Query psy64
Match_columns 115
No_of_seqs 107 out of 1916
Neff 10.7
Searched_HMMs 46136
Date Fri Aug 16 16:53:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy64.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/64hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 1.1E-25 2.4E-30 139.6 3.4 106 3-109 144-265 (279)
2 KOG2462|consensus 99.9 1.3E-25 2.8E-30 139.3 1.2 96 15-113 128-241 (279)
3 KOG1074|consensus 99.8 1.2E-20 2.6E-25 131.2 0.7 39 3-41 367-405 (958)
4 KOG3623|consensus 99.7 3.7E-19 8.1E-24 122.6 1.3 81 14-108 891-971 (1007)
5 KOG3623|consensus 99.7 1.1E-18 2.3E-23 120.5 3.1 106 3-109 224-331 (1007)
6 KOG1074|consensus 99.7 6.6E-19 1.4E-23 122.7 1.4 54 60-113 880-933 (958)
7 KOG3608|consensus 99.7 5.2E-17 1.1E-21 104.4 5.2 109 2-111 192-345 (467)
8 KOG3576|consensus 99.7 5.6E-18 1.2E-22 101.7 -1.0 81 14-108 114-194 (267)
9 KOG3576|consensus 99.6 2.5E-16 5.5E-21 94.6 0.5 95 3-111 131-236 (267)
10 PHA00733 hypothetical protein 99.4 7E-14 1.5E-18 80.1 1.0 89 13-112 36-124 (128)
11 PHA02768 hypothetical protein; 99.2 2.7E-12 5.8E-17 62.2 1.5 46 58-105 4-49 (55)
12 KOG3608|consensus 99.2 3.7E-11 7.9E-16 78.0 4.7 92 2-108 276-373 (467)
13 PF13465 zf-H2C2_2: Zinc-finge 99.1 8.5E-11 1.8E-15 49.1 2.3 25 74-98 1-25 (26)
14 PF13465 zf-H2C2_2: Zinc-finge 99.1 8.1E-11 1.8E-15 49.1 2.1 26 4-29 1-26 (26)
15 PHA02768 hypothetical protein; 99.0 1.5E-10 3.3E-15 56.1 1.6 43 17-75 5-47 (55)
16 PHA00733 hypothetical protein 99.0 9E-10 1.9E-14 63.2 4.9 62 5-83 62-123 (128)
17 KOG3993|consensus 98.9 5E-10 1.1E-14 74.1 1.1 78 5-82 283-379 (500)
18 PLN03086 PRLI-interacting fact 98.9 6.4E-09 1.4E-13 72.1 6.1 83 15-100 451-554 (567)
19 PHA00616 hypothetical protein 98.8 2.6E-09 5.6E-14 49.4 2.0 34 59-92 1-34 (44)
20 PLN03086 PRLI-interacting fact 98.8 8E-09 1.7E-13 71.6 3.6 101 3-110 420-537 (567)
21 PHA00732 hypothetical protein 98.6 2.2E-08 4.9E-13 52.7 1.9 45 59-109 1-46 (79)
22 PHA00732 hypothetical protein 98.5 9.5E-08 2E-12 50.3 2.4 48 17-83 1-48 (79)
23 KOG3993|consensus 98.5 1.2E-08 2.6E-13 67.8 -1.7 82 18-113 268-382 (500)
24 PHA00616 hypothetical protein 98.5 1.3E-07 2.8E-12 43.8 2.1 34 17-64 1-34 (44)
25 COG5189 SFP1 Putative transcri 98.3 2.3E-07 5E-12 59.9 1.6 53 56-108 346-419 (423)
26 PF05605 zf-Di19: Drought indu 98.3 1.6E-07 3.5E-12 46.0 0.6 50 59-111 2-53 (54)
27 PF00096 zf-C2H2: Zinc finger, 98.2 1.3E-06 2.9E-11 35.0 2.0 23 18-40 1-23 (23)
28 PF05605 zf-Di19: Drought indu 98.2 4.5E-06 9.7E-11 40.8 3.8 51 17-83 2-53 (54)
29 PF00096 zf-C2H2: Zinc finger, 98.1 2.3E-06 4.9E-11 34.3 2.1 22 60-81 1-22 (23)
30 PF13912 zf-C2H2_6: C2H2-type 98.0 1.3E-06 2.8E-11 36.5 -0.3 25 87-111 1-25 (27)
31 PF13894 zf-C2H2_4: C2H2-type 97.9 1.2E-05 2.5E-10 32.3 2.2 23 18-40 1-23 (24)
32 PF13912 zf-C2H2_6: C2H2-type 97.8 7.9E-06 1.7E-10 34.0 1.2 24 17-40 1-24 (27)
33 COG5189 SFP1 Putative transcri 97.8 3.8E-06 8.3E-11 54.5 -0.0 65 15-79 347-418 (423)
34 PRK04860 hypothetical protein; 97.7 1.7E-05 3.7E-10 47.3 1.8 41 58-102 118-158 (160)
35 PF13894 zf-C2H2_4: C2H2-type 97.7 3.9E-05 8.5E-10 30.6 2.2 23 60-82 1-23 (24)
36 PF12756 zf-C2H2_2: C2H2 type 97.7 4.2E-05 9.2E-10 41.7 2.9 62 19-82 1-73 (100)
37 PF09237 GAGA: GAGA factor; I 97.5 7E-05 1.5E-09 35.6 1.8 33 55-87 20-52 (54)
38 smart00355 ZnF_C2H2 zinc finge 97.4 0.00019 4.1E-09 29.0 2.1 23 18-40 1-23 (26)
39 PF12756 zf-C2H2_2: C2H2 type 97.4 2.8E-05 6.1E-10 42.4 -0.8 24 87-110 50-73 (100)
40 smart00355 ZnF_C2H2 zinc finge 97.2 0.00032 7E-09 28.3 2.0 23 60-82 1-23 (26)
41 PF12874 zf-met: Zinc-finger o 97.2 5.4E-05 1.2E-09 30.8 -0.7 22 88-109 1-22 (25)
42 PF12171 zf-C2H2_jaz: Zinc-fin 97.0 0.00019 4E-09 29.8 0.0 22 88-109 2-23 (27)
43 PF09237 GAGA: GAGA factor; I 96.9 0.0015 3.3E-08 31.1 2.7 29 13-41 20-48 (54)
44 PF12874 zf-met: Zinc-finger o 96.8 0.00075 1.6E-08 27.3 1.3 22 18-39 1-22 (25)
45 PRK04860 hypothetical protein; 96.7 0.0016 3.4E-08 39.0 2.4 40 16-73 118-157 (160)
46 PF13909 zf-H2C2_5: C2H2-type 96.6 0.0024 5.1E-08 25.6 1.9 22 18-40 1-22 (24)
47 PF13909 zf-H2C2_5: C2H2-type 96.2 0.0056 1.2E-07 24.4 1.9 21 60-81 1-21 (24)
48 cd00350 rubredoxin_like Rubred 96.1 0.0021 4.7E-08 28.0 0.6 24 60-95 2-25 (33)
49 PF13913 zf-C2HC_2: zinc-finge 95.6 0.011 2.3E-07 24.0 1.7 21 60-81 3-23 (25)
50 smart00451 ZnF_U1 U1-like zinc 95.4 0.0044 9.4E-08 27.1 0.1 22 87-108 3-24 (35)
51 KOG1146|consensus 95.2 0.013 2.9E-07 45.1 1.9 98 12-109 460-611 (1406)
52 smart00451 ZnF_U1 U1-like zinc 95.0 0.024 5.2E-07 24.6 1.9 23 17-39 3-25 (35)
53 COG5048 FOG: Zn-finger [Genera 94.9 0.0097 2.1E-07 40.2 0.6 55 58-112 288-348 (467)
54 COG1592 Rubrerythrin [Energy p 94.5 0.014 3E-07 35.1 0.5 25 58-95 133-157 (166)
55 cd00729 rubredoxin_SM Rubredox 94.2 0.018 3.9E-07 25.2 0.5 26 59-96 2-27 (34)
56 KOG2893|consensus 94.2 0.012 2.6E-07 37.3 -0.1 43 18-78 11-53 (341)
57 COG2888 Predicted Zn-ribbon RN 94.0 0.022 4.7E-07 28.1 0.5 33 58-95 26-58 (61)
58 TIGR02098 MJ0042_CXXC MJ0042 f 94.0 0.036 7.8E-07 24.7 1.2 34 60-98 3-36 (38)
59 PF09538 FYDLN_acid: Protein o 93.7 0.04 8.8E-07 30.8 1.4 30 18-72 10-39 (108)
60 smart00531 TFIIE Transcription 93.7 0.097 2.1E-06 30.9 3.0 46 8-71 90-135 (147)
61 PF13719 zinc_ribbon_5: zinc-r 93.7 0.051 1.1E-06 24.2 1.4 34 60-98 3-36 (37)
62 PF09986 DUF2225: Uncharacteri 93.5 0.0074 1.6E-07 37.8 -2.0 44 57-100 3-61 (214)
63 KOG1146|consensus 93.3 0.014 3E-07 45.0 -1.2 57 53-109 459-540 (1406)
64 TIGR00622 ssl1 transcription f 93.1 0.035 7.6E-07 31.2 0.5 90 15-110 13-104 (112)
65 COG5188 PRP9 Splicing factor 3 93.0 0.14 3.1E-06 34.4 3.2 30 79-108 366-396 (470)
66 PF13717 zinc_ribbon_4: zinc-r 92.9 0.076 1.7E-06 23.5 1.3 34 60-98 3-36 (36)
67 KOG2893|consensus 92.7 0.072 1.6E-06 33.9 1.5 45 57-106 9-53 (341)
68 PRK14890 putative Zn-ribbon RN 92.6 0.071 1.5E-06 26.3 1.1 33 58-96 24-57 (59)
69 COG4049 Uncharacterized protei 92.5 0.084 1.8E-06 25.7 1.3 29 11-39 11-39 (65)
70 TIGR00373 conserved hypothetic 92.4 0.15 3.2E-06 30.5 2.6 44 5-71 97-140 (158)
71 COG1997 RPL43A Ribosomal prote 92.2 0.073 1.6E-06 28.4 1.0 33 58-100 34-66 (89)
72 KOG2231|consensus 91.8 0.24 5.3E-06 36.1 3.4 86 20-110 118-235 (669)
73 PRK00464 nrdR transcriptional 91.8 0.022 4.8E-07 33.9 -1.4 16 87-102 28-43 (154)
74 smart00531 TFIIE Transcription 91.7 0.36 7.7E-06 28.5 3.6 40 55-98 95-134 (147)
75 KOG2186|consensus 91.7 0.15 3.3E-06 32.6 2.1 45 60-107 4-48 (276)
76 TIGR00373 conserved hypothetic 91.2 0.22 4.7E-06 29.8 2.3 36 54-98 104-139 (158)
77 PRK06266 transcription initiat 91.0 0.22 4.7E-06 30.5 2.3 41 8-71 108-148 (178)
78 KOG2186|consensus 91.0 0.16 3.5E-06 32.5 1.7 51 17-84 3-53 (276)
79 PRK00398 rpoP DNA-directed RNA 90.7 0.079 1.7E-06 24.8 0.1 31 58-98 2-32 (46)
80 KOG2593|consensus 90.4 0.32 7E-06 33.6 2.8 51 2-69 113-163 (436)
81 COG5048 FOG: Zn-finger [Genera 90.0 0.056 1.2E-06 36.5 -1.0 71 16-98 288-364 (467)
82 TIGR02605 CxxC_CxxC_SSSS putat 90.0 0.049 1.1E-06 26.1 -0.9 29 60-95 6-34 (52)
83 smart00834 CxxC_CXXC_SSSS Puta 89.8 0.051 1.1E-06 24.5 -0.9 30 59-95 5-34 (41)
84 COG4049 Uncharacterized protei 89.4 0.22 4.7E-06 24.3 1.0 28 55-82 13-40 (65)
85 PRK06266 transcription initiat 89.3 0.24 5.3E-06 30.3 1.5 35 55-98 113-147 (178)
86 smart00659 RPOLCX RNA polymera 89.2 0.23 5E-06 23.1 1.0 27 59-96 2-28 (44)
87 TIGR02300 FYDLN_acid conserved 88.9 0.26 5.6E-06 28.3 1.3 33 17-74 9-41 (129)
88 PF06524 NOA36: NOA36 protein; 88.3 0.27 5.9E-06 31.7 1.2 84 14-110 139-232 (314)
89 PRK09678 DNA-binding transcrip 86.4 0.17 3.8E-06 26.1 -0.3 44 60-105 2-47 (72)
90 KOG2636|consensus 85.4 0.37 8.1E-06 33.5 0.8 29 80-108 394-423 (497)
91 COG3357 Predicted transcriptio 85.2 0.4 8.7E-06 25.8 0.7 14 16-29 57-70 (97)
92 PTZ00255 60S ribosomal protein 85.2 0.38 8.2E-06 26.0 0.6 32 58-99 35-66 (90)
93 COG5236 Uncharacterized conser 85.0 0.62 1.3E-05 31.5 1.6 22 19-40 222-243 (493)
94 PF14353 CpXC: CpXC protein 85.0 0.61 1.3E-05 26.7 1.4 49 60-108 2-59 (128)
95 PHA00626 hypothetical protein 84.8 0.38 8.2E-06 23.5 0.4 16 85-100 21-36 (59)
96 PF07754 DUF1610: Domain of un 84.5 0.43 9.2E-06 19.2 0.4 11 57-67 14-24 (24)
97 COG1996 RPC10 DNA-directed RNA 84.5 0.5 1.1E-05 22.5 0.7 30 57-96 4-33 (49)
98 PRK00432 30S ribosomal protein 84.0 0.49 1.1E-05 22.6 0.6 13 86-98 36-48 (50)
99 KOG2785|consensus 84.0 0.46 1E-05 32.3 0.7 23 17-39 3-25 (390)
100 PF01780 Ribosomal_L37ae: Ribo 83.5 0.38 8.2E-06 26.0 0.1 32 58-99 34-65 (90)
101 PF13451 zf-trcl: Probable zin 83.4 0.67 1.5E-05 22.1 0.9 39 57-95 2-41 (49)
102 KOG2593|consensus 82.3 1.8 3.8E-05 30.2 2.9 39 54-95 123-161 (436)
103 TIGR00280 L37a ribosomal prote 82.2 0.52 1.1E-05 25.5 0.3 32 58-99 34-65 (91)
104 PF08274 PhnA_Zn_Ribbon: PhnA 81.7 0.49 1.1E-05 20.1 0.1 24 61-95 4-27 (30)
105 COG5236 Uncharacterized conser 80.5 1.5 3.2E-05 29.8 2.0 23 61-83 222-244 (493)
106 PF03604 DNA_RNApol_7kD: DNA d 80.4 1.1 2.3E-05 19.3 1.0 13 58-70 16-28 (32)
107 PF10571 UPF0547: Uncharacteri 80.4 0.42 9.1E-06 19.5 -0.3 9 89-97 16-24 (26)
108 PF13240 zinc_ribbon_2: zinc-r 80.2 0.45 9.8E-06 18.8 -0.2 6 90-95 16-21 (23)
109 smart00734 ZnF_Rad18 Rad18-lik 79.5 1.9 4.2E-05 17.5 1.6 20 18-38 2-21 (26)
110 PRK03824 hypA hydrogenase nick 79.4 0.49 1.1E-05 27.6 -0.4 39 58-96 69-116 (135)
111 PF12013 DUF3505: Protein of u 79.2 0.53 1.1E-05 26.2 -0.3 25 87-111 80-108 (109)
112 PF11672 DUF3268: Protein of u 79.0 0.58 1.3E-05 25.9 -0.1 38 58-95 1-39 (102)
113 KOG2071|consensus 79.0 1.5 3.3E-05 31.6 1.8 27 15-41 416-442 (579)
114 PRK03976 rpl37ae 50S ribosomal 78.6 0.74 1.6E-05 24.9 0.2 32 58-99 35-66 (90)
115 PF13453 zf-TFIIB: Transcripti 77.1 0.69 1.5E-05 20.9 -0.2 21 85-105 17-37 (41)
116 PF09723 Zn-ribbon_8: Zinc rib 76.9 1.3 2.7E-05 20.2 0.7 18 88-105 6-23 (42)
117 COG1773 Rubredoxin [Energy pro 76.8 1.4 3.1E-05 21.5 0.9 15 86-100 2-16 (55)
118 smart00440 ZnF_C2C2 C2C2 Zinc 76.7 0.27 5.8E-06 22.3 -1.6 11 88-98 29-39 (40)
119 COG1198 PriA Primosomal protei 76.7 1.6 3.5E-05 32.6 1.5 13 84-96 472-484 (730)
120 PF04959 ARS2: Arsenite-resist 76.6 2.3 5E-05 26.9 2.0 28 14-41 74-101 (214)
121 KOG2907|consensus 76.4 2.2 4.8E-05 24.0 1.7 36 60-98 75-113 (116)
122 KOG4124|consensus 76.2 0.4 8.6E-06 32.3 -1.5 50 57-106 347-417 (442)
123 smart00661 RPOL9 RNA polymeras 76.1 1.4 3.1E-05 20.8 0.8 16 87-102 20-35 (52)
124 COG3091 SprT Zn-dependent meta 75.8 1.5 3.3E-05 26.1 1.0 39 56-99 114-152 (156)
125 COG1655 Uncharacterized protei 75.4 0.36 7.7E-06 30.7 -1.8 39 57-95 17-70 (267)
126 PF07975 C1_4: TFIIH C1-like d 75.3 1.3 2.7E-05 21.3 0.5 26 85-110 19-44 (51)
127 TIGR01206 lysW lysine biosynth 75.2 1.2 2.7E-05 21.6 0.4 32 60-99 3-34 (54)
128 PF02176 zf-TRAF: TRAF-type zi 75.0 2.6 5.6E-05 20.4 1.6 43 58-100 8-55 (60)
129 PF02892 zf-BED: BED zinc fing 74.7 4.1 9E-05 18.5 2.2 24 56-79 13-40 (45)
130 PF08790 zf-LYAR: LYAR-type C2 73.8 0.86 1.9E-05 19.0 -0.3 9 61-69 2-10 (28)
131 KOG4167|consensus 73.7 1 2.2E-05 33.5 -0.1 27 57-83 790-816 (907)
132 PF07282 OrfB_Zn_ribbon: Putat 73.1 2.2 4.8E-05 21.5 1.1 28 61-98 30-57 (69)
133 PF15269 zf-C2H2_7: Zinc-finge 72.1 1.3 2.7E-05 20.6 0.1 23 88-110 21-43 (54)
134 KOG2482|consensus 72.1 12 0.00026 25.6 4.5 77 2-81 128-217 (423)
135 COG1571 Predicted DNA-binding 71.0 2.5 5.5E-05 29.4 1.3 18 56-73 364-381 (421)
136 PRK04351 hypothetical protein; 70.9 2.2 4.8E-05 25.3 0.9 34 59-100 112-145 (149)
137 KOG4173|consensus 70.8 2.5 5.5E-05 26.5 1.1 56 19-78 108-165 (253)
138 PF12013 DUF3505: Protein of u 70.4 4.6 9.9E-05 22.4 2.1 68 16-84 10-109 (109)
139 PF07295 DUF1451: Protein of u 69.7 1.4 3E-05 26.1 -0.1 9 18-26 113-121 (146)
140 PF04606 Ogr_Delta: Ogr/Delta- 69.4 0.76 1.7E-05 21.5 -1.0 41 61-103 1-43 (47)
141 COG5216 Uncharacterized conser 69.3 2.4 5.2E-05 20.9 0.7 33 59-97 22-54 (67)
142 smart00614 ZnF_BED BED zinc fi 68.6 5.7 0.00012 18.7 1.9 21 60-80 19-44 (50)
143 KOG1280|consensus 68.2 6.2 0.00013 26.9 2.6 39 57-95 77-117 (381)
144 TIGR00100 hypA hydrogenase nic 67.7 2 4.4E-05 24.3 0.3 26 59-96 70-95 (115)
145 COG1326 Uncharacterized archae 67.4 6.3 0.00014 24.5 2.3 36 60-99 7-42 (201)
146 PRK12380 hydrogenase nickel in 67.2 2.2 4.8E-05 24.1 0.4 25 59-95 70-94 (113)
147 PF08271 TF_Zn_Ribbon: TFIIB z 66.2 2 4.3E-05 19.6 0.0 31 60-99 1-31 (43)
148 COG1675 TFA1 Transcription ini 65.9 9.6 0.00021 23.4 2.9 44 5-71 101-144 (176)
149 PF04959 ARS2: Arsenite-resist 65.7 2.6 5.6E-05 26.7 0.5 27 57-83 75-101 (214)
150 PF14446 Prok-RING_1: Prokaryo 64.8 4.3 9.4E-05 19.7 1.1 11 18-28 6-16 (54)
151 KOG4167|consensus 64.7 0.71 1.5E-05 34.2 -2.3 27 86-112 791-817 (907)
152 PHA02998 RNA polymerase subuni 64.7 1.5 3.3E-05 26.8 -0.6 39 59-101 143-185 (195)
153 PF00301 Rubredoxin: Rubredoxi 64.3 2.7 5.9E-05 19.8 0.3 14 88-101 2-15 (47)
154 cd00730 rubredoxin Rubredoxin; 63.9 2.3 5E-05 20.3 0.0 13 88-100 2-14 (50)
155 PF12760 Zn_Tnp_IS1595: Transp 63.2 1.2 2.5E-05 20.8 -1.1 27 60-95 19-45 (46)
156 PRK00564 hypA hydrogenase nick 63.0 2.6 5.7E-05 23.9 0.1 26 59-96 71-97 (117)
157 smart00154 ZnF_AN1 AN1-like Zi 62.1 4.3 9.3E-05 18.2 0.7 14 17-30 12-25 (39)
158 TIGR00416 sms DNA repair prote 61.8 5.2 0.00011 28.3 1.4 13 16-28 6-18 (454)
159 PF04810 zf-Sec23_Sec24: Sec23 61.2 0.82 1.8E-05 20.7 -1.7 18 82-99 19-36 (40)
160 KOG2026|consensus 61.1 5 0.00011 27.8 1.2 25 85-114 39-63 (442)
161 PF02318 FYVE_2: FYVE-type zin 60.8 5.1 0.00011 22.7 1.1 15 82-96 89-103 (118)
162 KOG2482|consensus 60.8 16 0.00035 25.0 3.4 67 42-108 127-216 (423)
163 PF11931 DUF3449: Domain of un 60.8 2.8 6.1E-05 26.1 0.0 27 82-108 96-123 (196)
164 KOG2807|consensus 60.7 7.1 0.00015 26.4 1.8 22 16-37 289-310 (378)
165 PF05443 ROS_MUCR: ROS/MUCR tr 60.7 8 0.00017 22.6 1.8 26 59-87 72-97 (132)
166 PRK11823 DNA repair protein Ra 60.6 5.8 0.00012 28.0 1.5 13 16-28 6-18 (446)
167 COG5151 SSL1 RNA polymerase II 60.5 1.6 3.4E-05 29.2 -1.1 45 61-107 364-408 (421)
168 TIGR00595 priA primosomal prot 60.1 5 0.00011 28.8 1.1 10 19-28 215-224 (505)
169 COG4957 Predicted transcriptio 59.7 3.3 7.2E-05 24.2 0.2 22 88-112 77-98 (148)
170 KOG2071|consensus 59.0 2.6 5.7E-05 30.5 -0.4 29 84-112 415-443 (579)
171 PF01428 zf-AN1: AN1-like Zinc 58.9 2.5 5.5E-05 19.3 -0.3 13 87-99 13-25 (43)
172 PF04423 Rad50_zn_hook: Rad50 58.9 6.4 0.00014 18.8 1.1 11 89-99 22-32 (54)
173 PF01155 HypA: Hydrogenase exp 58.6 3.1 6.7E-05 23.4 -0.1 26 59-96 70-95 (113)
174 PF10263 SprT-like: SprT-like 58.2 4.6 0.0001 23.8 0.6 32 59-98 123-154 (157)
175 PRK14873 primosome assembly pr 57.7 6.2 0.00013 29.4 1.3 10 19-28 385-394 (665)
176 PLN02294 cytochrome c oxidase 57.5 4.9 0.00011 24.5 0.6 17 84-100 138-154 (174)
177 COG1327 Predicted transcriptio 57.2 1.5 3.3E-05 26.0 -1.5 12 88-99 29-40 (156)
178 PRK03681 hypA hydrogenase nick 57.0 3.1 6.7E-05 23.5 -0.2 27 59-96 70-96 (114)
179 KOG2231|consensus 56.5 28 0.0006 26.1 4.3 21 19-39 184-204 (669)
180 COG1594 RPB9 DNA-directed RNA 56.4 3.1 6.8E-05 23.5 -0.3 16 15-30 20-35 (113)
181 cd01121 Sms Sms (bacterial rad 56.2 6.9 0.00015 26.9 1.3 11 18-28 1-11 (372)
182 cd00924 Cyt_c_Oxidase_Vb Cytoc 55.5 5.5 0.00012 21.9 0.6 18 82-100 75-92 (97)
183 TIGR01384 TFS_arch transcripti 55.2 5.1 0.00011 22.0 0.4 13 87-99 16-28 (104)
184 PF05290 Baculo_IE-1: Baculovi 54.2 7.3 0.00016 22.8 1.0 46 56-102 77-136 (140)
185 PF10013 DUF2256: Uncharacteri 53.6 3.9 8.5E-05 18.8 -0.1 13 89-101 10-22 (42)
186 PF04780 DUF629: Protein of un 53.3 3 6.6E-05 29.5 -0.8 21 60-80 58-78 (466)
187 KOG3408|consensus 53.0 10 0.00022 21.7 1.4 28 55-82 53-80 (129)
188 PF12230 PRP21_like_P: Pre-mRN 52.4 4.7 0.0001 25.6 0.0 27 85-112 166-192 (229)
189 COG4640 Predicted membrane pro 52.3 7.3 0.00016 27.1 0.9 16 59-74 15-30 (465)
190 PF10276 zf-CHCC: Zinc-finger 52.3 6 0.00013 18.0 0.3 12 16-27 28-39 (40)
191 PRK05452 anaerobic nitric oxid 52.1 3.8 8.2E-05 29.1 -0.5 41 56-96 422-467 (479)
192 COG4888 Uncharacterized Zn rib 52.0 3.6 7.7E-05 22.7 -0.5 39 56-98 19-57 (104)
193 smart00731 SprT SprT homologue 51.6 9.7 0.00021 22.4 1.3 33 59-98 112-144 (146)
194 PRK14714 DNA polymerase II lar 50.9 11 0.00023 30.3 1.6 9 18-26 668-676 (1337)
195 PRK05580 primosome assembly pr 50.8 8.6 0.00019 28.7 1.1 9 59-67 421-429 (679)
196 PF14803 Nudix_N_2: Nudix N-te 50.7 5.7 0.00012 17.3 0.1 11 87-97 22-32 (34)
197 COG3677 Transposase and inacti 50.0 5.8 0.00012 23.0 0.1 37 60-101 31-67 (129)
