152 (244)
240 PF09845 DUF2072: Zn-ribbon co 28.7 40 0.00087 18.0 1.2 17 1-17 2-18 (131)
241 PF03884 DUF329: Domain of unk 28.2 20 0.00043 16.1 0.0 11 2-12 4-14 (57)
242 cd01413 SIR2_Af2 SIR2_Af2: Arc 28.1 1.2E+02 0.0027 17.4 3.2 41 27-72 105-145 (222)
243 PF14149 YhfH: YhfH-like prote 27.7 6.3 0.00014 16.0 -1.4 8 3-10 16-23 (37)
244 PF08209 Sgf11: Sgf11 (transcr 27.6 34 0.00073 13.5 0.6 21 35-56 4-24 (33)
245 PF02891 zf-MIZ: MIZ/SP-RING z 27.4 53 0.0011 14.1 1.3 9 63-71 41-49 (50)
246 PF14599 zinc_ribbon_6: Zinc-r 27.3 18 0.00039 16.5 -0.2 22 3-24 33-54 (61)
247 PLN02748 tRNA dimethylallyltra 27.3 65 0.0014 21.2 2.1 25 34-58 417-442 (468)
248 COG3024 Uncharacterized protei 27.2 29 0.00063 16.0 0.5 8 2-9 9-16 (65)
249 COG4391 Uncharacterized protei 27.0 44 0.00095 15.3 1.0 13 34-46 47-59 (62)
250 COG1655 Uncharacterized protei 26.6 27 0.00058 20.6 0.4 18 1-18 20-37 (267)
251 PF01194 RNA_pol_N: RNA polyme 26.5 57 0.0012 14.8 1.3 18 62-79 3-20 (60)
252 PF10263 SprT-like: SprT-like 26.3 32 0.0007 18.3 0.6 33 34-74 122-154 (157)
253 PF04216 FdhE: Protein involve 26.2 28 0.00061 20.9 0.4 36 34-70 210-245 (290)
254 TIGR00686 phnA alkylphosphonat 26.1 59 0.0013 16.7 1.5 13 34-46 18-30 (109)
255 KOG0717|consensus 26.1 58 0.0013 21.4 1.7 22 36-57 293-314 (508)
256 COG1644 RPB10 DNA-directed RNA 26.0 65 0.0014 14.8 1.4 12 35-46 4-15 (63)
257 PF08996 zf-DNA_Pol: DNA Polym 25.7 44 0.00095 18.8 1.1 38 1-46 19-56 (188)
258 PF01927 Mut7-C: Mut7-C RNAse 25.7 33 0.00071 18.4 0.6 13 63-75 124-136 (147)
259 TIGR01385 TFSII transcription 25.6 83 0.0018 19.3 2.3 37 35-73 258-296 (299)
260 COG0777 AccD Acetyl-CoA carbox 25.3 58 0.0013 19.9 1.5 8 36-43 29-36 (294)
261 KOG2879|consensus 25.3 51 0.0011 20.1 1.3 12 62-73 275-286 (298)
262 KOG1088|consensus 25.2 38 0.00082 17.7 0.7 21 28-48 91-111 (124)
263 smart00746 TRASH metallochaper 25.0 47 0.001 11.7 0.9 9 3-11 1-9 (39)
264 PRK00481 NAD-dependent deacety 24.7 1.2E+02 0.0027 17.7 2.8 38 27-72 114-151 (242)
265 PF14122 YokU: YokU-like prote 24.5 24 0.00052 17.3 -0.1 14 2-15 37-50 (87)
266 PRK08222 hydrogenase 4 subunit 24.5 73 0.0016 17.8 1.8 19 62-80 113-131 (181)
267 COG3357 Predicted transcriptio 24.4 41 0.00089 16.7 0.7 14 62-75 57-70 (97)
268 COG1885 Uncharacterized protei 24.3 39 0.00085 17.2 0.7 11 2-12 51-61 (115)
269 PF14354 Lar_restr_allev: Rest 24.2 36 0.00079 14.9 0.5 8 2-9 5-12 (61)
270 PLN03238 probable histone acet 24.1 1.5E+02 0.0032 18.3 3.0 25 33-57 46-70 (290)
271 PF10537 WAC_Acf1_DNA_bd: ATP- 24.0 1.1E+02 0.0025 15.4 3.8 35 36-71 4-38 (102)
272 PRK10220 hypothetical protein; 24.0 1E+02 0.0022 16.0 2.0 14 34-47 19-32 (111)
273 PF02146 SIR2: Sir2 family; I 23.9 24 0.00052 19.4 -0.1 43 27-73 97-139 (178)
274 PF09779 Ima1_N: Ima1 N-termin 23.9 1.2E+02 0.0027 15.9 2.5 9 35-43 20-28 (131)
275 PF13408 Zn_ribbon_recom: Reco 23.8 29 0.00063 14.8 0.1 11 2-12 7-17 (58)
276 PHA02446 hypothetical protein 23.7 37 0.0008 17.7 0.5 20 26-45 79-98 (166)
277 KOG3399|consensus 23.7 1E+02 0.0022 16.3 2.0 18 1-18 16-33 (122)
278 COG0675 Transposase and inacti 23.6 91 0.002 18.7 2.3 12 62-73 321-332 (364)
279 PF09297 zf-NADH-PPase: NADH p 23.6 27 0.00059 13.2 0.0 10 34-43 20-29 (32)
280 TIGR00570 cdk7 CDK-activating 23.6 1.1E+02 0.0023 19.0 2.5 9 1-9 4-12 (309)
281 PRK04016 DNA-directed RNA poly 23.4 94 0.002 14.3 1.8 13 35-47 4-16 (62)
282 PHA02942 putative transposase; 22.9 1.1E+02 0.0023 19.5 2.4 12 62-73 341-352 (383)
283 PF03966 Trm112p: Trm112p-like 22.8 31 0.00068 15.7 0.1 18 29-46 47-64 (68)
284 PF07295 DUF1451: Protein of u 22.7 17 0.00037 19.6 -0.8 29 33-71 110-138 (146)
285 PTZ00448 hypothetical protein; 22.3 90 0.0019 19.9 2.0 23 35-57 314-336 (373)
286 PF01363 FYVE: FYVE zinc finge 22.3 54 0.0012 14.7 0.9 10 2-11 11-20 (69)
287 smart00731 SprT SprT homologue 22.0 48 0.001 17.7 0.8 33 34-73 111-143 (146)
288 PF15616 TerY-C: TerY-C metal 22.0 71 0.0015 17.1 1.4 13 60-72 102-114 (131)
289 PRK00418 DNA gyrase inhibitor; 22.0 45 0.00098 15.3 0.6 9 2-10 8-16 (62)
290 TIGR00627 tfb4 transcription f 21.8 1.1E+02 0.0025 18.6 2.3 12 35-46 255-266 (279)
291 PTZ00043 cytochrome c oxidase 21.7 52 0.0011 19.5 0.9 16 32-47 178-193 (268)
292 PF13445 zf-RING_UBOX: RING-ty 21.7 44 0.00095 13.9 0.5 14 35-49 14-27 (43)
293 PRK12860 transcriptional activ 21.5 61 0.0013 18.5 1.1 29 34-70 133-161 (189)
294 cd00065 FYVE FYVE domain; Zinc 21.5 83 0.0018 13.4 1.4 10 3-12 5-14 (57)
295 KOG1994|consensus 21.4 55 0.0012 19.3 0.9 23 60-82 236-258 (268)
296 TIGR03826 YvyF flagellar opero 20.8 32 0.00069 18.5 -0.0 11 2-12 5-15 (137)
297 TIGR03655 anti_R_Lar restricti 20.8 44 0.00096 14.4 0.4 12 36-47 27-38 (53)
298 PRK12722 transcriptional activ 20.7 64 0.0014 18.4 1.1 29 35-71 134-162 (187)
299 PF01396 zf-C4_Topoisom: Topoi 20.7 39 0.00084 13.6 0.2 7 2-8 3-9 (39)
300 COG0846 SIR2 NAD-dependent pro 20.2 83 0.0018 18.8 1.5 41 27-71 114-154 (250)
301 COG2995 PqiA Uncharacterized p 20.2 1.1E+02 0.0023 19.9 2.0 16 2-18 20-35 (418)
No 1
>KOG2462|consensus
Probab=99.90 E-value=3.4e-24 Score=119.34 Aligned_cols=89 Identities=25% Similarity=0.428 Sum_probs=62.8
Q ss_pred CcccccccccccccccccccccCC------------------------CCCCCCCCCCceeCCCCCccCCCHHHHHHHHH
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRC------------------------SNMPRPDSSHLYVCFKCGYHQYNSDRMKRHIR 56 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~------------------------~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~ 56 (92)
|+|.+|++.+.+.++|-.|..-.+ .|.++|+ .++.|.+||+.|.....|+.|+|
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiR 208 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIR 208 (279)
T ss_pred eeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccc
Confidence 356666666666666665521111 3444444 46778888888888888888888
Q ss_pred HhhCCCCccCCcCccccCChHHHHHHHHHhccCCCC
Q psy5652 57 THTGERPFKCEFCAHSATSKSNLKMHIMVKHQNDFV 92 (92)
Q Consensus 57 ~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~h~~~~p 92 (92)
+|+|||||.|+.|+++|...+||..|+ ++|.+.|+
T Consensus 209 THTGEKPF~C~hC~kAFADRSNLRAHm-QTHS~~K~ 243 (279)
T KOG2462|consen 209 THTGEKPFSCPHCGKAFADRSNLRAHM-QTHSDVKK 243 (279)
T ss_pred cccCCCCccCCcccchhcchHHHHHHH-HhhcCCcc
Confidence 888888888888888888888888888 88877653
No 2
>KOG2462|consensus
Probab=99.87 E-value=9.7e-23 Score=113.60 Aligned_cols=76 Identities=20% Similarity=0.404 Sum_probs=70.6
Q ss_pred CcccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccccCChHHHH
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSATSKSNLK 80 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~ 80 (92)
++|.+|||.|.+.=.|+ .|.++|+++|||.|+.|+++|.+.++|..|+++|.+.|+|+|..|+|.|...+-|.
T Consensus 188 c~C~iCGKaFSRPWLLQ-------GHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLn 260 (279)
T KOG2462|consen 188 CECGICGKAFSRPWLLQ-------GHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLN 260 (279)
T ss_pred cccccccccccchHHhh-------cccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHH
Confidence 36788888888887777 68999999999999999999999999999999999999999999999999999999
Q ss_pred HHH
Q psy5652 81 MHI 83 (92)
Q Consensus 81 ~h~ 83 (92)
+|.
T Consensus 261 KH~ 263 (279)
T KOG2462|consen 261 KHS 263 (279)
T ss_pred Hhh
Confidence 997
No 3
>KOG3576|consensus
Probab=99.72 E-value=2.1e-19 Score=96.97 Aligned_cols=81 Identities=27% Similarity=0.547 Sum_probs=76.5
Q ss_pred CcccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccccCChHHHH
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSATSKSNLK 80 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~ 80 (92)
|.|.+|++.|....-|.+ |+..|.+.+.+-|..||++|-..-.|++|+++|+|.+||+|..|+++|.+.-.|.
T Consensus 118 ftCrvCgK~F~lQRmlnr-------h~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsle 190 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNR-------HLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLE 190 (267)
T ss_pred eeeehhhhhhhHHHHHHH-------HhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHH
Confidence 579999999999999984 7899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcc
Q psy5652 81 MHIMVKHQ 88 (92)
Q Consensus 81 ~h~~~~h~ 88 (92)
.|+++.|.
T Consensus 191 shl~kvhg 198 (267)
T KOG3576|consen 191 SHLKKVHG 198 (267)
T ss_pred HHHHHHcC
Confidence 99987774
No 4
>KOG3623|consensus
Probab=99.65 E-value=8.7e-18 Score=104.13 Aligned_cols=76 Identities=20% Similarity=0.493 Sum_probs=72.4
Q ss_pred CcccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccccCChHHHH
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSATSKSNLK 80 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~ 80 (92)
|.|..|++.|...+.|.+ |...|++.+||.|.+|.++|..+-.|..|.|.|.|+|||+|..|+|.|..++...
T Consensus 895 yaCDqCDK~FqKqSSLaR-------HKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYS 967 (1007)
T KOG3623|consen 895 YACDQCDKAFQKQSSLAR-------HKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYS 967 (1007)
T ss_pred chHHHHHHHHHhhHHHHH-------hhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchH
Confidence 679999999999999995 7889999999999999999999999999999999999999999999999999998
Q ss_pred HHH
Q psy5652 81 MHI 83 (92)
Q Consensus 81 ~h~ 83 (92)
.|+
T Consensus 968 QHM 970 (1007)
T KOG3623|consen 968 QHM 970 (1007)
T ss_pred hhh
Confidence 886
No 5
>KOG3623|consensus
Probab=99.46 E-value=6.2e-15 Score=91.81 Aligned_cols=83 Identities=19% Similarity=0.490 Sum_probs=68.8
Q ss_pred CcccccccccccccccccccccC--CC----CCCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccccC
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKR--CS----NMPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSAT 74 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~--~~----~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~ 74 (92)
|.|..|...|.+...|.+|+... +. +...-...+.|.|.+||++|..+-.|+.|+|+|.|+|||.|+.|+|.|.
T Consensus 241 fsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFS 320 (1007)
T KOG3623|consen 241 FSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFS 320 (1007)
T ss_pred CcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccc
Confidence 57999999999999998875332 11 1122233468999999999999999999999999999999999999999
Q ss_pred ChHHHHHHH
Q psy5652 75 SKSNLKMHI 83 (92)
Q Consensus 75 ~~~~l~~h~ 83 (92)
.++.+..|+
T Consensus 321 HSGSySSHm 329 (1007)
T KOG3623|consen 321 HSGSYSSHM 329 (1007)
T ss_pred cCCcccccc
Confidence 999888886
No 6
>PHA00733 hypothetical protein
Probab=99.40 E-value=5.7e-13 Score=68.65 Aligned_cols=83 Identities=19% Similarity=0.233 Sum_probs=66.6
Q ss_pred cccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccccCChHHHHH
Q psy5652 2 VCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSATSKSNLKM 81 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~ 81 (92)
.|.+|.+.|.....|..+..-. .++..++ .++|.|+.|++.|.....|..|++.+ ..+|.|..|++.|.....|..
T Consensus 42 ~~~~~~~~~~~~~~l~~~~~l~-~~~~~~~-~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~ 117 (128)
T PHA00733 42 IRAVVKTLIYNPQLLDESSYLY-KLLTSKA-VSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLD 117 (128)
T ss_pred HHHHHhhhccChhhhcchHHHH-hhcccCC-CCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHH
Confidence 5888999988887777542111 2334444 67999999999999999999999876 457999999999999999999
Q ss_pred HHHHhcc
Q psy5652 82 HIMVKHQ 88 (92)
Q Consensus 82 h~~~~h~ 88 (92)
|+...|.
T Consensus 118 H~~~~h~ 124 (128)
T PHA00733 118 HVCKKHN 124 (128)
T ss_pred HHHHhcC
Confidence 9977775
No 7
>PHA02768 hypothetical protein; Provisional
Probab=99.28 E-value=2.2e-12 Score=56.59 Aligned_cols=43 Identities=23% Similarity=0.400 Sum_probs=39.3
Q ss_pred ceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccccCChHHH
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSATSKSNL 79 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l 79 (92)
.|.|+.||+.|...+.|..|++.|+ ++++|..|++.|.+.+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 5899999999999999999999998 789999999999877665
No 8
>KOG3576|consensus
Probab=99.23 E-value=6.3e-12 Score=68.48 Aligned_cols=79 Identities=18% Similarity=0.401 Sum_probs=67.5
Q ss_pred cccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhC-----------CCCccCCcCc
Q psy5652 2 VCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTG-----------ERPFKCEFCA 70 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~-----------~~~~~c~~c~ 70 (92)
-|..||+.|.+--||.+ |+++|++.+||.|..|+++|...-.|..|.+.-.| ++-|.|.+||
T Consensus 147 lct~cgkgfndtfdlkr-------h~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg 219 (267)
T KOG3576|consen 147 LCTFCGKGFNDTFDLKR-------HTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCG 219 (267)
T ss_pred HHhhccCcccchhhhhh-------hhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccC
Confidence 48899999999999994 89999999999999999999999999988874333 4679999999
Q ss_pred cccCChHHHHHHHHHhc
Q psy5652 71 HSATSKSNLKMHIMVKH 87 (92)
Q Consensus 71 ~~~~~~~~l~~h~~~~h 87 (92)
..-.....+..|+..-|
T Consensus 220 ~t~~~~e~~~~h~~~~h 236 (267)
T KOG3576|consen 220 YTSERPEVYYLHLKLHH 236 (267)
T ss_pred CCCCChhHHHHHHHhcC
Confidence 88888888888884333
No 9
>KOG3608|consensus
Probab=99.17 E-value=2.5e-11 Score=70.86 Aligned_cols=83 Identities=16% Similarity=0.419 Sum_probs=42.6
Q ss_pred cccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCc--CccccCChHHH
Q psy5652 2 VCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEF--CAHSATSKSNL 79 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~--c~~~~~~~~~l 79 (92)
+|+.|++.....+.|..|+ +..|...++|.|..|+..+...+.|++|...|. +..|+|.. |...+++...+
T Consensus 265 kCplCdmtc~~~ssL~~H~------r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~ 337 (467)
T KOG3608|consen 265 KCPLCDMTCSSASSLTTHI------RYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQM 337 (467)
T ss_pred cccccccCCCChHHHHHHH------HhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHH
Confidence 3444444444444444332 344555566666666666666666666666554 33455543 55555555555
Q ss_pred HHHHHHhccCCC
Q psy5652 80 KMHIMVKHQNDF 91 (92)
Q Consensus 80 ~~h~~~~h~~~~ 91 (92)
.+|....|.|..
T Consensus 338 ~~H~~evhEg~n 349 (467)
T KOG3608|consen 338 RRHFLEVHEGNN 349 (467)
T ss_pred HHHHHHhccCCC
Confidence 555544444433
No 10
>KOG1074|consensus
Probab=99.17 E-value=2.2e-12 Score=81.53 Aligned_cols=80 Identities=23% Similarity=0.488 Sum_probs=67.2
Q ss_pred cccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhCC----CCccCC---cCccccC
Q psy5652 2 VCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGE----RPFKCE---FCAHSAT 74 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~----~~~~c~---~c~~~~~ 74 (92)
.|-+|.+.+...+.|++ |.++|++++||.|.+||++|..+.+|+.|+.+|... ..+.|+ .|.+-|.
T Consensus 607 qCiiC~rVlSC~saLqm-------HyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kft 679 (958)
T KOG1074|consen 607 QCIICLRVLSCPSALQM-------HYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFT 679 (958)
T ss_pred ceeeeeecccchhhhhh-------hhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccc
Confidence 48889999999999996 678999999999999999999999999999888754 347788 7888888
Q ss_pred ChHHHHHHHHHhccC
Q psy5652 75 SKSNLKMHIMVKHQN 89 (92)
Q Consensus 75 ~~~~l~~h~~~~h~~ 89 (92)
..-.|..|+ ++|++
T Consensus 680 n~V~lpQhI-riH~~ 693 (958)
T KOG1074|consen 680 NAVTLPQHI-RIHLG 693 (958)
T ss_pred ccccccceE-EeecC
Confidence 888888888 88873
No 11
>KOG3608|consensus
Probab=99.11 E-value=1.4e-11 Score=71.89 Aligned_cols=60 Identities=28% Similarity=0.602 Sum_probs=50.0
Q ss_pred CCCCCCCCCceeCCCCCccCCCHHHHHHHHHH-hhCCCCccCCcCccccCChHHHHHHHHHhcc
Q psy5652 26 NMPRPDSSHLYVCFKCGYHQYNSDRMKRHIRT-HTGERPFKCEFCAHSATSKSNLKMHIMVKHQ 88 (92)
Q Consensus 26 ~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~c~~c~~~~~~~~~l~~h~~~~h~ 88 (92)
|++.|.. .|.|+.|+.+....+.|..|++. |...+||+|..|.+.+.+.+.|.+|. ..|.
T Consensus 256 Hv~rHvn--~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~-~~HS 316 (467)
T KOG3608|consen 256 HVVRHVN--CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHV-QVHS 316 (467)
T ss_pred HHHHhhh--cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHH-Hhcc
Confidence 3444443 58999999999999999999987 66679999999999999999999998 6775
No 12
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.03 E-value=2.4e-10 Score=43.30 Aligned_cols=26 Identities=50% Similarity=1.210 Sum_probs=23.3
Q ss_pred HHHHHHHHhhCCCCccCCcCccccCC
Q psy5652 50 RMKRHIRTHTGERPFKCEFCAHSATS 75 (92)
Q Consensus 50 ~l~~h~~~~~~~~~~~c~~c~~~~~~ 75 (92)
+|..|++.|++++||.|..|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47899999999999999999998863
No 13
>KOG1074|consensus
Probab=99.00 E-value=2e-10 Score=73.03 Aligned_cols=54 Identities=41% Similarity=0.752 Sum_probs=50.6
Q ss_pred eeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccccCChHHHHHHHHHhccCC
Q psy5652 36 YVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSATSKSNLKMHIMVKHQND 90 (92)
Q Consensus 36 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~h~~~ 90 (92)
..|.+||+.|.+.+.|+.|+++|+++|||.|..|++.|....+|..|+ .+|...
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHM-gtH~w~ 933 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHM-GTHMWV 933 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhh-cccccc
Confidence 679999999999999999999999999999999999999999999999 788644
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.85 E-value=1.5e-10 Score=50.81 Aligned_cols=42 Identities=10% Similarity=0.240 Sum_probs=35.9
Q ss_pred CcccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCHHHH
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNSDRM 51 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l 51 (92)
|.|+.||+.|...+.|.. |+++|+ +++.|..|++.|...+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~-------H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMIT-------HLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHH-------HHHhcC--CcccCCcccceeccccee
Confidence 689999999999999995 678888 588999999988765544
No 15
>KOG3993|consensus
Probab=98.76 E-value=1.2e-09 Score=65.19 Aligned_cols=80 Identities=21% Similarity=0.425 Sum_probs=63.0
Q ss_pred CcccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhC--------CC----------
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTG--------ER---------- 62 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~--------~~---------- 62 (92)
|+|..|...|.+--.|.+|.|.+= ....|.|++|++.|.-..+|..|.|+|.- ..
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RI-------V~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~ra 340 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRI-------VHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRA 340 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCee-------EEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhh
Confidence 578899999999988988765221 22468999999999999999999887631 11
Q ss_pred ---------------CccCCcCccccCChHHHHHHHHHhcc
Q psy5652 63 ---------------PFKCEFCAHSATSKSNLKMHIMVKHQ 88 (92)
Q Consensus 63 ---------------~~~c~~c~~~~~~~~~l~~h~~~~h~ 88 (92)
-|.|..|++.|.+...|.+|+ .+|.
T Consensus 341 e~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHq-lthq 380 (500)
T KOG3993|consen 341 EVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQ-LTHQ 380 (500)
T ss_pred hhhhccccCCcccCceeecHHhhhhhHHHHHHHHhH-Hhhh
Confidence 278999999999999999998 6663
No 16
>PHA00616 hypothetical protein
Probab=98.70 E-value=1.1e-08 Score=42.99 Aligned_cols=34 Identities=18% Similarity=0.490 Sum_probs=28.2
Q ss_pred ceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCc
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEF 68 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~ 68 (92)
+|.|+.||..|.....+..|++.|+|++++.+..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 5788888888888888888888888888887653
No 17
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.69 E-value=1.9e-08 Score=62.67 Aligned_cols=61 Identities=21% Similarity=0.413 Sum_probs=39.2
Q ss_pred cccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccccC
Q psy5652 2 VCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSAT 74 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~ 74 (92)
.|..|++.|. ..+|..| +.++. +++.|+ |+..+ ....|..|+..+...+++.|..|+..+.
T Consensus 455 ~C~~Cgk~f~-~s~LekH-------~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~ 515 (567)
T PLN03086 455 HCEKCGQAFQ-QGEMEKH-------MKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQ 515 (567)
T ss_pred cCCCCCCccc-hHHHHHH-------HHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccc
Confidence 4677777774 4556643 33332 567777 77544 4566777777777777777777777663
No 18
>PHA00616 hypothetical protein
Probab=98.69 E-value=1e-08 Score=43.05 Aligned_cols=29 Identities=14% Similarity=0.287 Sum_probs=24.6
Q ss_pred CccCCcCccccCChHHHHHHHHHhccCCCC
Q psy5652 63 PFKCEFCAHSATSKSNLKMHIMVKHQNDFV 92 (92)
Q Consensus 63 ~~~c~~c~~~~~~~~~l~~h~~~~h~~~~p 92 (92)
||+|+.||+.|...+++..|+ ..|++++|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~-r~~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHL-LSVHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHH-HHhcCCCc
Confidence 688999999999999999998 77777765
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.57 E-value=1.3e-07 Score=59.09 Aligned_cols=77 Identities=23% Similarity=0.438 Sum_probs=60.1
Q ss_pred CcccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCC----------HHHHHHHHHHhhCCCCccCCcCc
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYN----------SDRMKRHIRTHTGERPFKCEFCA 70 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~----------~~~l~~h~~~~~~~~~~~c~~c~ 70 (92)
+.|+ |++.+ ...+|.. |..+|-..+++.|..|+..+.. .+.|..|.... |.+++.|..|+
T Consensus 479 v~Cp-Cg~~~-~R~~L~~-------H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cg 548 (567)
T PLN03086 479 LQCP-CGVVL-EKEQMVQ-------HQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCG 548 (567)
T ss_pred ccCC-CCCCc-chhHHHh-------hhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccC
Confidence 4699 99765 5577774 6778888899999999988742 35788998875 88999999999
Q ss_pred cccCChHHHHHHHHHhcc
Q psy5652 71 HSATSKSNLKMHIMVKHQ 88 (92)
Q Consensus 71 ~~~~~~~~l~~h~~~~h~ 88 (92)
+.+... .+..|+...|.
T Consensus 549 k~Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 549 RSVMLK-EMDIHQIAVHQ 565 (567)
T ss_pred Ceeeeh-hHHHHHHHhhc
Confidence 987554 67778756554
No 20
>PHA00732 hypothetical protein
Probab=98.54 E-value=9.2e-08 Score=45.46 Aligned_cols=44 Identities=11% Similarity=0.147 Sum_probs=25.7
Q ss_pred CcccccccccccccccccccccCCCCCC-CCCCCCceeCCCCCccCCCHHHHHHHHHH
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMP-RPDSSHLYVCFKCGYHQYNSDRMKRHIRT 57 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~-~~~~~~~~~c~~c~~~~~~~~~l~~h~~~ 57 (92)
|.|..|++.|.....|..| +. .|.+ +.|+.|++.|.+ +..|.++
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H-------~r~~H~~---~~C~~CgKsF~~---l~~H~~~ 46 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQH-------ARRNHTL---TKCPVCNKSYRR---LNQHFYS 46 (79)
T ss_pred ccCCCCCCccCCHHHHHHH-------hhcccCC---CccCCCCCEeCC---hhhhhcc
Confidence 4677777777777777753 32 2322 357777777663 4555543
No 21
>PHA00733 hypothetical protein
Probab=98.47 E-value=1.6e-07 Score=48.58 Aligned_cols=50 Identities=22% Similarity=0.347 Sum_probs=41.7
Q ss_pred CcccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCHHHHHHHHHHhh
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHT 59 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~ 59 (92)
|.|..|++.|.....|..|+ ..+ ..++.|.+|++.|.....|..|+....
T Consensus 74 y~C~~Cgk~Fss~s~L~~H~-------r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 74 YVCPLCLMPFSSSVSLKQHI-------RYT--EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred ccCCCCCCcCCCHHHHHHHH-------hcC--CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 67999999999999999654 433 246899999999999999999987644
No 22
>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=98.35 E-value=2.1e-06 Score=38.00 Aligned_cols=50 Identities=24% Similarity=0.587 Sum_probs=37.0
Q ss_pred ceeCCCCCccCCCHHHHHHHHHH-hhC-CCCccCCcCccccCChHHHHHHHHHhc
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRT-HTG-ERPFKCEFCAHSATSKSNLKMHIMVKH 87 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~-~~~-~~~~~c~~c~~~~~~~~~l~~h~~~~h 87 (92)
.|.|+.|++ ..+...|..|... |.. .+.+.|+.|...+. .+|..|+...|
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 478999999 5667789988765 544 35799999987543 48888885444
No 23
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.26 E-value=1.3e-06 Score=31.79 Aligned_cols=20 Identities=35% Similarity=0.682 Sum_probs=9.5
Q ss_pred eCCCCCccCCCHHHHHHHHH
Q psy5652 37 VCFKCGYHQYNSDRMKRHIR 56 (92)
Q Consensus 37 ~c~~c~~~~~~~~~l~~h~~ 56 (92)
.|+.|++.|.....|..|++
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHHh
Confidence 44444444444444444444
No 24
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.13 E-value=2.2e-06 Score=31.14 Aligned_cols=23 Identities=52% Similarity=0.961 Sum_probs=20.4
Q ss_pred ccCCcCccccCChHHHHHHHHHhc
Q psy5652 64 FKCEFCAHSATSKSNLKMHIMVKH 87 (92)
Q Consensus 64 ~~c~~c~~~~~~~~~l~~h~~~~h 87 (92)
|.|..|++.|.....|..|+ ..|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~-~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHM-RRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHH-HHH
T ss_pred CCCCCCCCccCCHHHHHHHH-hHC
Confidence 68999999999999999999 444
No 25
>KOG3993|consensus
Probab=98.07 E-value=2.3e-06 Score=51.70 Aligned_cols=59 Identities=19% Similarity=0.355 Sum_probs=43.6
Q ss_pred CcccccccccccccccccccccC----------CCC----------------CCCCCCCCceeCCCCCccCCCHHHHHHH
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKR----------CSN----------------MPRPDSSHLYVCFKCGYHQYNSDRMKRH 54 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~----------~~~----------------~~~~~~~~~~~c~~c~~~~~~~~~l~~h 54 (92)
|+|++|+|.|....+|..|..-. ... .+......-|.|.+|++.|.....|.+|
T Consensus 296 YrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKH 375 (500)
T KOG3993|consen 296 YRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKH 375 (500)
T ss_pred ecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHh
Confidence 78999999999999999984211 000 0001223369999999999999999999
Q ss_pred HHHhh
Q psy5652 55 IRTHT 59 (92)
Q Consensus 55 ~~~~~ 59 (92)
+.+|.
T Consensus 376 qlthq 380 (500)
T KOG3993|consen 376 QLTHQ 380 (500)
T ss_pred HHhhh
Confidence 87664
No 26
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.06 E-value=2e-06 Score=38.04 Aligned_cols=49 Identities=20% Similarity=0.392 Sum_probs=35.0
Q ss_pred CcccccccccccccccccccccCCCCCCCCCC-CCceeCCCCCccCCCHHHHHHHHHHh
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMPRPDS-SHLYVCFKCGYHQYNSDRMKRHIRTH 58 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~-~~~~~c~~c~~~~~~~~~l~~h~~~~ 58 (92)
|.|+.|++. .+...|..|. ...|.. .+.+.|++|...+. ..|..|+...
T Consensus 3 f~CP~C~~~-~~~~~L~~H~------~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 3 FTCPYCGKG-FSESSLVEHC------EDEHRSESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred cCCCCCCCc-cCHHHHHHHH------HhHCcCCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 789999995 5567788764 445543 35789999998644 3788887754
No 27
>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=98.05 E-value=8.5e-08 Score=36.17 Aligned_cols=21 Identities=24% Similarity=0.401 Sum_probs=18.8
Q ss_pred CCCCCCCCCceeCCCCCccCC
Q psy5652 26 NMPRPDSSHLYVCFKCGYHQY 46 (92)
Q Consensus 26 ~~~~~~~~~~~~c~~c~~~~~ 46 (92)
|+.+|.++++|.|+.|++.|.
T Consensus 5 H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 5 HMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHSSSSSEEESSSSEEES
T ss_pred HhhhcCCCCCCCCCCCcCeeC
Confidence 677899999999999999885
No 28
>PHA00732 hypothetical protein
Probab=97.90 E-value=3.5e-06 Score=40.08 Aligned_cols=43 Identities=33% Similarity=0.660 Sum_probs=36.2
Q ss_pred ceeCCCCCccCCCHHHHHHHHHH-hhCCCCccCCcCccccCChHHHHHHH
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRT-HTGERPFKCEFCAHSATSKSNLKMHI 83 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~c~~c~~~~~~~~~l~~h~ 83 (92)
+|.|..|++.|.....|..|++. |. ++.|..|++.|. .+..|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~ 44 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHF 44 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhh
Confidence 57899999999999999999984 65 368999999997 466665
No 29
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.86 E-value=2.6e-05 Score=28.22 Aligned_cols=19 Identities=42% Similarity=0.850 Sum_probs=7.9
Q ss_pred cCCcCccccCChHHHHHHH
Q psy5652 65 KCEFCAHSATSKSNLKMHI 83 (92)
Q Consensus 65 ~c~~c~~~~~~~~~l~~h~ 83 (92)
.|..|++.|.....|..|+
T Consensus 2 ~C~~C~~~~~~~~~l~~H~ 20 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHM 20 (24)
T ss_dssp E-SSTS-EESSHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHH
Confidence 3444444444444444444
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.83 E-value=2.6e-05 Score=38.30 Aligned_cols=19 Identities=21% Similarity=0.590 Sum_probs=0.0
Q ss_pred ccccccccccccccccccc
Q psy5652 2 VCIFCRQLLPMDADFILGH 20 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~ 20 (92)
.|.+|+..|.+...|..|+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~ 19 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHM 19 (100)
T ss_dssp -------------------
T ss_pred Ccccccccccccccccccc
Confidence 4899999999999999765
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.78 E-value=1.5e-05 Score=30.03 Aligned_cols=21 Identities=24% Similarity=0.569 Sum_probs=10.2
Q ss_pred eeCCCCCccCCCHHHHHHHHH
Q psy5652 36 YVCFKCGYHQYNSDRMKRHIR 56 (92)
Q Consensus 36 ~~c~~c~~~~~~~~~l~~h~~ 56 (92)
|.|..|++.|.+...|..|++
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~ 22 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKR 22 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHC
T ss_pred CCCCccCCccCChhHHHHHhH
Confidence 444455555555444444443
No 32
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.76 E-value=4.1e-05 Score=27.67 Aligned_cols=23 Identities=30% Similarity=0.742 Sum_probs=19.3
Q ss_pred eeCCCCCccCCCHHHHHHHHHHh
Q psy5652 36 YVCFKCGYHQYNSDRMKRHIRTH 58 (92)
Q Consensus 36 ~~c~~c~~~~~~~~~l~~h~~~~ 58 (92)
|.|+.|+..|.+...|..|+..+
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 68999999999999999999865
No 33
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.71 E-value=2.4e-05 Score=29.46 Aligned_cols=25 Identities=36% Similarity=0.689 Sum_probs=22.3
Q ss_pred CccCCcCccccCChHHHHHHHHHhcc
Q psy5652 63 PFKCEFCAHSATSKSNLKMHIMVKHQ 88 (92)
Q Consensus 63 ~~~c~~c~~~~~~~~~l~~h~~~~h~ 88 (92)
||.|..|++.|.....|..|+ +.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~-~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHK-RSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHH-CTTT
T ss_pred CCCCCccCCccCChhHHHHHh-HHhc
Confidence 689999999999999999999 6663
No 34
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.49 E-value=0.00019 Score=26.19 Aligned_cols=19 Identities=42% Similarity=0.705 Sum_probs=9.7
Q ss_pred cCCcCccccCChHHHHHHH
Q psy5652 65 KCEFCAHSATSKSNLKMHI 83 (92)
Q Consensus 65 ~c~~c~~~~~~~~~l~~h~ 83 (92)
.|..|++.|.....|..|+
T Consensus 2 ~C~~C~~~f~~~~~l~~H~ 20 (26)
T smart00355 2 RCPECGKVFKSKSALKEHM 20 (26)
T ss_pred CCCCCcchhCCHHHHHHHH
Confidence 3445555555555555554
No 35
>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=97.49 E-value=0.00018 Score=31.14 Aligned_cols=33 Identities=24% Similarity=0.446 Sum_probs=17.1
Q ss_pred CCCCceeCCCCCccCCCHHHHHHHHHHhhCCCC
Q psy5652 31 DSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERP 63 (92)
Q Consensus 31 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~ 63 (92)
..+.|..|++|+.......+|.+|+....+.+|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 344566777777777777777777665555443
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.48 E-value=0.0002 Score=26.14 Aligned_cols=24 Identities=38% Similarity=0.686 Sum_probs=18.4
Q ss_pred eeCCCCCccCCCHHHHHHHHHHhh
Q psy5652 36 YVCFKCGYHQYNSDRMKRHIRTHT 59 (92)
Q Consensus 36 ~~c~~c~~~~~~~~~l~~h~~~~~ 59 (92)
+.|..|++.|.....+..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 467888888888888888877553
No 37
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.40 E-value=0.00082 Score=29.11 Aligned_cols=33 Identities=21% Similarity=0.404 Sum_probs=21.7
Q ss_pred hCCCCccCCcCccccCChHHHHHHHHHhccCCCC
Q psy5652 59 TGERPFKCEFCAHSATSKSNLKMHIMVKHQNDFV 92 (92)
Q Consensus 59 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~h~~~~p 92 (92)
..+.|-.|+.|+..+.+..+|.+|+ .++.+.||
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHl-e~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHL-EIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHH-HHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHH-HHHhcccC
Confidence 4567999999999999999999999 44444443
No 38
>PRK04860 hypothetical protein; Provisional
Probab=97.36 E-value=0.00021 Score=38.44 Aligned_cols=39 Identities=28% Similarity=0.588 Sum_probs=32.8
Q ss_pred CceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccccCCh
Q psy5652 34 HLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSATSK 76 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~ 76 (92)
-+|.|. |+. ....+..|.++++++++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 379997 987 556689999999999999999999877543
No 39
>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=97.19 E-value=0.00015 Score=27.32 Aligned_cols=20 Identities=10% Similarity=0.310 Sum_probs=14.6
Q ss_pred Cccccccccccccccccccc
Q psy5652 1 MVCIFCRQLLPMDADFILGH 20 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~ 20 (92)
|.|.+|++.|.++..+..|+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHM 21 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCT
T ss_pred CCcccCCCCcCCHHHHHHHH
Confidence 56777888888877777654
No 40
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.13 E-value=0.00014 Score=42.95 Aligned_cols=20 Identities=10% Similarity=0.225 Sum_probs=17.0
Q ss_pred Ccccc--ccccccccccccccc
Q psy5652 1 MVCIF--CRQLLPMDADFILGH 20 (92)
Q Consensus 1 ~~C~~--C~~~f~~~~~l~~h~ 20 (92)
|+|++ |++.+.....|..|+
T Consensus 350 ykCpV~gC~K~YknqnGLKYH~ 371 (423)
T COG5189 350 YKCPVEGCNKKYKNQNGLKYHM 371 (423)
T ss_pred ecCCCCCchhhhccccchhhhh
Confidence 67877 999999999999875
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.06 E-value=0.00051 Score=25.17 Aligned_cols=20 Identities=20% Similarity=0.542 Sum_probs=9.9
Q ss_pred eCCCCCccCCCHHHHHHHHH
Q psy5652 37 VCFKCGYHQYNSDRMKRHIR 56 (92)
Q Consensus 37 ~c~~c~~~~~~~~~l~~h~~ 56 (92)
.|..|+..|.+...+..|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 44555555555555554443
No 42
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.03 E-value=0.00013 Score=43.04 Aligned_cols=51 Identities=27% Similarity=0.618 Sum_probs=41.7
Q ss_pred CCceeCCC--CCccCCCHHHHHHHHHH-h------------------hCCCCccCCcCccccCChHHHHHHH
Q psy5652 33 SHLYVCFK--CGYHQYNSDRMKRHIRT-H------------------TGERPFKCEFCAHSATSKSNLKMHI 83 (92)
Q Consensus 33 ~~~~~c~~--c~~~~~~~~~l~~h~~~-~------------------~~~~~~~c~~c~~~~~~~~~l~~h~ 83 (92)
++||.|++ |.+.|.+...|+-|+.. | ...|||.|..|+|.+.....|.-|+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 58999976 77999999999988763 2 1248999999999999988887776
No 43
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.39 E-value=0.0058 Score=22.07 Aligned_cols=19 Identities=53% Similarity=1.006 Sum_probs=9.3
Q ss_pred ccCCcCccccCChHHHHHHH
Q psy5652 64 FKCEFCAHSATSKSNLKMHI 83 (92)
Q Consensus 64 ~~c~~c~~~~~~~~~l~~h~ 83 (92)
|+|..|..... ...|..|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~ 19 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHL 19 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHH
Confidence 34555555444 55565555
No 44
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.37 E-value=0.0052 Score=22.68 Aligned_cols=20 Identities=35% Similarity=0.722 Sum_probs=13.0
Q ss_pred eeCCCCCccCCCHHHHHHHHH
Q psy5652 36 YVCFKCGYHQYNSDRMKRHIR 56 (92)
Q Consensus 36 ~~c~~c~~~~~~~~~l~~h~~ 56 (92)
..|+.||+.| ..+.|..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3577777777 5556666654
No 45
>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=95.21 E-value=0.015 Score=22.93 Aligned_cols=24 Identities=38% Similarity=0.984 Sum_probs=13.1
Q ss_pred eeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcc
Q psy5652 36 YVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAH 71 (92)
Q Consensus 36 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 71 (92)
|.|.+||..+.... .++.|+.|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 55666665543321 4666666653
No 46
>KOG2186|consensus
Probab=95.09 E-value=0.012 Score=33.98 Aligned_cols=46 Identities=20% Similarity=0.480 Sum_probs=27.9
Q ss_pred ceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccccCChHHHHHHH
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSATSKSNLKMHI 83 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~ 83 (92)
-|.|.+||....-+ .+..|+..-++ ..|.|..|++.|.. .....|.
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhh
Confidence 36677777765443 35556665555 56777777777755 3444444
No 47
>PRK04860 hypothetical protein; Provisional
Probab=95.05 E-value=0.0038 Score=33.71 Aligned_cols=37 Identities=16% Similarity=0.358 Sum_probs=27.3
Q ss_pred CcccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCH
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNS 48 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~ 48 (92)
|.|. |+. ....+. .|..++.++++|.|..|+..+...
T Consensus 120 Y~C~-C~~---~~~~~r-------rH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 120 YRCK-CQE---HQLTVR-------RHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEcC-CCC---eeCHHH-------HHHHHhcCCccEECCCCCceeEEe
Confidence 4576 775 444555 477889999999999999877543
No 48
>KOG2893|consensus
Probab=94.77 E-value=0.0078 Score=34.51 Aligned_cols=39 Identities=23% Similarity=0.511 Sum_probs=18.9
Q ss_pred CCCccCCCHHHHHHHHHHhhCCCCccCCcCccccCChHHHHHH
Q psy5652 40 KCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSATSKSNLKMH 82 (92)
Q Consensus 40 ~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h 82 (92)
+|.+.|....-|..|++ .+.|+|..|-+..-+...|..|
T Consensus 15 ycnrefddekiliqhqk----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 15 YCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred ecccccchhhhhhhhhh----hccceeeeehhhhccCCCceee
Confidence 45555555555554443 3445555555444344444444
No 49
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=94.54 E-value=0.039 Score=24.73 Aligned_cols=33 Identities=18% Similarity=0.520 Sum_probs=22.9
Q ss_pred CceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcc
Q psy5652 34 HLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAH 71 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 71 (92)
..|.|+.||+..... ..+......+|.|+.||.
T Consensus 26 v~F~CPnCGe~~I~R-----c~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYR-----CAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeeh-----hhhHHHcCCceECCCcCc
Confidence 479999999654332 233444467999999983
No 50
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.53 E-value=0.051 Score=21.30 Aligned_cols=21 Identities=24% Similarity=0.648 Sum_probs=15.7
Q ss_pred CccCCcCccccCChHHHHHHH
Q psy5652 63 PFKCEFCAHSATSKSNLKMHI 83 (92)
Q Consensus 63 ~~~c~~c~~~~~~~~~l~~h~ 83 (92)
+|.|..|+..|.....+..|+
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~ 23 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHL 23 (35)
T ss_pred CeEccccCCccCCHHHHHHHH
Confidence 467777888777777777776
No 51
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=94.35 E-value=0.033 Score=22.44 Aligned_cols=32 Identities=28% Similarity=0.545 Sum_probs=18.6
Q ss_pred cccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccC
Q psy5652 2 VCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQ 45 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~ 45 (92)
.|+.|+..|...++.. ........|..|+..|
T Consensus 4 ~Cp~C~~~y~i~d~~i------------p~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKI------------PPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHC------------CCCCcEEECCCCCCEe
Confidence 4677777766665533 1333456677776554
No 52
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=94.28 E-value=0.03 Score=31.74 Aligned_cols=48 Identities=17% Similarity=0.325 Sum_probs=27.1
Q ss_pred CcccccccccccccccccccccC--CCCCCCC-CCC-----CceeCCCCCccCCCH
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKR--CSNMPRP-DSS-----HLYVCFKCGYHQYNS 48 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~--~~~~~~~-~~~-----~~~~c~~c~~~~~~~ 48 (92)
++|++|++.|.++.-......-. -.....+ .+. ..+.|+.||.++...
T Consensus 6 ~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 6 ITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred eECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 46999999999886554322110 0000111 111 147899999877644
No 53
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=93.90 E-value=0.084 Score=25.65 Aligned_cols=25 Identities=16% Similarity=0.457 Sum_probs=21.7
Q ss_pred ceeCCCCCccCCCHHHHHHHHHHhh
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRTHT 59 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~~~ 59 (92)
.+.|..|+..|.+...|..|++.+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 6899999999999999999999753
No 54
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=93.83 E-value=0.035 Score=22.42 Aligned_cols=14 Identities=14% Similarity=0.392 Sum_probs=8.8
Q ss_pred cccccccccccccc
Q psy5652 2 VCIFCRQLLPMDAD 15 (92)
Q Consensus 2 ~C~~C~~~f~~~~~ 15 (92)
.|+.|+..|....+
T Consensus 4 ~CP~C~~~~~v~~~ 17 (38)
T TIGR02098 4 QCPNCKTSFRVVDS 17 (38)
T ss_pred ECCCCCCEEEeCHH
Confidence 46777766666554
No 55
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.81 E-value=0.031 Score=33.98 Aligned_cols=59 Identities=22% Similarity=0.332 Sum_probs=37.2
Q ss_pred cccccccccccccccccccccCCCCCC--CCCCC--CceeCC--CCCccCCCHHHHHHHHHHhhCCCCccCC
Q psy5652 2 VCIFCRQLLPMDADFILGHCKRCSNMP--RPDSS--HLYVCF--KCGYHQYNSDRMKRHIRTHTGERPFKCE 67 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~--~~~~~--~~~~c~--~c~~~~~~~~~l~~h~~~~~~~~~~~c~ 67 (92)
.|..|...|.....+.. +.. .|..+ +++.|+ .|+..|.....+..|...+.+..++.+.