198 PF13878 zf-C2H2_3: zinc-finge 49.9 21 0.00045 16.1 1.9 23 18-40 14-38 (41)
199 PF11789 zf-Nse: Zinc-finger o 49.9 10 0.00023 18.5 1.0 31 58-92 23-53 (57)
200 PF14311 DUF4379: Domain of un 49.0 8 0.00017 18.6 0.5 14 60-73 29-42 (55)
201 PRK00762 hypA hydrogenase nick 48.3 5.2 0.00011 23.0 -0.2 31 59-95 70-100 (124)
202 PTZ00448 hypothetical protein; 48.1 5.4 0.00012 27.4 -0.2 23 87-109 314-336 (373)
203 PF05191 ADK_lid: Adenylate ki 48.1 6.9 0.00015 17.2 0.2 13 88-100 2-14 (36)
204 PF09963 DUF2197: Uncharacteri 47.4 10 0.00022 18.6 0.8 40 60-99 3-43 (56)
205 PF09845 DUF2072: Zn-ribbon co 47.4 9 0.00019 22.3 0.6 15 17-31 1-15 (131)
206 PLN02748 tRNA dimethylallyltra 47.4 5.3 0.00012 28.4 -0.3 24 86-109 417-441 (468)
207 PRK12496 hypothetical protein; 47.0 14 0.0003 22.3 1.5 13 17-29 127-139 (164)
208 COG0675 Transposase and inacti 46.8 9.2 0.0002 25.3 0.7 23 61-98 311-333 (364)
209 PF01286 XPA_N: XPA protein N- 46.1 4.2 9.2E-05 17.8 -0.6 13 89-101 5-17 (34)
210 PF15135 UPF0515: Uncharacteri 46.0 22 0.00047 23.2 2.2 11 16-26 111-121 (278)
211 PF01927 Mut7-C: Mut7-C RNAse 45.3 17 0.00037 21.4 1.6 21 57-77 122-142 (147)
212 PRK05978 hypothetical protein; 45.0 5.1 0.00011 23.8 -0.6 32 60-100 34-65 (148)
213 TIGR00686 phnA alkylphosphonat 44.2 15 0.00032 20.7 1.1 14 59-72 19-32 (109)
214 KOG0717|consensus 43.7 11 0.00023 26.9 0.7 22 88-109 293-314 (508)
215 PF04641 Rtf2: Rtf2 RING-finge 43.7 20 0.00044 23.3 1.9 14 15-28 111-124 (260)
216 KOG4727|consensus 43.3 14 0.0003 22.6 1.0 26 87-112 75-102 (193)
217 PF10537 WAC_Acf1_DNA_bd: ATP- 42.4 55 0.0012 18.2 3.2 36 59-95 3-38 (102)
218 PF01096 TFIIS_C: Transcriptio 42.3 13 0.00027 16.6 0.6 10 88-97 29-38 (39)
219 COG4391 Uncharacterized protei 42.0 15 0.00033 18.4 0.9 14 16-29 47-60 (62)
220 KOG2923|consensus 41.8 15 0.00032 18.5 0.8 33 60-98 23-55 (67)
221 PF02591 DUF164: Putative zinc 41.7 24 0.00052 16.9 1.6 14 55-68 42-55 (56)
222 PF01215 COX5B: Cytochrome c o 41.5 13 0.00027 21.9 0.6 15 57-71 110-124 (136)
223 PF13824 zf-Mss51: Zinc-finger 41.0 16 0.00034 17.9 0.8 22 13-34 10-32 (55)
224 COG4338 Uncharacterized protei 40.6 6 0.00013 18.7 -0.6 13 89-101 14-26 (54)
225 PF08792 A2L_zn_ribbon: A2L zi 39.7 14 0.0003 15.9 0.5 12 87-98 21-32 (33)
226 PRK06260 threonine synthase; V 38.9 18 0.0004 25.0 1.2 11 18-28 4-14 (397)
227 PF06397 Desulfoferrod_N: Desu 37.5 17 0.00038 16.1 0.6 12 16-27 5-16 (36)
228 COG1066 Sms Predicted ATP-depe 37.1 19 0.00042 25.4 1.1 13 16-28 6-18 (456)
229 KOG2785|consensus 36.4 81 0.0018 22.1 3.8 64 16-81 165-242 (390)
230 COG4530 Uncharacterized protei 36.0 20 0.00043 20.3 0.8 15 14-28 23-37 (129)
231 PF05741 zf-nanos: Nanos RNA b 35.4 7.4 0.00016 19.0 -0.8 15 86-100 32-46 (55)
232 PTZ00043 cytochrome c oxidase 35.1 16 0.00035 23.5 0.5 18 84-101 178-195 (268)
233 PRK10220 hypothetical protein; 35.0 28 0.00061 19.6 1.3 14 59-72 20-33 (111)
234 KOG0978|consensus 34.9 12 0.00026 28.0 -0.1 45 60-104 644-695 (698)
235 COG2331 Uncharacterized protei 34.9 18 0.00039 19.0 0.5 8 60-67 13-20 (82)
236 PF01363 FYVE: FYVE zinc finge 34.5 18 0.00039 18.0 0.5 12 60-71 10-21 (69)
237 TIGR03831 YgiT_finger YgiT-typ 34.3 21 0.00046 15.9 0.7 15 57-71 30-44 (46)
238 PRK14892 putative transcriptio 34.0 10 0.00023 20.9 -0.4 36 57-99 19-54 (99)
239 PF10164 DUF2367: Uncharacteri 33.8 14 0.0003 20.3 0.0 13 85-97 86-98 (98)
240 PRK00420 hypothetical protein; 33.4 32 0.00069 19.5 1.4 15 58-72 39-53 (112)
241 cd04476 RPA1_DBD_C RPA1_DBD_C: 33.2 16 0.00034 21.9 0.2 26 61-97 36-61 (166)
242 PF08209 Sgf11: Sgf11 (transcr 33.1 50 0.0011 14.2 2.0 23 59-82 4-26 (33)
243 PF12773 DZR: Double zinc ribb 33.0 14 0.00031 17.1 -0.0 26 61-97 14-39 (50)
244 COG3364 Zn-ribbon containing p 32.7 21 0.00046 19.9 0.6 15 59-73 2-16 (112)
245 smart00064 FYVE Protein presen 32.7 20 0.00043 17.8 0.5 10 61-70 12-21 (68)
246 KOG1842|consensus 32.5 28 0.0006 24.8 1.3 25 58-82 14-38 (505)
247 PRK11032 hypothetical protein; 32.5 18 0.00038 21.9 0.3 9 18-26 125-133 (160)
248 KOG0782|consensus 32.3 14 0.0003 27.3 -0.2 30 72-101 238-267 (1004)
249 PRK12860 transcriptional activ 31.9 18 0.00038 22.6 0.3 27 60-94 135-161 (189)
250 PF09082 DUF1922: Domain of un 31.8 12 0.00027 19.1 -0.4 15 84-99 17-31 (68)
251 KOG2906|consensus 31.6 12 0.00025 20.7 -0.5 15 87-101 21-35 (105)
252 PF03811 Zn_Tnp_IS1: InsA N-te 31.4 6.3 0.00014 17.4 -1.3 30 60-93 6-35 (36)
253 cd00065 FYVE FYVE domain; Zinc 31.3 23 0.00051 16.7 0.6 11 60-70 19-29 (57)
254 KOG1088|consensus 31.3 21 0.00047 20.4 0.5 25 79-103 90-114 (124)
255 COG0068 HypF Hydrogenase matur 30.7 12 0.00025 28.2 -0.7 11 58-68 172-182 (750)
256 CHL00174 accD acetyl-CoA carbo 30.2 22 0.00048 23.8 0.5 16 59-74 57-72 (296)
257 TIGR00319 desulf_FeS4 desulfof 30.2 24 0.00052 15.0 0.5 11 87-97 7-17 (34)
258 PRK12722 transcriptional activ 29.9 21 0.00045 22.2 0.3 28 60-95 135-162 (187)
259 PLN03239 histone acetyltransfe 29.4 15 0.00033 25.1 -0.3 24 85-108 104-127 (351)
260 PF02148 zf-UBP: Zn-finger in 29.4 8.7 0.00019 19.0 -1.1 14 86-99 10-23 (63)
261 cd00974 DSRD Desulforedoxin (D 29.1 25 0.00055 14.9 0.5 11 87-97 4-14 (34)
262 PF02891 zf-MIZ: MIZ/SP-RING z 28.4 14 0.0003 17.5 -0.5 8 88-95 42-49 (50)
263 TIGR00515 accD acetyl-CoA carb 28.1 26 0.00056 23.3 0.6 15 60-74 46-60 (285)
264 cd01410 SIRT7 SIRT7: Eukaryoti 27.8 47 0.001 20.8 1.7 41 53-96 89-129 (206)
265 PRK07218 replication factor A; 27.8 23 0.00049 25.0 0.3 21 60-96 298-318 (423)
266 KOG0696|consensus 27.5 11 0.00024 26.8 -1.2 39 59-97 92-131 (683)
267 PHA02942 putative transposase; 27.0 37 0.00081 23.6 1.2 27 61-98 327-353 (383)
268 PTZ00064 histone acetyltransfe 26.0 17 0.00037 26.3 -0.6 25 84-108 277-301 (552)
269 PRK05654 acetyl-CoA carboxylas 25.9 25 0.00054 23.5 0.2 16 59-74 46-61 (292)
270 PF09332 Mcm10: Mcm10 replicat 25.9 12 0.00025 25.7 -1.4 44 57-100 250-298 (344)
271 PLN00104 MYST -like histone ac 25.8 16 0.00034 26.0 -0.8 25 84-108 195-219 (450)
272 PF14690 zf-ISL3: zinc-finger 25.6 34 0.00074 15.5 0.6 10 17-26 2-11 (47)
273 PRK08222 hydrogenase 4 subunit 25.2 27 0.00059 21.4 0.3 19 85-103 112-130 (181)
274 PRK06450 threonine synthase; V 25.1 33 0.00072 23.3 0.7 30 60-102 4-33 (338)
275 COG1656 Uncharacterized conser 24.8 52 0.0011 20.1 1.4 22 57-78 128-149 (165)
276 TIGR00627 tfb4 transcription f 24.7 34 0.00073 22.7 0.6 10 88-97 256-265 (279)
277 PF06689 zf-C4_ClpX: ClpX C4-t 24.6 6.7 0.00015 17.8 -1.9 30 61-96 3-33 (41)
278 PF12907 zf-met2: Zinc-binding 24.5 39 0.00085 15.3 0.6 22 60-81 2-26 (40)
279 PRK07591 threonine synthase; V 24.2 47 0.001 23.3 1.3 12 17-28 18-29 (421)
280 cd01413 SIR2_Af2 SIR2_Af2: Arc 24.1 52 0.0011 20.9 1.4 38 54-96 108-145 (222)
281 KOG1984|consensus 24.0 24 0.00051 27.4 -0.2 45 57-107 336-380 (1007)
282 smart00647 IBR In Between Ring 23.8 39 0.00084 16.2 0.6 38 61-106 20-59 (64)
283 PF05876 Terminase_GpA: Phage 23.7 14 0.00031 26.9 -1.3 42 59-100 200-242 (557)
284 COG1998 RPS31 Ribosomal protei 23.5 43 0.00092 16.0 0.7 11 87-97 37-47 (51)
285 PF14255 Cys_rich_CPXG: Cystei 23.1 32 0.00069 16.6 0.2 12 61-72 2-13 (52)
286 COG4896 Uncharacterized protei 23.1 64 0.0014 16.2 1.3 8 88-95 32-39 (68)
287 PF00130 C1_1: Phorbol esters/ 22.8 55 0.0012 15.2 1.0 30 57-97 9-38 (53)
288 PF04438 zf-HIT: HIT zinc fing 22.8 29 0.00062 14.5 0.0 11 87-97 13-23 (30)
289 PRK14138 NAD-dependent deacety 22.4 63 0.0014 20.9 1.5 40 53-96 113-152 (244)
290 TIGR00244 transcriptional regu 22.2 26 0.00057 20.9 -0.2 12 88-99 29-40 (147)
291 KOG3352|consensus 22.0 41 0.0009 20.2 0.6 14 57-70 131-144 (153)
292 KOG2747|consensus 21.7 20 0.00043 25.0 -0.9 27 83-109 154-180 (396)
293 TIGR01385 TFSII transcription 21.5 16 0.00034 24.5 -1.4 37 59-98 258-297 (299)
294 TIGR03829 YokU_near_AblA uncha 21.4 72 0.0016 17.3 1.4 19 57-75 33-51 (89)
295 PRK12387 formate hydrogenlyase 21.4 34 0.00074 20.9 0.2 19 85-103 112-130 (180)
296 COG1631 RPL42A Ribosomal prote 20.9 42 0.00091 18.3 0.4 13 87-99 68-80 (94)
297 PF14369 zf-RING_3: zinc-finge 20.8 43 0.00094 14.5 0.4 10 19-28 23-32 (35)
298 PF02146 SIR2: Sir2 family; I 20.8 38 0.00082 20.5 0.3 40 54-97 100-139 (178)
299 PF06353 DUF1062: Protein of u 20.7 41 0.00089 19.9 0.4 12 87-98 13-24 (142)
300 PRK11788 tetratricopeptide rep 20.3 65 0.0014 21.7 1.3 10 57-66 366-375 (389)
301 KOG4602|consensus 20.3 31 0.00067 22.7 -0.2 48 60-107 234-288 (318)
302 KOG2857|consensus 20.2 32 0.00069 20.4 -0.1 20 88-107 18-37 (157)
303 COG5152 Uncharacterized conser 20.0 47 0.001 21.0 0.5 16 15-30 194-209 (259)
No 1
>KOG2462|consensus
Probab=99.92 E-value=1.1e-25 Score=139.57 Aligned_cols=106 Identities=25% Similarity=0.427 Sum_probs=85.7
Q ss_pred HHHHHHHHhcCC---CCCeecCCChhhccChhhHHHHHHHhc------------Chh-HHHHHHHHhhcCCCceeccccc
Q psy64 3 RQLKEHMAVHTT---DRPFVCNMCPSTFKLKKHLRQHYKVHL------------KMD-TLENHMKAVHEKIRDFQCKVCD 66 (115)
Q Consensus 3 ~~l~~h~~~h~~---~~~~~C~~C~~~~~~~~~l~~h~~~h~------------~~~-~l~~h~~~~h~~~~~~~C~~c~ 66 (115)
++|.+|.+.|.. .+.+.|++||+.|.+...|..|+++|. .+. .|+-|+| +|+|+|||.|+.|+
T Consensus 144 snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiR-THTGEKPF~C~hC~ 222 (279)
T KOG2462|consen 144 SNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIR-THTGEKPFSCPHCG 222 (279)
T ss_pred cccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccc-cccCCCCccCCccc
Confidence 456677776632 455777777777777777777777775 111 3556666 78999999999999
Q ss_pred ccccChhhHHHHHHHhcCCCceeEEeecceehhhhhhccCCcc
Q psy64 67 RAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVVIYAKKFSLDI 109 (115)
Q Consensus 67 ~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~~~~h~~~ 109 (115)
++|.+.++|..|+++|.+.|+|.|..|+|+|...+-|..|..+
T Consensus 223 kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 223 KAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred chhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 9999999999999999999999999999999999999998753
No 2
>KOG2462|consensus
Probab=99.91 E-value=1.3e-25 Score=139.28 Aligned_cols=96 Identities=23% Similarity=0.421 Sum_probs=88.9
Q ss_pred CCCeecCCChhhccChhhHHHHHHHhc------------------ChhHHHHHHHHhhcCCCceecccccccccChhhHH
Q psy64 15 DRPFVCNMCPSTFKLKKHLRQHYKVHL------------------KMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLK 76 (115)
Q Consensus 15 ~~~~~C~~C~~~~~~~~~l~~h~~~h~------------------~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l~ 76 (115)
...|+|++||+.|...++|.+|++.|. .+..|++|++ +| ..+.+|..||+.|.+...|+
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHir-TH--~l~c~C~iCGKaFSRPWLLQ 204 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIR-TH--TLPCECGICGKAFSRPWLLQ 204 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhh-cc--CCCcccccccccccchHHhh
Confidence 345999999999999999999999885 6788999999 44 47899999999999999999
Q ss_pred HHHHHhcCCCceeEEeecceehhhhhhccCCcccccc
Q psy64 77 LHMRIHTGEKKYIFIVVKKIIVVIYAKKFSLDIEILC 113 (115)
Q Consensus 77 ~h~~~h~~~~~~~C~~C~~~~~~~~~~~~h~~~h~~~ 113 (115)
-|+++|+|||||.|.+|++.|.+++.|+.|+.+|..+
T Consensus 205 GHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~ 241 (279)
T KOG2462|consen 205 GHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDV 241 (279)
T ss_pred cccccccCCCCccCCcccchhcchHHHHHHHHhhcCC
Confidence 9999999999999999999999999999999999764
No 3
>KOG1074|consensus
Probab=99.79 E-value=1.2e-20 Score=131.19 Aligned_cols=39 Identities=38% Similarity=0.801 Sum_probs=35.5
Q ss_pred HHHHHHHHhcCCCCCeecCCChhhccChhhHHHHHHHhc
Q psy64 3 RQLKEHMAVHTTDRPFVCNMCPSTFKLKKHLRQHYKVHL 41 (115)
Q Consensus 3 ~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~ 41 (115)
+.|+.|++.|+|++||+|++||..|..+.+|..|...|.
T Consensus 367 SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~ 405 (958)
T KOG1074|consen 367 SALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHR 405 (958)
T ss_pred hhhhhhhhccCCCCCeeecccccccccccceeeeeeecc
Confidence 678999999999999999999999999999999876553
No 4
>KOG3623|consensus
Probab=99.74 E-value=3.7e-19 Score=122.64 Aligned_cols=81 Identities=26% Similarity=0.462 Sum_probs=75.9
Q ss_pred CCCCeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccChhhHHHHHHHhcCCCceeEEee
Q psy64 14 TDRPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVV 93 (115)
Q Consensus 14 ~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C 93 (115)
.+-+|.|..|+++|...++|.+|.. -|+|++||+|.+|.++|..+-.|..|.+.|.|||||.|+.|
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKY--------------EHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKC 956 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKY--------------EHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKC 956 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhh--------------hhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhh
Confidence 3457999999999999999999987 45899999999999999999999999999999999999999
Q ss_pred cceehhhhhhccCCc
Q psy64 94 KKIIVVIYAKKFSLD 108 (115)
Q Consensus 94 ~~~~~~~~~~~~h~~ 108 (115)
+|.|..+++...|+.
T Consensus 957 lKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 957 LKRFSHSGSYSQHMN 971 (1007)
T ss_pred hhhcccccchHhhhc
Confidence 999999999998875
No 5
>KOG3623|consensus
Probab=99.74 E-value=1.1e-18 Score=120.46 Aligned_cols=106 Identities=28% Similarity=0.467 Sum_probs=84.9
Q ss_pred HHHHHHHHh-c-CCCCCeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccChhhHHHHHH
Q psy64 3 RQLKEHMAV-H-TTDRPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLHMR 80 (115)
Q Consensus 3 ~~l~~h~~~-h-~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~ 80 (115)
..|+.|+.- | .++..|.|..|.++|.+.+.|.+|+..|.....-..+.- .....+.|+|.+||++|..+-.|+.|++
T Consensus 224 tslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~slt-qsa~lRKFKCtECgKAFKfKHHLKEHlR 302 (1007)
T KOG3623|consen 224 TSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLT-QSALLRKFKCTECGKAFKFKHHLKEHLR 302 (1007)
T ss_pred HHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCccccccc-chhhhccccccccchhhhhHHHHHhhhe
Confidence 356778773 4 345569999999999999999999998852111111111 2234567999999999999999999999
Q ss_pred HhcCCCceeEEeecceehhhhhhccCCcc
Q psy64 81 IHTGEKKYIFIVVKKIIVVIYAKKFSLDI 109 (115)
Q Consensus 81 ~h~~~~~~~C~~C~~~~~~~~~~~~h~~~ 109 (115)
+|.|||||.|+.|+|.|..++++..|+.+
T Consensus 303 IHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 303 IHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred eecCCCCcCCcccccccccCCcccccccc
Confidence 99999999999999999999999999863
No 6
>KOG1074|consensus
Probab=99.73 E-value=6.6e-19 Score=122.66 Aligned_cols=54 Identities=24% Similarity=0.455 Sum_probs=51.1
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecceehhhhhhccCCcccccc
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVVIYAKKFSLDIEILC 113 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~~~~h~~~h~~~ 113 (115)
..|..||+.|..++.|+.|+++|+++|||.|..|++.|..+..|..|+..|.-+
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~ 933 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWV 933 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhcccccc
Confidence 569999999999999999999999999999999999999999999999988643
No 7
>KOG3608|consensus
Probab=99.68 E-value=5.2e-17 Score=104.43 Aligned_cols=109 Identities=21% Similarity=0.395 Sum_probs=86.0
Q ss_pred hHHHHHHHHhcCCCCCeecCCChhhccChhhHHHHHHHhc----------------------------------------
Q psy64 2 KRQLKEHMAVHTTDRPFVCNMCPSTFKLKKHLRQHYKVHL---------------------------------------- 41 (115)
Q Consensus 2 k~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~---------------------------------------- 41 (115)
|..|.+|++.|++++...|+.||.-|+..+.|-.|.+-.+
T Consensus 192 k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdm 271 (467)
T KOG3608|consen 192 KYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDM 271 (467)
T ss_pred HHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhccccccccc
Confidence 5789999999999999999999999999999888875432
Q ss_pred ---ChhHHHHHHHHhhcCCCceecccccccccChhhHHHHHHHhcCCCceeEEe--ecceehhhhhhccCCcccc
Q psy64 42 ---KMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIV--VKKIIVVIYAKKFSLDIEI 111 (115)
Q Consensus 42 ---~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~--C~~~~~~~~~~~~h~~~h~ 111 (115)
..+.|..|++..|..++||+|+.|.+.+.+.+.|+.|...|+ +..|.|.. |.+.+.....+.+|++.+.