T Consensus 291 ~~~~~~~~~s~~~~l~~-------~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 291 KSKQCNISFSRSSPLTR-------HLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred CCccccCCccccccccc-------cccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 45666666777766664 333 56666 677776 5777777776666666666665555443
No 56
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.51 E-value=0.049 Score=24.08 Aligned_cols=26 Identities=23% Similarity=0.510 Sum_probs=14.2
Q ss_pred CCCCceeCCCCCccCCCHHHHHHHHH
Q psy5652 31 DSSHLYVCFKCGYHQYNSDRMKRHIR 56 (92)
Q Consensus 31 ~~~~~~~c~~c~~~~~~~~~l~~h~~ 56 (92)
.++.-+.|+-|+..|........|.-
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhh
Confidence 34445566666666655555555543
No 57
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.49 E-value=0.047 Score=22.08 Aligned_cols=14 Identities=21% Similarity=0.548 Sum_probs=7.9
Q ss_pred cccccccccccccc
Q psy5652 2 VCIFCRQLLPMDAD 15 (92)
Q Consensus 2 ~C~~C~~~f~~~~~ 15 (92)
.|+.|+..|...++
T Consensus 4 ~CP~C~~~f~v~~~ 17 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD 17 (37)
T ss_pred ECCCCCceEEcCHH
Confidence 36666666555544
No 58
>KOG2893|consensus
Probab=93.33 E-value=0.0077 Score=34.54 Aligned_cols=43 Identities=14% Similarity=0.417 Sum_probs=32.2
Q ss_pred ccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCHHHHHHHHH
Q psy5652 3 CIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNSDRMKRHIR 56 (92)
Q Consensus 3 C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~ 56 (92)
|..|++.|.++.-|.+|+ . .+.|.|.+|-+...+-..|..|..
T Consensus 13 cwycnrefddekiliqhq-------k----akhfkchichkkl~sgpglsihcm 55 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQ-------K----AKHFKCHICHKKLFSGPGLSIHCM 55 (341)
T ss_pred eeecccccchhhhhhhhh-------h----hccceeeeehhhhccCCCceeehh
Confidence 889999999999988643 2 367888888877666666665543
No 59
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.22 E-value=0.0099 Score=36.09 Aligned_cols=57 Identities=30% Similarity=0.562 Sum_probs=49.8
Q ss_pred CceeCCCCCccCCCHHHHHHHHH--HhhCC--CCccCC--cCccccCChHHHHHHHHHhccCCC
Q psy5652 34 HLYVCFKCGYHQYNSDRMKRHIR--THTGE--RPFKCE--FCAHSATSKSNLKMHIMVKHQNDF 91 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~~~l~~h~~--~~~~~--~~~~c~--~c~~~~~~~~~l~~h~~~~h~~~~ 91 (92)
.++.|..|...+.....+..|.+ .|.++ +++.|+ .|++.|.+...+..|. ..|.+.+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~-~~~~~~~ 350 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHI-LLHTSIS 350 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCc-ccccCCC
Confidence 36889999999999999999999 89999 999999 7999999999988888 7776543
No 60
>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=93.17 E-value=0.14 Score=25.98 Aligned_cols=30 Identities=23% Similarity=0.611 Sum_probs=21.2
Q ss_pred eeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccccCCh
Q psy5652 36 YVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSATSK 76 (92)
Q Consensus 36 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~ 76 (92)
..|+.||..|... ...|..|++||..|...
T Consensus 10 R~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 4788888877553 23578888888877644
No 61
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=93.12 E-value=0.22 Score=22.39 Aligned_cols=34 Identities=18% Similarity=0.514 Sum_probs=22.5
Q ss_pred CCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcc
Q psy5652 33 SHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAH 71 (92)
Q Consensus 33 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 71 (92)
...|.|+.||+..... ..+-.....+|.|+.||.
T Consensus 23 ~~~F~CPnCG~~~I~R-----C~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVIIYR-----CEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCeeEee-----chhHHhcCCceECCCCCC
Confidence 4579999999762222 223334457899999984
No 62
>KOG1146|consensus
Probab=91.85 E-value=0.093 Score=36.99 Aligned_cols=22 Identities=9% Similarity=0.155 Sum_probs=18.7
Q ss_pred Cccccccccccccccccccccc
Q psy5652 1 MVCIFCRQLLPMDADFILGHCK 22 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~ 22 (92)
++|+.|+..|+....|..|++.
T Consensus 466 ~~cpkc~~~yk~a~~L~vhmRs 487 (1406)
T KOG1146|consen 466 LKCPKCNWHYKLAQTLGVHMRS 487 (1406)
T ss_pred ccCCccchhhhhHHHhhhcccc
Confidence 5799999999999999987644
No 63
>KOG1146|consensus
Probab=91.63 E-value=0.18 Score=35.73 Aligned_cols=54 Identities=26% Similarity=0.569 Sum_probs=44.5
Q ss_pred CCCCceeCCCCCccCCCHHHHHHHHHHh-------------------------hCCCCccCCcCccccCChHHHHHHHH
Q psy5652 31 DSSHLYVCFKCGYHQYNSDRMKRHIRTH-------------------------TGERPFKCEFCAHSATSKSNLKMHIM 84 (92)
Q Consensus 31 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~-------------------------~~~~~~~c~~c~~~~~~~~~l~~h~~ 84 (92)
...+.+.|+.|.+.|.....|-.|+|.. -+.++|.|..|...+....+|..|++
T Consensus 461 S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 461 SFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred cccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 3347899999999999999999999870 01356888999999999999999985
No 64
>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=91.57 E-value=0.16 Score=20.16 Aligned_cols=25 Identities=40% Similarity=0.949 Sum_probs=14.3
Q ss_pred ceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcc
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAH 71 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 71 (92)
.|.|.+||..+... ..|..|+.|+.
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCcCCCC
Confidence 36677777554332 14567777764
No 65
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=91.47 E-value=0.098 Score=27.90 Aligned_cols=38 Identities=16% Similarity=0.363 Sum_probs=25.2
Q ss_pred CCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcccc
Q psy5652 32 SSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSA 73 (92)
Q Consensus 32 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~ 73 (92)
+...|.|+.|+..|.....+..- .. ...|.|+.|+...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~---d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLL---DM-DGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhc---CC-CCcEECCCCCCEE
Confidence 44578999999888866544321 11 3349999998654
No 66
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=91.45 E-value=0.21 Score=33.43 Aligned_cols=12 Identities=25% Similarity=0.520 Sum_probs=6.8
Q ss_pred CCceeCCCCCcc
Q psy5652 33 SHLYVCFKCGYH 44 (92)
Q Consensus 33 ~~~~~c~~c~~~ 44 (92)
..|..|+.||..
T Consensus 473 ~~p~~Cp~Cgs~ 484 (730)
T COG1198 473 PIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCC
Confidence 345566666653
No 67
>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=91.23 E-value=0.24 Score=26.83 Aligned_cols=34 Identities=15% Similarity=0.365 Sum_probs=26.4
Q ss_pred CCCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcccc
Q psy5652 31 DSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSA 73 (92)
Q Consensus 31 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~ 73 (92)
.+..-|.|+.|+..|.....+. -.|.|+.||...
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 3456799999999888777664 269999999754
No 68
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=91.23 E-value=0.2 Score=27.37 Aligned_cols=25 Identities=44% Similarity=1.095 Sum_probs=19.9
Q ss_pred CceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcc
Q psy5652 34 HLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAH 71 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 71 (92)
+.|.|++||.. +.|+.|.+||.|+.
T Consensus 133 ~~~vC~vCGy~-------------~~ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGYT-------------HEGEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCCc-------------ccCCCCCcCCCCCC
Confidence 37999999864 35578999999983
No 69
>PHA00626 hypothetical protein
Probab=91.11 E-value=0.31 Score=21.63 Aligned_cols=14 Identities=43% Similarity=1.087 Sum_probs=10.4
Q ss_pred CceeCCCCCccCCC
Q psy5652 34 HLYVCFKCGYHQYN 47 (92)
Q Consensus 34 ~~~~c~~c~~~~~~ 47 (92)
..|.|+.||..|..
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 46888888876654
No 70
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.47 E-value=0.19 Score=21.26 Aligned_cols=11 Identities=36% Similarity=0.688 Sum_probs=7.0
Q ss_pred ceeCCCCCccC
Q psy5652 35 LYVCFKCGYHQ 45 (92)
Q Consensus 35 ~~~c~~c~~~~ 45 (92)
...|+.||..+
T Consensus 21 ~~~Cp~CG~~~ 31 (46)
T PRK00398 21 GVRCPYCGYRI 31 (46)
T ss_pred ceECCCCCCeE
Confidence 45777777544
No 71
>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=90.31 E-value=0.14 Score=21.28 Aligned_cols=15 Identities=13% Similarity=0.246 Sum_probs=9.0
Q ss_pred Ccccccccccccccc
Q psy5652 1 MVCIFCRQLLPMDAD 15 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~ 15 (92)
|.|..||..|.....
T Consensus 6 y~C~~Cg~~fe~~~~ 20 (42)
T PF09723_consen 6 YRCEECGHEFEVLQS 20 (42)
T ss_pred EEeCCCCCEEEEEEE
Confidence 467777766654433
No 72
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=90.21 E-value=0.29 Score=26.44 Aligned_cols=17 Identities=24% Similarity=0.491 Sum_probs=12.4
Q ss_pred CceeCCCCCccCCCHHH
Q psy5652 34 HLYVCFKCGYHQYNSDR 50 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~~~ 50 (92)
+.+.|+.||..|.....
T Consensus 27 ~~~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 27 RRRECLACGKRFTTFER 43 (154)
T ss_pred eeeeccccCCcceEeEe
Confidence 34889999988866543
No 73
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=89.45 E-value=0.38 Score=26.63 Aligned_cols=34 Identities=18% Similarity=0.502 Sum_probs=25.7
Q ss_pred CCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccccC
Q psy5652 32 SSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSAT 74 (92)
Q Consensus 32 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~ 74 (92)
+..-|.|+.|+..|.....+. -.|.|+.||....
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 345799999998888776542 3699999996553
No 74
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=89.26 E-value=0.26 Score=23.14 Aligned_cols=40 Identities=10% Similarity=0.286 Sum_probs=23.9
Q ss_pred CcccccccccccccccccccccCCCCCCCCCCCCceeCC--CCCccCCCHH
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCF--KCGYHQYNSD 49 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~--~c~~~~~~~~ 49 (92)
+.|+.|+......+.-. ......+.-++|. +||..|....
T Consensus 2 m~CP~Cg~~a~irtSr~---------~s~~~~~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 2 FHCPLCQHAAHARTSRY---------ITDTTKERYHQCQNVNCSATFITYE 43 (72)
T ss_pred ccCCCCCCccEEEEChh---------cChhhheeeeecCCCCCCCEEEEEE
Confidence 46888887654443322 1222455677887 8888776543
No 75
>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=88.39 E-value=0.8 Score=16.71 Aligned_cols=9 Identities=33% Similarity=0.947 Sum_probs=6.1
Q ss_pred CceeCCCCC
Q psy5652 34 HLYVCFKCG 42 (92)
Q Consensus 34 ~~~~c~~c~ 42 (92)
..|.|+.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 467777776
No 76
>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=88.28 E-value=0.41 Score=24.99 Aligned_cols=14 Identities=14% Similarity=-0.204 Sum_probs=8.3
Q ss_pred ceeCCCCCccCCCH
Q psy5652 35 LYVCFKCGYHQYNS 48 (92)
Q Consensus 35 ~~~c~~c~~~~~~~ 48 (92)
|-.|+.||..|...
T Consensus 26 p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 26 PAVSPYTGEQFPPE 39 (129)
T ss_pred CccCCCcCCccCcc
Confidence 45666666665544
No 77
>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=88.27 E-value=0.68 Score=19.18 Aligned_cols=22 Identities=36% Similarity=0.699 Sum_probs=8.8
Q ss_pred CccCCcCccccCC----hHHHHHHHH
Q psy5652 63 PFKCEFCAHSATS----KSNLKMHIM 84 (92)
Q Consensus 63 ~~~c~~c~~~~~~----~~~l~~h~~ 84 (92)
...|..|++.+.. .++|..|+.
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHHH
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 3445555544433 245555553
No 78
>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=88.15 E-value=0.83 Score=19.84 Aligned_cols=13 Identities=15% Similarity=0.416 Sum_probs=8.9
Q ss_pred Ccccccccccccc
Q psy5652 1 MVCIFCRQLLPMD 13 (92)
Q Consensus 1 ~~C~~C~~~f~~~ 13 (92)
|+|.+|+..+.-.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 5688888666544
No 79
>KOG4173|consensus
Probab=87.83 E-value=0.15 Score=28.79 Aligned_cols=51 Identities=20% Similarity=0.411 Sum_probs=35.8
Q ss_pred eCCCCCccCCCHHHHHHHHHH----------hhCCCCccCCc--CccccCChHHHHHHHHHhc
Q psy5652 37 VCFKCGYHQYNSDRMKRHIRT----------HTGERPFKCEF--CAHSATSKSNLKMHIMVKH 87 (92)
Q Consensus 37 ~c~~c~~~~~~~~~l~~h~~~----------~~~~~~~~c~~--c~~~~~~~~~l~~h~~~~h 87 (92)
.|.+|.+.|+..-.|..|+.. -.|.--|+|.. |+..|.+......|+-.+|
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhc
Confidence 678888888888777777752 23334477765 8877888777777765555
No 80
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=87.83 E-value=0.27 Score=21.21 Aligned_cols=13 Identities=15% Similarity=0.386 Sum_probs=8.8
Q ss_pred Ccccccccccccc
Q psy5652 1 MVCIFCRQLLPMD 13 (92)
Q Consensus 1 ~~C~~C~~~f~~~ 13 (92)
|+|..|+..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (52)
T TIGR02605 6 YRCTACGHRFEVL 18 (52)
T ss_pred EEeCCCCCEeEEE
Confidence 5677888776643
No 81
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=86.91 E-value=0.5 Score=26.99 Aligned_cols=24 Identities=25% Similarity=0.642 Sum_probs=12.2
Q ss_pred ccCCcCccccCChHHHHHHHHHhc
Q psy5652 64 FKCEFCAHSATSKSNLKMHIMVKH 87 (92)
Q Consensus 64 ~~c~~c~~~~~~~~~l~~h~~~~h 87 (92)
|.|..|+|.|.-..-+.+|+...|
T Consensus 78 ~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp EEE-SSS-EESSHHHHHHHHHHH-
T ss_pred ECCCCCCcccCChHHHHHHHhhcC
Confidence 555556666665555555555554
No 82
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=86.56 E-value=0.9 Score=19.48 Aligned_cols=10 Identities=30% Similarity=0.574 Sum_probs=5.0
Q ss_pred eeCCCCCccC
Q psy5652 36 YVCFKCGYHQ 45 (92)
Q Consensus 36 ~~c~~c~~~~ 45 (92)
..|..|++.+
T Consensus 19 a~C~~C~~~l 28 (50)
T smart00614 19 AKCKYCGKKL 28 (50)
T ss_pred EEecCCCCEe
Confidence 4455555544
No 83
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=85.74 E-value=0.76 Score=19.36 Aligned_cols=10 Identities=40% Similarity=1.192 Sum_probs=5.4
Q ss_pred eeCCCCCccC
Q psy5652 36 YVCFKCGYHQ 45 (92)
Q Consensus 36 ~~c~~c~~~~ 45 (92)
|.|..||..+
T Consensus 3 Y~C~~Cg~~~ 12 (44)
T smart00659 3 YICGECGREN 12 (44)
T ss_pred EECCCCCCEe
Confidence 5555555544
No 84
>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=85.02 E-value=0.55 Score=20.11 Aligned_cols=15 Identities=13% Similarity=0.383 Sum_probs=9.3
Q ss_pred Ccccccccccccccc
Q psy5652 1 MVCIFCRQLLPMDAD 15 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~ 15 (92)
|.|.+|+..+.....
T Consensus 2 y~C~~CgyvYd~~~G 16 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKG 16 (47)
T ss_dssp EEETTTSBEEETTTB
T ss_pred cCCCCCCEEEcCCcC
Confidence 467777766555543
No 85
>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=84.09 E-value=1.3 Score=28.51 Aligned_cols=10 Identities=30% Similarity=0.627 Sum_probs=6.0
Q ss_pred CceeCCCCCc
Q psy5652 34 HLYVCFKCGY 43 (92)
Q Consensus 34 ~~~~c~~c~~ 43 (92)
.+..|+.|+.
T Consensus 252 ~~~~Cp~C~s 261 (505)
T TIGR00595 252 IPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCC
Confidence 3556666665
No 86
>KOG2593|consensus
Probab=84.06 E-value=0.5 Score=29.65 Aligned_cols=19 Identities=21% Similarity=0.441 Sum_probs=9.7
Q ss_pred CceeCCCCCccCCCHHHHH
Q psy5652 34 HLYVCFKCGYHQYNSDRMK 52 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~~~l~ 52 (92)
..|.|+.|.+.|.....++
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~ 145 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQ 145 (436)
T ss_pred ccccCCccccchhhhHHHH
Confidence 3455555555555544433
No 87
>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=83.94 E-value=0.27 Score=18.68 Aligned_cols=18 Identities=17% Similarity=0.357 Sum_probs=11.0
Q ss_pred Ccccccccccccccccccc
Q psy5652 1 MVCIFCRQLLPMDADFILG 19 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h 19 (92)
|.|-.|++.| ...+++.|
T Consensus 1 ~sCiDC~~~F-~~~~y~~H 18 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSH 18 (28)
T ss_dssp EEETTTTEEE-EGGGTTT-
T ss_pred CeeecCCCCc-CcCCcCCC
Confidence 4577788888 44555543
No 88
>PRK14873 primosome assembly protein PriA; Provisional
Probab=83.41 E-value=1.2 Score=29.83 Aligned_cols=10 Identities=30% Similarity=0.836 Sum_probs=5.4
Q ss_pred ceeCCCCCcc
Q psy5652 35 LYVCFKCGYH 44 (92)
Q Consensus 35 ~~~c~~c~~~ 44 (92)
++.|+.|+..
T Consensus 422 p~~Cp~Cgs~ 431 (665)
T PRK14873 422 DWRCPRCGSD 431 (665)
T ss_pred CccCCCCcCC
Confidence 4556666543
No 89
>COG1773 Rubredoxin [Energy production and conversion]
Probab=82.38 E-value=1.8 Score=19.24 Aligned_cols=15 Identities=13% Similarity=0.372 Sum_probs=9.6
Q ss_pred Ccccccccccccccc
Q psy5652 1 MVCIFCRQLLPMDAD 15 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~ 15 (92)
|+|..|+-.|.-..-
T Consensus 4 ~~C~~CG~vYd~e~G 18 (55)
T COG1773 4 WRCSVCGYVYDPEKG 18 (55)
T ss_pred eEecCCceEeccccC
Confidence 467777776665543
No 90
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=82.31 E-value=2 Score=15.83 Aligned_cols=18 Identities=17% Similarity=0.355 Sum_probs=9.1
Q ss_pred eCCCCCccCCCHHHHHHHH
Q psy5652 37 VCFKCGYHQYNSDRMKRHI 55 (92)
Q Consensus 37 ~c~~c~~~~~~~~~l~~h~ 55 (92)
.|++|++.+ ....+..|+
T Consensus 3 ~CPiC~~~v-~~~~in~HL 20 (26)
T smart00734 3 QCPVCFREV-PENLINSHL 20 (26)
T ss_pred cCCCCcCcc-cHHHHHHHH
Confidence 466666655 333444443
No 91
>KOG2186|consensus
Probab=79.76 E-value=0.48 Score=27.70 Aligned_cols=50 Identities=20% Similarity=0.354 Sum_probs=33.4
Q ss_pred CcccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhC
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTG 60 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~ 60 (92)
|.|.+||....-...-+ |+..-.+ .-|.|..|+..|.. .....|...-+.
T Consensus 4 FtCnvCgEsvKKp~vek--------H~srCrn-~~fSCIDC~k~F~~-~sYknH~kCITE 53 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQVEK--------HMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCITE 53 (276)
T ss_pred EehhhhhhhccccchHH--------HHHhccC-CeeEEeeccccccc-chhhhhhhhcch
Confidence 57888988776655433 3322233 57899999999988 457777765443
No 92
>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=79.08 E-value=1.1 Score=16.62 Aligned_cols=8 Identities=25% Similarity=0.650 Sum_probs=3.8
Q ss_pred cccccccc
Q psy5652 3 CIFCRQLL 10 (92)
Q Consensus 3 C~~C~~~f 10 (92)
|+.||..|
T Consensus 17 Cp~CG~~F 24 (26)
T PF10571_consen 17 CPHCGYDF 24 (26)
T ss_pred CCCCCCCC
Confidence 44555444
No 93
>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=77.88 E-value=1.8 Score=17.63 Aligned_cols=36 Identities=22% Similarity=0.444 Sum_probs=16.9
Q ss_pred CcccccccccccccccccccccCCCCCCCCCCC--CceeCCCCCccC
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMPRPDSS--HLYVCFKCGYHQ 45 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~--~~~~c~~c~~~~ 45 (92)
++|+.|+..-.....++ .++..+. .-|.|..|+..+
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q---------~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQ---------TRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp S--SSS-SSEEEEEEES---------SSSSSSSSEEEEEESSSTEEE
T ss_pred CCCcCCCCCeEEEEEee---------ccCCCCCCeEEEEeCCCCCee
Confidence 46888876533333322 2222221 357888888654
No 94
>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=77.26 E-value=0.89 Score=18.76 Aligned_cols=14 Identities=29% Similarity=0.634 Sum_probs=9.5
Q ss_pred CceeCCCCCccCCC
Q psy5652 34 HLYVCFKCGYHQYN 47 (92)
Q Consensus 34 ~~~~c~~c~~~~~~ 47 (92)
..+.|+.||+.+.+
T Consensus 31 p~~~C~~CGE~~~~ 44 (46)
T TIGR03831 31 PALVCPQCGEEYLD 44 (46)
T ss_pred CccccccCCCEeeC
Confidence 34678888876654
No 95
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=77.04 E-value=1.3 Score=19.57 Aligned_cols=16 Identities=19% Similarity=0.505 Sum_probs=11.8
Q ss_pred cccccccccccccccc
Q psy5652 2 VCIFCRQLLPMDADFI 17 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~ 17 (92)
+|.+|++.|...++..
T Consensus 7 ~C~~Cg~~~~~~dDiV 22 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIV 22 (54)
T ss_pred cChhhCCcccCCCCEE
Confidence 5889998888666543
No 96
>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=76.90 E-value=0.86 Score=18.39 Aligned_cols=13 Identities=15% Similarity=0.299 Sum_probs=8.2
Q ss_pred Ccccccccccccc
Q psy5652 1 MVCIFCRQLLPMD 13 (92)
Q Consensus 1 ~~C~~C~~~f~~~ 13 (92)
|.|..|+..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (41)
T smart00834 6 YRCEDCGHTFEVL 18 (41)
T ss_pred EEcCCCCCEEEEE
Confidence 4677777666543
No 97
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=76.61 E-value=0.91 Score=30.49 Aligned_cols=31 Identities=23% Similarity=0.484 Sum_probs=21.3
Q ss_pred eCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcccc
Q psy5652 37 VCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSA 73 (92)
Q Consensus 37 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~ 73 (92)
-|+.|.+-|.+...- |.| ..|..|+.||...
T Consensus 153 lC~~C~~EY~dP~nR----RfH--AQp~aCp~CGP~~ 183 (750)
T COG0068 153 LCPFCDKEYKDPLNR----RFH--AQPIACPKCGPHL 183 (750)
T ss_pred CCHHHHHHhcCcccc----ccc--cccccCcccCCCe
Confidence 488888877776542 334 4588999999633
No 98
>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=76.58 E-value=3.6 Score=16.53 Aligned_cols=14 Identities=29% Similarity=0.774 Sum_probs=7.0
Q ss_pred CCCCCCCceeCCCC
Q psy5652 28 PRPDSSHLYVCFKC 41 (92)
Q Consensus 28 ~~~~~~~~~~c~~c 41 (92)
....+...|.|..|
T Consensus 22 ~~~~G~qryrC~~C 35 (36)
T PF03811_consen 22 KSPSGHQRYRCKDC 35 (36)
T ss_pred CCCCCCEeEecCcC
Confidence 33344445666555
No 99
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=76.43 E-value=3.1 Score=23.92 Aligned_cols=26 Identities=19% Similarity=0.395 Sum_probs=20.9
Q ss_pred CCCceeCCCCCccCCCHHHHHHHHHH
Q psy5652 32 SSHLYVCFKCGYHQYNSDRMKRHIRT 57 (92)
Q Consensus 32 ~~~~~~c~~c~~~~~~~~~l~~h~~~ 57 (92)
++..|.|..|++.|.....+.+|+..
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 44569999999999999999999975
No 100
>KOG3408|consensus
Probab=75.49 E-value=2.4 Score=22.03 Aligned_cols=25 Identities=20% Similarity=0.547 Sum_probs=22.0
Q ss_pred CCceeCCCCCccCCCHHHHHHHHHH
Q psy5652 33 SHLYVCFKCGYHQYNSDRMKRHIRT 57 (92)
Q Consensus 33 ~~~~~c~~c~~~~~~~~~l~~h~~~ 57 (92)
...|.|..|.+-|.+...|+.|.++
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHhc
Confidence 3469999999999999999999875
No 101
>PRK05580 primosome assembly protein PriA; Validated
Probab=75.40 E-value=3.8 Score=27.59 Aligned_cols=11 Identities=27% Similarity=0.555 Sum_probs=7.1
Q ss_pred CceeCCCCCcc
Q psy5652 34 HLYVCFKCGYH 44 (92)
Q Consensus 34 ~~~~c~~c~~~ 44 (92)
.+..|+.|+..
T Consensus 420 ~~~~Cp~Cg~~ 430 (679)
T PRK05580 420 IPKACPECGST 430 (679)
T ss_pred CCCCCCCCcCC
Confidence 45667777654
No 102
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=75.34 E-value=1.4 Score=18.22 Aligned_cols=10 Identities=30% Similarity=0.607 Sum_probs=5.0
Q ss_pred cccccccccc
Q psy5652 3 CIFCRQLLPM 12 (92)
Q Consensus 3 C~~C~~~f~~ 12 (92)
|+.|++.|..
T Consensus 16 C~~CgM~Y~~ 25 (41)
T PF13878_consen 16 CPTCGMLYSP 25 (41)
T ss_pred CCCCCCEECC
Confidence 5555555443
No 103
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=75.24 E-value=4.3 Score=17.23 Aligned_cols=12 Identities=50% Similarity=1.184 Sum_probs=8.8
Q ss_pred ceeCCCCCccCC
Q psy5652 35 LYVCFKCGYHQY 46 (92)
Q Consensus 35 ~~~c~~c~~~~~ 46 (92)
.+.|+.||..+.
T Consensus 20 ~~vC~~Cg~~~~ 31 (52)
T smart00661 20 RFVCRKCGYEEP 31 (52)
T ss_pred EEECCcCCCeEE
Confidence 678888886543
No 104
>PF15269 zf-C2H2_7: Zinc-finger
Probab=75.17 E-value=2.9 Score=17.69 Aligned_cols=20 Identities=35% Similarity=0.688 Sum_probs=13.8
Q ss_pred ccCCcCccccCChHHHHHHH
Q psy5652 64 FKCEFCAHSATSKSNLKMHI 83 (92)
Q Consensus 64 ~~c~~c~~~~~~~~~l~~h~ 83 (92)
|+|.+|.....-.+.|..|+
T Consensus 21 ykcfqcpftc~~kshl~nhm 40 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHM 40 (54)
T ss_pred ceeecCCcccchHHHHHHHH
Confidence 56777766666677777776
No 105
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=75.00 E-value=2.9 Score=20.44 Aligned_cols=30 Identities=27% Similarity=0.443 Sum_probs=17.6
Q ss_pred ceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccccC
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSAT 74 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~ 74 (92)
.+.|+.|++. ...+.. ..-|.|..|+..|.
T Consensus 35 ~~~Cp~C~~~--------~VkR~a--~GIW~C~kCg~~fA 64 (89)
T COG1997 35 KHVCPFCGRT--------TVKRIA--TGIWKCRKCGAKFA 64 (89)
T ss_pred CCcCCCCCCc--------ceeeec--cCeEEcCCCCCeec
Confidence 5778888754 112222 33578888876664
No 106
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=74.99 E-value=5 Score=20.64 Aligned_cols=84 Identities=13% Similarity=0.176 Sum_probs=46.7
Q ss_pred cccccccccccccccccccccC---CCCCCCCCC--CCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccccCCh
Q psy5652 2 VCIFCRQLLPMDADFILGHCKR---CSNMPRPDS--SHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSATSK 76 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~---~~~~~~~~~--~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~ 76 (92)
+|++|+-.+....+|.+-+--. ....++... ...-.|--|...|........ ..-.....|.|..|...|=-.
T Consensus 17 ~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~FC~d 94 (112)
T TIGR00622 17 ECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNVFCVD 94 (112)
T ss_pred cCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCCccccc
Confidence 5899999988888888642110 001111111 111247777777765421110 001223478999999888777
Q ss_pred HHHHHHHHHhcc
Q psy5652 77 SNLKMHIMVKHQ 88 (92)
Q Consensus 77 ~~l~~h~~~~h~ 88 (92)
-+...|. ..|+
T Consensus 95 CD~fiHe-~Lh~ 105 (112)
T TIGR00622 95 CDVFVHE-SLHC 105 (112)
T ss_pred cchhhhh-hccC
Confidence 7777776 5553
No 107
>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=74.72 E-value=1.6 Score=16.82 Aligned_cols=9 Identities=56% Similarity=1.287 Sum_probs=4.8
Q ss_pred CceeCCCCC
Q psy5652 34 HLYVCFKCG 42 (92)
Q Consensus 34 ~~~~c~~c~ 42 (92)
..+.|++|+
T Consensus 18 ~~~vCp~C~ 26 (30)
T PF08274_consen 18 ELLVCPECG 26 (30)
T ss_dssp SSEEETTTT
T ss_pred CEEeCCccc
Confidence 345565555
No 108
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=74.40 E-value=5 Score=16.40 Aligned_cols=12 Identities=50% Similarity=1.040 Sum_probs=8.2
Q ss_pred CceeCCCCCccC
Q psy5652 34 HLYVCFKCGYHQ 45 (92)
Q Consensus 34 ~~~~c~~c~~~~ 45 (92)
.-|.|..|+..+
T Consensus 27 ~fy~C~~C~~~w 38 (40)
T smart00440 27 VFYVCTKCGHRW 38 (40)
T ss_pred EEEEeCCCCCEe
Confidence 357888887654
No 109
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=74.03 E-value=3.4 Score=28.14 Aligned_cols=47 Identities=19% Similarity=0.404 Sum_probs=33.5
Q ss_pred ccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccc
Q psy5652 3 CIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHS 72 (92)
Q Consensus 3 C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~ 72 (92)
|..||..+.....-. .+.-|.......|..||.. ...|..|+.|+..
T Consensus 438 C~~Cg~v~~Cp~Cd~--------~lt~H~~~~~L~CH~Cg~~---------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 438 CRDCGYIAECPNCDS--------PLTLHKATGQLRCHYCGYQ---------------EPIPQSCPECGSE 484 (730)
T ss_pred cccCCCcccCCCCCc--------ceEEecCCCeeEeCCCCCC---------------CCCCCCCCCCCCC
Confidence 777777777766433 4666776678899999842 2468899999854
No 110
>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=73.61 E-value=2.6 Score=22.27 Aligned_cols=24 Identities=42% Similarity=0.912 Sum_probs=15.5
Q ss_pred ceeCCCCCccCCCHHHHHHHHHHhhCC
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRTHTGE 61 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~~~~~ 61 (92)
.-.|-+||+.|.. |.+|++.|.|-
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 4689999999887 58899888653
No 111
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.01 E-value=2.8 Score=21.44 Aligned_cols=14 Identities=14% Similarity=-0.133 Sum_probs=8.2
Q ss_pred CceeCCCCCccCCC
Q psy5652 34 HLYVCFKCGYHQYN 47 (92)
Q Consensus 34 ~~~~c~~c~~~~~~ 47 (92)
.|..|+.||+.|+.
T Consensus 25 dPiVsPytG~s~P~ 38 (129)
T COG4530 25 DPIVSPYTGKSYPR 38 (129)
T ss_pred CccccCcccccchH
Confidence 35566666666643
No 112
>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=72.99 E-value=1.6 Score=17.35 Aligned_cols=16 Identities=13% Similarity=0.042 Sum_probs=8.5
Q ss_pred cccccccccccccccc
Q psy5652 2 VCIFCRQLLPMDADFI 17 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~ 17 (92)
+|.+|++.|.++..+.
T Consensus 5 ~C~eC~~~f~dSyL~~ 20 (34)
T PF01286_consen 5 KCDECGKPFMDSYLLN 20 (34)
T ss_dssp E-TTT--EES-SSCCC
T ss_pred hHhHhCCHHHHHHHHH
Confidence 4888998888776544
No 113
>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=72.09 E-value=4.8 Score=15.47 Aligned_cols=12 Identities=17% Similarity=0.335 Sum_probs=7.1
Q ss_pred cccccccccccc
Q psy5652 2 VCIFCRQLLPMD 13 (92)
Q Consensus 2 ~C~~C~~~f~~~ 13 (92)
+|..|++.+...
T Consensus 1 ~C~~C~~~i~~~ 12 (39)
T smart00132 1 KCAGCGKPIRGG 12 (39)
T ss_pred CccccCCcccCC
Confidence 366677665554
No 114
>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=71.72 E-value=3.5 Score=22.46 Aligned_cols=17 Identities=18% Similarity=0.337 Sum_probs=12.3
Q ss_pred CceeCCCCCccCCCHHH
Q psy5652 34 HLYVCFKCGYHQYNSDR 50 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~~~ 50 (92)
.|..|..||+.|++...
T Consensus 67 ~PsYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 67 APSYCHNCGKPYPWTEN 83 (158)
T ss_pred CChhHHhCCCCCchHHH
Confidence 57778888888877644
No 115
>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=71.41 E-value=1.4 Score=18.68 Aligned_cols=14 Identities=14% Similarity=0.396 Sum_probs=8.0
Q ss_pred cccccccccccccc
Q psy5652 2 VCIFCRQLLPMDAD 15 (92)
Q Consensus 2 ~C~~C~~~f~~~~~ 15 (92)
.|+.||........
T Consensus 1 ~CP~Cg~~a~ir~S 14 (47)
T PF04606_consen 1 RCPHCGSKARIRTS 14 (47)
T ss_pred CcCCCCCeeEEEEc
Confidence 36777765544443
No 116
>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=71.06 E-value=3.5 Score=21.10 Aligned_cols=22 Identities=23% Similarity=0.465 Sum_probs=16.0
Q ss_pred CCCceeCCCCCccCCCHHHHHH
Q psy5652 32 SSHLYVCFKCGYHQYNSDRMKR 53 (92)
Q Consensus 32 ~~~~~~c~~c~~~~~~~~~l~~ 53 (92)
....+.|+.||..+.+......
T Consensus 28 ~~~~~~C~~CGe~~~~~e~~~~ 49 (127)
T TIGR03830 28 GVPGWYCPACGEELLDPEESKR 49 (127)
T ss_pred eeeeeECCCCCCEEEcHHHHHH
Confidence 3346889999998887765443
No 117
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.40 E-value=5.1 Score=21.03 Aligned_cols=42 Identities=17% Similarity=0.143 Sum_probs=23.3
Q ss_pred cccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCHH
Q psy5652 2 VCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNSD 49 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~ 49 (92)
.|+.|....+-...+.. ....-+.=+.|..|..||..|++..
T Consensus 41 qcp~csasirgd~~veg------vlglg~dye~psfchncgs~fpwte 82 (160)
T COG4306 41 QCPICSASIRGDYYVEG------VLGLGGDYEPPSFCHNCGSRFPWTE 82 (160)
T ss_pred cCCccCCcccccceeee------eeccCCCCCCcchhhcCCCCCCcHH
Confidence 36666655544443331 1112223345777889999888764
No 118
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=70.07 E-value=2.1 Score=18.52 Aligned_cols=10 Identities=20% Similarity=0.554 Sum_probs=7.9
Q ss_pred Cccccccccc
Q psy5652 1 MVCIFCRQLL 10 (92)
Q Consensus 1 ~~C~~C~~~f 10 (92)
|+|..|++.|
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 5688888887
No 119
>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=69.99 E-value=7 Score=19.63 Aligned_cols=23 Identities=35% Similarity=0.817 Sum_probs=15.2
Q ss_pred eeC----CCCCccCCCHHHHHHHHHHh
Q psy5652 36 YVC----FKCGYHQYNSDRMKRHIRTH 58 (92)
Q Consensus 36 ~~c----~~c~~~~~~~~~l~~h~~~~ 58 (92)
|.| ..|+....+...+..|.+..
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~ 107 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKE 107 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHh
Confidence 666 67777666666666666543
No 120
>KOG1842|consensus
Probab=69.62 E-value=3.4 Score=26.43 Aligned_cols=26 Identities=15% Similarity=0.319 Sum_probs=19.8
Q ss_pred CceeCCCCCccCCCHHHHHHHHHHhh
Q psy5652 34 HLYVCFKCGYHQYNSDRMKRHIRTHT 59 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~~~l~~h~~~~~ 59 (92)
..|.|+.|...|.+...|..|.-.-.
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH 39 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEH 39 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhc
Confidence 46788888888888888888876533
No 121
>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=68.68 E-value=1.7 Score=18.97 Aligned_cols=9 Identities=33% Similarity=0.608 Sum_probs=2.7
Q ss_pred CCCCCccCC
Q psy5652 38 CFKCGYHQY 46 (92)
Q Consensus 38 c~~c~~~~~ 46 (92)
||+|++.|.
T Consensus 23 CPlC~r~l~ 31 (54)
T PF04423_consen 23 CPLCGRPLD 31 (54)
T ss_dssp -TTT--EE-
T ss_pred CCCCCCCCC
Confidence 555555544
No 122
>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=68.67 E-value=1.2 Score=26.33 Aligned_cols=23 Identities=22% Similarity=0.557 Sum_probs=14.5
Q ss_pred CCCccCCcCccccCChHHHHHHH
Q psy5652 61 ERPFKCEFCAHSATSKSNLKMHI 83 (92)
Q Consensus 61 ~~~~~c~~c~~~~~~~~~l~~h~ 83 (92)
.+++.|+.|+........|....
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmSt 229 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMST 229 (314)
T ss_pred CCCCCCCCCCCcccccccceeee
Confidence 36788888886655555554443
No 123
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=68.32 E-value=2.4 Score=24.02 Aligned_cols=35 Identities=26% Similarity=0.466 Sum_probs=19.8
Q ss_pred cccccccccccccccccccccCCCCCCCC-CCC---CceeCCCCCccCC
Q psy5652 2 VCIFCRQLLPMDADFILGHCKRCSNMPRP-DSS---HLYVCFKCGYHQY 46 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~-~~~---~~~~c~~c~~~~~ 46 (92)
.|+.|+..+.....+. .++ .++ ..+.|..||+.+.
T Consensus 16 ~CPvCg~~l~~~~~~~----------~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 16 DCPVCGGTLKAHMYLY----------DIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred cCCcccceeeEEEeee----------cCCccceEEEEEEEccccCCccc
Confidence 5899987554444333 222 232 2577888886544
No 124
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=67.89 E-value=2.4 Score=22.25 Aligned_cols=17 Identities=12% Similarity=0.311 Sum_probs=12.7
Q ss_pred Ccccccccccccccccc
Q psy5652 1 MVCIFCRQLLPMDADFI 17 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~ 17 (92)
|+|+.|++.|.....-.
T Consensus 54 yrC~~C~~tf~~~~~~~ 70 (129)
T COG3677 54 YKCKSCGSTFTVETGSP 70 (129)
T ss_pred cccCCcCcceeeeccCc
Confidence 67899998887776533
No 125
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=67.54 E-value=3.2 Score=20.43 Aligned_cols=12 Identities=17% Similarity=0.697 Sum_probs=7.7
Q ss_pred CccCCcCccccC
Q psy5652 63 PFKCEFCAHSAT 74 (92)
Q Consensus 63 ~~~c~~c~~~~~ 74 (92)
.|.|..|++.|.
T Consensus 54 IW~C~~C~~~~A 65 (90)
T PTZ00255 54 IWRCKGCKKTVA 65 (90)
T ss_pred EEEcCCCCCEEe
Confidence 577777776553
No 126
>PF14353 CpXC: CpXC protein
Probab=67.48 E-value=2.3 Score=22.05 Aligned_cols=18 Identities=11% Similarity=0.479 Sum_probs=13.7
Q ss_pred Cccccccccccccccccc
Q psy5652 1 MVCIFCRQLLPMDADFIL 18 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~ 18 (92)
|.|+.||..|.....+..
T Consensus 39 ~~CP~Cg~~~~~~~p~lY 56 (128)
T PF14353_consen 39 FTCPSCGHKFRLEYPLLY 56 (128)
T ss_pred EECCCCCCceecCCCEEE
Confidence 468888888887776664
No 127
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=67.45 E-value=1.1 Score=19.95 Aligned_cols=36 Identities=28% Similarity=0.532 Sum_probs=17.0
Q ss_pred cccccccccccccccccccccCCCCCCCCCCCCceeCCCCCc
Q psy5652 2 VCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGY 43 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~ 43 (92)
+|-+|++.+...++-.. .-....-.-..|-|.+|..
T Consensus 4 kC~lCdk~~~Id~~~~~------aKrLrnrPi~tYmC~eC~~ 39 (56)
T PF09963_consen 4 KCILCDKKEEIDEDTPE------AKRLRNRPIHTYMCDECKE 39 (56)
T ss_pred EEEecCCEEEeccCCHH------HHHhhcCCCcceeChhHHH
Confidence 46677766554432111 0112222334677777754
No 128
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=67.30 E-value=3.1 Score=18.39 Aligned_cols=30 Identities=20% Similarity=0.523 Sum_probs=18.5
Q ss_pred CcccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccC
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQ 45 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~ 45 (92)
|+|+.|+..+.-..+.. + ....|+.||-.+
T Consensus 3 ~~CP~CG~~iev~~~~~--------------G-eiV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPEL--------------G-ELVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCcc--------------C-CEEeCCCCCCEE
Confidence 57999998764433311 1 245888888544
No 129
>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=67.09 E-value=6.4 Score=25.43 Aligned_cols=25 Identities=16% Similarity=0.401 Sum_probs=12.4
Q ss_pred ccCCcCccccCChHHHHHHHHHhcc
Q psy5652 64 FKCEFCAHSATSKSNLKMHIMVKHQ 88 (92)
Q Consensus 64 ~~c~~c~~~~~~~~~l~~h~~~~h~ 88 (92)
+.|+.|.+.|.....+..|+...|.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~ 82 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHP 82 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhh
Confidence 3444455555555555555544443
No 130
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=66.84 E-value=6 Score=17.60 Aligned_cols=10 Identities=30% Similarity=0.793 Sum_probs=5.8
Q ss_pred CceeCCCCCc
Q psy5652 34 HLYVCFKCGY 43 (92)
Q Consensus 34 ~~~~c~~c~~ 43 (92)
..|.|+.||-
T Consensus 13 v~~~Cp~cGi 22 (55)
T PF13824_consen 13 VNFECPDCGI 22 (55)
T ss_pred cCCcCCCCCC
Confidence 4566666664
No 131
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=65.81 E-value=17 Score=19.99 Aligned_cols=56 Identities=16% Similarity=0.235 Sum_probs=37.5
Q ss_pred ceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCc--CccccCChHHHHHHHHHhccCCCC
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEF--CAHSATSKSNLKMHIMVKHQNDFV 92 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~--c~~~~~~~~~l~~h~~~~h~~~~p 92 (92)
...|+.|........... -.|.+...|+-.|.. |.. ..+...|.+|.+..|...+|
T Consensus 80 ~L~CPLCRG~V~GWtvve-~AR~~LN~K~RsC~~e~C~F-~GtY~eLrKHar~~HP~~rP 137 (162)
T PF07800_consen 80 ELACPLCRGEVKGWTVVE-PARRFLNAKKRSCSQESCSF-SGTYSELRKHARSEHPSARP 137 (162)
T ss_pred cccCccccCceeceEEch-HHHHHhccCCccCccccccc-ccCHHHHHHHHHhhCCCCCC
Confidence 567888865443332222 245566677878866 543 34778999999999988876
No 132
>KOG2907|consensus
Probab=65.33 E-value=6 Score=20.34 Aligned_cols=39 Identities=23% Similarity=0.468 Sum_probs=24.7
Q ss_pred CceeCCCCCccCCCHHHHHHHHHH-hhCCC-CccCCcCccccC
Q psy5652 34 HLYVCFKCGYHQYNSDRMKRHIRT-HTGER-PFKCEFCAHSAT 74 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~~~l~~h~~~-~~~~~-~~~c~~c~~~~~ 74 (92)
....|+.||..-.....+|. |+ ..|+- =|.|+.|+..|.
T Consensus 73 I~~kCpkCghe~m~Y~T~Ql--RSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 73 IKHKCPKCGHEEMSYHTLQL--RSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred hhccCcccCCchhhhhhhhc--ccccCCceEEEEcCccceeee
Confidence 44678888876666655553 33 34443 378888886654
No 133
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.57 E-value=2 Score=19.52 Aligned_cols=37 Identities=22% Similarity=0.486 Sum_probs=20.5
Q ss_pred cccccccc-cccccccccccccCCCCCCCCCCCCceeCCCCCccC
Q psy5652 2 VCIFCRQL-LPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQ 45 (92)
Q Consensus 2 ~C~~C~~~-f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~ 45 (92)
+|.+|++. +.+...+. ..+.....-+.|-|++|....
T Consensus 4 kCiiCd~v~~iD~rt~~-------tKrLrN~PIrtymC~eC~~Rv 41 (68)
T COG4896 4 KCIICDRVDEIDNRTFK-------TKRLRNKPIRTYMCPECEHRV 41 (68)
T ss_pred eEEEecceeeecchhHH-------HHHhhCCCceeEechhhHhhh
Confidence 57788765 33333333 123333444678898886543
No 134
>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=64.31 E-value=3 Score=16.29 Aligned_cols=11 Identities=18% Similarity=0.449 Sum_probs=6.9
Q ss_pred Ccccccccccc
Q psy5652 1 MVCIFCRQLLP 11 (92)
Q Consensus 1 ~~C~~C~~~f~ 11 (92)
|+|..|+..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 46777776655
No 135
>KOG2785|consensus
Probab=64.18 E-value=16 Score=23.01 Aligned_cols=50 Identities=20% Similarity=0.390 Sum_probs=38.0
Q ss_pred ceeCCCCCccCCCHHHHHHHHHHhhCC-----------------------CCccCCcCc---cccCChHHHHHHHH
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRTHTGE-----------------------RPFKCEFCA---HSATSKSNLKMHIM 84 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~~~~~-----------------------~~~~c~~c~---~~~~~~~~l~~h~~ 84 (92)
|-.|-.|+..+.....-..|+..+.|- +.+.|..|+ +.|........|+.
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 467889999988888888888765541 236888888 78888888888864
No 136
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=63.45 E-value=2.5 Score=22.32 Aligned_cols=15 Identities=20% Similarity=0.401 Sum_probs=11.1
Q ss_pred CceeCCCCCccCCCH
Q psy5652 34 HLYVCFKCGYHQYNS 48 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~ 48 (92)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 468899999776553
No 137
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=62.40 E-value=3.3 Score=20.42 Aligned_cols=12 Identities=17% Similarity=0.537 Sum_probs=7.5
Q ss_pred CccCCcCccccC
Q psy5652 63 PFKCEFCAHSAT 74 (92)
Q Consensus 63 ~~~c~~c~~~~~ 74 (92)
.|.|..|++.|.
T Consensus 53 IW~C~~C~~~~A 64 (91)
T TIGR00280 53 IWTCRKCGAKFA 64 (91)
T ss_pred EEEcCCCCCEEe
Confidence 467777766553
No 138
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=62.38 E-value=2.7 Score=18.19 Aligned_cols=17 Identities=12% Similarity=0.413 Sum_probs=11.3
Q ss_pred CCccCCcCccccCChHH
Q psy5652 62 RPFKCEFCAHSATSKSN 78 (92)
Q Consensus 62 ~~~~c~~c~~~~~~~~~ 78 (92)
+.+.|..||..|.....