T Consensus 272 tc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 272 TCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred CCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhc
Confidence 567788888888888888888888888888888888888776 55666654 6666666666666665443
No 8
>KOG3576|consensus
Probab=99.66 E-value=5.6e-18 Score=101.66 Aligned_cols=81 Identities=28% Similarity=0.613 Sum_probs=61.6
Q ss_pred CCCCeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccChhhHHHHHHHhcCCCceeEEee
Q psy64 14 TDRPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVV 93 (115)
Q Consensus 14 ~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C 93 (115)
+...|.|.+|+++|....-|.+|++-| ...+.+.|.-||+.|...-.|++|.++|+|.+||+|+.|
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch--------------~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c 179 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCH--------------SDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLC 179 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhc--------------cHHHHHHHhhccCcccchhhhhhhhccccCccccchhhh
Confidence 456699999999999999999998855 455666777777777777777777777777777777777
Q ss_pred cceehhhhhhccCCc
Q psy64 94 KKIIVVIYAKKFSLD 108 (115)
Q Consensus 94 ~~~~~~~~~~~~h~~ 108 (115)
++.|+++.+|..|++
T Consensus 180 ~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 180 EKAFTQRCSLESHLK 194 (267)
T ss_pred hHHHHhhccHHHHHH
Confidence 777777777777665
No 9
>KOG3576|consensus
Probab=99.58 E-value=2.5e-16 Score=94.60 Aligned_cols=95 Identities=21% Similarity=0.430 Sum_probs=83.8
Q ss_pred HHHHHHHHhcCCCCCeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccChhhHHHHHHHh
Q psy64 3 RQLKEHMAVHTTDRPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLHMRIH 82 (115)
Q Consensus 3 ~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~h 82 (115)
.-|.+|+..|...+.+-|..||+.|.....|.+|+++ |+|.+||+|..|+++|...-.|..|.+.-
T Consensus 131 Rmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rt--------------htgvrpykc~~c~kaftqrcsleshl~kv 196 (267)
T KOG3576|consen 131 RMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRT--------------HTGVRPYKCSLCEKAFTQRCSLESHLKKV 196 (267)
T ss_pred HHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhcc--------------ccCccccchhhhhHHHHhhccHHHHHHHH
Confidence 4578999999999999999999999999999999984 58999999999999999999999997643
Q ss_pred c-----------CCCceeEEeecceehhhhhhccCCcccc
Q psy64 83 T-----------GEKKYIFIVVKKIIVVIYAKKFSLDIEI 111 (115)
Q Consensus 83 ~-----------~~~~~~C~~C~~~~~~~~~~~~h~~~h~ 111 (115)
. .+|.|+|+.||++-........|++.|+
T Consensus 197 hgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~h 236 (267)
T KOG3576|consen 197 HGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHH 236 (267)
T ss_pred cCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcC
Confidence 3 4578999999999999888888888765
No 10
>PHA00733 hypothetical protein
Probab=99.39 E-value=7e-14 Score=80.06 Aligned_cols=89 Identities=13% Similarity=0.141 Sum_probs=71.2
Q ss_pred CCCCCeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccChhhHHHHHHHhcCCCceeEEe
Q psy64 13 TTDRPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIV 92 (115)
Q Consensus 13 ~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~ 92 (115)
...+++.|.+|...|.....|..+.. |..++ .+.+.+||.|+.||+.|.....|..|++.+ +.+|.|++
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~-------l~~~~--~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~ 104 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSY-------LYKLL--TSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPV 104 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHH-------HHhhc--ccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCC
Confidence 34577889999999988877776632 22222 234588999999999999999999999876 46899999
Q ss_pred ecceehhhhhhccCCccccc
Q psy64 93 VKKIIVVIYAKKFSLDIEIL 112 (115)
Q Consensus 93 C~~~~~~~~~~~~h~~~h~~ 112 (115)
|++.|.....|..|+...+.
T Consensus 105 CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 105 CGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCccCCHHHHHHHHHHhcC
Confidence 99999999999999876543
No 11
>PHA02768 hypothetical protein; Provisional
Probab=99.24 E-value=2.7e-12 Score=62.17 Aligned_cols=46 Identities=15% Similarity=0.310 Sum_probs=41.9
Q ss_pred CceecccccccccChhhHHHHHHHhcCCCceeEEeecceehhhhhhcc
Q psy64 58 RDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVVIYAKKF 105 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~~~~ 105 (115)
..|+|+.||+.|.....|..|+++|+ +||.|..|++.|...+.|..
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeEE
Confidence 35899999999999999999999998 79999999999998877754
No 12
>KOG3608|consensus
Probab=99.18 E-value=3.7e-11 Score=77.95 Aligned_cols=92 Identities=21% Similarity=0.393 Sum_probs=70.5
Q ss_pred hHHHHHHHHh-cCCCCCeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceeccc--ccccccChhhHHHH
Q psy64 2 KRQLKEHMAV-HTTDRPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKV--CDRAFFDVYNLKLH 78 (115)
Q Consensus 2 k~~l~~h~~~-h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~--c~~~~~~~~~l~~h 78 (115)
.++|..|++. |...+||+|..|++.+...+.|..|...| . +..|.|.. |...+.+...+..|
T Consensus 276 ~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~H--------------S-~~~y~C~h~~C~~s~r~~~q~~~H 340 (467)
T KOG3608|consen 276 ASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVH--------------S-KTVYQCEHPDCHYSVRTYTQMRRH 340 (467)
T ss_pred hHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhc--------------c-ccceecCCCCCcHHHHHHHHHHHH
Confidence 4678888884 78889999999999999999999998866 2 45677766 77777777777777
Q ss_pred HHHhc-CCC--ceeEEeecceehhhhhhccCCc
Q psy64 79 MRIHT-GEK--KYIFIVVKKIIVVIYAKKFSLD 108 (115)
Q Consensus 79 ~~~h~-~~~--~~~C~~C~~~~~~~~~~~~h~~ 108 (115)
..-+. |.. +|.|..|.+.|+.-.+|..|+.
T Consensus 341 ~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~ 373 (467)
T KOG3608|consen 341 FLEVHEGNNPILYACHCCDRFFTSGKSLSAHLM 373 (467)
T ss_pred HHHhccCCCCCceeeecchhhhccchhHHHHHH
Confidence 66544 433 4788888888888777777765
No 13
>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=99.09 E-value=8.5e-11 Score=49.06 Aligned_cols=25 Identities=48% Similarity=0.607 Sum_probs=19.3
Q ss_pred hHHHHHHHhcCCCceeEEeecceeh
Q psy64 74 NLKLHMRIHTGEKKYIFIVVKKIIV 98 (115)
Q Consensus 74 ~l~~h~~~h~~~~~~~C~~C~~~~~ 98 (115)
+|..|++.|++++||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 3667888888888888888888775
No 14
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.08 E-value=8.1e-11 Score=49.13 Aligned_cols=26 Identities=35% Similarity=0.862 Sum_probs=23.9
Q ss_pred HHHHHHHhcCCCCCeecCCChhhccC
Q psy64 4 QLKEHMAVHTTDRPFVCNMCPSTFKL 29 (115)
Q Consensus 4 ~l~~h~~~h~~~~~~~C~~C~~~~~~ 29 (115)
+|..|++.|++++||.|+.|+++|..
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 58899999999999999999999863
No 15
>PHA02768 hypothetical protein; Provisional
Probab=99.01 E-value=1.5e-10 Score=56.07 Aligned_cols=43 Identities=16% Similarity=0.456 Sum_probs=37.9
Q ss_pred CeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccChhhH
Q psy64 17 PFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNL 75 (115)
Q Consensus 17 ~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l 75 (115)
-|.|++||+.|...++|..|++.| . ++++|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H--------------~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKH--------------N--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhc--------------C--CcccCCcccceeccccee
Confidence 478999999999999999999966 3 689999999999977655
No 16
>PHA00733 hypothetical protein
Probab=99.00 E-value=9e-10 Score=63.20 Aligned_cols=62 Identities=23% Similarity=0.435 Sum_probs=50.9
Q ss_pred HHHHHHhcCCCCCeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccChhhHHHHHHHhc
Q psy64 5 LKEHMAVHTTDRPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLHMRIHT 83 (115)
Q Consensus 5 l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~h~ 83 (115)
|..|+..+ +.+||.|+.||+.|.....|..|++.+ ..+|.|..|++.|.....|..|+....
T Consensus 62 l~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~h----------------~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 62 LYKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIRYT----------------EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred HHhhcccC-CCCCccCCCCCCcCCCHHHHHHHHhcC----------------CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 45554444 578999999999999999999887633 346899999999999999999977654
No 17
>KOG3993|consensus
Probab=98.89 E-value=5e-10 Score=74.15 Aligned_cols=78 Identities=19% Similarity=0.339 Sum_probs=55.2
Q ss_pred HHHHHHhcCCCCCeecCCChhhccChhhHHHHHHHhcChhHHH------------------HHHH-HhhcCCCceecccc
Q psy64 5 LKEHMAVHTTDRPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLE------------------NHMK-AVHEKIRDFQCKVC 65 (115)
Q Consensus 5 l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~------------------~h~~-~~h~~~~~~~C~~c 65 (115)
|.+|.........|+|++|+|.|.-..+|..|.++|.-+.... +-.+ .....+..|.|..|
T Consensus 283 LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C 362 (500)
T KOG3993|consen 283 LAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTC 362 (500)
T ss_pred HhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHh
Confidence 4555555555567999999999999999999999996222211 0000 00123447899999
Q ss_pred cccccChhhHHHHHHHh
Q psy64 66 DRAFFDVYNLKLHMRIH 82 (115)
Q Consensus 66 ~~~~~~~~~l~~h~~~h 82 (115)
++.|.+..+|..|+-+|
T Consensus 363 ~KkFrRqAYLrKHqlth 379 (500)
T KOG3993|consen 363 GKKFRRQAYLRKHQLTH 379 (500)
T ss_pred hhhhHHHHHHHHhHHhh
Confidence 99999999999997666
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.87 E-value=6.4e-09 Score=72.11 Aligned_cols=83 Identities=16% Similarity=0.342 Sum_probs=47.9
Q ss_pred CCCeecCCChhhccChhhHHHHHHHhc-----------ChhHHHHHHHHhhcCCCceecccccccccC----------hh
Q psy64 15 DRPFVCNMCPSTFKLKKHLRQHYKVHL-----------KMDTLENHMKAVHEKIRDFQCKVCDRAFFD----------VY 73 (115)
Q Consensus 15 ~~~~~C~~C~~~~~~~~~l~~h~~~h~-----------~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~----------~~ 73 (115)
++.+.|+.|++.|. ...|..|+..++ .+..|..|.. .+...+++.|+.|+..+.. ..
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~Hkpv~CpCg~~~~R~~L~~H~~-thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s 528 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFHEPLQCPCGVVLEKEQMVQHQA-STCPLRLITCRFCGDMVQAGGSAMDVRDRLR 528 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcCCCccCCCCCCcchhHHHhhhh-ccCCCCceeCCCCCCccccCccccchhhhhh
Confidence 34455666666553 344555554321 1223333433 4566777788888777642 23
Q ss_pred hHHHHHHHhcCCCceeEEeecceehhh
Q psy64 74 NLKLHMRIHTGEKKYIFIVVKKIIVVI 100 (115)
Q Consensus 74 ~l~~h~~~h~~~~~~~C~~C~~~~~~~ 100 (115)
.|..|.... |.+++.|..|++.+..+
T Consensus 529 ~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr 554 (567)
T PLN03086 529 GMSEHESIC-GSRTAPCDSCGRSVMLK 554 (567)
T ss_pred hHHHHHHhc-CCcceEccccCCeeeeh
Confidence 677776664 77778887787776654
No 19
>PHA00616 hypothetical protein
Probab=98.82 E-value=2.6e-09 Score=49.44 Aligned_cols=34 Identities=18% Similarity=0.247 Sum_probs=32.2
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCceeEEe
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIV 92 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~ 92 (115)
||+|+.||+.|...+.+..|++.+++++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999999874
No 20
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.76 E-value=8e-09 Score=71.64 Aligned_cols=101 Identities=17% Similarity=0.310 Sum_probs=68.9
Q ss_pred HHHHHHHHhcCCCCCeecCC--ChhhccChhhHHHHHHH-h----cChhHHHHHHHHhhcCCCceecccccccccChhhH
Q psy64 3 RQLKEHMAVHTTDRPFVCNM--CPSTFKLKKHLRQHYKV-H----LKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNL 75 (115)
Q Consensus 3 ~~l~~h~~~h~~~~~~~C~~--C~~~~~~~~~l~~h~~~-h----~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l 75 (115)
.+|..|.... ....-.|+. ||..|.. ..+..|..- + .....+..|+...| +++.|+ ||..+ ....|
T Consensus 420 ~~l~lHe~~C-~r~~V~Cp~~~Cg~v~~r-~el~~H~~C~~Cgk~f~~s~LekH~~~~H---kpv~Cp-Cg~~~-~R~~L 492 (567)
T PLN03086 420 RSIALHEAYC-SRHNVVCPHDGCGIVLRV-EEAKNHVHCEKCGQAFQQGEMEKHMKVFH---EPLQCP-CGVVL-EKEQM 492 (567)
T ss_pred hHHHHHHhhC-CCcceeCCcccccceeec-cccccCccCCCCCCccchHHHHHHHHhcC---CCccCC-CCCCc-chhHH
Confidence 3455565432 223445874 9988853 345555410 0 14567889988433 789999 99755 66899
Q ss_pred HHHHHHhcCCCceeEEeecceehh----------hhhhccCCccc
Q psy64 76 KLHMRIHTGEKKYIFIVVKKIIVV----------IYAKKFSLDIE 110 (115)
Q Consensus 76 ~~h~~~h~~~~~~~C~~C~~~~~~----------~~~~~~h~~~h 110 (115)
..|...+..++|+.|..|++.+.. ...|..|..+.
T Consensus 493 ~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C 537 (567)
T PLN03086 493 VQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC 537 (567)
T ss_pred HhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc
Confidence 999999999999999999999941 34677776543
No 21
>PHA00732 hypothetical protein
Probab=98.61 E-value=2.2e-08 Score=52.65 Aligned_cols=45 Identities=24% Similarity=0.304 Sum_probs=38.0
Q ss_pred ceecccccccccChhhHHHHHHH-hcCCCceeEEeecceehhhhhhccCCcc
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRI-HTGEKKYIFIVVKKIIVVIYAKKFSLDI 109 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~-h~~~~~~~C~~C~~~~~~~~~~~~h~~~ 109 (115)
||.|..||+.|.....|..|++. |. ++.|+.|++.|. .+..|+++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhcc
Confidence 58999999999999999999984 55 468999999998 46677654
No 22
>PHA00732 hypothetical protein
Probab=98.50 E-value=9.5e-08 Score=50.29 Aligned_cols=48 Identities=27% Similarity=0.494 Sum_probs=38.2
Q ss_pred CeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccChhhHHHHHHHhc
Q psy64 17 PFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLHMRIHT 83 (115)
Q Consensus 17 ~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~h~ 83 (115)
||.|+.|++.|.....|..|++.+ |. ++.|+.||+.|. .+..|..+..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~-------------H~---~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRN-------------HT---LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcc-------------cC---CCccCCCCCEeC---ChhhhhcccC
Confidence 689999999999999999998732 12 358999999998 4667776554
No 23
>KOG3993|consensus
Probab=98.47 E-value=1.2e-08 Score=67.75 Aligned_cols=82 Identities=18% Similarity=0.241 Sum_probs=66.9
Q ss_pred eecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccChhhHHHHHHHhc--------------
Q psy64 18 FVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLHMRIHT-------------- 83 (115)
Q Consensus 18 ~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~h~-------------- 83 (115)
|.|..|-..|.+...|..|.-.- .---.|+|++|++.|.-..+|.+|.+=|.
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~R--------------IV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k 333 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPR--------------IVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPK 333 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCe--------------eEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChh
Confidence 78999999999998888885321 11235999999999999999999977551
Q ss_pred -------------------CCCceeEEeecceehhhhhhccCCcccccc
Q psy64 84 -------------------GEKKYIFIVVKKIIVVIYAKKFSLDIEILC 113 (115)
Q Consensus 84 -------------------~~~~~~C~~C~~~~~~~~~~~~h~~~h~~~ 113 (115)
.+..|.|..|+|+|....-|..|..+|++.
T Consensus 334 ~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~ 382 (500)
T KOG3993|consen 334 QAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRA 382 (500)
T ss_pred hhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhcc
Confidence 123589999999999999999999888764
No 24
>PHA00616 hypothetical protein
Probab=98.46 E-value=1.3e-07 Score=43.83 Aligned_cols=34 Identities=21% Similarity=0.366 Sum_probs=29.4
Q ss_pred CeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceeccc
Q psy64 17 PFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKV 64 (115)
Q Consensus 17 ~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~ 64 (115)
||+|+.||+.|.....|..|++.+ .+++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~--------------hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSV--------------HKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHh--------------cCCCccceeE
Confidence 689999999999999999999854 6778888765
No 25
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.33 E-value=2.3e-07 Score=59.94 Aligned_cols=53 Identities=25% Similarity=0.432 Sum_probs=44.4
Q ss_pred CCCceeccc--ccccccChhhHHHHHHH-h------------------cCCCceeEEeecceehhhhhhccCCc
Q psy64 56 KIRDFQCKV--CDRAFFDVYNLKLHMRI-H------------------TGEKKYIFIVVKKIIVVIYAKKFSLD 108 (115)
Q Consensus 56 ~~~~~~C~~--c~~~~~~~~~l~~h~~~-h------------------~~~~~~~C~~C~~~~~~~~~~~~h~~ 108 (115)
+.|||+|+. |.+.|.....|+-|+.- | ..+|||+|++|+|.+.+.-.|.-|+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 359999988 99999999999888542 2 13599999999999999999988875
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=98.32 E-value=1.6e-07 Score=45.99 Aligned_cols=50 Identities=20% Similarity=0.279 Sum_probs=38.6
Q ss_pred ceecccccccccChhhHHHHHHH-hcCC-CceeEEeecceehhhhhhccCCcccc
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRI-HTGE-KKYIFIVVKKIIVVIYAKKFSLDIEI 111 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~-h~~~-~~~~C~~C~~~~~~~~~~~~h~~~h~ 111 (115)
.|.||.|++ ......|..|... |..+ +.++|++|...+.. +|..|+.+++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~--~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVTD--NLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhhh--HHHHHHHHhc
Confidence 489999999 5667789999665 5443 57999999986553 7888887665
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.20 E-value=1.3e-06 Score=35.03 Aligned_cols=23 Identities=30% Similarity=0.843 Sum_probs=20.9
Q ss_pred eecCCChhhccChhhHHHHHHHh
Q psy64 18 FVCNMCPSTFKLKKHLRQHYKVH 40 (115)
Q Consensus 18 ~~C~~C~~~~~~~~~l~~h~~~h 40 (115)
|.|+.|++.|..+..|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 68999999999999999998753
No 28
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.16 E-value=4.5e-06 Score=40.82 Aligned_cols=51 Identities=22% Similarity=0.435 Sum_probs=37.3
Q ss_pred CeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcC-CCceecccccccccChhhHHHHHHHhc
Q psy64 17 PFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEK-IRDFQCKVCDRAFFDVYNLKLHMRIHT 83 (115)
Q Consensus 17 ~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~-~~~~~C~~c~~~~~~~~~l~~h~~~h~ 83 (115)
.|.|++|++ ..+...|..|.... |.. .+.+.||+|...+. .+|..|+..+.
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~-------------H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDE-------------HRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhH-------------CcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 488999999 56677888887643 333 45789999997544 47888877654
No 29
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.14 E-value=2.3e-06 Score=34.33 Aligned_cols=22 Identities=41% Similarity=0.886 Sum_probs=13.6
Q ss_pred eecccccccccChhhHHHHHHH
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRI 81 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~ 81 (115)
|+|+.|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4566666666666666666554
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.97 E-value=1.3e-06 Score=36.52 Aligned_cols=25 Identities=8% Similarity=-0.121 Sum_probs=17.3
Q ss_pred ceeEEeecceehhhhhhccCCcccc
Q psy64 87 KYIFIVVKKIIVVIYAKKFSLDIEI 111 (115)
Q Consensus 87 ~~~C~~C~~~~~~~~~~~~h~~~h~ 111 (115)
||.|+.|++.|.+...|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 4677777777777777777776653
No 31
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.92 E-value=1.2e-05 Score=32.27 Aligned_cols=23 Identities=43% Similarity=0.974 Sum_probs=19.2
Q ss_pred eecCCChhhccChhhHHHHHHHh
Q psy64 18 FVCNMCPSTFKLKKHLRQHYKVH 40 (115)
Q Consensus 18 ~~C~~C~~~~~~~~~l~~h~~~h 40 (115)
|.|++|+..|.+...|..|+..+
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 68999999999999999998865
No 32
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.85 E-value=7.9e-06 Score=34.04 Aligned_cols=24 Identities=42% Similarity=0.848 Sum_probs=22.2
Q ss_pred CeecCCChhhccChhhHHHHHHHh
Q psy64 17 PFVCNMCPSTFKLKKHLRQHYKVH 40 (115)
Q Consensus 17 ~~~C~~C~~~~~~~~~l~~h~~~h 40 (115)
||.|..|++.|.+...|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 689999999999999999999765
No 33
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.83 E-value=3.8e-06 Score=54.46 Aligned_cols=65 Identities=23% Similarity=0.557 Sum_probs=46.6
Q ss_pred CCCeecCC--ChhhccChhhHHHHHHHhcChhH-----HHHHHHHhhcCCCceecccccccccChhhHHHHH
Q psy64 15 DRPFVCNM--CPSTFKLKKHLRQHYKVHLKMDT-----LENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLHM 79 (115)
Q Consensus 15 ~~~~~C~~--C~~~~~~~~~l~~h~~~h~~~~~-----l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l~~h~ 79 (115)
++||+|++ |.++|+..-.|+-|+..=+..+. -...+......+|||.|+.|++.|.....|+-|.
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 59999998 99999999999999753221000 0011111346789999999999999998887664
No 34
>PRK04860 hypothetical protein; Provisional
Probab=97.74 E-value=1.7e-05 Score=47.26 Aligned_cols=41 Identities=22% Similarity=0.402 Sum_probs=35.0
Q ss_pred CceecccccccccChhhHHHHHHHhcCCCceeEEeecceehhhhh
Q psy64 58 RDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVVIYA 102 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~ 102 (115)
-+|.|. |+. ....+..|.++++++++|.|..|+..|.....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~~ 158 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKGE 158 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEecc
Confidence 368998 987 66778899999999999999999999876543
No 35
>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=97.71 E-value=3.9e-05 Score=30.64 Aligned_cols=23 Identities=43% Similarity=0.959 Sum_probs=11.7
Q ss_pred eecccccccccChhhHHHHHHHh
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIH 82 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h 82 (115)
|.|+.|++.|.....|..|+..+
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 45555666666655555555543
No 36
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.70 E-value=4.2e-05 Score=41.69 Aligned_cols=62 Identities=27% Similarity=0.515 Sum_probs=17.1
Q ss_pred ecCCChhhccChhhHHHHHHHhcCh-----------hHHHHHHHHhhcCCCceecccccccccChhhHHHHHHHh
Q psy64 19 VCNMCPSTFKLKKHLRQHYKVHLKM-----------DTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLHMRIH 82 (115)
Q Consensus 19 ~C~~C~~~~~~~~~l~~h~~~h~~~-----------~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~h 82 (115)
+|..|+..|.....|..|+...+.. ..+....+. .-...+.|..|++.|.....|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~--~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRK--KVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp --------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Ccccccccccccccccccccccccccccccccccccccccccccc--ccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 4899999999999999998654421 111111110 1112467777777777777777777754
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=97.53 E-value=7e-05 Score=35.60 Aligned_cols=33 Identities=21% Similarity=0.395 Sum_probs=22.2
Q ss_pred cCCCceecccccccccChhhHHHHHHHhcCCCc
Q psy64 55 EKIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKK 87 (115)
Q Consensus 55 ~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~ 87 (115)
..+.|-.|++|+..+....+|.+|+....+.||
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 456778899999888888889888888877766
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.37 E-value=0.00019 Score=28.99 Aligned_cols=23 Identities=35% Similarity=0.800 Sum_probs=20.5
Q ss_pred eecCCChhhccChhhHHHHHHHh
Q psy64 18 FVCNMCPSTFKLKKHLRQHYKVH 40 (115)
Q Consensus 18 ~~C~~C~~~~~~~~~l~~h~~~h 40 (115)
|.|+.|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 57999999999999999998755
No 39
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.35 E-value=2.8e-05 Score=42.38 Aligned_cols=24 Identities=8% Similarity=-0.078 Sum_probs=21.2
Q ss_pred ceeEEeecceehhhhhhccCCccc
Q psy64 87 KYIFIVVKKIIVVIYAKKFSLDIE 110 (115)
Q Consensus 87 ~~~C~~C~~~~~~~~~~~~h~~~h 110 (115)
.+.|..|++.|.+...|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 689999999999999999999864
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.23 E-value=0.00032 Score=28.26 Aligned_cols=23 Identities=39% Similarity=0.798 Sum_probs=14.4
Q ss_pred eecccccccccChhhHHHHHHHh
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIH 82 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h 82 (115)
|.|..|++.|.....+..|+..|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 35666666666666666666544
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.17 E-value=5.4e-05 Score=30.82 Aligned_cols=22 Identities=9% Similarity=0.015 Sum_probs=11.9
Q ss_pred eeEEeecceehhhhhhccCCcc
Q psy64 88 YIFIVVKKIIVVIYAKKFSLDI 109 (115)
Q Consensus 88 ~~C~~C~~~~~~~~~~~~h~~~ 109 (115)
|.|.+|.+.|.+...+..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 3455555555555555555543
No 42
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.98 E-value=0.00019 Score=29.84 Aligned_cols=22 Identities=9% Similarity=-0.037 Sum_probs=18.3
Q ss_pred eeEEeecceehhhhhhccCCcc
Q psy64 88 YIFIVVKKIIVVIYAKKFSLDI 109 (115)
Q Consensus 88 ~~C~~C~~~~~~~~~~~~h~~~ 109 (115)
|.|+.|++.|.+...+..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6788888888888888888876
No 43
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.88 E-value=0.0015 Score=31.11 Aligned_cols=29 Identities=21% Similarity=0.694 Sum_probs=20.7
Q ss_pred CCCCCeecCCChhhccChhhHHHHHHHhc
Q psy64 13 TTDRPFVCNMCPSTFKLKKHLRQHYKVHL 41 (115)
Q Consensus 13 ~~~~~~~C~~C~~~~~~~~~l~~h~~~h~ 41 (115)
..+.|..|++|+..+++..+|++|+...+
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H 48 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRH 48 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHT
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHh
Confidence 45678999999999999999999997653
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.82 E-value=0.00075 Score=27.29 Aligned_cols=22 Identities=36% Similarity=0.911 Sum_probs=19.9
Q ss_pred eecCCChhhccChhhHHHHHHH
Q psy64 18 FVCNMCPSTFKLKKHLRQHYKV 39 (115)
Q Consensus 18 ~~C~~C~~~~~~~~~l~~h~~~ 39 (115)
|.|.+|+..|.+...+..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 6799999999999999999864
No 45
>PRK04860 hypothetical protein; Provisional
Probab=96.69 E-value=0.0016 Score=38.97 Aligned_cols=40 Identities=20% Similarity=0.514 Sum_probs=31.1
Q ss_pred CCeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccChh
Q psy64 16 RPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVY 73 (115)
Q Consensus 16 ~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~ 73 (115)
-+|.|. |+. ....+..|.+ .+.++++|.|..|+..|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~r--------------i~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNR--------------VVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHH--------------HhcCCccEECCCCCceeEEec
Confidence 468998 987 5556777777 458899999999998876543
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.57 E-value=0.0024 Score=25.55 Aligned_cols=22 Identities=32% Similarity=0.727 Sum_probs=17.2
Q ss_pred eecCCChhhccChhhHHHHHHHh
Q psy64 18 FVCNMCPSTFKLKKHLRQHYKVH 40 (115)
Q Consensus 18 ~~C~~C~~~~~~~~~l~~h~~~h 40 (115)
|+|+.|+.... ...|..|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 68999999998 88999998764
No 47
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.17 E-value=0.0056 Score=24.41 Aligned_cols=21 Identities=29% Similarity=0.573 Sum_probs=9.6
Q ss_pred eecccccccccChhhHHHHHHH
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRI 81 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~ 81 (115)
|+|+.|+.... ...|..|++.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 34555555444 4455555544
No 48
>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=96.12 E-value=0.0021 Score=27.98 Aligned_cols=24 Identities=17% Similarity=0.386 Sum_probs=18.3
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecc
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKK 95 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 95 (115)
|+|..||..+.... .++.|++|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 68899987665442 6789999986
No 49
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.64 E-value=0.011 Score=24.04 Aligned_cols=21 Identities=33% Similarity=0.770 Sum_probs=14.2
Q ss_pred eecccccccccChhhHHHHHHH
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRI 81 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~ 81 (115)
.+|+.||+.| ....+..|+..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3688888888 55566667543
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=95.40 E-value=0.0044 Score=27.09 Aligned_cols=22 Identities=5% Similarity=-0.028 Sum_probs=14.8
Q ss_pred ceeEEeecceehhhhhhccCCc
Q psy64 87 KYIFIVVKKIIVVIYAKKFSLD 108 (115)
Q Consensus 87 ~~~C~~C~~~~~~~~~~~~h~~ 108 (115)
+|.|+.|++.|.+...+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4667777777776666666654
No 51
>KOG1146|consensus
Probab=95.15 E-value=0.013 Score=45.06 Aligned_cols=98 Identities=16% Similarity=0.295 Sum_probs=69.1
Q ss_pred cCCCCCeecCCChhhccChhhHHHHHHHh-cChhH-----HHHHHHH-----hhcCCCceecccccccccChhhHHHHHH
Q psy64 12 HTTDRPFVCNMCPSTFKLKKHLRQHYKVH-LKMDT-----LENHMKA-----VHEKIRDFQCKVCDRAFFDVYNLKLHMR 80 (115)
Q Consensus 12 h~~~~~~~C~~C~~~~~~~~~l~~h~~~h-~~~~~-----l~~h~~~-----~h~~~~~~~C~~c~~~~~~~~~l~~h~~ 80 (115)
+.-.+.+.|+.|++.|+....|-.|++.- ..... ...|.+. ...+.++|.|..|...+...+.|..|+.