T Consensus 3 k~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAG 19 (49)
T ss_pred eeEEcccCCCeEEEehh
Confidence 45778888877765543
No 139
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=61.74 E-value=4.3 Score=20.75 Aligned_cols=14 Identities=14% Similarity=0.245 Sum_probs=8.6
Q ss_pred ceeCCCCCccCCCH
Q psy5652 35 LYVCFKCGYHQYNS 48 (92)
Q Consensus 35 ~~~c~~c~~~~~~~ 48 (92)
.+.|..|+..|...
T Consensus 70 ~~~C~~Cg~~~~~~ 83 (113)
T PRK12380 70 QAWCWDCSQVVEIH 83 (113)
T ss_pred EEEcccCCCEEecC
Confidence 46677777655543
No 140
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=61.73 E-value=2.9 Score=24.62 Aligned_cols=12 Identities=25% Similarity=0.454 Sum_probs=7.0
Q ss_pred ceeCCCCCccCC
Q psy5652 35 LYVCFKCGYHQY 46 (92)
Q Consensus 35 ~~~c~~c~~~~~ 46 (92)
.|.|+.|+..|.
T Consensus 155 ef~C~~C~h~F~ 166 (278)
T PF15135_consen 155 EFHCPKCRHNFR 166 (278)
T ss_pred eeecccccccch
Confidence 466666665554
No 141
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=61.04 E-value=4.5 Score=21.96 Aligned_cols=34 Identities=29% Similarity=0.656 Sum_probs=23.8
Q ss_pred CceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccc
Q psy5652 34 HLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHS 72 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~ 72 (92)
-+|.|. |+..|... ..|-..-.|+ .|.|..|+..
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 479998 99886653 4444445566 8999999853
No 142
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=59.38 E-value=4.8 Score=22.09 Aligned_cols=11 Identities=55% Similarity=1.413 Sum_probs=8.1
Q ss_pred CceeCCCCCcc
Q psy5652 34 HLYVCFKCGYH 44 (92)
Q Consensus 34 ~~~~c~~c~~~ 44 (92)
..+.|+.||..
T Consensus 27 ~sf~C~~CGyr 37 (163)
T TIGR00340 27 STYICEKCGYR 37 (163)
T ss_pred EEEECCCCCCc
Confidence 36888888854
No 143
>PF14369 zf-RING_3: zinc-finger
Probab=58.91 E-value=4.4 Score=16.09 Aligned_cols=10 Identities=20% Similarity=0.355 Sum_probs=6.4
Q ss_pred cccccccccc
Q psy5652 3 CIFCRQLLPM 12 (92)
Q Consensus 3 C~~C~~~f~~ 12 (92)
|+.|+..|..
T Consensus 24 CP~C~~gFvE 33 (35)
T PF14369_consen 24 CPRCHGGFVE 33 (35)
T ss_pred CcCCCCcEeE
Confidence 6777766643
No 144
>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=58.88 E-value=8.6 Score=16.08 Aligned_cols=12 Identities=25% Similarity=0.600 Sum_probs=6.1
Q ss_pred cCCcCccccCCh
Q psy5652 65 KCEFCAHSATSK 76 (92)
Q Consensus 65 ~c~~c~~~~~~~ 76 (92)
.|+.|++.|.+.
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 345555555544
No 145
>KOG4167|consensus
Probab=57.97 E-value=2 Score=29.11 Aligned_cols=26 Identities=23% Similarity=0.621 Sum_probs=22.7
Q ss_pred ceeCCCCCccCCCHHHHHHHHHHhhC
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRTHTG 60 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~~~~ 60 (92)
-|.|.+|++.|.-...+..|+++|.-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 59999999999988888999988764
No 146
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=57.95 E-value=4.3 Score=16.52 Aligned_cols=13 Identities=23% Similarity=0.570 Sum_probs=7.1
Q ss_pred Ccccccccccccc
Q psy5652 1 MVCIFCRQLLPMD 13 (92)
Q Consensus 1 ~~C~~C~~~f~~~ 13 (92)
|+|..|++.|=.+
T Consensus 13 f~C~~C~~~FC~~ 25 (39)
T smart00154 13 FKCRHCGNLFCGE 25 (39)
T ss_pred eECCccCCccccc
Confidence 3466666665444
No 147
>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=57.66 E-value=13 Score=15.07 Aligned_cols=14 Identities=29% Similarity=0.807 Sum_probs=8.5
Q ss_pred CCCCceeCCCCCcc
Q psy5652 31 DSSHLYVCFKCGYH 44 (92)
Q Consensus 31 ~~~~~~~c~~c~~~ 44 (92)
.+.+.|.|+.|+..
T Consensus 20 ~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 20 DGGKTWICNFCGTK 33 (40)
T ss_dssp TTTTEEEETTT--E
T ss_pred CCCCEEECcCCCCc
Confidence 35567888888753
No 148
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=57.03 E-value=5.6 Score=21.76 Aligned_cols=11 Identities=36% Similarity=1.105 Sum_probs=8.0
Q ss_pred ceeCCCCCccC
Q psy5652 35 LYVCFKCGYHQ 45 (92)
Q Consensus 35 ~~~c~~c~~~~ 45 (92)
.+.|+.||...
T Consensus 29 sf~C~~CGyk~ 39 (160)
T smart00709 29 SFECEHCGYRN 39 (160)
T ss_pred EEECCCCCCcc
Confidence 68888888543
No 149
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=56.36 E-value=8.5 Score=20.54 Aligned_cols=26 Identities=35% Similarity=0.613 Sum_probs=16.5
Q ss_pred eeCCCCCccCCCHHHHHHHHHHhhCCCCc
Q psy5652 36 YVCFKCGYHQYNSDRMKRHIRTHTGERPF 64 (92)
Q Consensus 36 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~ 64 (92)
-.|-++|+.|.+ |++|+++|.+--|-
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTPd 102 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTPD 102 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCHH
Confidence 456677776644 67777777665444
No 150
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=56.09 E-value=5.7 Score=19.33 Aligned_cols=33 Identities=18% Similarity=0.437 Sum_probs=23.4
Q ss_pred cccccccccccccccccccccCCCCCCCCCCCCceeCCCCCc
Q psy5652 2 VCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGY 43 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~ 43 (92)
.|..|+..+.....+. ..+....+.|-|.-|..
T Consensus 2 ~C~HCg~~~p~~~~~~---------~~~~g~~~~FCC~GC~~ 34 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKIT---------VEIDGEERPFCCPGCQA 34 (88)
T ss_pred CCCCCCCCCCCCCCee---------eeeCCCccccccHHHHH
Confidence 6899998887665544 45555667888887753
No 151
>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=55.65 E-value=13 Score=24.14 Aligned_cols=26 Identities=15% Similarity=0.560 Sum_probs=22.6
Q ss_pred ceeCCCCCccCCCHHHHHHHHHH-hhC
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRT-HTG 60 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~-~~~ 60 (92)
-|.|+.|.+.|.....+..|+.. |.+
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 58899999999999999999974 554
No 152
>PRK12496 hypothetical protein; Provisional
Probab=55.65 E-value=8.6 Score=21.10 Aligned_cols=10 Identities=30% Similarity=0.521 Sum_probs=4.7
Q ss_pred eeCCCCCccC
Q psy5652 36 YVCFKCGYHQ 45 (92)
Q Consensus 36 ~~c~~c~~~~ 45 (92)
+.|.-|++.|
T Consensus 128 ~~C~gC~~~~ 137 (164)
T PRK12496 128 KVCKGCKKKY 137 (164)
T ss_pred EECCCCCccc
Confidence 4444444444
No 153
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=55.60 E-value=14 Score=16.01 Aligned_cols=14 Identities=36% Similarity=0.619 Sum_probs=10.2
Q ss_pred ceeCCCCCccCCCH
Q psy5652 35 LYVCFKCGYHQYNS 48 (92)
Q Consensus 35 ~~~c~~c~~~~~~~ 48 (92)
-+.|+.|+..+...
T Consensus 28 ~W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 28 WWKCPKCGHEWKAS 41 (55)
T ss_pred EEECCCCCCeeEcc
Confidence 58889888766554
No 154
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=55.41 E-value=17 Score=24.08 Aligned_cols=40 Identities=18% Similarity=0.408 Sum_probs=21.4
Q ss_pred cccccccccccc-cccccccccCCCCCCCCCCCCceeCCCCCccCCCH
Q psy5652 2 VCIFCRQLLPMD-ADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNS 48 (92)
Q Consensus 2 ~C~~C~~~f~~~-~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~ 48 (92)
.|+.|+..+.-. +++. .........-.|.|+.||......
T Consensus 202 pCPhCg~~~~l~~~~l~-------w~~~~~~~~a~y~C~~Cg~~i~e~ 242 (557)
T PF05876_consen 202 PCPHCGEEQVLEWENLK-------WDKGEAPETARYVCPHCGCEIEEH 242 (557)
T ss_pred cCCCCCCCcccccccee-------ecCCCCccceEEECCCCcCCCCHH
Confidence 577887776654 3333 111112233467788887665443
No 155
>KOG1280|consensus
Probab=55.28 E-value=21 Score=22.32 Aligned_cols=38 Identities=21% Similarity=0.602 Sum_probs=26.7
Q ss_pred CCceeCCCCCccCCCHHHHHHHHHHhhCCC--CccCCcCc
Q psy5652 33 SHLYVCFKCGYHQYNSDRMKRHIRTHTGER--PFKCEFCA 70 (92)
Q Consensus 33 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~--~~~c~~c~ 70 (92)
...|.|++|+..-.....++.|...-..+. ...|+.|.
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 346999999998888889999987633222 34556555
No 156
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=54.81 E-value=6.7 Score=19.76 Aligned_cols=11 Identities=27% Similarity=0.942 Sum_probs=5.9
Q ss_pred CceeCCCCCcc
Q psy5652 34 HLYVCFKCGYH 44 (92)
Q Consensus 34 ~~~~c~~c~~~ 44 (92)
+.|+|+.|+..
T Consensus 21 k~FtCp~Cghe 31 (104)
T COG4888 21 KTFTCPRCGHE 31 (104)
T ss_pred ceEecCccCCe
Confidence 34556666543
No 157
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=53.69 E-value=2.8 Score=20.82 Aligned_cols=17 Identities=18% Similarity=0.421 Sum_probs=10.6
Q ss_pred Ccccccccccccccccc
Q psy5652 1 MVCIFCRQLLPMDADFI 17 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~ 17 (92)
|+|.+|+.....-..+.
T Consensus 7 wkC~VCg~~iieGqkFT 23 (103)
T COG4847 7 WKCYVCGGTIIEGQKFT 23 (103)
T ss_pred eeEeeeCCEeeeccEEE
Confidence 56777777665555444
No 158
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=53.40 E-value=8 Score=24.10 Aligned_cols=17 Identities=29% Similarity=0.663 Sum_probs=9.5
Q ss_pred ccccccccccccccccc
Q psy5652 3 CIFCRQLLPMDADFILG 19 (92)
Q Consensus 3 C~~C~~~f~~~~~l~~h 19 (92)
|.+|...|.+.+.|..|
T Consensus 223 C~FC~~~FYdDDEL~~H 239 (493)
T COG5236 223 CIFCKIYFYDDDELRRH 239 (493)
T ss_pred hhhccceecChHHHHHH
Confidence 55555555555555543
No 159
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=53.34 E-value=3.8 Score=18.16 Aligned_cols=16 Identities=19% Similarity=0.528 Sum_probs=13.1
Q ss_pred cccccccccccccccc
Q psy5652 3 CIFCRQLLPMDADFIL 18 (92)
Q Consensus 3 C~~C~~~f~~~~~l~~ 18 (92)
|..|+..|.+..+|..
T Consensus 30 C~~Cg~~Y~d~~dL~~ 45 (55)
T PF13821_consen 30 CFWCGTKYDDEEDLER 45 (55)
T ss_pred eeeeCCccCCHHHHHh
Confidence 7888888888888764
No 160
>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=53.11 E-value=6.5 Score=20.17 Aligned_cols=26 Identities=15% Similarity=0.319 Sum_probs=17.3
Q ss_pred CceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcc
Q psy5652 34 HLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAH 71 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 71 (92)
-...|..|+..|.... ..+.|+.|+.
T Consensus 69 ~~~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (115)
T TIGR00100 69 VECECEDCSEEVSPEI------------DLYRCPKCHG 94 (115)
T ss_pred cEEEcccCCCEEecCC------------cCccCcCCcC
Confidence 3578889987665432 1467888874
No 161
>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=52.25 E-value=8 Score=16.90 Aligned_cols=20 Identities=30% Similarity=0.350 Sum_probs=8.8
Q ss_pred CCceeCCCCCccCCCHHHHH
Q psy5652 33 SHLYVCFKCGYHQYNSDRMK 52 (92)
Q Consensus 33 ~~~~~c~~c~~~~~~~~~l~ 52 (92)
...|.|+.|...|-..=.+-
T Consensus 19 ~~~y~C~~C~~~FC~dCD~f 38 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVF 38 (51)
T ss_dssp -EEE--TTTT--B-HHHHHT
T ss_pred CCeEECCCCCCccccCcChh
Confidence 45788888887775544333
No 162
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=51.31 E-value=13 Score=23.75 Aligned_cols=12 Identities=33% Similarity=0.692 Sum_probs=5.8
Q ss_pred ceeCCCCCccCC
Q psy5652 35 LYVCFKCGYHQY 46 (92)
Q Consensus 35 ~~~c~~c~~~~~ 46 (92)
-|.|+.||..+.
T Consensus 367 g~rC~kCg~~~~ 378 (421)
T COG1571 367 GFRCKKCGTRAR 378 (421)
T ss_pred CcccccccccCC
Confidence 455555554443
No 163
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=51.00 E-value=28 Score=21.57 Aligned_cols=22 Identities=23% Similarity=0.617 Sum_probs=13.7
Q ss_pred CCccCCcCccccCChHHHHHHH
Q psy5652 62 RPFKCEFCAHSATSKSNLKMHI 83 (92)
Q Consensus 62 ~~~~c~~c~~~~~~~~~l~~h~ 83 (92)
..|.|..|...|-..-+...|.
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred cceechhhhhhhhhhhHHHHHH
Confidence 4577777766666555555554
No 164
>KOG2482|consensus
Probab=50.58 E-value=14 Score=23.11 Aligned_cols=21 Identities=29% Similarity=0.689 Sum_probs=18.6
Q ss_pred ccCCcCccccCChHHHHHHHH
Q psy5652 64 FKCEFCAHSATSKSNLKMHIM 84 (92)
Q Consensus 64 ~~c~~c~~~~~~~~~l~~h~~ 84 (92)
+.|..|.++|+.+..|..|++
T Consensus 196 ~~CLyCekifrdkntLkeHMr 216 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMR 216 (423)
T ss_pred heeeeeccccCCcHHHHHHHH
Confidence 688899999999999999985
No 165
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=50.38 E-value=5.4 Score=17.45 Aligned_cols=38 Identities=18% Similarity=0.517 Sum_probs=19.2
Q ss_pred ceeCCC--CCccCCCHHHHHHHHHHhhCCCCccCCc----Ccccc
Q psy5652 35 LYVCFK--CGYHQYNSDRMKRHIRTHTGERPFKCEF----CAHSA 73 (92)
Q Consensus 35 ~~~c~~--c~~~~~~~~~l~~h~~~~~~~~~~~c~~----c~~~~ 73 (92)
+..|+. |...+.. ..|..|+...-..++..|.. |...+
T Consensus 9 ~v~C~~~cc~~~i~r-~~l~~H~~~~C~~~~v~C~~~~~GC~~~~ 52 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPR-KELDDHLENECPKRPVPCPYSPYGCKERV 52 (60)
T ss_dssp EEE-TT--S-BEEEC-CCHHHHHHTTSTTSEEE-SS----S--EE
T ss_pred EeeCCCCCcccceeH-HHHHHHHHccCCCCcEECCCCCCCCCCcc
Confidence 456766 4443433 35777777544556677777 76554
No 166
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=50.15 E-value=14 Score=23.97 Aligned_cols=40 Identities=18% Similarity=0.277 Sum_probs=22.5
Q ss_pred CCCCceeCCCCCccCCCHHHHHHHHHHhhC------CCCccCCcCcc
Q psy5652 31 DSSHLYVCFKCGYHQYNSDRMKRHIRTHTG------ERPFKCEFCAH 71 (92)
Q Consensus 31 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~------~~~~~c~~c~~ 71 (92)
.....|.|..||..|.-...-.. .....| ...|.|+.|+.
T Consensus 421 ~~~~~~~c~~c~~~yd~~~g~~~-~~~~~gt~~~~lp~~~~cp~c~~ 466 (479)
T PRK05452 421 DLGPRMQCSVCQWIYDPAKGEPM-QDVAPGTPWSEVPDNFLCPECSL 466 (479)
T ss_pred CCCCeEEECCCCeEECCCCCCcc-cCCCCCCChhhCCCCCcCcCCCC
Confidence 34567999999987764321110 111111 23589999874
No 167
>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=49.92 E-value=10 Score=14.24 Aligned_cols=8 Identities=38% Similarity=1.132 Sum_probs=3.6
Q ss_pred ceeCCCCC
Q psy5652 35 LYVCFKCG 42 (92)
Q Consensus 35 ~~~c~~c~ 42 (92)
.|.|..|.
T Consensus 15 ~Y~C~~c~ 22 (30)
T PF03107_consen 15 FYHCSECC 22 (30)
T ss_pred eEEeCCCC
Confidence 44444443
No 168
>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=49.85 E-value=4.6 Score=16.70 Aligned_cols=12 Identities=17% Similarity=0.548 Sum_probs=5.1
Q ss_pred cccccccccccc
Q psy5652 2 VCIFCRQLLPMD 13 (92)
Q Consensus 2 ~C~~C~~~f~~~ 13 (92)
+|..|++.|=.+
T Consensus 15 ~C~~C~~~FC~~ 26 (43)
T PF01428_consen 15 KCKHCGKSFCLK 26 (43)
T ss_dssp E-TTTS-EE-TT
T ss_pred ECCCCCcccCcc
Confidence 466666665444
No 169
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=48.53 E-value=21 Score=20.29 Aligned_cols=36 Identities=19% Similarity=0.404 Sum_probs=21.2
Q ss_pred CcccccccccccccccccccccCCCCCCCCC-CC---CceeCCCCCccC
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMPRPD-SS---HLYVCFKCGYHQ 45 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~-~~---~~~~c~~c~~~~ 45 (92)
+.|+.|++.......+.. + ++. ++ ..+.|+.||...
T Consensus 1 ~~Cp~C~~~~~~~~~~~~-------~--IP~F~evii~sf~C~~CGyr~ 40 (192)
T TIGR00310 1 IDCPSCGGECETVMKTVN-------D--IPYFGEVLETSTICEHCGYRS 40 (192)
T ss_pred CcCCCCCCCCEEEEEEEc-------C--CCCcceEEEEEEECCCCCCcc
Confidence 469999876555444441 1 332 22 368899998643
No 170
>KOG2231|consensus
Probab=47.79 E-value=23 Score=24.16 Aligned_cols=16 Identities=25% Similarity=0.644 Sum_probs=9.4
Q ss_pred cccccccccccccccc
Q psy5652 3 CIFCRQLLPMDADFIL 18 (92)
Q Consensus 3 C~~C~~~f~~~~~l~~ 18 (92)
|.+|...|.+...|..
T Consensus 185 C~~C~~~fld~~el~r 200 (669)
T KOG2231|consen 185 CKFCHERFLDDDELYR 200 (669)
T ss_pred chhhhhhhccHHHHHH
Confidence 5556666666666554
No 171
>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=47.50 E-value=5.1 Score=16.14 Aligned_cols=9 Identities=22% Similarity=0.770 Sum_probs=3.3
Q ss_pred Ccccccccc
Q psy5652 1 MVCIFCRQL 9 (92)
Q Consensus 1 ~~C~~C~~~ 9 (92)
|+|..|+..
T Consensus 7 YkC~~CGni 15 (36)
T PF06397_consen 7 YKCEHCGNI 15 (36)
T ss_dssp EE-TTT--E
T ss_pred EEccCCCCE
Confidence 456666644
No 172
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=46.32 E-value=4 Score=20.57 Aligned_cols=17 Identities=18% Similarity=0.370 Sum_probs=11.9
Q ss_pred Ccccccccccccccccc
Q psy5652 1 MVCIFCRQLLPMDADFI 17 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~ 17 (92)
|+|.+|++.+.....+.
T Consensus 3 WkC~iCg~~I~~gqlFT 19 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFT 19 (101)
T ss_pred eEEEecCCeeeecceEE
Confidence 57888887776666554
No 173
>KOG0402|consensus
Probab=46.08 E-value=6.7 Score=19.03 Aligned_cols=9 Identities=33% Similarity=0.977 Sum_probs=5.3
Q ss_pred Ccccccccc
Q psy5652 1 MVCIFCRQL 9 (92)
Q Consensus 1 ~~C~~C~~~ 9 (92)
|.|++|++.
T Consensus 37 y~CsfCGK~ 45 (92)
T KOG0402|consen 37 YTCSFCGKK 45 (92)
T ss_pred hhhhhcchh
Confidence 456667644
No 174
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=45.96 E-value=14 Score=13.04 Aligned_cols=7 Identities=29% Similarity=0.634 Sum_probs=3.3
Q ss_pred ccccccc
Q psy5652 3 CIFCRQL 9 (92)
Q Consensus 3 C~~C~~~ 9 (92)
|+.|+..
T Consensus 2 Cp~CG~~ 8 (23)
T PF13240_consen 2 CPNCGAE 8 (23)
T ss_pred CcccCCC
Confidence 4445543
No 175
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=45.85 E-value=8.7 Score=15.05 Aligned_cols=6 Identities=50% Similarity=1.110 Sum_probs=2.9
Q ss_pred cccccc
Q psy5652 2 VCIFCR 7 (92)
Q Consensus 2 ~C~~C~ 7 (92)
+|..|+
T Consensus 10 ~C~~C~ 15 (32)
T PF13696_consen 10 VCHRCG 15 (32)
T ss_pred EeecCC
Confidence 455554
No 176
>KOG0801|consensus
Probab=45.63 E-value=12 Score=20.73 Aligned_cols=13 Identities=38% Similarity=1.017 Sum_probs=10.0
Q ss_pred Ccccccccccccc
Q psy5652 1 MVCIFCRQLLPMD 13 (92)
Q Consensus 1 ~~C~~C~~~f~~~ 13 (92)
++|++|.|.....
T Consensus 139 ~KCPvC~K~V~sD 151 (205)
T KOG0801|consen 139 MKCPVCHKVVPSD 151 (205)
T ss_pred ccCCccccccCCC
Confidence 6899999876544
No 177
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=45.24 E-value=8.1 Score=15.14 Aligned_cols=8 Identities=50% Similarity=1.377 Sum_probs=3.8
Q ss_pred cccccccc
Q psy5652 3 CIFCRQLL 10 (92)
Q Consensus 3 C~~C~~~f 10 (92)
|.+|+..|
T Consensus 24 C~~Cg~~~ 31 (33)
T PF08792_consen 24 CIFCGSSF 31 (33)
T ss_pred cccCCcEe
Confidence 45555443
No 178
>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=44.99 E-value=14 Score=15.78 Aligned_cols=14 Identities=21% Similarity=0.380 Sum_probs=10.1
Q ss_pred Cccccccccccccc
Q psy5652 1 MVCIFCRQLLPMDA 14 (92)
Q Consensus 1 ~~C~~C~~~f~~~~ 14 (92)
|+|..|++.+....
T Consensus 27 f~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 27 FKCSKCGKPLNDGD 40 (58)
T ss_dssp SBETTTTCBTTTSS
T ss_pred cccCCCCCccCCCe
Confidence 56888887776665
No 179
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=44.46 E-value=12 Score=14.87 Aligned_cols=10 Identities=30% Similarity=0.743 Sum_probs=4.1
Q ss_pred eeCCCCCccC
Q psy5652 36 YVCFKCGYHQ 45 (92)
Q Consensus 36 ~~c~~c~~~~ 45 (92)
-.|..||..+
T Consensus 22 isC~~CGPr~ 31 (35)
T PF07503_consen 22 ISCTNCGPRY 31 (35)
T ss_dssp --BTTCC-SC
T ss_pred ccCCCCCCCE
Confidence 3566666543
No 180
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=43.17 E-value=12 Score=19.28 Aligned_cols=14 Identities=14% Similarity=0.100 Sum_probs=9.7
Q ss_pred CceeCCCCCccCCC
Q psy5652 34 HLYVCFKCGYHQYN 47 (92)
Q Consensus 34 ~~~~c~~c~~~~~~ 47 (92)
-.+.|..|+..|..
T Consensus 70 ~~~~C~~Cg~~~~~ 83 (117)
T PRK00564 70 VELECKDCSHVFKP 83 (117)
T ss_pred CEEEhhhCCCcccc
Confidence 35788889866544
No 181
>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=42.88 E-value=8.8 Score=23.13 Aligned_cols=11 Identities=36% Similarity=0.588 Sum_probs=5.2
Q ss_pred ceeCCCCCccC
Q psy5652 35 LYVCFKCGYHQ 45 (92)
Q Consensus 35 ~~~c~~c~~~~ 45 (92)
...|+.|+...
T Consensus 26 ~~~c~~c~~~~ 36 (285)
T TIGR00515 26 WTKCPKCGQVL 36 (285)
T ss_pred eeECCCCcchh
Confidence 34455555443
No 182
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=42.54 E-value=31 Score=19.33 Aligned_cols=33 Identities=24% Similarity=0.564 Sum_probs=20.7
Q ss_pred CCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcccc
Q psy5652 32 SSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSA 73 (92)
Q Consensus 32 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~ 73 (92)
+..-|.|+.|...+...... .. .|.|+.||...
T Consensus 110 ~~~~y~C~~~~~r~sfdeA~------~~---~F~Cp~Cg~~L 142 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEAM------EL---GFTCPKCGEDL 142 (176)
T ss_pred cCCceeCCCCCCcccHHHHH------Hh---CCCCCCCCchh
Confidence 34468888887666544322 22 28999998654
No 183
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=42.52 E-value=22 Score=18.29 Aligned_cols=38 Identities=26% Similarity=0.436 Sum_probs=20.0
Q ss_pred ceeCCCCCccCCCHHHHHHHHHH-hhCC-CCccCCcCccccC
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRT-HTGE-RPFKCEFCAHSAT 74 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~-~~~~c~~c~~~~~ 74 (92)
...|+.||..=.....+| .|+ ..+. .=|.|..||..|+
T Consensus 72 ~~~CpkCg~~ea~y~~~Q--tRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQ--TRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred cccCCCCCCceeEEEeee--hhccCCCceEEEEecccCCEee
Confidence 357888885433322222 332 2222 2378888887654
No 184
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=42.38 E-value=15 Score=18.38 Aligned_cols=35 Identities=14% Similarity=0.228 Sum_probs=13.2
Q ss_pred cccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCCCH
Q psy5652 2 VCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQYNS 48 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~~~ 48 (92)
.|..|+..+.+.. ..+.....-|.|..|...|.+.
T Consensus 16 ~CalCG~tWg~~y------------~Ev~G~rLfFCCd~ca~EF~nm 50 (105)
T PF11494_consen 16 GCALCGATWGDYY------------EEVDGERLFFCCDDCAKEFKNM 50 (105)
T ss_dssp S-SS---S---SS-------------B-TT--BSSS--SSSS-TTS-
T ss_pred cccccCCcHHHHH------------HhhcCCEEEEEcHHHHHHHHHH
Confidence 3777777766332 3444454567788998888875
No 185
>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=42.36 E-value=10 Score=15.59 Aligned_cols=9 Identities=33% Similarity=0.630 Sum_probs=5.8
Q ss_pred Ccccccccc
Q psy5652 1 MVCIFCRQL 9 (92)
Q Consensus 1 ~~C~~C~~~ 9 (92)
|+|+.|+..
T Consensus 1 m~Cp~Cg~~ 9 (43)
T PF08271_consen 1 MKCPNCGSK 9 (43)
T ss_dssp ESBTTTSSS
T ss_pred CCCcCCcCC
Confidence 467777754
No 186
>PLN02294 cytochrome c oxidase subunit Vb
Probab=42.23 E-value=17 Score=20.30 Aligned_cols=15 Identities=13% Similarity=0.142 Sum_probs=11.2
Q ss_pred CCceeCCCCCccCCC
Q psy5652 33 SHLYVCFKCGYHQYN 47 (92)
Q Consensus 33 ~~~~~c~~c~~~~~~ 47 (92)
+++..|++||.-|.-
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 468889999987643
No 187
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=42.03 E-value=5 Score=17.84 Aligned_cols=10 Identities=50% Similarity=1.039 Sum_probs=2.9
Q ss_pred CceeCCCCCc
Q psy5652 34 HLYVCFKCGY 43 (92)
Q Consensus 34 ~~~~c~~c~~ 43 (92)
+.|.|+.||-
T Consensus 32 r~y~Cp~CgA 41 (55)
T PF05741_consen 32 RKYVCPICGA 41 (55)
T ss_dssp GG---TTT--
T ss_pred hcCcCCCCcC
Confidence 3466666664
No 188
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=41.69 E-value=17 Score=14.38 Aligned_cols=13 Identities=31% Similarity=0.774 Sum_probs=7.9
Q ss_pred CCCceeCCCCCcc
Q psy5652 32 SSHLYVCFKCGYH 44 (92)
Q Consensus 32 ~~~~~~c~~c~~~ 44 (92)
+...+.|+.|+..
T Consensus 19 ~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 19 DRERLVCPACGFI 31 (34)
T ss_dssp SS-EEEETTTTEE
T ss_pred CccceECCCCCCE
Confidence 4456788888753
No 189
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=41.19 E-value=17 Score=14.86 Aligned_cols=16 Identities=25% Similarity=0.486 Sum_probs=7.6
Q ss_pred cccccccccccccccc
Q psy5652 2 VCIFCRQLLPMDADFI 17 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~ 17 (92)
.|++|++.-..-..|.
T Consensus 3 ~CSFCgr~~~~v~~li 18 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLI 18 (41)
T ss_dssp B-TTT--BTTTSSSEE
T ss_pred CccCCCCCHHHHhcee
Confidence 5888887755444443
No 190
>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=41.15 E-value=38 Score=15.26 Aligned_cols=14 Identities=29% Similarity=0.679 Sum_probs=8.8
Q ss_pred CCCccCCcCccccC
Q psy5652 61 ERPFKCEFCAHSAT 74 (92)
Q Consensus 61 ~~~~~c~~c~~~~~ 74 (92)
.+.|.|+.||..+.
T Consensus 44 ~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 44 GRVFTCPNCGFEMD 57 (69)
T ss_pred cceEEcCCCCCEEC
Confidence 45677777775543
No 191
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.77 E-value=12 Score=16.13 Aligned_cols=13 Identities=15% Similarity=0.513 Sum_probs=7.1
Q ss_pred cCCcCccccCChH
Q psy5652 65 KCEFCAHSATSKS 77 (92)
Q Consensus 65 ~c~~c~~~~~~~~ 77 (92)
.|+.|++.|.+..
T Consensus 14 ICpvCqRPFsWRk 26 (54)
T COG4338 14 ICPVCQRPFSWRK 26 (54)
T ss_pred hhhhhcCchHHHH
Confidence 4555666555543
No 192
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=40.68 E-value=9.1 Score=14.82 Aligned_cols=10 Identities=20% Similarity=0.760 Sum_probs=5.5
Q ss_pred Cccccccccc
Q psy5652 1 MVCIFCRQLL 10 (92)
Q Consensus 1 ~~C~~C~~~f 10 (92)
|+|..|+..+
T Consensus 8 ykC~~Cgniv 17 (34)
T TIGR00319 8 YKCEVCGNIV 17 (34)
T ss_pred EEcCCCCcEE
Confidence 4566666544
No 193
>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=40.67 E-value=9.3 Score=14.82 Aligned_cols=10 Identities=20% Similarity=0.790 Sum_probs=5.7
Q ss_pred Cccccccccc
Q psy5652 1 MVCIFCRQLL 10 (92)
Q Consensus 1 ~~C~~C~~~f 10 (92)
|+|..|+..+
T Consensus 5 ykC~~CGniv 14 (34)
T cd00974 5 YKCEICGNIV 14 (34)
T ss_pred EEcCCCCcEE
Confidence 4566666554
No 194
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=40.65 E-value=10 Score=23.03 Aligned_cols=11 Identities=45% Similarity=1.180 Sum_probs=5.0
Q ss_pred eeCCCCCccCC
Q psy5652 36 YVCFKCGYHQY 46 (92)
Q Consensus 36 ~~c~~c~~~~~ 46 (92)
+.|+.|+..|.
T Consensus 58 ~vcp~c~~h~r 68 (296)
T CHL00174 58 NICEQCGYHLK 68 (296)
T ss_pred CCCCCCCCCcC
Confidence 34455554443
No 195
>KOG2231|consensus
Probab=40.53 E-value=31 Score=23.65 Aligned_cols=21 Identities=29% Similarity=0.581 Sum_probs=12.8
Q ss_pred eCCCCCccCCCHHHHHHHHHH
Q psy5652 37 VCFKCGYHQYNSDRMKRHIRT 57 (92)
Q Consensus 37 ~c~~c~~~~~~~~~l~~h~~~ 57 (92)
.|..|...|.....+..|++.
T Consensus 184 ~C~~C~~~fld~~el~rH~~~ 204 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRF 204 (669)
T ss_pred cchhhhhhhccHHHHHHhhcc
Confidence 455666666666666666553
No 196
>KOG3507|consensus
Probab=40.12 E-value=27 Score=15.83 Aligned_cols=30 Identities=23% Similarity=0.673 Sum_probs=17.3
Q ss_pred CCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcccc
Q psy5652 33 SHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSA 73 (92)
Q Consensus 33 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~ 73 (92)
..-|.|.+|+..- .|+ ..-++.|.+||...
T Consensus 18 ~miYiCgdC~~en----~lk-------~~D~irCReCG~RI 47 (62)
T KOG3507|consen 18 TMIYICGDCGQEN----TLK-------RGDVIRCRECGYRI 47 (62)
T ss_pred cEEEEeccccccc----ccc-------CCCcEehhhcchHH
Confidence 3468888887421 111 12467888887544
No 197
>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=40.10 E-value=10 Score=18.70 Aligned_cols=11 Identities=36% Similarity=0.927 Sum_probs=6.7
Q ss_pred ceeCCCCCccC
Q psy5652 35 LYVCFKCGYHQ 45 (92)
Q Consensus 35 ~~~c~~c~~~~ 45 (92)
-|.|..|+..|
T Consensus 53 IW~C~~C~~~~ 63 (90)
T PF01780_consen 53 IWKCKKCGKKF 63 (90)
T ss_dssp EEEETTTTEEE
T ss_pred EeecCCCCCEE
Confidence 36677776544
No 198
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=39.53 E-value=20 Score=12.92 Aligned_cols=7 Identities=29% Similarity=0.771 Sum_probs=3.8
Q ss_pred ccccccc
Q psy5652 2 VCIFCRQ 8 (92)
Q Consensus 2 ~C~~C~~ 8 (92)
.|+.|+.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 3555654
No 199
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=39.07 E-value=12 Score=13.94 Aligned_cols=13 Identities=23% Similarity=0.534 Sum_probs=5.1
Q ss_pred ccccccccccccc
Q psy5652 2 VCIFCRQLLPMDA 14 (92)
Q Consensus 2 ~C~~C~~~f~~~~ 14 (92)
.|++|+.......
T Consensus 1 ~CP~C~s~l~~~~ 13 (28)
T PF03119_consen 1 TCPVCGSKLVREE 13 (28)
T ss_dssp B-TTT--BEEE-C
T ss_pred CcCCCCCEeEcCC
Confidence 3777776655433
No 200
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=38.64 E-value=21 Score=21.69 Aligned_cols=11 Identities=27% Similarity=0.600 Sum_probs=6.8
Q ss_pred ccCCcCccccC
Q psy5652 64 FKCEFCAHSAT 74 (92)
Q Consensus 64 ~~c~~c~~~~~ 74 (92)
+.|+.|+.-|.
T Consensus 47 ~vc~~c~~h~r 57 (292)
T PRK05654 47 NVCPKCGHHMR 57 (292)
T ss_pred CCCCCCCCCee
Confidence 56666766554
No 201
>PRK01343 zinc-binding protein; Provisional
Probab=37.84 E-value=17 Score=16.34 Aligned_cols=9 Identities=22% Similarity=0.401 Sum_probs=6.2
Q ss_pred ccccccccc
Q psy5652 2 VCIFCRQLL 10 (92)
Q Consensus 2 ~C~~C~~~f 10 (92)
.|++|++.+
T Consensus 11 ~CP~C~k~~ 19 (57)
T PRK01343 11 PCPECGKPS 19 (57)
T ss_pred cCCCCCCcC
Confidence 477787664
No 202
>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=37.79 E-value=12 Score=17.97 Aligned_cols=13 Identities=23% Similarity=0.508 Sum_probs=6.9
Q ss_pred ceeCCCCCccCCC
Q psy5652 35 LYVCFKCGYHQYN 47 (92)
Q Consensus 35 ~~~c~~c~~~~~~ 47 (92)
...|..|+..|..
T Consensus 46 ~~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 46 ILSCRVCGESFQT 58 (81)
T ss_dssp EEEESSS--EEEE
T ss_pred EEEecCCCCeEEE
Confidence 4577777765543
No 203
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=37.69 E-value=24 Score=14.55 Aligned_cols=12 Identities=33% Similarity=0.537 Sum_probs=8.6
Q ss_pred CceeCCCCCccC
Q psy5652 34 HLYVCFKCGYHQ 45 (92)
Q Consensus 34 ~~~~c~~c~~~~ 45 (92)
.+..|+.|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 467888888655
No 204
>KOG3214|consensus
Probab=37.63 E-value=18 Score=18.30 Aligned_cols=14 Identities=21% Similarity=0.560 Sum_probs=8.3
Q ss_pred CccCCcCccccCCh
Q psy5652 63 PFKCEFCAHSATSK 76 (92)
Q Consensus 63 ~~~c~~c~~~~~~~ 76 (92)
...|..|+..|...
T Consensus 47 ~~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 47 KASCRICEESFQTT 60 (109)
T ss_pred eeeeeehhhhhccc
Confidence 35666666666543
No 205
>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=37.52 E-value=22 Score=17.83 Aligned_cols=13 Identities=23% Similarity=0.317 Sum_probs=10.5
Q ss_pred CceeCCCCCccCC
Q psy5652 34 HLYVCFKCGYHQY 46 (92)
Q Consensus 34 ~~~~c~~c~~~~~ 46 (92)
++..|.+||.-|.
T Consensus 78 ~~~rC~eCG~~fk 90 (97)
T cd00924 78 KPKRCPECGHVFK 90 (97)
T ss_pred CceeCCCCCcEEE
Confidence 6889999997764
No 206
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=37.51 E-value=15 Score=19.87 Aligned_cols=16 Identities=13% Similarity=0.247 Sum_probs=13.6
Q ss_pred cccccccccccccccc
Q psy5652 2 VCIFCRQLLPMDADFI 17 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~ 17 (92)
.|..|++.|.+..-+.
T Consensus 30 eC~~C~~RFTTyErve 45 (147)
T TIGR00244 30 ECLECHERFTTFERAE 45 (147)
T ss_pred cCCccCCccceeeecc
Confidence 4899999999998766
No 207
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=37.40 E-value=18 Score=14.44 Aligned_cols=7 Identities=29% Similarity=0.833 Sum_probs=4.3
Q ss_pred ccccccc
Q psy5652 3 CIFCRQL 9 (92)
Q Consensus 3 C~~C~~~ 9 (92)
|..|+..
T Consensus 11 C~~C~~~ 17 (36)
T PF11781_consen 11 CPVCGSR 17 (36)
T ss_pred CCCCCCe
Confidence 6666654
No 208
>KOG4602|consensus
Probab=36.84 E-value=17 Score=21.74 Aligned_cols=9 Identities=56% Similarity=1.132 Sum_probs=5.0
Q ss_pred ceeCCCCCc
Q psy5652 35 LYVCFKCGY 43 (92)
Q Consensus 35 ~~~c~~c~~ 43 (92)
.|.|++||-
T Consensus 268 ~YVCPiCGA 276 (318)
T KOG4602|consen 268 SYVCPICGA 276 (318)
T ss_pred hhcCccccc
Confidence 455666654
No 209
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=35.63 E-value=26 Score=17.79 Aligned_cols=26 Identities=19% Similarity=0.342 Sum_probs=17.1
Q ss_pred ceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCc
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCA 70 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~ 70 (92)
++.|..||..|..-+.. .--.|+.||
T Consensus 2 pH~CtrCG~vf~~g~~~----------il~GCp~CG 27 (112)
T COG3364 2 PHQCTRCGEVFDDGSEE----------ILSGCPKCG 27 (112)
T ss_pred CceecccccccccccHH----------HHccCcccc
Confidence 56788888887764322 136788877
No 210
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=35.58 E-value=17 Score=14.80 Aligned_cols=16 Identities=13% Similarity=0.453 Sum_probs=6.3
Q ss_pred cccccccccccccccc
Q psy5652 3 CIFCRQLLPMDADFIL 18 (92)
Q Consensus 3 C~~C~~~f~~~~~l~~ 18 (92)
|..|++.+.....+..
T Consensus 1 C~~C~~~~~~~~~~~v 16 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHV 16 (47)
T ss_dssp -TTT--B--GG-GEEE
T ss_pred CCCCCCcCccCcceEe
Confidence 6778888777644443
No 211
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=35.37 E-value=18 Score=17.92 Aligned_cols=12 Identities=33% Similarity=0.783 Sum_probs=6.9
Q ss_pred ceeCCCCCccCC
Q psy5652 35 LYVCFKCGYHQY 46 (92)
Q Consensus 35 ~~~c~~c~~~~~ 46 (92)
.|.|..|+..|.
T Consensus 54 IW~C~~C~~~~A 65 (90)
T PRK03976 54 IWECRKCGAKFA 65 (90)
T ss_pred EEEcCCCCCEEe
Confidence 466666665443
No 212
>PHA02998 RNA polymerase subunit; Provisional
Probab=34.89 E-value=50 Score=18.71 Aligned_cols=12 Identities=17% Similarity=0.462 Sum_probs=8.0
Q ss_pred ccCCcCccccCC
Q psy5652 64 FKCEFCAHSATS 75 (92)
Q Consensus 64 ~~c~~c~~~~~~ 75 (92)
|.|..|+..|..
T Consensus 172 YkC~~CG~~wkp 183 (195)
T PHA02998 172 HACRDCKKHFKP 183 (195)
T ss_pred EEcCCCCCccCC
Confidence 677777766643
No 213
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=34.67 E-value=20 Score=15.70 Aligned_cols=15 Identities=20% Similarity=0.658 Sum_probs=9.5
Q ss_pred Ccccccccccccccc
Q psy5652 1 MVCIFCRQLLPMDAD 15 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~ 15 (92)
+.|+.||..+...-+
T Consensus 1 i~CPyCge~~~~~iD 15 (52)
T PF14255_consen 1 IQCPYCGEPIEILID 15 (52)
T ss_pred CCCCCCCCeeEEEEe
Confidence 357888877655433
No 214
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=34.14 E-value=14 Score=18.18 Aligned_cols=15 Identities=27% Similarity=0.700 Sum_probs=7.7
Q ss_pred CCCCCccCCCHHHHH
Q psy5652 38 CFKCGYHQYNSDRMK 52 (92)
Q Consensus 38 c~~c~~~~~~~~~l~ 52 (92)
|+.||..|.+.+...
T Consensus 38 C~~CGe~y~~dev~~ 52 (89)
T TIGR03829 38 CSHCGMEYQDDTTVK 52 (89)
T ss_pred ccCCCcEeecHHHHH
Confidence 555555555544433
No 215
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=34.02 E-value=23 Score=17.37 Aligned_cols=12 Identities=25% Similarity=0.515 Sum_probs=8.7
Q ss_pred cccccccccccc
Q psy5652 2 VCIFCRQLLPMD 13 (92)
Q Consensus 2 ~C~~C~~~f~~~ 13 (92)
.|.+|++.+...
T Consensus 80 ~C~vC~k~l~~~ 91 (109)
T PF10367_consen 80 KCSVCGKPLGNS 91 (109)
T ss_pred CccCcCCcCCCc
Confidence 488888877663
No 216
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=33.11 E-value=28 Score=15.15 Aligned_cols=12 Identities=8% Similarity=0.387 Sum_probs=7.0
Q ss_pred Cccccccccccc
Q psy5652 1 MVCIFCRQLLPM 12 (92)
Q Consensus 1 ~~C~~C~~~f~~ 12 (92)
+.|++|+..+.+
T Consensus 2 ~~Cpi~~~~~~~ 13 (63)
T smart00504 2 FLCPISLEVMKD 13 (63)
T ss_pred cCCcCCCCcCCC
Confidence 356777665544
No 217
>PRK05978 hypothetical protein; Provisional
Probab=33.09 E-value=37 Score=18.47 Aligned_cols=16 Identities=25% Similarity=0.418 Sum_probs=7.3
Q ss_pred eCCCCCccCCCHHHHH
Q psy5652 37 VCFKCGYHQYNSDRMK 52 (92)
Q Consensus 37 ~c~~c~~~~~~~~~l~ 52 (92)
.|+.||++-.....|+
T Consensus 35 rCP~CG~G~LF~g~Lk 50 (148)
T PRK05978 35 RCPACGEGKLFRAFLK 50 (148)
T ss_pred cCCCCCCCcccccccc
Confidence 4555555444443333
No 218
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=32.66 E-value=5.6 Score=21.77 Aligned_cols=10 Identities=40% Similarity=1.192 Sum_probs=4.8
Q ss_pred ceeCCCCCcc
Q psy5652 35 LYVCFKCGYH 44 (92)
Q Consensus 35 ~~~c~~c~~~ 44 (92)
.|.|+.||..
T Consensus 30 sf~C~~CGyk 39 (161)
T PF03367_consen 30 SFECEHCGYK 39 (161)
T ss_dssp EEE-TTT--E
T ss_pred EeECCCCCCE
Confidence 5778888753
No 219
>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=32.56 E-value=16 Score=22.90 Aligned_cols=10 Identities=20% Similarity=0.395 Sum_probs=5.6
Q ss_pred eeCCCCCccC
Q psy5652 36 YVCFKCGYHQ 45 (92)
Q Consensus 36 ~~c~~c~~~~ 45 (92)
.+|++|...|
T Consensus 341 ~~CPtCRa~F 350 (358)
T PF10272_consen 341 CPCPTCRAKF 350 (358)
T ss_pred CCCCCCcccc
Confidence 4566665544
No 220
>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=32.55 E-value=54 Score=16.25 Aligned_cols=38 Identities=24% Similarity=0.343 Sum_probs=19.8
Q ss_pred ceeCCCCCccCCCHHHHHHHHHHhh-C-CCCccCCcCccccC
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRTHT-G-ERPFKCEFCAHSAT 74 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~~~-~-~~~~~c~~c~~~~~ 74 (92)
...|+.||..-..-..++ +++.. + ..-|.|..|+..+.
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q--~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQ--TRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred cCCCCCCCCCeeEEEEec--cCCCCCCcEEEEEeCCCCCeeE
Confidence 468888886433222222 22211 1 13478888886553
No 221
>PRK00420 hypothetical protein; Validated
Probab=32.05 E-value=50 Score=17.10 Aligned_cols=12 Identities=25% Similarity=0.121 Sum_probs=7.9
Q ss_pred ceeCCCCCccCC
Q psy5652 35 LYVCFKCGYHQY 46 (92)
Q Consensus 35 ~~~c~~c~~~~~ 46 (92)
...|+.||....
T Consensus 40 ~~~Cp~Cg~~~~ 51 (112)
T PRK00420 40 EVVCPVHGKVYI 51 (112)
T ss_pred ceECCCCCCeee
Confidence 457888877444
No 222
>smart00507 HNHc HNH nucleases.
Probab=31.99 E-value=42 Score=13.45 Aligned_cols=11 Identities=27% Similarity=0.791 Sum_probs=6.6
Q ss_pred ccccccccccc
Q psy5652 2 VCIFCRQLLPM 12 (92)
Q Consensus 2 ~C~~C~~~f~~ 12 (92)
.|..|+..+..