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 34457899999999999999999999873 21111 1111110 1234568999999999999998888866
Q ss_pred Hhc-------------------------------------CC------CceeEEeecceehhhhhhccCCcc
Q psy64 81 IHT-------------------------------------GE------KKYIFIVVKKIIVVIYAKKFSLDI 109 (115)
Q Consensus 81 ~h~-------------------------------------~~------~~~~C~~C~~~~~~~~~~~~h~~~ 109 (115)
.-. +. -.|.|.+|++-......|.-|+..
T Consensus 540 S~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmts 611 (1406)
T KOG1146|consen 540 SDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTA 611 (1406)
T ss_pred HHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhcccccccc
Confidence 420 01 237899999988888888888764
No 52
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.98 E-value=0.024 Score=24.64 Aligned_cols=23 Identities=30% Similarity=0.600 Sum_probs=20.2
Q ss_pred CeecCCChhhccChhhHHHHHHH
Q psy64 17 PFVCNMCPSTFKLKKHLRQHYKV 39 (115)
Q Consensus 17 ~~~C~~C~~~~~~~~~l~~h~~~ 39 (115)
+|.|++|+..|.+...+..|...
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 68899999999999999888753
No 53
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.89 E-value=0.0097 Score=40.23 Aligned_cols=55 Identities=24% Similarity=0.275 Sum_probs=50.8
Q ss_pred CceecccccccccChhhHHHHHH--HhcCC--CceeEE--eecceehhhhhhccCCccccc
Q psy64 58 RDFQCKVCDRAFFDVYNLKLHMR--IHTGE--KKYIFI--VVKKIIVVIYAKKFSLDIEIL 112 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~~~l~~h~~--~h~~~--~~~~C~--~C~~~~~~~~~~~~h~~~h~~ 112 (115)
.++.|..|...|.....+..|.+ .|.++ +|+.|+ .|++.|.....+..|..+|..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~ 348 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTS 348 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccC
Confidence 46889999999999999999999 89999 999999 799999999999999998864
No 54
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=94.47 E-value=0.014 Score=35.10 Aligned_cols=25 Identities=24% Similarity=0.522 Sum_probs=20.8
Q ss_pred CceecccccccccChhhHHHHHHHhcCCCceeEEeecc
Q psy64 58 RDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKK 95 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 95 (115)
+.|.|+.||. ++.|+.|.+|++||.
T Consensus 133 ~~~vC~vCGy-------------~~~ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGY-------------THEGEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCC-------------cccCCCCCcCCCCCC
Confidence 3799999986 356788999999995
No 55
>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=94.24 E-value=0.018 Score=25.23 Aligned_cols=26 Identities=15% Similarity=0.131 Sum_probs=18.2
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCceeEEeecce
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKI 96 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 96 (115)
.|.|..||..+... +.|..|++|+..
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCcCCCCc
Confidence 47899998765432 256789999863
No 56
>KOG2893|consensus
Probab=94.24 E-value=0.012 Score=37.27 Aligned_cols=43 Identities=33% Similarity=0.665 Sum_probs=33.0
Q ss_pred eecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccChhhHHHH
Q psy64 18 FVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLH 78 (115)
Q Consensus 18 ~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l~~h 78 (115)
-.|.+|++.|..+.-|..|++ .|.|+|.+|.+....-..|..|
T Consensus 11 pwcwycnrefddekiliqhqk------------------akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQK------------------AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred ceeeecccccchhhhhhhhhh------------------hccceeeeehhhhccCCCceee
Confidence 369999999999998887765 5779999998766555555444
No 57
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=93.99 E-value=0.022 Score=28.08 Aligned_cols=33 Identities=12% Similarity=0.107 Sum_probs=21.7
Q ss_pred CceecccccccccChhhHHHHHHHhcCCCceeEEeecc
Q psy64 58 RDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKK 95 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 95 (115)
-.|.|+.||..--..- .+-..-..+|+|+.||.
T Consensus 26 v~F~CPnCGe~~I~Rc-----~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRC-----AKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehh-----hhHHHcCCceECCCcCc
Confidence 3589999995443332 22223357899999995
No 58
>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=93.97 E-value=0.036 Score=24.72 Aligned_cols=34 Identities=18% Similarity=0.140 Sum_probs=24.0
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecceeh
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIV 98 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 98 (115)
+.|+.|+..|.-..... ........|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~-----~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-----GANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc-----CCCCCEEECCCCCCEEE
Confidence 57999998888776432 12223578999998875
No 59
>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=93.73 E-value=0.04 Score=30.81 Aligned_cols=30 Identities=20% Similarity=0.382 Sum_probs=24.5
Q ss_pred eecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccCh
Q psy64 18 FVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDV 72 (115)
Q Consensus 18 ~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~ 72 (115)
..|+.||..|... +..|..||.||..|...
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 5799999999863 23688999999988776
No 60
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=93.71 E-value=0.097 Score=30.90 Aligned_cols=46 Identities=15% Similarity=0.395 Sum_probs=28.2
Q ss_pred HHHhcCCCCCeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccC
Q psy64 8 HMAVHTTDRPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFD 71 (115)
Q Consensus 8 h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~ 71 (115)
-+..-.+...|.|+.|+..|.....+.. ... ...|.||.||.....
T Consensus 90 ~l~~e~~~~~Y~Cp~C~~~y~~~ea~~~-----------------~d~-~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 90 KLEDETNNAYYKCPNCQSKYTFLEANQL-----------------LDM-DGTFTCPRCGEELEE 135 (147)
T ss_pred HHhcccCCcEEECcCCCCEeeHHHHHHh-----------------cCC-CCcEECCCCCCEEEE
Confidence 3333445667999999988886443221 011 233899999976543
No 61
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.69 E-value=0.051 Score=24.22 Aligned_cols=34 Identities=15% Similarity=0.244 Sum_probs=24.9
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecceeh
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIV 98 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 98 (115)
..|+.|+..|.-...- .-.+....+|+.|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~-----l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-----LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH-----cccCCcEEECCCCCcEee
Confidence 4799999888877642 234455789999998874
No 62
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=93.48 E-value=0.0074 Score=37.83 Aligned_cols=44 Identities=14% Similarity=0.221 Sum_probs=28.8
Q ss_pred CCceecccccccccChhhHHHHHHH---h-------cCCCc-----eeEEeecceehhh
Q psy64 57 IRDFQCKVCDRAFFDVYNLKLHMRI---H-------TGEKK-----YIFIVVKKIIVVI 100 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~~~~l~~h~~~---h-------~~~~~-----~~C~~C~~~~~~~ 100 (115)
++.+.||.|+..|....-.....+. . .+..| ++|+.||+.+...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 4668999999999976433222221 1 23444 4899999988754
No 63
>KOG1146|consensus
Probab=93.27 E-value=0.014 Score=44.99 Aligned_cols=57 Identities=18% Similarity=0.239 Sum_probs=47.4
Q ss_pred hhcCCCceecccccccccChhhHHHHHHHh-------------------------cCCCceeEEeecceehhhhhhccCC
Q psy64 53 VHEKIRDFQCKVCDRAFFDVYNLKLHMRIH-------------------------TGEKKYIFIVVKKIIVVIYAKKFSL 107 (115)
Q Consensus 53 ~h~~~~~~~C~~c~~~~~~~~~l~~h~~~h-------------------------~~~~~~~C~~C~~~~~~~~~~~~h~ 107 (115)
.+...+.++|+.|+..|.....|..|++.- .+.++|.|..|.+.+.....|..|+
T Consensus 459 L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihl 538 (1406)
T KOG1146|consen 459 LHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHL 538 (1406)
T ss_pred eecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHH
Confidence 344558899999999999999999998871 1337899999999999999999887
Q ss_pred cc
Q psy64 108 DI 109 (115)
Q Consensus 108 ~~ 109 (115)
..
T Consensus 539 qS 540 (1406)
T KOG1146|consen 539 QS 540 (1406)
T ss_pred HH
Confidence 63
No 64
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.08 E-value=0.035 Score=31.16 Aligned_cols=90 Identities=19% Similarity=0.280 Sum_probs=55.0
Q ss_pred CCCeecCCChhhccChhhHHHHHHHhcC--hhHHHHHHHHhhcCCCceecccccccccChhhHHHHHHHhcCCCceeEEe
Q psy64 15 DRPFVCNMCPSTFKLKKHLRQHYKVHLK--MDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIV 92 (115)
Q Consensus 15 ~~~~~C~~C~~~~~~~~~l~~h~~~h~~--~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~ 92 (115)
+-|-.|++||...-+..+|.+.- |+. ...+.+-.. ........|-.|+..|....... ...-.....|+|+.
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSy--HHLfPl~~f~ev~~--~~~~~~~~C~~C~~~f~~~~~~~--~~~~~~~~~y~C~~ 86 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSY--HHLFPLKAFQEIPL--EEYNGSRFCFGCQGPFPKPPVSP--FDELKDSHRYVCAV 86 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhh--hccCCCcccccccc--cccCCCCcccCcCCCCCCccccc--ccccccccceeCCC
Confidence 35788999999999999888763 321 111111000 00111224888998887654211 01123345799999
Q ss_pred ecceehhhhhhccCCccc
Q psy64 93 VKKIIVVIYAKKFSLDIE 110 (115)
Q Consensus 93 C~~~~~~~~~~~~h~~~h 110 (115)
|...|-...+...|-..|
T Consensus 87 C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 87 CKNVFCVDCDVFVHESLH 104 (112)
T ss_pred CCCccccccchhhhhhcc
Confidence 999999888887777665
No 65
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=92.95 E-value=0.14 Score=34.41 Aligned_cols=30 Identities=3% Similarity=-0.037 Sum_probs=25.9
Q ss_pred HHHhcCCCceeEEeec-ceehhhhhhccCCc
Q psy64 79 MRIHTGEKKYIFIVVK-KIIVVIYAKKFSLD 108 (115)
Q Consensus 79 ~~~h~~~~~~~C~~C~-~~~~~~~~~~~h~~ 108 (115)
.+.|.-++.|.|++|| +.+..+..+.+|+.
T Consensus 366 ~klhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 366 CKLHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred HHhcCCCcceeeeecccccccchHHHHhhhh
Confidence 3567778899999999 89999999999975
No 66
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.88 E-value=0.076 Score=23.53 Aligned_cols=34 Identities=12% Similarity=0.144 Sum_probs=24.3
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecceeh
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIV 98 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 98 (115)
..|+.|+..|.-.... .-......+|+.|+..|.
T Consensus 3 i~Cp~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHHH-----CCCCCcEEECCCCCCEeC
Confidence 5799999888877653 223345679999998873
No 67
>KOG2893|consensus
Probab=92.68 E-value=0.072 Score=33.91 Aligned_cols=45 Identities=20% Similarity=0.228 Sum_probs=36.2
Q ss_pred CCceecccccccccChhhHHHHHHHhcCCCceeEEeecceehhhhhhccC
Q psy64 57 IRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVVIYAKKFS 106 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~~~~h 106 (115)
.|+ .|=.|++.|....-|.+|++. |-|+|.+|.|...+-..|..|
T Consensus 9 ~kp-wcwycnrefddekiliqhqka----khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 9 DKP-WCWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred CCc-eeeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceee
Confidence 566 488999999999999988765 459999999987777666555
No 68
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=92.58 E-value=0.071 Score=26.30 Aligned_cols=33 Identities=12% Similarity=0.226 Sum_probs=21.4
Q ss_pred Cceeccccccc-ccChhhHHHHHHHhcCCCceeEEeecce
Q psy64 58 RDFQCKVCDRA-FFDVYNLKLHMRIHTGEKKYIFIVVKKI 96 (115)
Q Consensus 58 ~~~~C~~c~~~-~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 96 (115)
-.|.|+.||.. ..+-..- -.-..+|.|+.||..
T Consensus 24 ~~F~CPnCG~~~I~RC~~C------Rk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCEKC------RKQSNPYTCPKCGFE 57 (59)
T ss_pred CEeeCCCCCCeeEeechhH------HhcCCceECCCCCCc
Confidence 45899999986 3332221 122468999999953
No 69
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=92.50 E-value=0.084 Score=25.69 Aligned_cols=29 Identities=17% Similarity=0.348 Sum_probs=24.6
Q ss_pred hcCCCCCeecCCChhhccChhhHHHHHHH
Q psy64 11 VHTTDRPFVCNMCPSTFKLKKHLRQHYKV 39 (115)
Q Consensus 11 ~h~~~~~~~C~~C~~~~~~~~~l~~h~~~ 39 (115)
...||..+.|+-||..|+......+|.-.
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 34678889999999999999999988754
No 70
>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=92.45 E-value=0.15 Score=30.55 Aligned_cols=44 Identities=20% Similarity=0.467 Sum_probs=30.3
Q ss_pred HHHHHHhcCCCCCeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccC
Q psy64 5 LKEHMAVHTTDRPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFD 71 (115)
Q Consensus 5 l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~ 71 (115)
+..-+...++..-|.|+.|+..|.....+. ..|.||.||.....
T Consensus 97 lk~~l~~e~~~~~Y~Cp~c~~r~tf~eA~~-----------------------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 97 LREKLEFETNNMFFICPNMCVRFTFNEAME-----------------------LNFTCPRCGAMLDY 140 (158)
T ss_pred HHHHHhhccCCCeEECCCCCcEeeHHHHHH-----------------------cCCcCCCCCCEeee
Confidence 334444455667799999998888766532 25899999966443
No 71
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=92.25 E-value=0.073 Score=28.39 Aligned_cols=33 Identities=9% Similarity=0.070 Sum_probs=23.5
Q ss_pred CceecccccccccChhhHHHHHHHhcCCCceeEEeecceehhh
Q psy64 58 RDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVVI 100 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~ 100 (115)
..|.|+.|++.-. . -.+...|.|..|++.|..-
T Consensus 34 ~~~~Cp~C~~~~V--------k--R~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRTTV--------K--RIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCcce--------e--eeccCeEEcCCCCCeeccc
Confidence 4689999986411 1 2345689999999998753
No 72
>KOG2231|consensus
Probab=91.82 E-value=0.24 Score=36.14 Aligned_cols=86 Identities=19% Similarity=0.254 Sum_probs=50.5
Q ss_pred cCCChhhccChhhHHHHHHHhc----------------------ChhHHHHHHHHhhcCCC----ceecccccccccChh
Q psy64 20 CNMCPSTFKLKKHLRQHYKVHL----------------------KMDTLENHMKAVHEKIR----DFQCKVCDRAFFDVY 73 (115)
Q Consensus 20 C~~C~~~~~~~~~l~~h~~~h~----------------------~~~~l~~h~~~~h~~~~----~~~C~~c~~~~~~~~ 73 (115)
|..| ..|.....|..|+...+ .+..|..|+.....++. --.|..|...|....
T Consensus 118 ~~~c-~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~ 196 (669)
T KOG2231|consen 118 CLHC-TEFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDD 196 (669)
T ss_pred Cccc-cchhHHHHHHHHHHHhhhhhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHH
Confidence 4444 44447778888874322 56667777763222111 136888888888888
Q ss_pred hHHHHHHHhcCCCceeEEeec------ceehhhhhhccCCccc
Q psy64 74 NLKLHMRIHTGEKKYIFIVVK------KIIVVIYAKKFSLDIE 110 (115)
Q Consensus 74 ~l~~h~~~h~~~~~~~C~~C~------~~~~~~~~~~~h~~~h 110 (115)
.+..|++... |.|-.|. -.|.+-.+|..|.+.+
T Consensus 197 el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~ 235 (669)
T KOG2231|consen 197 ELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKG 235 (669)
T ss_pred HHHHhhccce----eheeecCcccccchhcccchHHHHHhhhc
Confidence 8888877654 3444442 3444455555555543
No 73
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=91.80 E-value=0.022 Score=33.87 Aligned_cols=16 Identities=6% Similarity=-0.025 Sum_probs=12.5
Q ss_pred ceeEEeecceehhhhh
Q psy64 87 KYIFIVVKKIIVVIYA 102 (115)
Q Consensus 87 ~~~C~~C~~~~~~~~~ 102 (115)
.+.|+.||++|..-..
T Consensus 28 ~~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 28 RRECLACGKRFTTFER 43 (154)
T ss_pred eeeccccCCcceEeEe
Confidence 4899999999976543
No 74
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=91.70 E-value=0.36 Score=28.51 Aligned_cols=40 Identities=8% Similarity=0.127 Sum_probs=27.4
Q ss_pred cCCCceecccccccccChhhHHHHHHHhcCCCceeEEeecceeh
Q psy64 55 EKIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIV 98 (115)
Q Consensus 55 ~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 98 (115)
.+...|.|+.|+..|.....+.. -..+.-|.|+.||....
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~----~d~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQL----LDMDGTFTCPRCGEELE 134 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHh----cCCCCcEECCCCCCEEE
Confidence 45567899999998886544321 11234499999998763
No 75
>KOG2186|consensus
Probab=91.67 E-value=0.15 Score=32.65 Aligned_cols=45 Identities=20% Similarity=0.248 Sum_probs=29.1
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecceehhhhhhccCC
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVVIYAKKFSL 107 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~~~~h~ 107 (115)
|.|..||....-+. +-.|+....+ .-|.|-.|+++|.. .+...|.
T Consensus 4 FtCnvCgEsvKKp~-vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhccccc-hHHHHHhccC-CeeEEeeccccccc-chhhhhh
Confidence 67788877655443 4457766666 55788888888876 4444443
No 76
>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=91.22 E-value=0.22 Score=29.85 Aligned_cols=36 Identities=8% Similarity=-0.025 Sum_probs=28.3
Q ss_pred hcCCCceecccccccccChhhHHHHHHHhcCCCceeEEeecceeh
Q psy64 54 HEKIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIV 98 (115)
Q Consensus 54 h~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 98 (115)
..+..-|.|+.|+..|+....+. .-|.|+.||....
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEee
Confidence 34566789999999888887764 2699999998653
No 77
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=91.04 E-value=0.22 Score=30.46 Aligned_cols=41 Identities=17% Similarity=0.504 Sum_probs=28.4
Q ss_pred HHHhcCCCCCeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccC
Q psy64 8 HMAVHTTDRPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFD 71 (115)
Q Consensus 8 h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~ 71 (115)
-+..-....-|.|+.|+..|.....+ +..|.|+.||.....
T Consensus 108 ~l~~e~~~~~Y~Cp~C~~rytf~eA~-----------------------~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 108 QLEEEENNMFFFCPNCHIRFTFDEAM-----------------------EYGFRCPQCGEMLEE 148 (178)
T ss_pred HhhhccCCCEEECCCCCcEEeHHHHh-----------------------hcCCcCCCCCCCCee
Confidence 33334455679999999998876542 135899999976554
No 78
>KOG2186|consensus
Probab=90.95 E-value=0.16 Score=32.55 Aligned_cols=51 Identities=25% Similarity=0.494 Sum_probs=35.7
Q ss_pred CeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccChhhHHHHHHHhcC
Q psy64 17 PFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLHMRIHTG 84 (115)
Q Consensus 17 ~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~ 84 (115)
-|.|..||.+..-+ .+..|+.. -++ .-|.|..||+.|.. ..+..|..--++
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~sr--------------Crn-~~fSCIDC~k~F~~-~sYknH~kCITE 53 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSR--------------CRN-AYFSCIDCGKTFER-VSYKNHTKCITE 53 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHh--------------ccC-CeeEEeeccccccc-chhhhhhhhcch
Confidence 47899999987754 35556542 234 56899999999999 455667655443
No 79
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.71 E-value=0.079 Score=24.76 Aligned_cols=31 Identities=13% Similarity=0.068 Sum_probs=21.7
Q ss_pred CceecccccccccChhhHHHHHHHhcCCCceeEEeecceeh
Q psy64 58 RDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIV 98 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 98 (115)
..|.|+.||..+...... ....|+.||..+.
T Consensus 2 ~~y~C~~CG~~~~~~~~~----------~~~~Cp~CG~~~~ 32 (46)
T PRK00398 2 AEYKCARCGREVELDEYG----------TGVRCPYCGYRIL 32 (46)
T ss_pred CEEECCCCCCEEEECCCC----------CceECCCCCCeEE
Confidence 358899999877664321 1679999987554
No 80
>KOG2593|consensus
Probab=90.37 E-value=0.32 Score=33.56 Aligned_cols=51 Identities=18% Similarity=0.546 Sum_probs=34.3
Q ss_pred hHHHHHHHHhcCCCCCeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccc
Q psy64 2 KRQLKEHMAVHTTDRPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAF 69 (115)
Q Consensus 2 k~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~ 69 (115)
+..|..-++.-+....|.|+.|.+.|.....++. .-...-.|.|..|+--.
T Consensus 113 ~krled~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L-----------------~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 113 RKRLEDRLRDDTNVAGYVCPNCQKKYTSLEALQL-----------------LDNETGEFHCENCGGEL 163 (436)
T ss_pred HHHHHHHhhhccccccccCCccccchhhhHHHHh-----------------hcccCceEEEecCCCch
Confidence 3445555566677788999999999987765442 11234568898887443
No 81
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.04 E-value=0.056 Score=36.54 Aligned_cols=71 Identities=21% Similarity=0.331 Sum_probs=55.8
Q ss_pred CCeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCC--Cceecc--cccccccChhhHHHHHHHhcCCCceeEE
Q psy64 16 RPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKI--RDFQCK--VCDRAFFDVYNLKLHMRIHTGEKKYIFI 91 (115)
Q Consensus 16 ~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~--~~~~C~--~c~~~~~~~~~l~~h~~~h~~~~~~~C~ 91 (115)
.++.|..|...|.....+..|.+. ..|.++ +++.|+ .|++.|.+...+..|...|.+..++.+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~------------~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRS------------VNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred cCCCCccccCCccccccccccccc------------cccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 468899999999999988888772 024677 899999 7999999999999999999887776653
Q ss_pred --eecceeh
Q psy64 92 --VVKKIIV 98 (115)
Q Consensus 92 --~C~~~~~ 98 (115)
.|.+.+.