T Consensus 12 ~C~~C~~~~~~ 22 (52)
T smart00507 12 VCAYCGKPASE 22 (52)
T ss_pred CCcCCcCCCCC
Confidence 56667666543
No 223
>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 TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=31.48 E-value=12 Score=25.61 Aligned_cols=31 Identities=23% Similarity=0.520 Sum_probs=18.1
Q ss_pred eCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcccc
Q psy5652 37 VCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSA 73 (92)
Q Consensus 37 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~ 73 (92)
.|+.|.+-+.+... .|.| ..+..|..||...
T Consensus 120 ~C~~C~~ey~~p~~----rr~h--~~~~~C~~Cgp~l 150 (711)
T TIGR00143 120 LCPDCAKEYKDPLD----RRFH--AQPIACPRCGPQL 150 (711)
T ss_pred CCHHHHHHhcCCcc----ccCC--CCCccCCCCCcEE
Confidence 57777666555432 2222 3567888888543
No 225
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=31.20 E-value=52 Score=19.18 Aligned_cols=13 Identities=31% Similarity=0.748 Sum_probs=8.6
Q ss_pred CceeCCCCCccCC
Q psy5652 34 HLYVCFKCGYHQY 46 (92)
Q Consensus 34 ~~~~c~~c~~~~~ 46 (92)
....|+.||.-+.
T Consensus 34 ~v~~C~~Cg~~~~ 46 (236)
T PF04981_consen 34 EVTICPKCGRYRI 46 (236)
T ss_pred CceECCCCCCEEC
Confidence 4567888886443
No 226
>KOG0978|consensus
Probab=30.98 E-value=17 Score=24.90 Aligned_cols=21 Identities=19% Similarity=0.292 Sum_probs=14.6
Q ss_pred hhCCCCccCCcCccccCChHH
Q psy5652 58 HTGERPFKCEFCAHSATSKSN 78 (92)
Q Consensus 58 ~~~~~~~~c~~c~~~~~~~~~ 78 (92)
....+--+||.|+.+|.....
T Consensus 673 r~etRqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 673 RYETRQRKCPKCNAAFGANDV 693 (698)
T ss_pred HHHHhcCCCCCCCCCCCcccc
Confidence 334456789999999876543
No 227
>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=30.91 E-value=20 Score=14.33 Aligned_cols=13 Identities=15% Similarity=0.649 Sum_probs=7.6
Q ss_pred ccccccccccccc
Q psy5652 2 VCIFCRQLLPMDA 14 (92)
Q Consensus 2 ~C~~C~~~f~~~~ 14 (92)
.|+.|++.|....
T Consensus 3 ~C~~Cg~~Yh~~~ 15 (36)
T PF05191_consen 3 ICPKCGRIYHIEF 15 (36)
T ss_dssp EETTTTEEEETTT
T ss_pred CcCCCCCcccccc
Confidence 4677776655433
No 228
>KOG2906|consensus
Probab=30.60 E-value=29 Score=17.53 Aligned_cols=13 Identities=23% Similarity=0.552 Sum_probs=8.4
Q ss_pred CceeCCCCCccCC
Q psy5652 34 HLYVCFKCGYHQY 46 (92)
Q Consensus 34 ~~~~c~~c~~~~~ 46 (92)
..|.|..|++.+.
T Consensus 20 ~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 20 NRFSCRTCPYVFP 32 (105)
T ss_pred eeEEcCCCCceee
Confidence 3567777776554
No 229
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=30.40 E-value=27 Score=14.94 Aligned_cols=11 Identities=18% Similarity=0.437 Sum_probs=6.1
Q ss_pred ccccccccccc
Q psy5652 3 CIFCRQLLPMD 13 (92)
Q Consensus 3 C~~C~~~f~~~ 13 (92)
|+.|+..|.-.
T Consensus 1 CP~Cg~~f~C~ 11 (50)
T PF14375_consen 1 CPRCGAPFECG 11 (50)
T ss_pred CCCCCCcCCCC
Confidence 55566555544
No 230
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=30.30 E-value=74 Score=18.30 Aligned_cols=10 Identities=30% Similarity=0.747 Sum_probs=4.8
Q ss_pred CccCCcCccc
Q psy5652 63 PFKCEFCAHS 72 (92)
Q Consensus 63 ~~~c~~c~~~ 72 (92)
-+.|..||..
T Consensus 30 lvrC~eCG~V 39 (201)
T COG1326 30 LVRCEECGTV 39 (201)
T ss_pred EEEccCCCcE
Confidence 3455555543
No 231
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=30.22 E-value=29 Score=16.93 Aligned_cols=12 Identities=17% Similarity=0.293 Sum_probs=6.6
Q ss_pred cccccccccccc
Q psy5652 2 VCIFCRQLLPMD 13 (92)
Q Consensus 2 ~C~~C~~~f~~~ 13 (92)
.|+.||..|...
T Consensus 10 ~C~~CG~d~~~~ 21 (86)
T PF06170_consen 10 RCPHCGLDYSHA 21 (86)
T ss_pred cccccCCccccC
Confidence 366666555443
No 232
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=30.21 E-value=18 Score=14.62 Aligned_cols=13 Identities=23% Similarity=0.375 Sum_probs=6.7
Q ss_pred cCCcCccccCChH
Q psy5652 65 KCEFCAHSATSKS 77 (92)
Q Consensus 65 ~c~~c~~~~~~~~ 77 (92)
.|+.|++.|.+.+
T Consensus 4 ~CprC~kg~Hwa~ 16 (36)
T PF14787_consen 4 LCPRCGKGFHWAS 16 (36)
T ss_dssp C-TTTSSSCS-TT
T ss_pred cCcccCCCcchhh
Confidence 4666776665543
No 233
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=29.99 E-value=1.1e+02 Score=17.42 Aligned_cols=43 Identities=19% Similarity=0.325 Sum_probs=25.2
Q ss_pred CCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccc
Q psy5652 27 MPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHS 72 (92)
Q Consensus 27 ~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~ 72 (92)
...|..-....|..|+..+....... ........-.|+.|+..
T Consensus 87 ielHG~~~~~~C~~C~~~~~~~~~~~---~~~~~~~~p~C~~Cgg~ 129 (206)
T cd01410 87 SELHGNMFIEVCKSCGPEYVRDDVVE---TRGDKETGRRCHACGGI 129 (206)
T ss_pred EEecCCcCcccCCCCCCccchHHHHH---HhhcCCCCCcCCCCcCc
Confidence 45666666788999997765543221 11122234568888754
No 234
>KOG2636|consensus
Probab=29.84 E-value=47 Score=21.68 Aligned_cols=28 Identities=25% Similarity=0.450 Sum_probs=20.3
Q ss_pred CCCCCceeCCCCC-ccCCCHHHHHHHHHH
Q psy5652 30 PDSSHLYVCFKCG-YHQYNSDRMKRHIRT 57 (92)
Q Consensus 30 ~~~~~~~~c~~c~-~~~~~~~~l~~h~~~ 57 (92)
|.=.+.|.|.+|| +.+.-...+++|-.-
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF~E 424 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHFNE 424 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHhHH
Confidence 3434569999999 677777778888654
No 235
>KOG2272|consensus
Probab=29.76 E-value=20 Score=21.41 Aligned_cols=21 Identities=24% Similarity=0.360 Sum_probs=13.6
Q ss_pred CCCCCCCCceeCCCCCccCCC
Q psy5652 27 MPRPDSSHLYVCFKCGYHQYN 47 (92)
Q Consensus 27 ~~~~~~~~~~~c~~c~~~~~~ 47 (92)
+..|+-...|.|..|.+.|.-
T Consensus 213 mgKhWHveHFvCa~CekPFlG 233 (332)
T KOG2272|consen 213 MGKHWHVEHFVCAKCEKPFLG 233 (332)
T ss_pred hccccchhheeehhcCCcccc
Confidence 455555556777777776654
No 236
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=29.70 E-value=30 Score=19.66 Aligned_cols=16 Identities=13% Similarity=0.245 Sum_probs=11.3
Q ss_pred cccccccccccccccc
Q psy5652 2 VCIFCRQLLPMDADFI 17 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~ 17 (92)
+|.+|+..|.-...++
T Consensus 8 KCKvCg~~F~P~~s~q 23 (189)
T PF05766_consen 8 KCKVCGEWFVPARSNQ 23 (189)
T ss_pred cCcccCCccccCCCce
Confidence 5888888887655544
No 237
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=29.64 E-value=25 Score=19.24 Aligned_cols=17 Identities=18% Similarity=0.280 Sum_probs=13.7
Q ss_pred ccccccccccccccccc
Q psy5652 2 VCIFCRQLLPMDADFIL 18 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~ 18 (92)
.|..|+..|.+...+..
T Consensus 30 eC~~C~~RFTTfE~~El 46 (156)
T COG1327 30 ECLECGERFTTFERAEL 46 (156)
T ss_pred cccccccccchhheeee
Confidence 48999999999876553
No 238
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=29.49 E-value=29 Score=17.76 Aligned_cols=25 Identities=12% Similarity=0.260 Sum_probs=20.2
Q ss_pred CCCceeCCCCCccCCCHHHHHHHHH
Q psy5652 32 SSHLYVCFKCGYHQYNSDRMKRHIR 56 (92)
Q Consensus 32 ~~~~~~c~~c~~~~~~~~~l~~h~~ 56 (92)
+...+.|.+|.+-|.....|..|.+
T Consensus 52 GlGqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 52 GLGQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred CCceeeeehhHHHHHHHHHHHHHhc
Confidence 3446889999999999888888875
No 239
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=29.37 E-value=1.3e+02 Score=17.76 Aligned_cols=42 Identities=17% Similarity=0.419 Sum_probs=25.6
Q ss_pred CCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccc
Q psy5652 27 MPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHS 72 (92)
Q Consensus 27 ~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~ 72 (92)
...|..-....|..|+..+....... ..... ..-.|+.|+..
T Consensus 111 ielHG~~~~~~C~~C~~~~~~~~~~~---~~~~~-~~p~Cp~Cgg~ 152 (244)
T PRK14138 111 IELHGNVEEYYCVRCGKRYTVEDVIE---KLEKS-DVPRCDDCSGL 152 (244)
T ss_pred EEccCCcCeeEECCCCCcccHHHHHH---HHhcC-CCCCCCCCCCe
Confidence 45667667788999998877654433 11112 23468888743
No 240
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=28.65 E-value=40 Score=17.96 Aligned_cols=17 Identities=18% Similarity=0.372 Sum_probs=12.4
Q ss_pred Ccccccccccccccccc
Q psy5652 1 MVCIFCRQLLPMDADFI 17 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~ 17 (92)
++|.-|++.|.+-+.-.
T Consensus 2 H~Ct~Cg~~f~dgs~ei 18 (131)
T PF09845_consen 2 HQCTKCGRVFEDGSKEI 18 (131)
T ss_pred cccCcCCCCcCCCcHHH
Confidence 46888888888777433
No 241
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=28.23 E-value=20 Score=16.08 Aligned_cols=11 Identities=18% Similarity=0.552 Sum_probs=4.1
Q ss_pred ccccccccccc
Q psy5652 2 VCIFCRQLLPM 12 (92)
Q Consensus 2 ~C~~C~~~f~~ 12 (92)
.|++|++.+..
T Consensus 4 ~CP~C~k~~~~ 14 (57)
T PF03884_consen 4 KCPICGKPVEW 14 (57)
T ss_dssp E-TTT--EEE-
T ss_pred cCCCCCCeecc
Confidence 46777765444
No 242
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=28.05 E-value=1.2e+02 Score=17.44 Aligned_cols=41 Identities=15% Similarity=0.256 Sum_probs=24.1
Q ss_pred CCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccc
Q psy5652 27 MPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHS 72 (92)
Q Consensus 27 ~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~ 72 (92)
...|..-....|..|+..+..... . .......-.|+.|+..
T Consensus 105 ~elHG~l~~~~C~~C~~~~~~~~~-~----~~~~~~~p~C~~Cgg~ 145 (222)
T cd01413 105 IELHGTLQTAYCVNCGSKYDLEEV-K----YAKKHEVPRCPKCGGI 145 (222)
T ss_pred EEccCCcCcceECCCCCCcchhHH-H----HhccCCCCcCCCCCCc
Confidence 456666667889999987765532 1 1111223468778643
No 243
>PF14149 YhfH: YhfH-like protein
Probab=27.73 E-value=6.3 Score=16.00 Aligned_cols=8 Identities=25% Similarity=0.791 Sum_probs=4.4
Q ss_pred cccccccc
Q psy5652 3 CIFCRQLL 10 (92)
Q Consensus 3 C~~C~~~f 10 (92)
|..||+.+
T Consensus 16 C~~CG~~i 23 (37)
T PF14149_consen 16 CTECGKEI 23 (37)
T ss_pred cHHHHHHH
Confidence 55666543
No 244
>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=27.59 E-value=34 Score=13.45 Aligned_cols=21 Identities=29% Similarity=0.526 Sum_probs=11.4
Q ss_pred ceeCCCCCccCCCHHHHHHHHH
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIR 56 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~ 56 (92)
.+.|+.|++..... .+..|+.
T Consensus 4 ~~~C~nC~R~v~a~-RfA~HLe 24 (33)
T PF08209_consen 4 YVECPNCGRPVAAS-RFAPHLE 24 (33)
T ss_dssp EEE-TTTSSEEEGG-GHHHHHH
T ss_pred eEECCCCcCCcchh-hhHHHHH
Confidence 46788887755433 3455543
No 245
>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=27.44 E-value=53 Score=14.07 Aligned_cols=9 Identities=33% Similarity=1.110 Sum_probs=3.6
Q ss_pred CccCCcCcc
Q psy5652 63 PFKCEFCAH 71 (92)
Q Consensus 63 ~~~c~~c~~ 71 (92)
.|.|+.|++
T Consensus 41 ~W~CPiC~~ 49 (50)
T PF02891_consen 41 KWKCPICNK 49 (50)
T ss_dssp --B-TTT--
T ss_pred CeECcCCcC
Confidence 489998864
No 246
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=27.31 E-value=18 Score=16.46 Aligned_cols=22 Identities=23% Similarity=0.582 Sum_probs=7.4
Q ss_pred ccccccccccccccccccccCC
Q psy5652 3 CIFCRQLLPMDADFILGHCKRC 24 (92)
Q Consensus 3 C~~C~~~f~~~~~l~~h~~~~~ 24 (92)
|.+|++..........|.|..|
T Consensus 33 CNDC~~~s~v~fH~lg~KC~~C 54 (61)
T PF14599_consen 33 CNDCNAKSEVPFHFLGHKCSHC 54 (61)
T ss_dssp ESSS--EEEEE--TT----TTT
T ss_pred CCCCCCccceeeeHhhhcCCCC
Confidence 6666665544444444444444
No 247
>PLN02748 tRNA dimethylallyltransferase
Probab=27.31 E-value=65 Score=21.16 Aligned_cols=25 Identities=24% Similarity=0.490 Sum_probs=19.6
Q ss_pred CceeCCCCCc-cCCCHHHHHHHHHHh
Q psy5652 34 HLYVCFKCGY-HQYNSDRMKRHIRTH 58 (92)
Q Consensus 34 ~~~~c~~c~~-~~~~~~~l~~h~~~~ 58 (92)
+.|.|..|+. .+.....+..|+...
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr 442 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGR 442 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcch
Confidence 5788999997 687888888887653
No 248
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.16 E-value=29 Score=15.99 Aligned_cols=8 Identities=25% Similarity=0.609 Sum_probs=4.8
Q ss_pred cccccccc
Q psy5652 2 VCIFCRQL 9 (92)
Q Consensus 2 ~C~~C~~~ 9 (92)
+|+.|++-
T Consensus 9 ~CP~Cgkp 16 (65)
T COG3024 9 PCPTCGKP 16 (65)
T ss_pred cCCCCCCc
Confidence 46666654
No 249
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.02 E-value=44 Score=15.30 Aligned_cols=13 Identities=23% Similarity=0.278 Sum_probs=8.3
Q ss_pred CceeCCCCCccCC
Q psy5652 34 HLYVCFKCGYHQY 46 (92)
Q Consensus 34 ~~~~c~~c~~~~~ 46 (92)
..-.|+.|+..|.
T Consensus 47 gev~CPYC~t~y~ 59 (62)
T COG4391 47 GEVVCPYCSTRYR 59 (62)
T ss_pred CcEecCccccEEE
Confidence 3456777776654
No 250
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.57 E-value=27 Score=20.64 Aligned_cols=18 Identities=11% Similarity=0.202 Sum_probs=14.2
Q ss_pred Cccccccccccccccccc
Q psy5652 1 MVCIFCRQLLPMDADFIL 18 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~ 18 (92)
+.|++|+-.|..+.-+..
T Consensus 20 ieCPvC~tkFkkeev~tg 37 (267)
T COG1655 20 IECPVCNTKFKKEEVKTG 37 (267)
T ss_pred eccCcccchhhhhheecc
Confidence 469999999988876553
No 251
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=26.50 E-value=57 Score=14.83 Aligned_cols=18 Identities=22% Similarity=0.408 Sum_probs=11.3
Q ss_pred CCccCCcCccccCChHHH
Q psy5652 62 RPFKCEFCAHSATSKSNL 79 (92)
Q Consensus 62 ~~~~c~~c~~~~~~~~~l 79 (92)
.|..|..||+.......-
T Consensus 3 iPVRCFTCGkvi~~~~e~ 20 (60)
T PF01194_consen 3 IPVRCFTCGKVIGNKWEE 20 (60)
T ss_dssp -SSS-STTTSBTCGHHHH
T ss_pred CceecCCCCCChhHhHHH
Confidence 477888899877655443
No 252
>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=26.32 E-value=32 Score=18.28 Aligned_cols=33 Identities=21% Similarity=0.589 Sum_probs=20.4
Q ss_pred CceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccccC
Q psy5652 34 HLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSAT 74 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~ 74 (92)
-.|.|..|+..+..... . ....|.|..|+..+.
T Consensus 122 ~~~~C~~C~~~~~r~~~------~--~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 122 YVYRCPSCGREYKRHRR------S--KRKRYRCGRCGGPLV 154 (157)
T ss_pred eEEEcCCCCCEeeeecc------c--chhhEECCCCCCEEE
Confidence 46889999876633322 2 223488988886553
No 253
>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=26.16 E-value=28 Score=20.89 Aligned_cols=36 Identities=19% Similarity=0.280 Sum_probs=13.5
Q ss_pred CceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCc
Q psy5652 34 HLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCA 70 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~ 70 (92)
....|+.||..-........ .....+.+...|..|+
T Consensus 210 ~R~~Cp~Cg~~~~~~l~~~~-~e~~~~~rve~C~~C~ 245 (290)
T PF04216_consen 210 VRIKCPYCGNTDHEKLEYFT-VEGEPAYRVEVCESCG 245 (290)
T ss_dssp -TTS-TTT---SS-EEE---------SEEEEEETTTT
T ss_pred cCCCCcCCCCCCCcceeeEe-cCCCCcEEEEECCccc
Confidence 34578888875443322110 1122344567787777
No 254
>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=26.07 E-value=59 Score=16.75 Aligned_cols=13 Identities=23% Similarity=0.519 Sum_probs=8.1
Q ss_pred CceeCCCCCccCC
Q psy5652 34 HLYVCFKCGYHQY 46 (92)
Q Consensus 34 ~~~~c~~c~~~~~ 46 (92)
..|.|++|+..+.
T Consensus 18 ~~~iCpeC~~EW~ 30 (109)
T TIGR00686 18 TQLICPSCLYEWN 30 (109)
T ss_pred CeeECcccccccc
Confidence 3467777775544
No 255
>KOG0717|consensus
Probab=26.07 E-value=58 Score=21.45 Aligned_cols=22 Identities=18% Similarity=0.428 Sum_probs=19.5
Q ss_pred eeCCCCCccCCCHHHHHHHHHH
Q psy5652 36 YVCFKCGYHQYNSDRMKRHIRT 57 (92)
Q Consensus 36 ~~c~~c~~~~~~~~~l~~h~~~ 57 (92)
+.|.+|.+.|.+.-.+..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999988764
No 256
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=26.01 E-value=65 Score=14.78 Aligned_cols=12 Identities=33% Similarity=0.592 Sum_probs=5.7
Q ss_pred ceeCCCCCccCC
Q psy5652 35 LYVCFKCGYHQY 46 (92)
Q Consensus 35 ~~~c~~c~~~~~ 46 (92)
|-.|-.||+...
T Consensus 4 PiRCFsCGkvi~ 15 (63)
T COG1644 4 PVRCFSCGKVIG 15 (63)
T ss_pred ceEeecCCCCHH
Confidence 334555555433
No 257
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 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 DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=25.74 E-value=44 Score=18.76 Aligned_cols=38 Identities=16% Similarity=0.177 Sum_probs=14.8
Q ss_pred CcccccccccccccccccccccCCCCCCCCCCCCceeCCCCCccCC
Q psy5652 1 MVCIFCRQLLPMDADFILGHCKRCSNMPRPDSSHLYVCFKCGYHQY 46 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~~~~c~~c~~~~~ 46 (92)
++|+.|+..|....-... ...........|+.|+..+.
T Consensus 19 ~~C~~C~~~~~f~g~~~~--------~~~~~~~~~~~C~~C~~~~~ 56 (188)
T PF08996_consen 19 LTCPSCGTEFEFPGVFEE--------DGDDVSPSGLQCPNCSTPLS 56 (188)
T ss_dssp EE-TTT--EEEE-SSS----------SSEEEETTEEEETTT--B--
T ss_pred eECCCCCCCccccccccC--------CccccccCcCcCCCCCCcCC
Confidence 358888877766654331 00101123467888887443
No 258
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=25.69 E-value=33 Score=18.35 Aligned_cols=13 Identities=15% Similarity=0.350 Sum_probs=10.1
Q ss_pred CccCCcCccccCC
Q psy5652 63 PFKCEFCAHSATS 75 (92)
Q Consensus 63 ~~~c~~c~~~~~~ 75 (92)
=+.|+.|++.|=.
T Consensus 124 f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 124 FWRCPGCGKIYWE 136 (147)
T ss_pred EEECCCCCCEecc
Confidence 4789999998733
No 259
>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=25.59 E-value=83 Score=19.34 Aligned_cols=37 Identities=22% Similarity=0.462 Sum_probs=17.1
Q ss_pred ceeCCCCCccCCCHHHHHHHHHHhhC--CCCccCCcCcccc
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRTHTG--ERPFKCEFCAHSA 73 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~~~~--~~~~~c~~c~~~~ 73 (92)
.+.|+.|+..=.....++ .+.... ..-|.|..|+..+
T Consensus 258 ~~~C~~C~~~~~~~~q~Q--trsaDEpmT~f~~C~~Cg~~w 296 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQ--TRSADEPMTTFVTCEECGNRW 296 (299)
T ss_pred cccCCCCCCccceEEEec--ccCCCCCCeEEEEcCCCCCee
Confidence 467777774322222222 222111 1225777777554
No 260
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=25.29 E-value=58 Score=19.88 Aligned_cols=8 Identities=38% Similarity=0.816 Sum_probs=3.6
Q ss_pred eeCCCCCc
Q psy5652 36 YVCFKCGY 43 (92)
Q Consensus 36 ~~c~~c~~ 43 (92)
-.|+.|+.
T Consensus 29 ~KCp~c~~ 36 (294)
T COG0777 29 TKCPSCGE 36 (294)
T ss_pred eECCCccc
Confidence 34444443
No 261
>KOG2879|consensus
Probab=25.26 E-value=51 Score=20.07 Aligned_cols=12 Identities=25% Similarity=0.924 Sum_probs=8.4
Q ss_pred CCccCCcCcccc
Q psy5652 62 RPFKCEFCAHSA 73 (92)
Q Consensus 62 ~~~~c~~c~~~~ 73 (92)
..|.|+.||...
T Consensus 275 asf~Cp~Cg~~~ 286 (298)
T KOG2879|consen 275 ASFTCPLCGENV 286 (298)
T ss_pred hhcccCccCCCC
Confidence 457888888654
No 262
>KOG1088|consensus
Probab=25.21 E-value=38 Score=17.71 Aligned_cols=21 Identities=19% Similarity=-0.061 Sum_probs=14.4
Q ss_pred CCCCCCCceeCCCCCccCCCH
Q psy5652 28 PRPDSSHLYVCFKCGYHQYNS 48 (92)
Q Consensus 28 ~~~~~~~~~~c~~c~~~~~~~ 48 (92)
.++-.+....|++||+.|+-+
T Consensus 91 e~~v~EG~l~CpetG~vfpI~ 111 (124)
T KOG1088|consen 91 EIDVIEGELVCPETGRVFPIS 111 (124)
T ss_pred hhhhccceEecCCCCcEeecc
Confidence 444455567899998887654
No 263
>smart00746 TRASH metallochaperone-like domain.
Probab=25.03 E-value=47 Score=11.74 Aligned_cols=9 Identities=33% Similarity=0.903 Sum_probs=5.5
Q ss_pred ccccccccc
Q psy5652 3 CIFCRQLLP 11 (92)
Q Consensus 3 C~~C~~~f~ 11 (92)
|+.|++.+.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 566666654
No 264
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=24.73 E-value=1.2e+02 Score=17.67 Aligned_cols=38 Identities=26% Similarity=0.388 Sum_probs=22.8
Q ss_pred CCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCccc
Q psy5652 27 MPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHS 72 (92)
Q Consensus 27 ~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~ 72 (92)
...|..-....|..|++.+.....+. .. .-.|+.|+..
T Consensus 114 ~elHG~~~~~~C~~C~~~~~~~~~~~-------~~-~p~C~~Cgg~ 151 (242)
T PRK00481 114 IELHGSLLRARCTKCGQTYDLDEYLK-------PE-PPRCPKCGGI 151 (242)
T ss_pred eeccCCcCceeeCCCCCCcChhhhcc-------CC-CCCCCCCCCc
Confidence 46667667788888987765543221 11 2238888743
No 265
>PF14122 YokU: YokU-like protein
Probab=24.55 E-value=24 Score=17.30 Aligned_cols=14 Identities=21% Similarity=0.468 Sum_probs=8.1
Q ss_pred cccccccccccccc
Q psy5652 2 VCIFCRQLLPMDAD 15 (92)
Q Consensus 2 ~C~~C~~~f~~~~~ 15 (92)
.|..||+.+.+..-
T Consensus 37 ~C~~CgmvYq~d~v 50 (87)
T PF14122_consen 37 ICSNCGMVYQDDEV 50 (87)
T ss_pred eecCCCcEEehhHH
Confidence 46666666655543
No 266
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=24.50 E-value=73 Score=17.79 Aligned_cols=19 Identities=11% Similarity=0.380 Sum_probs=14.8
Q ss_pred CCccCCcCccccCChHHHH
Q psy5652 62 RPFKCEFCAHSATSKSNLK 80 (92)
Q Consensus 62 ~~~~c~~c~~~~~~~~~l~ 80 (92)
....|..|++.|.....+.
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVA 131 (181)
T ss_pred ccCcCcccCCccCcHhHHH
Confidence 5788999999998765544
No 267
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=24.36 E-value=41 Score=16.74 Aligned_cols=14 Identities=29% Similarity=0.766 Sum_probs=10.8
Q ss_pred CCccCCcCccccCC
Q psy5652 62 RPFKCEFCAHSATS 75 (92)
Q Consensus 62 ~~~~c~~c~~~~~~ 75 (92)
+|-.|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 57788889877764
No 268
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.28 E-value=39 Score=17.24 Aligned_cols=11 Identities=18% Similarity=0.443 Sum_probs=7.1
Q ss_pred ccccccccccc
Q psy5652 2 VCIFCRQLLPM 12 (92)
Q Consensus 2 ~C~~C~~~f~~ 12 (92)
.|+.||..|..
T Consensus 51 ~CP~Cg~~~e~ 61 (115)
T COG1885 51 SCPKCGEPFES 61 (115)
T ss_pred cCCCCCCccce
Confidence 47777766543
No 269
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=24.22 E-value=36 Score=14.90 Aligned_cols=8 Identities=38% Similarity=0.982 Sum_probs=5.5
Q ss_pred cccccccc
Q psy5652 2 VCIFCRQL 9 (92)
Q Consensus 2 ~C~~C~~~ 9 (92)
.|++||..
T Consensus 5 PCPFCG~~ 12 (61)
T PF14354_consen 5 PCPFCGSA 12 (61)
T ss_pred CCCCCCCc
Confidence 48888744
No 270
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=24.13 E-value=1.5e+02 Score=18.33 Aligned_cols=25 Identities=24% Similarity=0.499 Sum_probs=20.5
Q ss_pred CCceeCCCCCccCCCHHHHHHHHHH
Q psy5652 33 SHLYVCFKCGYHQYNSDRMKRHIRT 57 (92)
Q Consensus 33 ~~~~~c~~c~~~~~~~~~l~~h~~~ 57 (92)
...|.|..|-+-+.+...+..|+..
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHh
Confidence 3568899999888888888888763
No 271
>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=24.01 E-value=1.1e+02 Score=15.43 Aligned_cols=35 Identities=11% Similarity=0.186 Sum_probs=14.6
Q ss_pred eeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcc
Q psy5652 36 YVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAH 71 (92)
Q Consensus 36 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 71 (92)
|.|+.-++.|.+.......+.. -.++.|.|...|+
T Consensus 4 f~i~~T~EiF~dYe~Y~~R~~~-y~~~vwtC~~TGk 38 (102)
T PF10537_consen 4 FYIPFTGEIFRDYEEYLKRMIL-YNQRVWTCEITGK 38 (102)
T ss_pred EEeCCCCcccCCHHHHHHHHHH-HhCCeeEEecCCC
Confidence 4444444445444443333222 1234455544443
No 272
>PRK10220 hypothetical protein; Provisional
Probab=23.98 E-value=1e+02 Score=16.00 Aligned_cols=14 Identities=21% Similarity=0.702 Sum_probs=8.4
Q ss_pred CceeCCCCCccCCC
Q psy5652 34 HLYVCFKCGYHQYN 47 (92)
Q Consensus 34 ~~~~c~~c~~~~~~ 47 (92)
-.|.|++|+.-+..
T Consensus 19 ~~~vCpeC~hEW~~ 32 (111)
T PRK10220 19 GMYICPECAHEWND 32 (111)
T ss_pred CeEECCcccCcCCc
Confidence 35677777755443
No 273
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=23.95 E-value=24 Score=19.35 Aligned_cols=43 Identities=23% Similarity=0.376 Sum_probs=26.6
Q ss_pred CCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcccc
Q psy5652 27 MPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSA 73 (92)
Q Consensus 27 ~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~ 73 (92)
...|..-....|..|++.+....... . ... ...-.|+.|+...
T Consensus 97 ielHG~l~~~~C~~C~~~~~~~~~~~-~--~~~-~~~~~C~~C~~~l 139 (178)
T PF02146_consen 97 IELHGSLFRLRCSKCGKEYDREDIVD-S--IDE-EEPPRCPKCGGLL 139 (178)
T ss_dssp EETTEEEEEEEETTTSBEEEGHHHHH-H--HHT-TSSCBCTTTSCBE
T ss_pred HHHHhhhceeeecCCCccccchhhcc-c--ccc-cccccccccCccC
Confidence 45666666789999999887654322 1 122 2334888888644
No 274
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=23.87 E-value=1.2e+02 Score=15.95 Aligned_cols=9 Identities=22% Similarity=0.681 Sum_probs=5.5
Q ss_pred ceeCCCCCc
Q psy5652 35 LYVCFKCGY 43 (92)
Q Consensus 35 ~~~c~~c~~ 43 (92)
.|.|+.|+.
T Consensus 20 ~w~C~~C~q 28 (131)
T PF09779_consen 20 NWTCPHCEQ 28 (131)
T ss_pred eeECCCCCC
Confidence 366766663
No 275
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=23.80 E-value=29 Score=14.81 Aligned_cols=11 Identities=18% Similarity=0.446 Sum_probs=7.9
Q ss_pred ccccccccccc
Q psy5652 2 VCIFCRQLLPM 12 (92)
Q Consensus 2 ~C~~C~~~f~~ 12 (92)
.|..||..+..
T Consensus 7 ~C~~CG~~m~~ 17 (58)
T PF13408_consen 7 RCGHCGSKMTR 17 (58)
T ss_pred EcccCCcEeEE
Confidence 58888877655
No 276
>PHA02446 hypothetical protein
Probab=23.71 E-value=37 Score=17.70 Aligned_cols=20 Identities=15% Similarity=0.067 Sum_probs=11.2
Q ss_pred CCCCCCCCCceeCCCCCccC
Q psy5652 26 NMPRPDSSHLYVCFKCGYHQ 45 (92)
Q Consensus 26 ~~~~~~~~~~~~c~~c~~~~ 45 (92)
.+..|.+..-..|+..|...
T Consensus 79 ~~eahpd~l~qecplsgqsv 98 (166)
T PHA02446 79 IVEAHPDKLLQECPLSGQSV 98 (166)
T ss_pred ccccCcHHHHHhCCCCCCcc
Confidence 34555555555666666543
No 277
>KOG3399|consensus
Probab=23.70 E-value=1e+02 Score=16.32 Aligned_cols=18 Identities=28% Similarity=0.611 Sum_probs=10.9
Q ss_pred Cccccccccccccccccc
Q psy5652 1 MVCIFCRQLLPMDADFIL 18 (92)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~ 18 (92)
|.|..|..-|....++..
T Consensus 16 y~C~~C~thla~~~dliS 33 (122)
T KOG3399|consen 16 YSCAHCKTHLARHDDLIS 33 (122)
T ss_pred EeccCCcccccchhhccc
Confidence 456666666666666653
No 278
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.64 E-value=91 Score=18.67 Aligned_cols=12 Identities=42% Similarity=0.847 Sum_probs=6.5
Q ss_pred CCccCCcCcccc
Q psy5652 62 RPFKCEFCAHSA 73 (92)
Q Consensus 62 ~~~~c~~c~~~~ 73 (92)
+.|.|+.||..+
T Consensus 321 r~~~C~~cg~~~ 332 (364)
T COG0675 321 RLFKCPRCGFVH 332 (364)
T ss_pred eeEECCCCCCee
Confidence 346666666443
No 279
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=23.62 E-value=27 Score=13.22 Aligned_cols=10 Identities=30% Similarity=0.597 Sum_probs=4.3
Q ss_pred CceeCCCCCc
Q psy5652 34 HLYVCFKCGY 43 (92)
Q Consensus 34 ~~~~c~~c~~ 43 (92)
..-.|+.|+.
T Consensus 20 ~~r~C~~Cg~ 29 (32)
T PF09297_consen 20 WARRCPSCGH 29 (32)
T ss_dssp S-EEESSSS-
T ss_pred CEeECCCCcC
Confidence 4445555553
No 280
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.57 E-value=1.1e+02 Score=19.05 Aligned_cols=9 Identities=22% Similarity=0.530 Sum_probs=5.9
Q ss_pred Ccccccccc
Q psy5652 1 MVCIFCRQL 9 (92)
Q Consensus 1 ~~C~~C~~~ 9 (92)
+.|++|...
T Consensus 4 ~~CP~Ck~~ 12 (309)
T TIGR00570 4 QGCPRCKTT 12 (309)
T ss_pred CCCCcCCCC
Confidence 358888653
No 281
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=23.40 E-value=94 Score=14.27 Aligned_cols=13 Identities=31% Similarity=0.616 Sum_probs=7.4
Q ss_pred ceeCCCCCccCCC
Q psy5652 35 LYVCFKCGYHQYN 47 (92)
Q Consensus 35 ~~~c~~c~~~~~~ 47 (92)
|-.|-.||+...+
T Consensus 4 PvRCFTCGkvi~~ 16 (62)
T PRK04016 4 PVRCFTCGKVIAE 16 (62)
T ss_pred CeEecCCCCChHH
Confidence 4456666665444
No 282
>PHA02942 putative transposase; Provisional
Probab=22.89 E-value=1.1e+02 Score=19.53 Aligned_cols=12 Identities=33% Similarity=0.753 Sum_probs=7.0
Q ss_pred CCccCCcCcccc
Q psy5652 62 RPFKCEFCAHSA 73 (92)
Q Consensus 62 ~~~~c~~c~~~~ 73 (92)
+.|.|+.||...
T Consensus 341 r~f~C~~CG~~~ 352 (383)
T PHA02942 341 RYFHCPSCGYEN 352 (383)
T ss_pred CEEECCCCCCEe
Confidence 456666666443
No 283
>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=22.78 E-value=31 Score=15.72 Aligned_cols=18 Identities=17% Similarity=0.235 Sum_probs=12.4
Q ss_pred CCCCCCceeCCCCCccCC
Q psy5652 29 RPDSSHLYVCFKCGYHQY 46 (92)
Q Consensus 29 ~~~~~~~~~c~~c~~~~~ 46 (92)
.+..+....|+.|++.|+
T Consensus 47 ~~i~eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 47 VEIVEGELICPECGREYP 64 (68)
T ss_dssp EETTTTEEEETTTTEEEE
T ss_pred ccccCCEEEcCCCCCEEe
Confidence 344445778899988775
No 284
>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=22.67 E-value=17 Score=19.64 Aligned_cols=29 Identities=34% Similarity=0.576 Sum_probs=17.9
Q ss_pred CCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcc
Q psy5652 33 SHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAH 71 (92)
Q Consensus 33 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 71 (92)
...+.|..||..... .+++ .--.|+.|+.
T Consensus 110 ~G~l~C~~Cg~~~~~---------~~~~-~l~~Cp~C~~ 138 (146)
T PF07295_consen 110 PGTLVCENCGHEVEL---------THPE-RLPPCPKCGH 138 (146)
T ss_pred CceEecccCCCEEEe---------cCCC-cCCCCCCCCC
Confidence 346899999965322 1233 3347888884
No 285
>PTZ00448 hypothetical protein; Provisional
Probab=22.34 E-value=90 Score=19.90 Aligned_cols=23 Identities=26% Similarity=0.697 Sum_probs=19.2
Q ss_pred ceeCCCCCccCCCHHHHHHHHHH
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRT 57 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~ 57 (92)
.|.|..|+-.|.+......|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57899999999888778888775
No 286
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=22.29 E-value=54 Score=14.72 Aligned_cols=10 Identities=20% Similarity=0.836 Sum_probs=3.7
Q ss_pred cccccccccc
Q psy5652 2 VCIFCRQLLP 11 (92)
Q Consensus 2 ~C~~C~~~f~ 11 (92)
.|..|++.|.
T Consensus 11 ~C~~C~~~F~ 20 (69)
T PF01363_consen 11 NCMICGKKFS 20 (69)
T ss_dssp B-TTT--B-B
T ss_pred cCcCcCCcCC
Confidence 3677777773
No 287
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=22.02 E-value=48 Score=17.66 Aligned_cols=33 Identities=21% Similarity=0.516 Sum_probs=20.1
Q ss_pred CceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcccc
Q psy5652 34 HLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSA 73 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~ 73 (92)
-.|.|..|+..+... +.+.....|.|..|+..+
T Consensus 111 ~~y~C~~C~~~~~~~-------rr~~~~~~y~C~~C~g~l 143 (146)
T smart00731 111 YPYRCTGCGQRYLRV-------RRSNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEEECCCCCCCCceE-------ccccCcceEEcCCCCCEE
Confidence 378898898766421 112222458888887654
No 288
>PF15616 TerY-C: TerY-C metal binding domain
Probab=22.02 E-value=71 Score=17.06 Aligned_cols=13 Identities=31% Similarity=0.945 Sum_probs=8.6
Q ss_pred CCCCccCCcCccc
Q psy5652 60 GERPFKCEFCAHS 72 (92)
Q Consensus 60 ~~~~~~c~~c~~~ 72 (92)
++....|+.|+..
T Consensus 102 g~~~~~CPwCg~~ 114 (131)
T PF15616_consen 102 GEGEVTCPWCGNE 114 (131)
T ss_pred CCCCEECCCCCCe
Confidence 4556778888754
No 289
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=22.00 E-value=45 Score=15.27 Aligned_cols=9 Identities=22% Similarity=0.593 Sum_probs=5.6
Q ss_pred ccccccccc
Q psy5652 2 VCIFCRQLL 10 (92)
Q Consensus 2 ~C~~C~~~f 10 (92)
.|+.|++..
T Consensus 8 ~CP~C~k~~ 16 (62)
T PRK00418 8 NCPTCGKPV 16 (62)
T ss_pred cCCCCCCcc
Confidence 477777643
No 290
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.80 E-value=1.1e+02 Score=18.58 Aligned_cols=12 Identities=25% Similarity=0.340 Sum_probs=8.0
Q ss_pred ceeCCCCCccCC
Q psy5652 35 LYVCFKCGYHQY 46 (92)
Q Consensus 35 ~~~c~~c~~~~~ 46 (92)
.|.|+.|...|-
T Consensus 255 GyvCs~Clsi~C 266 (279)
T TIGR00627 255 GFVCSVCLSVLC 266 (279)
T ss_pred eEECCCccCCcC
Confidence 477777766554
No 291
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=21.74 E-value=52 Score=19.45 Aligned_cols=16 Identities=25% Similarity=0.411 Sum_probs=12.3
Q ss_pred CCCceeCCCCCccCCC
Q psy5652 32 SSHLYVCFKCGYHQYN 47 (92)
Q Consensus 32 ~~~~~~c~~c~~~~~~ 47 (92)
.+++..|++||.-|.-
T Consensus 178 EGkpqRCpECGqVFKL 193 (268)
T PTZ00043 178 EGFLYRCGECDQIFML 193 (268)
T ss_pred CCCCccCCCCCcEEEE
Confidence 3468899999987754
No 292
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=21.73 E-value=44 Score=13.87 Aligned_cols=14 Identities=21% Similarity=0.109 Sum_probs=6.4
Q ss_pred ceeCCCCCccCCCHH
Q psy5652 35 LYVCFKCGYHQYNSD 49 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~ 49 (92)
|..-+ ||..|....
T Consensus 14 P~~L~-CGH~~c~~c 27 (43)
T PF13445_consen 14 PMVLP-CGHVFCKDC 27 (43)
T ss_dssp EEE-S-SS-EEEHHH
T ss_pred CEEEe-CccHHHHHH
Confidence 44433 777665543
No 293
>PRK12860 transcriptional activator FlhC; Provisional
Probab=21.54 E-value=61 Score=18.49 Aligned_cols=29 Identities=28% Similarity=0.649 Sum_probs=18.4
Q ss_pred CceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCc
Q psy5652 34 HLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCA 70 (92)
Q Consensus 34 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~ 70 (92)
....|..|+..|.... +.....|.|+.|.
T Consensus 133 ~l~~C~~Cgg~fv~~~--------~e~~~~f~CplC~ 161 (189)
T PRK12860 133 QLARCCRCGGKFVTHA--------HDLRHNFVCGLCQ 161 (189)
T ss_pred eeccCCCCCCCeeccc--------cccCCCCcCCCCC
Confidence 3467888887776321 2333578888886
No 294
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=21.47 E-value=83 Score=13.36 Aligned_cols=10 Identities=20% Similarity=0.780 Sum_probs=6.2
Q ss_pred cccccccccc
Q psy5652 3 CIFCRQLLPM 12 (92)
Q Consensus 3 C~~C~~~f~~ 12 (92)
|..|++.|..
T Consensus 5 C~~C~~~F~~ 14 (57)
T cd00065 5 CMGCGKPFTL 14 (57)
T ss_pred CcccCccccC
Confidence 6666666654
No 295
>KOG1994|consensus
Probab=21.39 E-value=55 Score=19.34 Aligned_cols=23 Identities=22% Similarity=0.492 Sum_probs=19.3
Q ss_pred CCCCccCCcCccccCChHHHHHH
Q psy5652 60 GERPFKCEFCAHSATSKSNLKMH 82 (92)
Q Consensus 60 ~~~~~~c~~c~~~~~~~~~l~~h 82 (92)
....|-|..||..|.....|..|
T Consensus 236 R~eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 236 RSEHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred hccceEEEEeccccCCHHHHHHh
Confidence 34579999999999999888777
No 296
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=20.83 E-value=32 Score=18.45 Aligned_cols=11 Identities=27% Similarity=0.552 Sum_probs=9.0
Q ss_pred ccccccccccc
Q psy5652 2 VCIFCRQLLPM 12 (92)
Q Consensus 2 ~C~~C~~~f~~ 12 (92)
.|+.||+.|..
T Consensus 5 nC~~CgklF~~ 15 (137)
T TIGR03826 5 NCPKCGRLFVK 15 (137)
T ss_pred cccccchhhhh
Confidence 48889988887
No 297
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=20.79 E-value=44 Score=14.38 Aligned_cols=12 Identities=25% Similarity=0.595 Sum_probs=7.2
Q ss_pred eeCCCCCccCCC
Q psy5652 36 YVCFKCGYHQYN 47 (92)
Q Consensus 36 ~~c~~c~~~~~~ 47 (92)
+.|..|+-....
T Consensus 27 ~~C~~Cga~~~~ 38 (53)
T TIGR03655 27 FECSTCGASGPV 38 (53)
T ss_pred EECCCCCCCccc
Confidence 467777755443
No 298
>PRK12722 transcriptional activator FlhC; Provisional
Probab=20.70 E-value=64 Score=18.36 Aligned_cols=29 Identities=31% Similarity=0.612 Sum_probs=17.6
Q ss_pred ceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcc
Q psy5652 35 LYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAH 71 (92)
Q Consensus 35 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 71 (92)
...|..|+..|.... +.....|.|+.|..
T Consensus 134 l~~C~~Cgg~fv~~~--------~e~~~~f~CplC~~ 162 (187)
T PRK12722 134 LSSCNCCGGHFVTHA--------HDPVGSFVCGLCQP 162 (187)
T ss_pred eccCCCCCCCeeccc--------cccCCCCcCCCCCC
Confidence 456777887775322 12234688888764
No 299
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=20.66 E-value=39 Score=13.62 Aligned_cols=7 Identities=29% Similarity=0.638 Sum_probs=4.7
Q ss_pred ccccccc
Q psy5652 2 VCIFCRQ 8 (92)
Q Consensus 2 ~C~~C~~ 8 (92)
.|+.|+.
T Consensus 3 ~CP~Cg~ 9 (39)
T PF01396_consen 3 KCPKCGG 9 (39)
T ss_pred CCCCCCc
Confidence 4777773
No 300
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=20.22 E-value=83 Score=18.77 Aligned_cols=41 Identities=27% Similarity=0.460 Sum_probs=24.4
Q ss_pred CCCCCCCCceeCCCCCccCCCHHHHHHHHHHhhCCCCccCCcCcc
Q psy5652 27 MPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAH 71 (92)
Q Consensus 27 ~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 71 (92)
...|.+-..+.|..|+..+........ ...+ .+=.|+.|+.
T Consensus 114 i~lHGsl~~~~C~~C~~~~~~~~~~~~---~~~~-~~p~C~~Cg~ 154 (250)
T COG0846 114 IELHGSLKRVRCSKCGNQYYDEDVIKF---IEDG-LIPRCPKCGG 154 (250)
T ss_pred EEeccceeeeEeCCCcCccchhhhhhh---cccC-CCCcCccCCC
Confidence 345666677889999887764441111 1111 3457888886
No 301
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=20.17 E-value=1.1e+02 Score=19.88 Aligned_cols=16 Identities=19% Similarity=0.441 Sum_probs=11.0
Q ss_pred ccccccccccccccccc
Q psy5652 2 VCIFCRQLLPMDADFIL 18 (92)
Q Consensus 2 ~C~~C~~~f~~~~~l~~ 18 (92)
.|++||..+.-. .|..
T Consensus 20 ~C~eCd~~~~~P-~l~~ 35 (418)
T COG2995 20 LCPECDMLVSLP-RLDS 35 (418)
T ss_pred cCCCCCceeccc-cCCC
Confidence 488888887776 3443
Done!