T Consensus 356 ~~~~~~~~~ 364 (467)
T COG5048 356 LLNSSSKFS 364 (467)
T ss_pred cccCccccc
Confidence 3444433
No 82
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=90.02 E-value=0.049 Score=26.08 Aligned_cols=29 Identities=10% Similarity=0.273 Sum_probs=20.3
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecc
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKK 95 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 95 (115)
|.|..||..|.....+. . +.+-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~------~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMS------D-DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecC------C-CCCCCCCCCCC
Confidence 78999999888654321 1 34567999986
No 83
>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=89.81 E-value=0.051 Score=24.51 Aligned_cols=30 Identities=10% Similarity=0.303 Sum_probs=20.8
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCceeEEeecc
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKK 95 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 95 (115)
.|+|+.||..|...... .....-.|+.||.
T Consensus 5 ~y~C~~Cg~~fe~~~~~-------~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKI-------SDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEec-------CCCCCCCCCCCCC
Confidence 37899999888765442 1144567999987
No 84
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=89.39 E-value=0.22 Score=24.29 Aligned_cols=28 Identities=14% Similarity=0.234 Sum_probs=21.2
Q ss_pred cCCCceecccccccccChhhHHHHHHHh
Q psy64 55 EKIRDFQCKVCDRAFFDVYNLKLHMRIH 82 (115)
Q Consensus 55 ~~~~~~~C~~c~~~~~~~~~l~~h~~~h 82 (115)
.|+.-+.||-||..|.....+..|...-
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKa 40 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKA 40 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHH
Confidence 5666678888888888888887776543
No 85
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=89.31 E-value=0.24 Score=30.26 Aligned_cols=35 Identities=14% Similarity=0.134 Sum_probs=26.9
Q ss_pred cCCCceecccccccccChhhHHHHHHHhcCCCceeEEeecceeh
Q psy64 55 EKIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIV 98 (115)
Q Consensus 55 ~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 98 (115)
.+..-|.|+.|+..|+....+. .-|.|+.||....
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 3456789999999888876652 3699999998653
No 86
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=89.22 E-value=0.23 Score=23.08 Aligned_cols=27 Identities=11% Similarity=-0.023 Sum_probs=18.5
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCceeEEeecce
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKI 96 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 96 (115)
.|.|..||..|... ...+..|+.||..
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC-----------CCCceECCCCCce
Confidence 37888888766643 2345788888864
No 87
>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=88.92 E-value=0.26 Score=28.31 Aligned_cols=33 Identities=15% Similarity=0.014 Sum_probs=25.2
Q ss_pred CeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccChhh
Q psy64 17 PFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYN 74 (115)
Q Consensus 17 ~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~~ 74 (115)
...|+.||..|... +..|..|+.||..|.....
T Consensus 9 Kr~Cp~cg~kFYDL-------------------------nk~p~vcP~cg~~~~~~~~ 41 (129)
T TIGR02300 9 KRICPNTGSKFYDL-------------------------NRRPAVSPYTGEQFPPEEA 41 (129)
T ss_pred cccCCCcCcccccc-------------------------CCCCccCCCcCCccCcchh
Confidence 35799999998863 3468899999998866633
No 88
>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=88.28 E-value=0.27 Score=31.74 Aligned_cols=84 Identities=15% Similarity=0.103 Sum_probs=47.8
Q ss_pred CCCCeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccChh------hHHHHHHH----hc
Q psy64 14 TDRPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVY------NLKLHMRI----HT 83 (115)
Q Consensus 14 ~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~~------~l~~h~~~----h~ 83 (115)
|.+.|+|..|..-+-.... -.|+..- +......|+|..|++.-..+= .-..|.+. ..
T Consensus 139 GGrif~CsfC~~flCEDDQ-FEHQAsC------------QvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~ 205 (314)
T PF06524_consen 139 GGRIFKCSFCDNFLCEDDQ-FEHQASC------------QVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYE 205 (314)
T ss_pred CCeEEEeecCCCeeeccch-hhhhhhh------------hhhhcccccccccccccchhhhheeeeehhhhhhhcccccc
Confidence 5678999999765544333 3344321 122345678888876554431 11223332 22
Q ss_pred CCCceeEEeecceehhhhhhccCCccc
Q psy64 84 GEKKYIFIVVKKIIVVIYAKKFSLDIE 110 (115)
Q Consensus 84 ~~~~~~C~~C~~~~~~~~~~~~h~~~h 110 (115)
..+++.|+.|++......+|.--.++|
T Consensus 206 k~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 206 KGKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred cCCCCCCCCCCCcccccccceeeeecc
Confidence 347889999998877776665444443
No 89
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=86.45 E-value=0.17 Score=26.13 Aligned_cols=44 Identities=14% Similarity=0.144 Sum_probs=26.9
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEE--eecceehhhhhhcc
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFI--VVKKIIVVIYAKKF 105 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~--~C~~~~~~~~~~~~ 105 (115)
+.|+.||........-... ....+.-+.|. .||.+|..-.++.+
T Consensus 2 m~CP~Cg~~a~irtSr~~s--~~~~~~Y~qC~N~eCg~tF~t~es~s~ 47 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYIT--DTTKERYHQCQNVNCSATFITYESVQR 47 (72)
T ss_pred ccCCCCCCccEEEEChhcC--hhhheeeeecCCCCCCCEEEEEEEEEE
Confidence 4688898655333322111 22455668897 89999987665543
No 90
>KOG2636|consensus
Probab=85.41 E-value=0.37 Score=33.46 Aligned_cols=29 Identities=10% Similarity=0.031 Sum_probs=25.3
Q ss_pred HHhcCCCceeEEeec-ceehhhhhhccCCc
Q psy64 80 RIHTGEKKYIFIVVK-KIIVVIYAKKFSLD 108 (115)
Q Consensus 80 ~~h~~~~~~~C~~C~-~~~~~~~~~~~h~~ 108 (115)
+.|.-...|.|++|| +++..+..+.+|+.
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 456777889999999 99999999999986
No 91
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=85.18 E-value=0.4 Score=25.82 Aligned_cols=14 Identities=36% Similarity=0.752 Sum_probs=12.6
Q ss_pred CCeecCCChhhccC
Q psy64 16 RPFVCNMCPSTFKL 29 (115)
Q Consensus 16 ~~~~C~~C~~~~~~ 29 (115)
+|..|..||..|+.
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 68899999999987
No 92
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=85.16 E-value=0.38 Score=25.99 Aligned_cols=32 Identities=13% Similarity=0.208 Sum_probs=23.2
Q ss_pred CceecccccccccChhhHHHHHHHhcCCCceeEEeecceehh
Q psy64 58 RDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVV 99 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~ 99 (115)
..|.|+.||+.-... .+...|.|..|+++|..
T Consensus 35 a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHAVKR----------QAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCceee----------eeeEEEEcCCCCCEEeC
Confidence 568999998643222 23468999999999875
No 93
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=85.02 E-value=0.62 Score=31.49 Aligned_cols=22 Identities=27% Similarity=0.643 Sum_probs=18.5
Q ss_pred ecCCChhhccChhhHHHHHHHh
Q psy64 19 VCNMCPSTFKLKKHLRQHYKVH 40 (115)
Q Consensus 19 ~C~~C~~~~~~~~~l~~h~~~h 40 (115)
.|..|..-|.+...|..|++..
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~ 243 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLR 243 (493)
T ss_pred hhhhccceecChHHHHHHHHhh
Confidence 4999999999999999988753
No 94
>PF14353 CpXC: CpXC protein
Probab=84.95 E-value=0.61 Score=26.73 Aligned_cols=49 Identities=12% Similarity=0.158 Sum_probs=27.9
Q ss_pred eecccccccccChhhHHHH--------HHHhcCC-CceeEEeecceehhhhhhccCCc
Q psy64 60 FQCKVCDRAFFDVYNLKLH--------MRIHTGE-KKYIFIVVKKIIVVIYAKKFSLD 108 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h--------~~~h~~~-~~~~C~~C~~~~~~~~~~~~h~~ 108 (115)
..||.||..|......... .+.-.|+ ..|.|+.||..|.-...+.-|-.
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~ 59 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDP 59 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcC
Confidence 3688888877654211111 1122222 45889999988877666554443
No 95
>PHA00626 hypothetical protein
Probab=84.83 E-value=0.38 Score=23.48 Aligned_cols=16 Identities=6% Similarity=-0.184 Sum_probs=12.4
Q ss_pred CCceeEEeecceehhh
Q psy64 85 EKKYIFIVVKKIIVVI 100 (115)
Q Consensus 85 ~~~~~C~~C~~~~~~~ 100 (115)
...|+|..||+.|+..
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 3579999999988754
No 96
>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=84.51 E-value=0.43 Score=19.15 Aligned_cols=11 Identities=27% Similarity=0.618 Sum_probs=8.5
Q ss_pred CCceecccccc
Q psy64 57 IRDFQCKVCDR 67 (115)
Q Consensus 57 ~~~~~C~~c~~ 67 (115)
.-+|.|+.||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 35789999984
No 97
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=84.50 E-value=0.5 Score=22.50 Aligned_cols=30 Identities=10% Similarity=0.275 Sum_probs=20.3
Q ss_pred CCceecccccccccChhhHHHHHHHhcCCCceeEEeecce
Q psy64 57 IRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKI 96 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 96 (115)
...|.|..||+.|. .-.......|+.||..
T Consensus 4 ~~~Y~C~~Cg~~~~----------~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVE----------LDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeee----------hhhccCceeCCCCCcE
Confidence 34689999998872 1223456789888864
No 98
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=84.03 E-value=0.49 Score=22.62 Aligned_cols=13 Identities=0% Similarity=-0.210 Sum_probs=10.8
Q ss_pred CceeEEeecceeh
Q psy64 86 KKYIFIVVKKIIV 98 (115)
Q Consensus 86 ~~~~C~~C~~~~~ 98 (115)
..+.|..||+++.
T Consensus 36 ~r~~C~~Cgyt~~ 48 (50)
T PRK00432 36 DRWHCGKCGYTEF 48 (50)
T ss_pred CcEECCCcCCEEe
Confidence 5789999998764
No 99
>KOG2785|consensus
Probab=84.02 E-value=0.46 Score=32.30 Aligned_cols=23 Identities=39% Similarity=0.761 Sum_probs=20.0
Q ss_pred CeecCCChhhccChhhHHHHHHH
Q psy64 17 PFVCNMCPSTFKLKKHLRQHYKV 39 (115)
Q Consensus 17 ~~~C~~C~~~~~~~~~l~~h~~~ 39 (115)
.|.|..|...|......+.|.+.
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKS 25 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKS 25 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhh
Confidence 47899999999999888888764
No 100
>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=83.49 E-value=0.38 Score=25.98 Aligned_cols=32 Identities=9% Similarity=0.201 Sum_probs=22.1
Q ss_pred CceecccccccccChhhHHHHHHHhcCCCceeEEeecceehh
Q psy64 58 RDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVV 99 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~ 99 (115)
..|.|+.||+.-... .....|.|..|+++|..
T Consensus 34 ~ky~Cp~Cgk~~vkR----------~a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKR----------VATGIWKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSEEEE----------EETTEEEETTTTEEEE-
T ss_pred CCCcCCCCCCceeEE----------eeeEEeecCCCCCEEeC
Confidence 568999999754322 23457999999999864
No 101
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=83.36 E-value=0.67 Score=22.07 Aligned_cols=39 Identities=10% Similarity=0.076 Sum_probs=24.6
Q ss_pred CCceecccccccccChhhHHHHHHHhcC-CCceeEEeecc
Q psy64 57 IRDFQCKVCDRAFFDVYNLKLHMRIHTG-EKKYIFIVVKK 95 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~~~~l~~h~~~h~~-~~~~~C~~C~~ 95 (115)
++.+.|..||..|.....-+....--.- ..|-.|..|-.
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR~ 41 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCRQ 41 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHHH
Confidence 5678999999999887765544332111 13566766643
No 102
>KOG2593|consensus
Probab=82.33 E-value=1.8 Score=30.17 Aligned_cols=39 Identities=8% Similarity=0.293 Sum_probs=28.0
Q ss_pred hcCCCceecccccccccChhhHHHHHHHhcCCCceeEEeecc
Q psy64 54 HEKIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKK 95 (115)
Q Consensus 54 h~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 95 (115)
-+....|.|+.|++.|..-..++ -.-...-.|.|+.|+-
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGG 161 (436)
T ss_pred ccccccccCCccccchhhhHHHH---hhcccCceEEEecCCC
Confidence 35667899999999888765543 2233345799999985
No 103
>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=82.17 E-value=0.52 Score=25.50 Aligned_cols=32 Identities=6% Similarity=0.171 Sum_probs=22.7
Q ss_pred CceecccccccccChhhHHHHHHHhcCCCceeEEeecceehh
Q psy64 58 RDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVV 99 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~ 99 (115)
..|.|+.||+.-.. -.+...|.|..|+++|..
T Consensus 34 a~y~CpfCgk~~vk----------R~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 34 AKYVCPFCGKKTVK----------RGSTGIWTCRKCGAKFAG 65 (91)
T ss_pred cCccCCCCCCCceE----------EEeeEEEEcCCCCCEEeC
Confidence 46899999864222 123458999999999864
No 104
>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=81.71 E-value=0.49 Score=20.06 Aligned_cols=24 Identities=8% Similarity=0.297 Sum_probs=10.4
Q ss_pred ecccccccccChhhHHHHHHHhcCCCceeEEeecc
Q psy64 61 QCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKK 95 (115)
Q Consensus 61 ~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 95 (115)
+|+.|+-.+.. .+.-.++|+.|+.
T Consensus 4 ~Cp~C~se~~y-----------~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTY-----------EDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----E-----------E-SSSEEETTTTE
T ss_pred CCCCCCCccee-----------ccCCEEeCCcccc
Confidence 57777654443 3345677877764
No 105
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=80.52 E-value=1.5 Score=29.79 Aligned_cols=23 Identities=30% Similarity=0.648 Sum_probs=15.0
Q ss_pred ecccccccccChhhHHHHHHHhc
Q psy64 61 QCKVCDRAFFDVYNLKLHMRIHT 83 (115)
Q Consensus 61 ~C~~c~~~~~~~~~l~~h~~~h~ 83 (115)
.|..|...|-....|..|.+...
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~H 244 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRH 244 (493)
T ss_pred hhhhccceecChHHHHHHHHhhh
Confidence 46667777777777766665543
No 106
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=80.45 E-value=1.1 Score=19.32 Aligned_cols=13 Identities=15% Similarity=0.644 Sum_probs=8.4
Q ss_pred Cceeccccccccc
Q psy64 58 RDFQCKVCDRAFF 70 (115)
Q Consensus 58 ~~~~C~~c~~~~~ 70 (115)
.+..|+.||....
T Consensus 16 ~~irC~~CG~RIl 28 (32)
T PF03604_consen 16 DPIRCPECGHRIL 28 (32)
T ss_dssp STSSBSSSS-SEE
T ss_pred CcEECCcCCCeEE
Confidence 3568999986543
No 107
>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=80.35 E-value=0.42 Score=19.53 Aligned_cols=9 Identities=0% Similarity=-0.381 Sum_probs=4.1
Q ss_pred eEEeeccee
Q psy64 89 IFIVVKKII 97 (115)
Q Consensus 89 ~C~~C~~~~ 97 (115)
.|+.||+.|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 344444444
No 108
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=80.20 E-value=0.45 Score=18.78 Aligned_cols=6 Identities=0% Similarity=-0.363 Sum_probs=2.7
Q ss_pred EEeecc
Q psy64 90 FIVVKK 95 (115)
Q Consensus 90 C~~C~~ 95 (115)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 444443
No 109
>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=79.46 E-value=1.9 Score=17.47 Aligned_cols=20 Identities=15% Similarity=0.433 Sum_probs=14.5
Q ss_pred eecCCChhhccChhhHHHHHH
Q psy64 18 FVCNMCPSTFKLKKHLRQHYK 38 (115)
Q Consensus 18 ~~C~~C~~~~~~~~~l~~h~~ 38 (115)
..|++|++.+ ....+..|..
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3599999998 5566777654
No 110
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=79.36 E-value=0.49 Score=27.59 Aligned_cols=39 Identities=10% Similarity=0.083 Sum_probs=22.6
Q ss_pred CceecccccccccChh---hH------HHHHHHhcCCCceeEEeecce
Q psy64 58 RDFQCKVCDRAFFDVY---NL------KLHMRIHTGEKKYIFIVVKKI 96 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~~---~l------~~h~~~h~~~~~~~C~~C~~~ 96 (115)
..+.|..||..|.... .+ ..|.-+-....-+.|+.||..
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 4579999998887651 11 111111122344779999954
No 111
>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=79.17 E-value=0.53 Score=26.21 Aligned_cols=25 Identities=12% Similarity=-0.149 Sum_probs=21.8
Q ss_pred ceeE----EeecceehhhhhhccCCcccc
Q psy64 87 KYIF----IVVKKIIVVIYAKKFSLDIEI 111 (115)
Q Consensus 87 ~~~C----~~C~~~~~~~~~~~~h~~~h~ 111 (115)
-|.| +.|++...+...+..|++.++
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 3889 999999999999999988765
No 112
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=79.02 E-value=0.58 Score=25.93 Aligned_cols=38 Identities=11% Similarity=0.083 Sum_probs=20.3
Q ss_pred CceecccccccccChhhHHHHHHHhcCCC-ceeEEeecc
Q psy64 58 RDFQCKVCDRAFFDVYNLKLHMRIHTGEK-KYIFIVVKK 95 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~~~l~~h~~~h~~~~-~~~C~~C~~ 95 (115)
||..|+.||....-...-...-......+ .|.|+.|+.
T Consensus 1 ~p~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~A 39 (102)
T PF11672_consen 1 KPIICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCDA 39 (102)
T ss_pred CCcccCCCCCeeEEcccchhcCccCCCCceeEECCCCCc
Confidence 46789999854443332222222222223 289988875
No 113
>KOG2071|consensus
Probab=78.99 E-value=1.5 Score=31.65 Aligned_cols=27 Identities=26% Similarity=0.516 Sum_probs=22.5
Q ss_pred CCCeecCCChhhccChhhHHHHHHHhc
Q psy64 15 DRPFVCNMCPSTFKLKKHLRQHYKVHL 41 (115)
Q Consensus 15 ~~~~~C~~C~~~~~~~~~l~~h~~~h~ 41 (115)
..|-.|..||..|........|+..|.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 456889999999999988888887763
No 114
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=78.59 E-value=0.74 Score=24.89 Aligned_cols=32 Identities=16% Similarity=0.195 Sum_probs=22.6
Q ss_pred CceecccccccccChhhHHHHHHHhcCCCceeEEeecceehh
Q psy64 58 RDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVV 99 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~ 99 (115)
..|.|+.|++.-... .+...|.|..|+++|..
T Consensus 35 a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKVKR----------VGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCceEE----------EEEEEEEcCCCCCEEeC
Confidence 468999997542222 23457999999998875
No 115
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=77.10 E-value=0.69 Score=20.94 Aligned_cols=21 Identities=5% Similarity=-0.293 Sum_probs=13.2
Q ss_pred CCceeEEeecceehhhhhhcc
Q psy64 85 EKKYIFIVVKKIIVVIYAKKF 105 (115)
Q Consensus 85 ~~~~~C~~C~~~~~~~~~~~~ 105 (115)
...+.|+.|+-.+-....+.+
T Consensus 17 ~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 17 VEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEEEECCCCCeEEccHHHHHH
Confidence 345667777777766666543
No 116
>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=76.93 E-value=1.3 Score=20.24 Aligned_cols=18 Identities=11% Similarity=-0.079 Sum_probs=12.9
Q ss_pred eeEEeecceehhhhhhcc
Q psy64 88 YIFIVVKKIIVVIYAKKF 105 (115)
Q Consensus 88 ~~C~~C~~~~~~~~~~~~ 105 (115)
|.|..||..|.....+..
T Consensus 6 y~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE 23 (42)
T ss_pred EEeCCCCCEEEEEEEcCC
Confidence 788999988876654433
No 117
>COG1773 Rubredoxin [Energy production and conversion]
Probab=76.79 E-value=1.4 Score=21.51 Aligned_cols=15 Identities=13% Similarity=0.007 Sum_probs=10.5
Q ss_pred CceeEEeecceehhh
Q psy64 86 KKYIFIVVKKIIVVI 100 (115)
Q Consensus 86 ~~~~C~~C~~~~~~~ 100 (115)
+.|+|.+||+.|.-.
T Consensus 2 ~~~~C~~CG~vYd~e 16 (55)
T COG1773 2 KRWRCSVCGYVYDPE 16 (55)
T ss_pred CceEecCCceEeccc
Confidence 357888888877543
No 118
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=76.75 E-value=0.27 Score=22.30 Aligned_cols=11 Identities=9% Similarity=0.036 Sum_probs=8.8
Q ss_pred eeEEeecceeh
Q psy64 88 YIFIVVKKIIV 98 (115)
Q Consensus 88 ~~C~~C~~~~~ 98 (115)
|.|..|+..+.
T Consensus 29 y~C~~C~~~w~ 39 (40)
T smart00440 29 YVCTKCGHRWR 39 (40)
T ss_pred EEeCCCCCEeC
Confidence 88988987764
No 119
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=76.67 E-value=1.6 Score=32.60 Aligned_cols=13 Identities=0% Similarity=-0.419 Sum_probs=7.5
Q ss_pred CCCceeEEeecce
Q psy64 84 GEKKYIFIVVKKI 96 (115)
Q Consensus 84 ~~~~~~C~~C~~~ 96 (115)
...|..|+.||-.
T Consensus 472 ~~~p~~Cp~Cgs~ 484 (730)
T COG1198 472 EPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCC
Confidence 3456666666643
No 120
>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=76.55 E-value=2.3 Score=26.88 Aligned_cols=28 Identities=21% Similarity=0.457 Sum_probs=21.2
Q ss_pred CCCCeecCCChhhccChhhHHHHHHHhc
Q psy64 14 TDRPFVCNMCPSTFKLKKHLRQHYKVHL 41 (115)
Q Consensus 14 ~~~~~~C~~C~~~~~~~~~l~~h~~~h~ 41 (115)
.+..|.|..|+|.|+-...+..|+..-+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcC
Confidence 3456999999999999999999987643
No 121
>KOG2907|consensus
Probab=76.39 E-value=2.2 Score=24.00 Aligned_cols=36 Identities=17% Similarity=0.216 Sum_probs=21.6
Q ss_pred eecccccccccChhhHHHHHHHhcCCCc---eeEEeecceeh
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKK---YIFIVVKKIIV 98 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~---~~C~~C~~~~~ 98 (115)
.+|+.||..=.....+ +-..+.|.. |.|+.|++.|.
T Consensus 75 ~kCpkCghe~m~Y~T~---QlRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTL---QLRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred ccCcccCCchhhhhhh---hcccccCCceEEEEcCccceeee
Confidence 4799998532222222 222344443 89999999885
No 122
>KOG4124|consensus
Probab=76.22 E-value=0.4 Score=32.35 Aligned_cols=50 Identities=28% Similarity=0.451 Sum_probs=36.3
Q ss_pred CCceeccc--ccccccChhhHHHHHHH---------------h----cCCCceeEEeecceehhhhhhccC
Q psy64 57 IRDFQCKV--CDRAFFDVYNLKLHMRI---------------H----TGEKKYIFIVVKKIIVVIYAKKFS 106 (115)
Q Consensus 57 ~~~~~C~~--c~~~~~~~~~l~~h~~~---------------h----~~~~~~~C~~C~~~~~~~~~~~~h 106 (115)
+++|+|+. |.+.+....++..|.-. | ...|+|+|++|.+.++....|.-|
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCce
Confidence 57888876 88988887777655322 1 134889999999998887665444
No 123
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=76.11 E-value=1.4 Score=20.76 Aligned_cols=16 Identities=0% Similarity=-0.124 Sum_probs=11.4
Q ss_pred ceeEEeecceehhhhh
Q psy64 87 KYIFIVVKKIIVVIYA 102 (115)
Q Consensus 87 ~~~C~~C~~~~~~~~~ 102 (115)
.|.|+.||+.+.....
T Consensus 20 ~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 20 RFVCRKCGYEEPIEQK 35 (52)
T ss_pred EEECCcCCCeEECCCc
Confidence 6888888887765433
No 124
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=75.84 E-value=1.5 Score=26.07 Aligned_cols=39 Identities=18% Similarity=0.442 Sum_probs=26.8
Q ss_pred CCCceecccccccccChhhHHHHHHHhcCCCceeEEeecceehh
Q psy64 56 KIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVV 99 (115)
Q Consensus 56 ~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~ 99 (115)
..-+|.|. |+..|.... .|-..-.|+ .|.|..|+.....
T Consensus 114 ~~~~Y~C~-C~q~~l~~R---Rhn~~~~g~-~YrC~~C~gkL~~ 152 (156)
T COG3091 114 TTYPYRCQ-CQQHYLRIR---RHNTVRRGE-VYRCGKCGGKLVF 152 (156)
T ss_pred cceeEEee-cCCccchhh---hcccccccc-eEEeccCCceEEe
Confidence 34578999 998766654 333444566 8999999876543
No 125
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.41 E-value=0.36 Score=30.69 Aligned_cols=39 Identities=18% Similarity=0.327 Sum_probs=26.2
Q ss_pred CCceecccccccccChhhHHHHHHHhcCC----------Cc-----eeEEeecc
Q psy64 57 IRDFQCKVCDRAFFDVYNLKLHMRIHTGE----------KK-----YIFIVVKK 95 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~~~~l~~h~~~h~~~----------~~-----~~C~~C~~ 95 (115)
.+.+.||.|+..|....-+..-.++-.|+ .| +.|+.|++
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~y 70 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYY 70 (267)
T ss_pred hceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhH
Confidence 46689999999998775544444444443 23 46888876
No 126
>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=75.33 E-value=1.3 Score=21.34 Aligned_cols=26 Identities=8% Similarity=0.013 Sum_probs=12.8
Q ss_pred CCceeEEeecceehhhhhhccCCccc
Q psy64 85 EKKYIFIVVKKIIVVIYAKKFSLDIE 110 (115)
Q Consensus 85 ~~~~~C~~C~~~~~~~~~~~~h~~~h 110 (115)
...|+|+.|...|-..-+.-.|...|
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CCeEECCCCCCccccCcChhhhcccc
Confidence 34577777777777776666666555
No 127
>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=75.15 E-value=1.2 Score=21.65 Aligned_cols=32 Identities=22% Similarity=0.180 Sum_probs=21.4
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecceehh
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVV 99 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~ 99 (115)
|+|+.||..+.-.... .|+ ...|+.||..+.-
T Consensus 3 ~~CP~CG~~iev~~~~-------~Ge-iV~Cp~CGaeleV 34 (54)
T TIGR01206 3 FECPDCGAEIELENPE-------LGE-LVICDECGAELEV 34 (54)
T ss_pred cCCCCCCCEEecCCCc-------cCC-EEeCCCCCCEEEE
Confidence 6899999876554331 133 5689999987643
No 128
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=74.96 E-value=2.6 Score=20.44 Aligned_cols=43 Identities=14% Similarity=0.148 Sum_probs=26.2
Q ss_pred Cceeccc-ccccccChhhHHHHHHHhcCCCceeEEe----ecceehhh
Q psy64 58 RDFQCKV-CDRAFFDVYNLKLHMRIHTGEKKYIFIV----VKKIIVVI 100 (115)
Q Consensus 58 ~~~~C~~-c~~~~~~~~~l~~h~~~h~~~~~~~C~~----C~~~~~~~ 100 (115)
.+..|+. |+..-.....|..|....-..++..|.. |...+...
T Consensus 8 ~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~ 55 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVPRE 55 (60)
T ss_dssp SEEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEEHH
T ss_pred CEeeCCCCCcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccchh
Confidence 4568888 4444344567889988777777888988 88877654
No 129
>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=74.75 E-value=4.1 Score=18.49 Aligned_cols=24 Identities=29% Similarity=0.534 Sum_probs=13.1
Q ss_pred CCCceecccccccccCh----hhHHHHH
Q psy64 56 KIRDFQCKVCDRAFFDV----YNLKLHM 79 (115)
Q Consensus 56 ~~~~~~C~~c~~~~~~~----~~l~~h~ 79 (115)
+....+|..|++.+... +.|..|+
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 34456888888777764 4666666
No 130
>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=73.76 E-value=0.86 Score=18.99 Aligned_cols=9 Identities=33% Similarity=1.039 Sum_probs=4.8
Q ss_pred ecccccccc
Q psy64 61 QCKVCDRAF 69 (115)
Q Consensus 61 ~C~~c~~~~ 69 (115)
.|..|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 455555555
No 131
>KOG4167|consensus
Probab=73.70 E-value=1 Score=33.47 Aligned_cols=27 Identities=30% Similarity=0.742 Sum_probs=23.8
Q ss_pred CCceecccccccccChhhHHHHHHHhc
Q psy64 57 IRDFQCKVCDRAFFDVYNLKLHMRIHT 83 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~~~~l~~h~~~h~ 83 (115)
+..|.|.+|++.|.....+..|+++|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 456899999999999999999999884
No 132
>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=73.05 E-value=2.2 Score=21.48 Aligned_cols=28 Identities=7% Similarity=0.086 Sum_probs=18.3
Q ss_pred ecccccccccChhhHHHHHHHhcCCCceeEEeecceeh
Q psy64 61 QCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIV 98 (115)
Q Consensus 61 ~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 98 (115)
.|+.||..... ....+.|.|+.||..+.
T Consensus 30 ~C~~CG~~~~~----------~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 30 TCPRCGHRNKK----------RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CccCccccccc----------ccccceEEcCCCCCEEC
Confidence 57778754333 23456789999987654
No 133
>PF15269 zf-C2H2_7: Zinc-finger
Probab=72.11 E-value=1.3 Score=20.62 Aligned_cols=23 Identities=4% Similarity=-0.229 Sum_probs=16.4
Q ss_pred eeEEeecceehhhhhhccCCccc
Q psy64 88 YIFIVVKKIIVVIYAKKFSLDIE 110 (115)
Q Consensus 88 ~~C~~C~~~~~~~~~~~~h~~~h 110 (115)
|.|-.|..+..-++.|..|++..
T Consensus 21 ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred ceeecCCcccchHHHHHHHHHHH
Confidence 56777777777777777776654
No 134
>KOG2482|consensus
Probab=72.09 E-value=12 Score=25.56 Aligned_cols=77 Identities=26% Similarity=0.442 Sum_probs=48.4
Q ss_pred hHHHHHHHHhcCCC-CCeecCCChhhcc-ChhhHHHHHHH-hc----------ChhHHHHHHHHhhcCCCceeccccccc
Q psy64 2 KRQLKEHMAVHTTD-RPFVCNMCPSTFK-LKKHLRQHYKV-HL----------KMDTLENHMKAVHEKIRDFQCKVCDRA 68 (115)
Q Consensus 2 k~~l~~h~~~h~~~-~~~~C~~C~~~~~-~~~~l~~h~~~-h~----------~~~~l~~h~~~~h~~~~~~~C~~c~~~ 68 (115)
+..|.++++.-++. ..-+|-.|...+. ..+.+..|+.. |. .-..+..|.+ ..-..++|..|.+.
T Consensus 128 ~eaLeqqQ~Eredt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLk---ekL~r~~CLyCeki 204 (423)
T KOG2482|consen 128 KEALEQQQKEREDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLK---EKLERLRCLYCEKI 204 (423)
T ss_pred HHHHHHHHHHhcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHH---HHHhhheeeeeccc
Confidence 44566666654332 3355888886654 44556666543 32 2233455554 22335789999999
Q ss_pred ccChhhHHHHHHH
Q psy64 69 FFDVYNLKLHMRI 81 (115)
Q Consensus 69 ~~~~~~l~~h~~~ 81 (115)
|.....|..|++.
T Consensus 205 frdkntLkeHMrk 217 (423)
T KOG2482|consen 205 FRDKNTLKEHMRK 217 (423)
T ss_pred cCCcHHHHHHHHh
Confidence 9999999999875
No 135
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=70.98 E-value=2.5 Score=29.43 Aligned_cols=18 Identities=22% Similarity=0.490 Sum_probs=13.3
Q ss_pred CCCceecccccccccChh
Q psy64 56 KIRDFQCKVCDRAFFDVY 73 (115)
Q Consensus 56 ~~~~~~C~~c~~~~~~~~ 73 (115)
|.+.|+|+.||..+....
T Consensus 364 G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 364 GRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCCcccccccccCCccc
Confidence 444889999998776654
No 136
>PRK04351 hypothetical protein; Provisional
Probab=70.88 E-value=2.2 Score=25.34 Aligned_cols=34 Identities=15% Similarity=0.394 Sum_probs=23.5
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCceeEEeecceehhh
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVVI 100 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~ 100 (115)
.|.|..||..+..... + ....|.|..|+-.+...
T Consensus 112 ~Y~C~~Cg~~~~r~Rr-------~-n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 112 LYECQSCGQQYLRKRR-------I-NTKRYRCGKCRGKLKLI 145 (149)
T ss_pred EEECCCCCCEeeeeee-------c-CCCcEEeCCCCcEeeec
Confidence 4789889876654321 1 34679999999877655
No 137
>KOG4173|consensus
Probab=70.78 E-value=2.5 Score=26.55 Aligned_cols=56 Identities=23% Similarity=0.385 Sum_probs=35.6
Q ss_pred ecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceeccc--ccccccChhhHHHH
Q psy64 19 VCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKV--CDRAFFDVYNLKLH 78 (115)
Q Consensus 19 ~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~--c~~~~~~~~~l~~h 78 (115)
.|..|.+.|.+...|..|+..++.. .++.- ...|...|+|.. |+..|.....-..|
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs-~Fqa~---veRG~dMy~ClvEgCt~KFkT~r~RkdH 165 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDS-LFQAL---VERGQDMYQCLVEGCTEKFKTSRDRKDH 165 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHH-HHHHH---HHcCccHHHHHHHhhhhhhhhhhhhhhH
Confidence 4888888888777777776544321 11111 234566788865 88888877766666
No 138
>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=70.35 E-value=4.6 Score=22.42 Aligned_cols=68 Identities=15% Similarity=0.398 Sum_probs=42.9
Q ss_pred CCeecCCChhhccChhhHHHHHHH-hcCh-----hHHHHHHHHhh-------------cC---------CCceec----c
Q psy64 16 RPFVCNMCPSTFKLKKHLRQHYKV-HLKM-----DTLENHMKAVH-------------EK---------IRDFQC----K 63 (115)
Q Consensus 16 ~~~~C~~C~~~~~~~~~l~~h~~~-h~~~-----~~l~~h~~~~h-------------~~---------~~~~~C----~ 63 (115)
+...|..|+.+..- ..+..|.+. |... ..+.+-.+... .. -..|.| .
T Consensus 10 ~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~~G~~C~~~~~ 88 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVYDGYRCQCDPP 88 (109)
T ss_pred CEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCCCCeeeecCCC
Confidence 34568999888765 778888874 3311 11222111100 00 124789 9
Q ss_pred cccccccChhhHHHHHHHhcC
Q psy64 64 VCDRAFFDVYNLKLHMRIHTG 84 (115)
Q Consensus 64 ~c~~~~~~~~~l~~h~~~h~~ 84 (115)
.|+........+..|++.+.|
T Consensus 89 ~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 89 HCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCcEeccHHHHHHHHHHhcC
Confidence 999999999999999887653
No 139
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=69.71 E-value=1.4 Score=26.12 Aligned_cols=9 Identities=33% Similarity=0.933 Sum_probs=4.6
Q ss_pred eecCCChhh
Q psy64 18 FVCNMCPST 26 (115)
Q Consensus 18 ~~C~~C~~~ 26 (115)
+.|..||..
T Consensus 113 l~C~~Cg~~ 121 (146)
T PF07295_consen 113 LVCENCGHE 121 (146)
T ss_pred EecccCCCE
Confidence 555555544
No 140
>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=69.43 E-value=0.76 Score=21.53 Aligned_cols=41 Identities=15% Similarity=0.002 Sum_probs=23.3
Q ss_pred ecccccccccChhhHHHHHHHhcCCCceeEEe--ecceehhhhhh
Q psy64 61 QCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIV--VKKIIVVIYAK 103 (115)
Q Consensus 61 ~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~--C~~~~~~~~~~ 103 (115)
.||.||........... .....+.=|.|.+ ||.+|....++
T Consensus 1 ~CP~Cg~~a~ir~S~~~--s~~~~~~Y~qC~N~~Cg~tfv~~~~~ 43 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQL--SPLTRELYCQCTNPECGHTFVANLEF 43 (47)
T ss_pred CcCCCCCeeEEEEchhh--CcceEEEEEEECCCcCCCEEEEEEEE
Confidence 37888865444433221 1222344578866 99999876544
No 141
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=69.28 E-value=2.4 Score=20.92 Aligned_cols=33 Identities=18% Similarity=0.327 Sum_probs=22.9
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCceeEEeeccee
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKII 97 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~ 97 (115)
.|.|| ||-.|..+-. ....||..-+|+.|+...
T Consensus 22 tyPCP-CGDRFeIsLe-----Dl~~GE~VArCPSCSLiv 54 (67)
T COG5216 22 TYPCP-CGDRFEISLE-----DLRNGEVVARCPSCSLIV 54 (67)
T ss_pred EecCC-CCCEeEEEHH-----HhhCCceEEEcCCceEEE
Confidence 35676 8877776542 235788999999998643
No 142
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=68.60 E-value=5.7 Score=18.67 Aligned_cols=21 Identities=33% Similarity=0.706 Sum_probs=16.5
Q ss_pred eecccccccccCh-----hhHHHHHH
Q psy64 60 FQCKVCDRAFFDV-----YNLKLHMR 80 (115)
Q Consensus 60 ~~C~~c~~~~~~~-----~~l~~h~~ 80 (115)
-.|..|++.+... +.|..|+.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 4899999988765 47777776
No 143
>KOG1280|consensus
Probab=68.19 E-value=6.2 Score=26.86 Aligned_cols=39 Identities=18% Similarity=0.256 Sum_probs=29.5
Q ss_pred CCceecccccccccChhhHHHHHHHhcCCCc--eeEEeecc
Q psy64 57 IRDFQCKVCDRAFFDVYNLKLHMRIHTGEKK--YIFIVVKK 95 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~--~~C~~C~~ 95 (115)
...|.|+.|+..-.....+..|....+-+-+ .+|++|..
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~ 117 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAA 117 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeecccc
Confidence 4479999999999999999999776554544 45677654
No 144
>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=67.68 E-value=2 Score=24.28 Aligned_cols=26 Identities=15% Similarity=0.305 Sum_probs=18.4
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCceeEEeecce
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKI 96 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 96 (115)
...|..||..|..... -+.|+.||..
T Consensus 70 ~~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (115)
T TIGR00100 70 ECECEDCSEEVSPEID------------LYRCPKCHGI 95 (115)
T ss_pred EEEcccCCCEEecCCc------------CccCcCCcCC
Confidence 4689999977765432 3679999853
No 145
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=67.43 E-value=6.3 Score=24.54 Aligned_cols=36 Identities=11% Similarity=0.081 Sum_probs=21.4
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecceehh
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVV 99 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~ 99 (115)
+.|+.|| +..- ...-++.-..+-.+.|+.||..+..
T Consensus 7 ~~Cp~Cg--~eev--~hEVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 7 IECPSCG--SEEV--SHEVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred EECCCCC--cchh--hHHHHHhcCCceEEEccCCCcEeec
Confidence 5899998 2211 1122333344456899999988844
No 146
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=67.21 E-value=2.2 Score=24.05 Aligned_cols=25 Identities=8% Similarity=-0.072 Sum_probs=17.0
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCceeEEeecc
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKK 95 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 95 (115)
.+.|..||..|.... ..+.|+.||.
T Consensus 70 ~~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred EEEcccCCCEEecCC------------cCccCcCCCC
Confidence 468999997665442 3356898884
No 147
>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=66.24 E-value=2 Score=19.60 Aligned_cols=31 Identities=6% Similarity=0.159 Sum_probs=16.1
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecceehh
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVV 99 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~ 99 (115)
|.|+.||..... ......-+.|+.||.....
T Consensus 1 m~Cp~Cg~~~~~---------~D~~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 1 MKCPNCGSKEIV---------FDPERGELVCPNCGLVLEE 31 (43)
T ss_dssp ESBTTTSSSEEE---------EETTTTEEEETTT-BBEE-
T ss_pred CCCcCCcCCceE---------EcCCCCeEECCCCCCEeec
Confidence 467888754311 1122334688888876543
No 148
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=65.87 E-value=9.6 Score=23.41 Aligned_cols=44 Identities=20% Similarity=0.575 Sum_probs=27.9
Q ss_pred HHHHHHhcCCCCCeecCCChhhccChhhHHHHHHHhcChhHHHHHHHHhhcCCCceecccccccccC
Q psy64 5 LKEHMAVHTTDRPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRAFFD 71 (115)
Q Consensus 5 l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~ 71 (115)
|..-+..-++..-|.|+.|...|.....+. ..|.||.||.....
T Consensus 101 Lk~~le~~~~~~~y~C~~~~~r~sfdeA~~-----------------------~~F~Cp~Cg~~L~~ 144 (176)
T COG1675 101 LKRKLEKETENNYYVCPNCHVKYSFDEAME-----------------------LGFTCPKCGEDLEE 144 (176)
T ss_pred HHHHHHhhccCCceeCCCCCCcccHHHHHH-----------------------hCCCCCCCCchhhh
Confidence 333344445667799988887776554321 23899999965443
No 149
>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=65.74 E-value=2.6 Score=26.67 Aligned_cols=27 Identities=15% Similarity=0.369 Sum_probs=17.1
Q ss_pred CCceecccccccccChhhHHHHHHHhc
Q psy64 57 IRDFQCKVCDRAFFDVYNLKLHMRIHT 83 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~~~~l~~h~~~h~ 83 (115)
+.-|.|+.|+|.|....-...|+..-+
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcC
Confidence 345788888888888777777766543
No 150
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=64.76 E-value=4.3 Score=19.75 Aligned_cols=11 Identities=36% Similarity=0.908 Sum_probs=7.3
Q ss_pred eecCCChhhcc
Q psy64 18 FVCNMCPSTFK 28 (115)
Q Consensus 18 ~~C~~C~~~~~ 28 (115)
..|+.||+.|.
T Consensus 6 ~~C~~Cg~~~~ 16 (54)
T PF14446_consen 6 CKCPVCGKKFK 16 (54)
T ss_pred ccChhhCCccc
Confidence 35777777765
No 151
>KOG4167|consensus
Probab=64.73 E-value=0.71 Score=34.20 Aligned_cols=27 Identities=7% Similarity=0.026 Sum_probs=24.6
Q ss_pred CceeEEeecceehhhhhhccCCccccc
Q psy64 86 KKYIFIVVKKIIVVIYAKKFSLDIEIL 112 (115)
Q Consensus 86 ~~~~C~~C~~~~~~~~~~~~h~~~h~~ 112 (115)
..|.|..|++.|.-..++..|+++|.+
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 458999999999999999999999975
No 152
>PHA02998 RNA polymerase subunit; Provisional
Probab=64.68 E-value=1.5 Score=26.79 Aligned_cols=39 Identities=13% Similarity=0.051 Sum_probs=23.6
Q ss_pred ceecccccccccChhhHHHHHHHh-cCCCc---eeEEeecceehhhh
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIH-TGEKK---YIFIVVKKIIVVIY 101 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h-~~~~~---~~C~~C~~~~~~~~ 101 (115)
..+|+.|+..-.....+ ++. .+|.+ |.|..||+.|..+.
T Consensus 143 ~v~CPkCg~~~A~f~ql----QTRSADEPmT~FYkC~~CG~~wkppk 185 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMI----QTRAADEPPLVRHACRDCKKHFKPPK 185 (195)
T ss_pred CCCCCCCCCCceEEEEE----eeccCCCCceEEEEcCCCCCccCCcc
Confidence 35799998543333222 233 33333 89999999887653
No 153
>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=64.28 E-value=2.7 Score=19.80 Aligned_cols=14 Identities=14% Similarity=-0.102 Sum_probs=10.3
Q ss_pred eeEEeecceehhhh
Q psy64 88 YIFIVVKKIIVVIY 101 (115)
Q Consensus 88 ~~C~~C~~~~~~~~ 101 (115)
|+|.+|++.+.-..
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 78888888776543
No 154
>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=63.90 E-value=2.3 Score=20.31 Aligned_cols=13 Identities=15% Similarity=-0.008 Sum_probs=9.4
Q ss_pred eeEEeecceehhh
Q psy64 88 YIFIVVKKIIVVI 100 (115)
Q Consensus 88 ~~C~~C~~~~~~~ 100 (115)
|+|.+||+.+...
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 6788888877643
No 155
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=63.18 E-value=1.2 Score=20.76 Aligned_cols=27 Identities=26% Similarity=0.575 Sum_probs=16.9
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecc
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKK 95 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 95 (115)
+.|+.||.. ....+ .....|.|..|++
T Consensus 19 ~~CP~Cg~~--~~~~~-------~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRL-------KTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEe-------CCCCeEECCCCCC
Confidence 679999854 11111 1156789988875
No 156
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=62.99 E-value=2.6 Score=23.92 Aligned_cols=26 Identities=19% Similarity=0.402 Sum_probs=17.1
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCce-eEEeecce
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKY-IFIVVKKI 96 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~-~C~~C~~~ 96 (115)
.+.|..||..|..... .| .|+.||..
T Consensus 71 ~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~ 97 (117)
T PRK00564 71 ELECKDCSHVFKPNAL------------DYGVCEKCHSK 97 (117)
T ss_pred EEEhhhCCCccccCCc------------cCCcCcCCCCC
Confidence 4689999976655422 33 49999853
No 157
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=62.15 E-value=4.3 Score=18.21 Aligned_cols=14 Identities=29% Similarity=0.588 Sum_probs=12.1
Q ss_pred CeecCCChhhccCh
Q psy64 17 PFVCNMCPSTFKLK 30 (115)
Q Consensus 17 ~~~C~~C~~~~~~~ 30 (115)
||.|..|+..|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 89999999998754
No 158
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=61.80 E-value=5.2 Score=28.27 Aligned_cols=13 Identities=31% Similarity=0.720 Sum_probs=10.2
Q ss_pred CCeecCCChhhcc
Q psy64 16 RPFVCNMCPSTFK 28 (115)
Q Consensus 16 ~~~~C~~C~~~~~ 28 (115)
..|.|..||..+.
T Consensus 6 ~~y~C~~Cg~~~~ 18 (454)
T TIGR00416 6 SKFVCQHCGADSP 18 (454)
T ss_pred CeEECCcCCCCCc
Confidence 3599999998844
No 159
>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=61.16 E-value=0.82 Score=20.65 Aligned_cols=18 Identities=17% Similarity=0.154 Sum_probs=9.9
Q ss_pred hcCCCceeEEeecceehh
Q psy64 82 HTGEKKYIFIVVKKIIVV 99 (115)
Q Consensus 82 h~~~~~~~C~~C~~~~~~ 99 (115)
..+.+.|.|+.|+.....
T Consensus 19 ~~~~~~w~C~~C~~~N~l 36 (40)
T PF04810_consen 19 DDGGKTWICNFCGTKNPL 36 (40)
T ss_dssp ETTTTEEEETTT--EEE-
T ss_pred cCCCCEEECcCCCCcCCC
Confidence 335567888888876543
No 160
>KOG2026|consensus
Probab=61.12 E-value=5 Score=27.75 Aligned_cols=25 Identities=12% Similarity=-0.015 Sum_probs=18.4
Q ss_pred CCceeEEeecceehhhhhhccCCccccccc
Q psy64 85 EKKYIFIVVKKIIVVIYAKKFSLDIEILCV 114 (115)
Q Consensus 85 ~~~~~C~~C~~~~~~~~~~~~h~~~h~~~~ 114 (115)
-.+|.|.+||+-|. .++.++|+.+|
T Consensus 39 LnvyAclvcg~y~q-----gr~~kS~A~~h 63 (442)
T KOG2026|consen 39 LNVYACLVCGKYFQ-----GRGEKSHAYTH 63 (442)
T ss_pred cceeeeeeeCchhh-----CcCccccchhc
Confidence 45788999998887 56666776655
No 161
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=60.82 E-value=5.1 Score=22.70 Aligned_cols=15 Identities=20% Similarity=0.222 Sum_probs=10.9
Q ss_pred hcCCCceeEEeecce
Q psy64 82 HTGEKKYIFIVVKKI 96 (115)
Q Consensus 82 h~~~~~~~C~~C~~~ 96 (115)
..++..|.|.+|.+.
T Consensus 89 ~~~~~~WlC~vC~k~ 103 (118)
T PF02318_consen 89 SKKEPIWLCKVCQKQ 103 (118)
T ss_dssp TSSSCCEEEHHHHHH
T ss_pred CCCCCCEEChhhHHH
Confidence 445678999988763
No 162
>KOG2482|consensus
Probab=60.80 E-value=16 Score=25.03 Aligned_cols=67 Identities=19% Similarity=0.301 Sum_probs=40.7
Q ss_pred ChhHHHHHHHHhhcCCCceecccccccccCh-hhHHHHHH-Hhc---C--C----------------CceeEEeecceeh
Q psy64 42 KMDTLENHMKAVHEKIRDFQCKVCDRAFFDV-YNLKLHMR-IHT---G--E----------------KKYIFIVVKKIIV 98 (115)
Q Consensus 42 ~~~~l~~h~~~~h~~~~~~~C~~c~~~~~~~-~~l~~h~~-~h~---~--~----------------~~~~C~~C~~~~~ 98 (115)
.+..|..+++........-+|-.|..-+... +..-.|+- .|. | + ..++|--|.+.|.
T Consensus 127 L~eaLeqqQ~Eredt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifr 206 (423)
T KOG2482|consen 127 LKEALEQQQKEREDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFR 206 (423)
T ss_pred HHHHHHHHHHHhcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccC
Confidence 3444555555432333344788888665543 33333422 221 1 1 2468999999999
Q ss_pred hhhhhccCCc
Q psy64 99 VIYAKKFSLD 108 (115)
Q Consensus 99 ~~~~~~~h~~ 108 (115)
++..|..|++
T Consensus 207 dkntLkeHMr 216 (423)
T KOG2482|consen 207 DKNTLKEHMR 216 (423)
T ss_pred CcHHHHHHHH
Confidence 9999999986
No 163
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=60.78 E-value=2.8 Score=26.14 Aligned_cols=27 Identities=11% Similarity=-0.097 Sum_probs=0.0
Q ss_pred hcCCCceeEEeecc-eehhhhhhccCCc
Q psy64 82 HTGEKKYIFIVVKK-IIVVIYAKKFSLD 108 (115)
Q Consensus 82 h~~~~~~~C~~C~~-~~~~~~~~~~h~~ 108 (115)
|--...|.|++||- +|..+..+.+|+.
T Consensus 96 hGL~~ey~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 96 HGLGVEYKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp ----------------------------
T ss_pred hCCCCeeeeEeCCCcceecHHHHHHhcC
Confidence 34456688999987 4558888888875
No 164
>KOG2807|consensus
Probab=60.74 E-value=7.1 Score=26.40 Aligned_cols=22 Identities=32% Similarity=0.698 Sum_probs=15.8
Q ss_pred CCeecCCChhhccChhhHHHHH
Q psy64 16 RPFVCNMCPSTFKLKKHLRQHY 37 (115)
Q Consensus 16 ~~~~C~~C~~~~~~~~~l~~h~ 37 (115)
-|-.|+.|+...-...+|.+..
T Consensus 289 LP~eCpiC~ltLVss~hLARSy 310 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLARSY 310 (378)
T ss_pred CCccCCccceeEecchHHHHHH
Confidence 3566888888887777777654
No 165
>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=60.66 E-value=8 Score=22.58 Aligned_cols=26 Identities=31% Similarity=0.591 Sum_probs=14.4
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCc
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKK 87 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~ 87 (115)
...|-+||+.|..- .+|+..|.|-.|
T Consensus 72 ~i~clecGk~~k~L---krHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECGKKFKTL---KRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--EESBH---HHHHHHTT-S-H
T ss_pred eeEEccCCcccchH---HHHHHHccCCCH
Confidence 45788888877654 678888865544
No 166
>PRK11823 DNA repair protein RadA; Provisional
Probab=60.64 E-value=5.8 Score=27.97 Aligned_cols=13 Identities=23% Similarity=0.675 Sum_probs=10.2
Q ss_pred CCeecCCChhhcc
Q psy64 16 RPFVCNMCPSTFK 28 (115)
Q Consensus 16 ~~~~C~~C~~~~~ 28 (115)
..|.|..||..+.
T Consensus 6 ~~y~C~~Cg~~~~ 18 (446)
T PRK11823 6 TAYVCQECGAESP 18 (446)
T ss_pred CeEECCcCCCCCc
Confidence 4699999998743
No 167
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=60.53 E-value=1.6 Score=29.17 Aligned_cols=45 Identities=16% Similarity=0.135 Sum_probs=26.6
Q ss_pred ecccccccccChhhHHHHHHHhcCCCceeEEeecceehhhhhhccCC
Q psy64 61 QCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVVIYAKKFSL 107 (115)
Q Consensus 61 ~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~~~~h~ 107 (115)
-|..|.-.|......... -.+....|.|+.|...|-.-.+...|-
T Consensus 364 ~Cf~CQ~~fp~~~~~~~~--~~~ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 364 HCFVCQGPFPKPPVSPFD--ESTSSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred cceeccCCCCCCCCCccc--ccccccceechhhhhhhhhhhHHHHHH
Confidence 366676656554432111 122345799999998888776655543
No 168
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=60.14 E-value=5 Score=28.76 Aligned_cols=10 Identities=20% Similarity=0.627 Sum_probs=5.3
Q ss_pred ecCCChhhcc
Q psy64 19 VCNMCPSTFK 28 (115)
Q Consensus 19 ~C~~C~~~~~ 28 (115)
.|..||+...
T Consensus 215 ~C~~Cg~~~~ 224 (505)
T TIGR00595 215 LCRSCGYILC 224 (505)
T ss_pred EhhhCcCccC
Confidence 3555655543
No 169
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=59.70 E-value=3.3 Score=24.15 Aligned_cols=22 Identities=18% Similarity=-0.070 Sum_probs=14.6
Q ss_pred eeEEeecceehhhhhhccCCccccc
Q psy64 88 YIFIVVKKIIVVIYAKKFSLDIEIL 112 (115)
Q Consensus 88 ~~C~~C~~~~~~~~~~~~h~~~h~~ 112 (115)
.+|-.+|+.|.+ |.+|+.+|.+
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccC
Confidence 367777777764 5677776543
No 170
>KOG2071|consensus
Probab=59.03 E-value=2.6 Score=30.50 Aligned_cols=29 Identities=7% Similarity=-0.199 Sum_probs=22.6
Q ss_pred CCCceeEEeecceehhhhhhccCCccccc
Q psy64 84 GEKKYIFIVVKKIIVVIYAKKFSLDIEIL 112 (115)
Q Consensus 84 ~~~~~~C~~C~~~~~~~~~~~~h~~~h~~ 112 (115)
...|..|..||..|.+......|+.+|..
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhhh
Confidence 45667899999999888887777777754
No 171
>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=58.89 E-value=2.5 Score=19.29 Aligned_cols=13 Identities=8% Similarity=0.018 Sum_probs=6.6
Q ss_pred ceeEEeecceehh
Q psy64 87 KYIFIVVKKIIVV 99 (115)
Q Consensus 87 ~~~C~~C~~~~~~ 99 (115)
|+.|..|++.|=.
T Consensus 13 ~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 13 PFKCKHCGKSFCL 25 (43)
T ss_dssp HEE-TTTS-EE-T
T ss_pred CeECCCCCcccCc
Confidence 5677777776654
No 172
>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=58.87 E-value=6.4 Score=18.84 Aligned_cols=11 Identities=0% Similarity=-0.170 Sum_probs=3.9
Q ss_pred eEEeecceehh
Q psy64 89 IFIVVKKIIVV 99 (115)
Q Consensus 89 ~C~~C~~~~~~ 99 (115)
.|++|+..|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 55666655543
No 173
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=58.57 E-value=3.1 Score=23.44 Aligned_cols=26 Identities=12% Similarity=0.084 Sum_probs=16.9
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCceeEEeecce
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKI 96 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 96 (115)
.+.|..||..|...... +.|+.|+..
T Consensus 70 ~~~C~~Cg~~~~~~~~~------------~~CP~Cgs~ 95 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEFD------------FSCPRCGSP 95 (113)
T ss_dssp EEEETTTS-EEECHHCC------------HH-SSSSSS
T ss_pred cEECCCCCCEEecCCCC------------CCCcCCcCC
Confidence 36899999888766532 348888865
No 174
>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=58.20 E-value=4.6 Score=23.77 Aligned_cols=32 Identities=19% Similarity=0.319 Sum_probs=20.7
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCceeEEeecceeh
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIV 98 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 98 (115)
.|.|..|+..+...... ....|.|..|+..+.
T Consensus 123 ~~~C~~C~~~~~r~~~~--------~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKRHRRS--------KRKRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeeeeccc--------chhhEECCCCCCEEE
Confidence 46888898766443322 223389999987764
No 175
>PRK14873 primosome assembly protein PriA; Provisional
Probab=57.71 E-value=6.2 Score=29.39 Aligned_cols=10 Identities=20% Similarity=0.740 Sum_probs=5.4
Q ss_pred ecCCChhhcc
Q psy64 19 VCNMCPSTFK 28 (115)
Q Consensus 19 ~C~~C~~~~~ 28 (115)
.|..||+.+.
T Consensus 385 ~C~~Cg~~~~ 394 (665)
T PRK14873 385 ACARCRTPAR 394 (665)
T ss_pred EhhhCcCeeE
Confidence 4666655543
No 176
>PLN02294 cytochrome c oxidase subunit Vb
Probab=57.47 E-value=4.9 Score=24.45 Aligned_cols=17 Identities=12% Similarity=0.059 Sum_probs=13.8
Q ss_pred CCCceeEEeecceehhh
Q psy64 84 GEKKYIFIVVKKIIVVI 100 (115)
Q Consensus 84 ~~~~~~C~~C~~~~~~~ 100 (115)
..+|++|+.||..|...
T Consensus 138 kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 138 KGKSFECPVCTQYFELE 154 (174)
T ss_pred CCCceeCCCCCCEEEEE
Confidence 34789999999998754
No 177
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=57.24 E-value=1.5 Score=26.04 Aligned_cols=12 Identities=0% Similarity=-0.155 Sum_probs=7.7
Q ss_pred eeEEeecceehh
Q psy64 88 YIFIVVKKIIVV 99 (115)
Q Consensus 88 ~~C~~C~~~~~~ 99 (115)
-.|+.|+..|+.
T Consensus 29 ReC~~C~~RFTT 40 (156)
T COG1327 29 RECLECGERFTT 40 (156)
T ss_pred hcccccccccch
Confidence 467777776654
No 178
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=56.97 E-value=3.1 Score=23.52 Aligned_cols=27 Identities=7% Similarity=0.073 Sum_probs=16.7
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCceeEEeecce
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKI 96 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 96 (115)
.+.|..||..|..... ..+.|+.||..
T Consensus 70 ~~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs~ 96 (114)
T PRK03681 70 ECWCETCQQYVTLLTQ-----------RVRRCPQCHGD 96 (114)
T ss_pred EEEcccCCCeeecCCc-----------cCCcCcCcCCC
Confidence 4689999965543321 11579999843
No 179
>KOG2231|consensus
Probab=56.49 E-value=28 Score=26.14 Aligned_cols=21 Identities=24% Similarity=0.649 Sum_probs=13.7
Q ss_pred ecCCChhhccChhhHHHHHHH
Q psy64 19 VCNMCPSTFKLKKHLRQHYKV 39 (115)
Q Consensus 19 ~C~~C~~~~~~~~~l~~h~~~ 39 (115)
.|..|...|.....|..|++.
T Consensus 184 ~C~~C~~~fld~~el~rH~~~ 204 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRF 204 (669)
T ss_pred cchhhhhhhccHHHHHHhhcc
Confidence 366677777766666666653
No 180
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=56.41 E-value=3.1 Score=23.50 Aligned_cols=16 Identities=19% Similarity=0.384 Sum_probs=12.0
Q ss_pred CCCeecCCChhhccCh
Q psy64 15 DRPFVCNMCPSTFKLK 30 (115)
Q Consensus 15 ~~~~~C~~C~~~~~~~ 30 (115)
...+.|..||+.+...
T Consensus 20 ~~~l~C~kCgye~~~~ 35 (113)
T COG1594 20 GGKLVCRKCGYEEEAS 35 (113)
T ss_pred CcEEECCCCCcchhcc
Confidence 3468899999887654
No 181
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=56.22 E-value=6.9 Score=26.94 Aligned_cols=11 Identities=27% Similarity=0.712 Sum_probs=7.7
Q ss_pred eecCCChhhcc
Q psy64 18 FVCNMCPSTFK 28 (115)
Q Consensus 18 ~~C~~C~~~~~ 28 (115)
|.|..||..+.
T Consensus 1 ~~c~~cg~~~~ 11 (372)
T cd01121 1 YVCSECGYVSP 11 (372)
T ss_pred CCCCCCCCCCC
Confidence 57888887743
No 182
>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=55.48 E-value=5.5 Score=21.90 Aligned_cols=18 Identities=11% Similarity=0.126 Sum_probs=13.7
Q ss_pred hcCCCceeEEeecceehhh
Q psy64 82 HTGEKKYIFIVVKKIIVVI 100 (115)
Q Consensus 82 h~~~~~~~C~~C~~~~~~~ 100 (115)
+.+ +|++|..||..|...
T Consensus 75 ~~g-~~~rC~eCG~~fkL~ 92 (97)
T cd00924 75 EKG-KPKRCPECGHVFKLV 92 (97)
T ss_pred eCC-CceeCCCCCcEEEEE
Confidence 344 789999999888653
No 183
>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=55.23 E-value=5.1 Score=22.01 Aligned_cols=13 Identities=8% Similarity=-0.171 Sum_probs=7.2
Q ss_pred ceeEEeecceehh
Q psy64 87 KYIFIVVKKIIVV 99 (115)
Q Consensus 87 ~~~C~~C~~~~~~ 99 (115)
.+.|+.|++.+..
T Consensus 16 ~~~C~~C~~~~~~ 28 (104)
T TIGR01384 16 VYVCPSCGYEKEK 28 (104)
T ss_pred eEECcCCCCcccc
Confidence 4566666655443
No 184
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=54.23 E-value=7.3 Score=22.75 Aligned_cols=46 Identities=13% Similarity=0.172 Sum_probs=27.4
Q ss_pred CCCceecccccccccChhhHH--------------HHHHHhcCCCceeEEeecceehhhhh
Q psy64 56 KIRDFQCKVCDRAFFDVYNLK--------------LHMRIHTGEKKYIFIVVKKIIVVIYA 102 (115)
Q Consensus 56 ~~~~~~C~~c~~~~~~~~~l~--------------~h~~~h~~~~~~~C~~C~~~~~~~~~ 102 (115)
+.+-|+|..|..++....-|+ ..+..+...-| +|++|.-+|.++..
T Consensus 77 d~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~yp-vCPvCkTSFKss~~ 136 (140)
T PF05290_consen 77 DPKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYP-VCPVCKTSFKSSSS 136 (140)
T ss_pred CCCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCC-CCCccccccccccc
Confidence 447899999987766543221 01111222222 78999999887754
No 185
>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=53.60 E-value=3.9 Score=18.76 Aligned_cols=13 Identities=15% Similarity=-0.077 Sum_probs=8.0
Q ss_pred eEEeecceehhhh
Q psy64 89 IFIVVKKIIVVIY 101 (115)
Q Consensus 89 ~C~~C~~~~~~~~ 101 (115)
.|.+|+..|.-+.
T Consensus 10 ~C~~C~rpf~WRK 22 (42)
T PF10013_consen 10 ICPVCGRPFTWRK 22 (42)
T ss_pred cCcccCCcchHHH
Confidence 5666776666443
No 186
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=53.34 E-value=3 Score=29.50 Aligned_cols=21 Identities=29% Similarity=0.589 Sum_probs=12.5
Q ss_pred eecccccccccChhhHHHHHH
Q psy64 60 FQCKVCDRAFFDVYNLKLHMR 80 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~ 80 (115)
+.|+.|.+.|.....+..|+.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~ 78 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHME 78 (466)
T ss_pred eeCCcccceeCCHHHHHHHHH
Confidence 356666666666666665544
No 187
>KOG3408|consensus
Probab=52.96 E-value=10 Score=21.75 Aligned_cols=28 Identities=32% Similarity=0.559 Sum_probs=22.8
Q ss_pred cCCCceecccccccccChhhHHHHHHHh
Q psy64 55 EKIRDFQCKVCDRAFFDVYNLKLHMRIH 82 (115)
Q Consensus 55 ~~~~~~~C~~c~~~~~~~~~l~~h~~~h 82 (115)
+|...|-|.+|.+.|.....|..|.++-
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhcc
Confidence 3444588999999999999999997753
No 188
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=52.38 E-value=4.7 Score=25.62 Aligned_cols=27 Identities=26% Similarity=0.266 Sum_probs=0.0
Q ss_pred CCceeEEeecceehhhhhhccCCccccc
Q psy64 85 EKKYIFIVVKKIIVVIYAKKFSLDIEIL 112 (115)
Q Consensus 85 ~~~~~C~~C~~~~~~~~~~~~h~~~h~~ 112 (115)
+....|++||...... .|..|+++.++
T Consensus 166 ~~~~~cPitGe~IP~~-e~~eHmRi~Ll 192 (229)
T PF12230_consen 166 EKMIICPITGEMIPAD-EMDEHMRIELL 192 (229)
T ss_dssp ----------------------------
T ss_pred cccccccccccccccc-ccccccccccc
Confidence 3446778887766543 56677777654
No 189
>COG4640 Predicted membrane protein [Function unknown]
Probab=52.27 E-value=7.3 Score=27.09 Aligned_cols=16 Identities=31% Similarity=0.665 Sum_probs=9.2
Q ss_pred ceecccccccccChhh
Q psy64 59 DFQCKVCDRAFFDVYN 74 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~ 74 (115)
...|+.||..|.....
T Consensus 15 ~~qC~qCG~~~t~~~s 30 (465)
T COG4640 15 DVQCTQCGHKFTSRQS 30 (465)
T ss_pred cccccccCCcCCchhh
Confidence 3446666666665543
No 190
>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=52.26 E-value=6 Score=17.96 Aligned_cols=12 Identities=33% Similarity=1.021 Sum_probs=9.9
Q ss_pred CCeecCCChhhc
Q psy64 16 RPFVCNMCPSTF 27 (115)
Q Consensus 16 ~~~~C~~C~~~~ 27 (115)
.+..|++||..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 467899999876
No 191
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=52.09 E-value=3.8 Score=29.14 Aligned_cols=41 Identities=10% Similarity=0.042 Sum_probs=24.1
Q ss_pred CCCceecccccccccChhhH-HHHHHHh----cCCCceeEEeecce
Q psy64 56 KIRDFQCKVCDRAFFDVYNL-KLHMRIH----TGEKKYIFIVVKKI 96 (115)
Q Consensus 56 ~~~~~~C~~c~~~~~~~~~l-~~h~~~h----~~~~~~~C~~C~~~ 96 (115)
..+.|+|..||..|.....- ......- .-.-.|.|++|+..
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred CCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 45578999999888865321 1111111 11224899999864
No 192
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=52.02 E-value=3.6 Score=22.73 Aligned_cols=39 Identities=10% Similarity=0.081 Sum_probs=22.7
Q ss_pred CCCceecccccccccChhhHHHHHHHhcCCCceeEEeecceeh
Q psy64 56 KIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIV 98 (115)
Q Consensus 56 ~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 98 (115)
-.+.|.|+.||..-...-.+. .-..---..|.+||..|.
T Consensus 19 L~k~FtCp~Cghe~vs~ctvk----k~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVK----KTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred CCceEecCccCCeeeeEEEEE----ecCceeEEEcccCcceEE
Confidence 457799999986544432211 111112357888888775
No 193
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=51.59 E-value=9.7 Score=22.37 Aligned_cols=33 Identities=12% Similarity=0.348 Sum_probs=19.4
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCceeEEeecceeh
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIV 98 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 98 (115)
.|.|..|+..+.... .+.....|.|..|+..+.
T Consensus 112 ~y~C~~C~~~~~~~r-------r~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRYLRVR-------RSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCCceEc-------cccCcceEEcCCCCCEEE
Confidence 577888876654221 122225688888886653
No 194
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=50.91 E-value=11 Score=30.32 Aligned_cols=9 Identities=22% Similarity=0.567 Sum_probs=6.3
Q ss_pred eecCCChhh
Q psy64 18 FVCNMCPST 26 (115)
Q Consensus 18 ~~C~~C~~~ 26 (115)
++|+.||..
T Consensus 668 rkCPkCG~~ 676 (1337)
T PRK14714 668 RRCPSCGTE 676 (1337)
T ss_pred EECCCCCCc
Confidence 667777764
No 195
>PRK05580 primosome assembly protein PriA; Validated
Probab=50.82 E-value=8.6 Score=28.68 Aligned_cols=9 Identities=22% Similarity=0.600 Sum_probs=4.9
Q ss_pred ceecccccc
Q psy64 59 DFQCKVCDR 67 (115)
Q Consensus 59 ~~~C~~c~~ 67 (115)
|..|+.||.
T Consensus 421 ~~~Cp~Cg~ 429 (679)
T PRK05580 421 PKACPECGS 429 (679)
T ss_pred CCCCCCCcC
Confidence 445666654
No 196
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=50.71 E-value=5.7 Score=17.30 Aligned_cols=11 Identities=9% Similarity=-0.001 Sum_probs=7.6
Q ss_pred ceeEEeeccee
Q psy64 87 KYIFIVVKKII 97 (115)
Q Consensus 87 ~~~C~~C~~~~ 97 (115)
.+.|+.|+...
T Consensus 22 R~vC~~Cg~Ih 32 (34)
T PF14803_consen 22 RLVCPACGFIH 32 (34)
T ss_dssp EEEETTTTEEE
T ss_pred ceECCCCCCEE
Confidence 47788887654
No 197
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=50.02 E-value=5.8 Score=23.00 Aligned_cols=37 Identities=16% Similarity=0.217 Sum_probs=23.0
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecceehhhh
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVVIY 101 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~ 101 (115)
-.||.|+...... .-..-.+...|+|..|+++|....
T Consensus 31 ~~cP~C~s~~~~k-----~g~~~~~~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 31 VNCPRCKSSNVVK-----IGGIRRGHQRYKCKSCGSTFTVET 67 (129)
T ss_pred CcCCCCCccceee-----ECCccccccccccCCcCcceeeec
Confidence 3688887544111 112234467899999999987653
No 198
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=49.91 E-value=21 Score=16.14 Aligned_cols=23 Identities=22% Similarity=0.427 Sum_probs=15.2
Q ss_pred eecCCChhhcc--ChhhHHHHHHHh
Q psy64 18 FVCNMCPSTFK--LKKHLRQHYKVH 40 (115)
Q Consensus 18 ~~C~~C~~~~~--~~~~l~~h~~~h 40 (115)
-.|+.||-.|. .+..-..|.+-|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 47999998875 444555565543
No 199
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=49.87 E-value=10 Score=18.53 Aligned_cols=31 Identities=16% Similarity=0.130 Sum_probs=16.0
Q ss_pred CceecccccccccChhhHHHHHHHhcCCCceeEEe
Q psy64 58 RDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIV 92 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~ 92 (115)
.|.....||..|...+-+. .+ ...+...|++
T Consensus 23 ~PV~s~~C~H~fek~aI~~-~i---~~~~~~~CPv 53 (57)
T PF11789_consen 23 DPVKSKKCGHTFEKEAILQ-YI---QRNGSKRCPV 53 (57)
T ss_dssp SEEEESSS--EEEHHHHHH-HC---TTTS-EE-SC
T ss_pred CCcCcCCCCCeecHHHHHH-HH---HhcCCCCCCC
Confidence 4666777888887765433 22 3345667766
No 200
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=48.98 E-value=8 Score=18.55 Aligned_cols=14 Identities=14% Similarity=0.581 Sum_probs=9.4
Q ss_pred eecccccccccChh
Q psy64 60 FQCKVCDRAFFDVY 73 (115)
Q Consensus 60 ~~C~~c~~~~~~~~ 73 (115)
++|+.||..|...-
T Consensus 29 W~C~~Cgh~w~~~v 42 (55)
T PF14311_consen 29 WKCPKCGHEWKASV 42 (55)
T ss_pred EECCCCCCeeEccH
Confidence 57888876666554
No 201
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.26 E-value=5.2 Score=22.97 Aligned_cols=31 Identities=13% Similarity=0.032 Sum_probs=17.6
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCceeEEeecc
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKK 95 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 95 (115)
.+.| .||..|........+ . ...+.|+.||.
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~----~-~~~~~CP~Cgs 100 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDH----Y-AAVIECPVCGN 100 (124)
T ss_pred eEEe-eCcCcccccccchhc----c-ccCCcCcCCCC
Confidence 4689 999777654310000 0 01357999984
No 202
>PTZ00448 hypothetical protein; Provisional
Probab=48.10 E-value=5.4 Score=27.38 Aligned_cols=23 Identities=9% Similarity=-0.162 Sum_probs=20.5
Q ss_pred ceeEEeecceehhhhhhccCCcc
Q psy64 87 KYIFIVVKKIIVVIYAKKFSLDI 109 (115)
Q Consensus 87 ~~~C~~C~~~~~~~~~~~~h~~~ 109 (115)
.|.|..|+..|.+....+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 68899999999999999999875
No 203
>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=48.08 E-value=6.9 Score=17.24 Aligned_cols=13 Identities=15% Similarity=0.013 Sum_probs=8.3
Q ss_pred eeEEeecceehhh
Q psy64 88 YIFIVVKKIIVVI 100 (115)
Q Consensus 88 ~~C~~C~~~~~~~ 100 (115)
+.|+.||+.|...
T Consensus 2 r~C~~Cg~~Yh~~ 14 (36)
T PF05191_consen 2 RICPKCGRIYHIE 14 (36)
T ss_dssp EEETTTTEEEETT
T ss_pred cCcCCCCCccccc
Confidence 4677777776543
No 204
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=47.42 E-value=10 Score=18.60 Aligned_cols=40 Identities=18% Similarity=0.165 Sum_probs=21.5
Q ss_pred eecccccccccChhhHHHHHHHh-cCCCceeEEeecceehh
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIH-TGEKKYIFIVVKKIIVV 99 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h-~~~~~~~C~~C~~~~~~ 99 (115)
.+|..|++.+.-......-.+.- ..-..|.|+.|......
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~RI~~ 43 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKERIRE 43 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHHHhH
Confidence 36778887766543322222222 12345888888765443
No 205
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=47.41 E-value=9 Score=22.31 Aligned_cols=15 Identities=27% Similarity=0.656 Sum_probs=12.4
Q ss_pred CeecCCChhhccChh
Q psy64 17 PFVCNMCPSTFKLKK 31 (115)
Q Consensus 17 ~~~C~~C~~~~~~~~ 31 (115)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 678999999998654
No 206
>PLN02748 tRNA dimethylallyltransferase
Probab=47.37 E-value=5.3 Score=28.40 Aligned_cols=24 Identities=4% Similarity=-0.058 Sum_probs=20.7
Q ss_pred CceeEEeecc-eehhhhhhccCCcc
Q psy64 86 KKYIFIVVKK-IIVVIYAKKFSLDI 109 (115)
Q Consensus 86 ~~~~C~~C~~-~~~~~~~~~~h~~~ 109 (115)
+.|.|++|++ ++.....+..|++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 5689999997 89999999988874
No 207
>PRK12496 hypothetical protein; Provisional
Probab=47.00 E-value=14 Score=22.34 Aligned_cols=13 Identities=23% Similarity=0.534 Sum_probs=10.1
Q ss_pred CeecCCChhhccC
Q psy64 17 PFVCNMCPSTFKL 29 (115)
Q Consensus 17 ~~~C~~C~~~~~~ 29 (115)
.+.|.-|++.|..
T Consensus 127 ~~~C~gC~~~~~~ 139 (164)
T PRK12496 127 RKVCKGCKKKYPE 139 (164)
T ss_pred eEECCCCCccccC
Confidence 3779999988763
No 208
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=46.79 E-value=9.2 Score=25.28 Aligned_cols=23 Identities=9% Similarity=0.193 Sum_probs=16.5
Q ss_pred ecccccccccChhhHHHHHHHhcCCCceeEEeecceeh
Q psy64 61 QCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIV 98 (115)
Q Consensus 61 ~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 98 (115)
.|+.||. -..+.|.|+.||..+.
T Consensus 311 ~C~~cg~---------------~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 311 TCPCCGH---------------LSGRLFKCPRCGFVHD 333 (364)
T ss_pred cccccCC---------------ccceeEECCCCCCeeh
Confidence 5888886 2256789999997654
No 209
>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=46.06 E-value=4.2 Score=17.75 Aligned_cols=13 Identities=15% Similarity=-0.084 Sum_probs=5.1
Q ss_pred eEEeecceehhhh
Q psy64 89 IFIVVKKIIVVIY 101 (115)
Q Consensus 89 ~C~~C~~~~~~~~ 101 (115)
.|..|++.|..+.
T Consensus 5 ~C~eC~~~f~dSy 17 (34)
T PF01286_consen 5 KCDECGKPFMDSY 17 (34)
T ss_dssp E-TTT--EES-SS
T ss_pred hHhHhCCHHHHHH
Confidence 4556666665554
No 210
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=45.95 E-value=22 Score=23.22 Aligned_cols=11 Identities=36% Similarity=0.987 Sum_probs=7.7
Q ss_pred CCeecCCChhh
Q psy64 16 RPFVCNMCPST 26 (115)
Q Consensus 16 ~~~~C~~C~~~ 26 (115)
+-|.|..|+..
T Consensus 111 rqFaC~~Cd~~ 121 (278)
T PF15135_consen 111 RQFACSSCDHM 121 (278)
T ss_pred eeeeccccchH
Confidence 55888888544
No 211
>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=45.27 E-value=17 Score=21.39 Aligned_cols=21 Identities=10% Similarity=0.406 Sum_probs=15.9
Q ss_pred CCceecccccccccChhhHHH
Q psy64 57 IRDFQCKVCDRAFFDVYNLKL 77 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~~~~l~~ 77 (115)
+.-+.|+.||+.|..-+.+..
T Consensus 122 ~~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 122 DEFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred CeEEECCCCCCEecccccHHH
Confidence 346799999999988765543
No 212
>PRK05978 hypothetical protein; Provisional
Probab=45.04 E-value=5.1 Score=23.85 Aligned_cols=32 Identities=13% Similarity=-0.034 Sum_probs=20.7
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecceehhh
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVVI 100 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~ 100 (115)
-+||.||+.=...+.|+. .-.|+.||..|...
T Consensus 34 grCP~CG~G~LF~g~Lkv---------~~~C~~CG~~~~~~ 65 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKP---------VDHCAACGEDFTHH 65 (148)
T ss_pred CcCCCCCCCccccccccc---------CCCccccCCccccC
Confidence 379999976555444331 23789999877654
No 213
>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=44.24 E-value=15 Score=20.69 Aligned_cols=14 Identities=14% Similarity=0.420 Sum_probs=10.4
Q ss_pred ceecccccccccCh
Q psy64 59 DFQCKVCDRAFFDV 72 (115)
Q Consensus 59 ~~~C~~c~~~~~~~ 72 (115)
-|.|++|+..+...
T Consensus 19 ~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 19 QLICPSCLYEWNEN 32 (109)
T ss_pred eeECcccccccccc
Confidence 48899998776544
No 214
>KOG0717|consensus
Probab=43.74 E-value=11 Score=26.88 Aligned_cols=22 Identities=14% Similarity=-0.059 Sum_probs=19.0
Q ss_pred eeEEeecceehhhhhhccCCcc
Q psy64 88 YIFIVVKKIIVVIYAKKFSLDI 109 (115)
Q Consensus 88 ~~C~~C~~~~~~~~~~~~h~~~ 109 (115)
+-|.+|.++|.+...+.-|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999998888753
No 215
>PF04641 Rtf2: Rtf2 RING-finger
Probab=43.68 E-value=20 Score=23.33 Aligned_cols=14 Identities=21% Similarity=0.686 Sum_probs=9.8
Q ss_pred CCCeecCCChhhcc
Q psy64 15 DRPFVCNMCPSTFK 28 (115)
Q Consensus 15 ~~~~~C~~C~~~~~ 28 (115)
..+|.|++.++.|.
T Consensus 111 ~~~~~CPvt~~~~~ 124 (260)
T PF04641_consen 111 EGRFICPVTGKEFN 124 (260)
T ss_pred CceeECCCCCcccC
Confidence 45678888877763
No 216
>KOG4727|consensus
Probab=43.30 E-value=14 Score=22.65 Aligned_cols=26 Identities=8% Similarity=-0.120 Sum_probs=22.1
Q ss_pred ceeEEeecceehhhhhhccCCc--cccc
Q psy64 87 KYIFIVVKKIIVVIYAKKFSLD--IEIL 112 (115)
Q Consensus 87 ~~~C~~C~~~~~~~~~~~~h~~--~h~~ 112 (115)
-|=|.+|.-++..+-.+..||. .|++
T Consensus 75 GyyCdVCdcvvKDSinflDHiNgKkHqr 102 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHINGKKHQR 102 (193)
T ss_pred ceeeeecceeehhhHHHHHHhccHHHHH
Confidence 4889999999999999999986 4544
No 217
>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=42.44 E-value=55 Score=18.17 Aligned_cols=36 Identities=14% Similarity=0.121 Sum_probs=23.4
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCceeEEeecc
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKK 95 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 95 (115)
.|.|+.-|..|.+...+...+... ..+.|.|...|+
T Consensus 3 Vf~i~~T~EiF~dYe~Y~~R~~~y-~~~vwtC~~TGk 38 (102)
T PF10537_consen 3 VFYIPFTGEIFRDYEEYLKRMILY-NQRVWTCEITGK 38 (102)
T ss_pred eEEeCCCCcccCCHHHHHHHHHHH-hCCeeEEecCCC
Confidence 466777777777776655444333 357788887776
No 218
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=42.28 E-value=13 Score=16.61 Aligned_cols=10 Identities=10% Similarity=0.072 Sum_probs=7.1
Q ss_pred eeEEeeccee
Q psy64 88 YIFIVVKKII 97 (115)
Q Consensus 88 ~~C~~C~~~~ 97 (115)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 6777777665
No 219
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.03 E-value=15 Score=18.35 Aligned_cols=14 Identities=29% Similarity=0.890 Sum_probs=10.5
Q ss_pred CCeecCCChhhccC
Q psy64 16 RPFVCNMCPSTFKL 29 (115)
Q Consensus 16 ~~~~C~~C~~~~~~ 29 (115)
..-.|++|+..|+.
T Consensus 47 gev~CPYC~t~y~l 60 (62)
T COG4391 47 GEVVCPYCSTRYRL 60 (62)
T ss_pred CcEecCccccEEEe
Confidence 34569999988864
No 220
>KOG2923|consensus
Probab=41.81 E-value=15 Score=18.53 Aligned_cols=33 Identities=21% Similarity=0.359 Sum_probs=22.0
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecceeh
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIV 98 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 98 (115)
|.|+ ||-.|.-... ....|+..-.|+.|+....
T Consensus 23 yPCp-CGDrf~It~e-----dL~~ge~Va~CpsCSL~I~ 55 (67)
T KOG2923|consen 23 YPCP-CGDRFQITLE-----DLENGEDVARCPSCSLIIR 55 (67)
T ss_pred cCCC-CCCeeeecHH-----HHhCCCeeecCCCceEEEE
Confidence 4565 8877765542 2356788889998886544
No 221
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=41.65 E-value=24 Score=16.95 Aligned_cols=14 Identities=21% Similarity=0.349 Sum_probs=10.4
Q ss_pred cCCCceeccccccc
Q psy64 55 EKIRDFQCKVCDRA 68 (115)
Q Consensus 55 ~~~~~~~C~~c~~~ 68 (115)
.++....|+.||+.
T Consensus 42 ~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 42 KGDEIVFCPNCGRI 55 (56)
T ss_pred cCCCeEECcCCCcc
Confidence 34567799999864
No 222
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=41.52 E-value=13 Score=21.91 Aligned_cols=15 Identities=20% Similarity=0.408 Sum_probs=11.9
Q ss_pred CCceecccccccccC
Q psy64 57 IRDFQCKVCDRAFFD 71 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~ 71 (115)
.++..|++||..|.-
T Consensus 110 g~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 110 GKPQRCPECGQVFKL 124 (136)
T ss_dssp TSEEEETTTEEEEEE
T ss_pred CCccCCCCCCeEEEE
Confidence 458899999988764
No 223
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=40.95 E-value=16 Score=17.90 Aligned_cols=22 Identities=18% Similarity=0.357 Sum_probs=14.8
Q ss_pred CCCCCeecCCChhhcc-ChhhHH
Q psy64 13 TTDRPFVCNMCPSTFK-LKKHLR 34 (115)
Q Consensus 13 ~~~~~~~C~~C~~~~~-~~~~l~ 34 (115)
.+...|.|+.||..+. +...+.
T Consensus 10 ~~~v~~~Cp~cGipthcS~ehw~ 32 (55)
T PF13824_consen 10 PAHVNFECPDCGIPTHCSEEHWE 32 (55)
T ss_pred ccccCCcCCCCCCcCccCHHHHH
Confidence 3456799999997754 444443
No 224
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.59 E-value=6 Score=18.71 Aligned_cols=13 Identities=15% Similarity=-0.036 Sum_probs=8.8
Q ss_pred eEEeecceehhhh
Q psy64 89 IFIVVKKIIVVIY 101 (115)
Q Consensus 89 ~C~~C~~~~~~~~ 101 (115)
+|++|+..|.-+.
T Consensus 14 ICpvCqRPFsWRk 26 (54)
T COG4338 14 ICPVCQRPFSWRK 26 (54)
T ss_pred hhhhhcCchHHHH
Confidence 5777777776544
No 225
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=39.74 E-value=14 Score=15.90 Aligned_cols=12 Identities=8% Similarity=-0.053 Sum_probs=6.9
Q ss_pred ceeEEeecceeh
Q psy64 87 KYIFIVVKKIIV 98 (115)
Q Consensus 87 ~~~C~~C~~~~~ 98 (115)
-+.|..|+..|.
T Consensus 21 ~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 21 YEVCIFCGSSFP 32 (33)
T ss_pred eEEcccCCcEee
Confidence 356666666553
No 226
>PRK06260 threonine synthase; Validated
Probab=38.92 E-value=18 Score=25.00 Aligned_cols=11 Identities=18% Similarity=0.682 Sum_probs=8.7
Q ss_pred eecCCChhhcc
Q psy64 18 FVCNMCPSTFK 28 (115)
Q Consensus 18 ~~C~~C~~~~~ 28 (115)
++|..||..|.
T Consensus 4 ~~C~~cg~~~~ 14 (397)
T PRK06260 4 LKCIECGKEYD 14 (397)
T ss_pred EEECCCCCCCC
Confidence 67888888865
No 227
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=37.55 E-value=17 Score=16.05 Aligned_cols=12 Identities=17% Similarity=0.595 Sum_probs=6.5
Q ss_pred CCeecCCChhhc
Q psy64 16 RPFVCNMCPSTF 27 (115)
Q Consensus 16 ~~~~C~~C~~~~ 27 (115)
+.|+|..||...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 458899998653
No 228
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=37.10 E-value=19 Score=25.43 Aligned_cols=13 Identities=31% Similarity=0.649 Sum_probs=10.3
Q ss_pred CCeecCCChhhcc
Q psy64 16 RPFVCNMCPSTFK 28 (115)
Q Consensus 16 ~~~~C~~C~~~~~ 28 (115)
.-|.|+.||+.+.
T Consensus 6 t~f~C~~CG~~s~ 18 (456)
T COG1066 6 TAFVCQECGYVSP 18 (456)
T ss_pred cEEEcccCCCCCc
Confidence 4599999998844
No 229
>KOG2785|consensus
Probab=36.40 E-value=81 Score=22.06 Aligned_cols=64 Identities=22% Similarity=0.279 Sum_probs=39.9
Q ss_pred CCeecCCChhhccChhhHHHHHHHhcC-----------hhHHHHHHHHhhcCCCceeccccc---ccccChhhHHHHHHH
Q psy64 16 RPFVCNMCPSTFKLKKHLRQHYKVHLK-----------MDTLENHMKAVHEKIRDFQCKVCD---RAFFDVYNLKLHMRI 81 (115)
Q Consensus 16 ~~~~C~~C~~~~~~~~~l~~h~~~h~~-----------~~~l~~h~~~~h~~~~~~~C~~c~---~~~~~~~~l~~h~~~ 81 (115)
.|-.|-.|++.+.+...-..||..+++ ...|..=+... . ...+.|..|+ +.|..-...+.|+..
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeK-V-~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEK-V-GIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHH-h-ccCceEEEeccccCcccccHHHHHHHhh
Confidence 456799999999999999999987652 11111100000 1 1345777777 777777777777654
No 230
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.03 E-value=20 Score=20.27 Aligned_cols=15 Identities=13% Similarity=0.332 Sum_probs=12.2
Q ss_pred CCCCeecCCChhhcc
Q psy64 14 TDRPFVCNMCPSTFK 28 (115)
Q Consensus 14 ~~~~~~C~~C~~~~~ 28 (115)
+..|..|++||++|.
T Consensus 23 NrdPiVsPytG~s~P 37 (129)
T COG4530 23 NRDPIVSPYTGKSYP 37 (129)
T ss_pred CCCccccCcccccch
Confidence 356788999999984
No 231
>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=35.41 E-value=7.4 Score=19.02 Aligned_cols=15 Identities=13% Similarity=0.091 Sum_probs=4.9
Q ss_pred CceeEEeecceehhh
Q psy64 86 KKYIFIVVKKIIVVI 100 (115)
Q Consensus 86 ~~~~C~~C~~~~~~~ 100 (115)
+.|.|++||.+-...
T Consensus 32 r~y~Cp~CgAtGd~A 46 (55)
T PF05741_consen 32 RKYVCPICGATGDNA 46 (55)
T ss_dssp GG---TTT---GGG-
T ss_pred hcCcCCCCcCcCccc
Confidence 457888888765444
No 232
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=35.15 E-value=16 Score=23.46 Aligned_cols=18 Identities=11% Similarity=0.056 Sum_probs=14.4
Q ss_pred CCCceeEEeecceehhhh
Q psy64 84 GEKKYIFIVVKKIIVVIY 101 (115)
Q Consensus 84 ~~~~~~C~~C~~~~~~~~ 101 (115)
..++.+|..||..|....
T Consensus 178 EGkpqRCpECGqVFKLVr 195 (268)
T PTZ00043 178 EGFLYRCGECDQIFMLVR 195 (268)
T ss_pred CCCCccCCCCCcEEEEEE
Confidence 456899999999998643
No 233
>PRK10220 hypothetical protein; Provisional
Probab=35.02 E-value=28 Score=19.64 Aligned_cols=14 Identities=21% Similarity=0.627 Sum_probs=10.3
Q ss_pred ceecccccccccCh
Q psy64 59 DFQCKVCDRAFFDV 72 (115)
Q Consensus 59 ~~~C~~c~~~~~~~ 72 (115)
.|.|++|+.-+...
T Consensus 20 ~~vCpeC~hEW~~~ 33 (111)
T PRK10220 20 MYICPECAHEWNDA 33 (111)
T ss_pred eEECCcccCcCCcc
Confidence 48999998766544
No 234
>KOG0978|consensus
Probab=34.90 E-value=12 Score=28.04 Aligned_cols=45 Identities=13% Similarity=0.200 Sum_probs=25.1
Q ss_pred eecccccccccChhhHH-HH------HHHhcCCCceeEEeecceehhhhhhc
Q psy64 60 FQCKVCDRAFFDVYNLK-LH------MRIHTGEKKYIFIVVKKIIVVIYAKK 104 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~-~h------~~~h~~~~~~~C~~C~~~~~~~~~~~ 104 (115)
-.|+.|...+....-.. -| +++-.+.+.-+||.|+..|..-.-..
T Consensus 644 LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~ 695 (698)
T KOG0978|consen 644 LKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHR 695 (698)
T ss_pred eeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccc
Confidence 36888874444332111 11 22333445568999999998764433
No 235
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.88 E-value=18 Score=18.98 Aligned_cols=8 Identities=25% Similarity=1.182 Sum_probs=3.7
Q ss_pred eecccccc
Q psy64 60 FQCKVCDR 67 (115)
Q Consensus 60 ~~C~~c~~ 67 (115)
|+|.+||.
T Consensus 13 Y~c~~cg~ 20 (82)
T COG2331 13 YECTECGN 20 (82)
T ss_pred Eeecccch
Confidence 44555543
No 236
>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=34.50 E-value=18 Score=18.02 Aligned_cols=12 Identities=25% Similarity=0.700 Sum_probs=5.1
Q ss_pred eecccccccccC
Q psy64 60 FQCKVCDRAFFD 71 (115)
Q Consensus 60 ~~C~~c~~~~~~ 71 (115)
-.|..|++.|..
T Consensus 10 ~~C~~C~~~F~~ 21 (69)
T PF01363_consen 10 SNCMICGKKFSL 21 (69)
T ss_dssp SB-TTT--B-BS
T ss_pred CcCcCcCCcCCC
Confidence 367888888743
No 237
>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=34.30 E-value=21 Score=15.94 Aligned_cols=15 Identities=20% Similarity=0.791 Sum_probs=10.2
Q ss_pred CCceecccccccccC
Q psy64 57 IRDFQCKVCDRAFFD 71 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~ 71 (115)
...+.|+.||..+..
T Consensus 30 vp~~~C~~CGE~~~~ 44 (46)
T TIGR03831 30 VPALVCPQCGEEYLD 44 (46)
T ss_pred CCccccccCCCEeeC
Confidence 445678888876643
No 238
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=34.02 E-value=10 Score=20.92 Aligned_cols=36 Identities=11% Similarity=0.043 Sum_probs=21.0
Q ss_pred CCceecccccccccChhhHHHHHHHhcCCCceeEEeecceehh
Q psy64 57 IRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVV 99 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~ 99 (115)
...|.|+.||.. .-.-.+.. +.--..|.+||..+..
T Consensus 19 pt~f~CP~Cge~-~v~v~~~k------~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRCGKV-SISVKIKK------NIAIITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCCCCe-EeeeecCC------CcceEECCCCCCccCE
Confidence 356899999942 22111111 2233589999987655
No 239
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=33.80 E-value=14 Score=20.34 Aligned_cols=13 Identities=0% Similarity=-0.207 Sum_probs=9.2
Q ss_pred CCceeEEeeccee
Q psy64 85 EKKYIFIVVKKII 97 (115)
Q Consensus 85 ~~~~~C~~C~~~~ 97 (115)
.+..+|..||..|
T Consensus 86 ~r~~rC~nCG~~f 98 (98)
T PF10164_consen 86 MRERRCSNCGATF 98 (98)
T ss_pred cCccccCCCCccC
Confidence 4566788888765
No 240
>PRK00420 hypothetical protein; Validated
Probab=33.40 E-value=32 Score=19.52 Aligned_cols=15 Identities=13% Similarity=0.395 Sum_probs=10.5
Q ss_pred CceecccccccccCh
Q psy64 58 RDFQCKVCDRAFFDV 72 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~ 72 (115)
....|+.||....-.
T Consensus 39 g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 39 GEVVCPVHGKVYIVK 53 (112)
T ss_pred CceECCCCCCeeeec
Confidence 346899999866543
No 241
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=33.23 E-value=16 Score=21.87 Aligned_cols=26 Identities=15% Similarity=0.332 Sum_probs=15.9
Q ss_pred ecccccccccChhhHHHHHHHhcCCCceeEEeeccee
Q psy64 61 QCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKII 97 (115)
Q Consensus 61 ~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~ 97 (115)
.|+.|.+...... +..|.|+.|+...
T Consensus 36 aC~~C~kkv~~~~-----------~~~~~C~~C~~~~ 61 (166)
T cd04476 36 ACPGCNKKVVEEG-----------NGTYRCEKCNKSV 61 (166)
T ss_pred cccccCcccEeCC-----------CCcEECCCCCCcC
Confidence 5777765433221 1568888888764
No 242
>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=33.09 E-value=50 Score=14.25 Aligned_cols=23 Identities=17% Similarity=0.368 Sum_probs=14.6
Q ss_pred ceecccccccccChhhHHHHHHHh
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIH 82 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h 82 (115)
.+.|+.|++.... +.+..|+...
T Consensus 4 ~~~C~nC~R~v~a-~RfA~HLekC 26 (33)
T PF08209_consen 4 YVECPNCGRPVAA-SRFAPHLEKC 26 (33)
T ss_dssp EEE-TTTSSEEEG-GGHHHHHHHH
T ss_pred eEECCCCcCCcch-hhhHHHHHHH
Confidence 4689999986554 4566776554
No 243
>PF12773 DZR: Double zinc ribbon
Probab=33.00 E-value=14 Score=17.12 Aligned_cols=26 Identities=15% Similarity=0.125 Sum_probs=14.4
Q ss_pred ecccccccccChhhHHHHHHHhcCCCceeEEeeccee
Q psy64 61 QCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKII 97 (115)
Q Consensus 61 ~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~ 97 (115)
-|+.||.... ........|+.|+...
T Consensus 14 fC~~CG~~l~-----------~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 14 FCPHCGTPLP-----------PPDQSKKICPNCGAEN 39 (50)
T ss_pred CChhhcCChh-----------hccCCCCCCcCCcCCC
Confidence 4677765444 2223345677777653
No 244
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=32.71 E-value=21 Score=19.85 Aligned_cols=15 Identities=33% Similarity=0.569 Sum_probs=12.2
Q ss_pred ceecccccccccChh
Q psy64 59 DFQCKVCDRAFFDVY 73 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~ 73 (115)
|.+|..||..|..-+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 678999999998754
No 245
>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 KOG1842|consensus
Probab=32.49 E-value=28 Score=24.81 Aligned_cols=25 Identities=20% Similarity=0.503 Sum_probs=21.7
Q ss_pred CceecccccccccChhhHHHHHHHh
Q psy64 58 RDFQCKVCDRAFFDVYNLKLHMRIH 82 (115)
Q Consensus 58 ~~~~C~~c~~~~~~~~~l~~h~~~h 82 (115)
..|.||.|...|.....|..|....
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~e 38 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVE 38 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhh
Confidence 4689999999999999999997753
No 247
>PRK11032 hypothetical protein; Provisional
Probab=32.47 E-value=18 Score=21.94 Aligned_cols=9 Identities=33% Similarity=0.973 Sum_probs=5.4
Q ss_pred eecCCChhh
Q psy64 18 FVCNMCPST 26 (115)
Q Consensus 18 ~~C~~C~~~ 26 (115)
..|..||..
T Consensus 125 LvC~~Cg~~ 133 (160)
T PRK11032 125 LVCEKCHHH 133 (160)
T ss_pred EEecCCCCE
Confidence 556666654
No 248
>KOG0782|consensus
Probab=32.32 E-value=14 Score=27.26 Aligned_cols=30 Identities=10% Similarity=-0.023 Sum_probs=19.8
Q ss_pred hhhHHHHHHHhcCCCceeEEeecceehhhh
Q psy64 72 VYNLKLHMRIHTGEKKYIFIVVKKIIVVIY 101 (115)
Q Consensus 72 ~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~ 101 (115)
.+.+.+|...|..-.--+|..|+|.|.++.
T Consensus 238 E~~fvrHHWVHrrRqeGkC~~CgKgFQQKf 267 (1004)
T KOG0782|consen 238 ESGFVRHHWVHRRRQEGKCNTCGKGFQQKF 267 (1004)
T ss_pred cccchHHhHhhHhhhccccchhhhhhhhhe
Confidence 346666666665444457888888888773
No 249
>PRK12860 transcriptional activator FlhC; Provisional
Probab=31.90 E-value=18 Score=22.57 Aligned_cols=27 Identities=15% Similarity=0.354 Sum_probs=18.1
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeec
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVK 94 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~ 94 (115)
..|..||-.|.... +.....|.|+.|.
T Consensus 135 ~~C~~Cgg~fv~~~--------~e~~~~f~CplC~ 161 (189)
T PRK12860 135 ARCCRCGGKFVTHA--------HDLRHNFVCGLCQ 161 (189)
T ss_pred ccCCCCCCCeeccc--------cccCCCCcCCCCC
Confidence 46888887776442 2334578999887
No 250
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=31.78 E-value=12 Score=19.11 Aligned_cols=15 Identities=33% Similarity=0.319 Sum_probs=8.2
Q ss_pred CCCceeEEeecceehh
Q psy64 84 GEKKYIFIVVKKIIVV 99 (115)
Q Consensus 84 ~~~~~~C~~C~~~~~~ 99 (115)
+.+--.| +||++..-
T Consensus 17 ~~kTkkC-~CG~~l~v 31 (68)
T PF09082_consen 17 GAKTKKC-VCGKTLKV 31 (68)
T ss_dssp T-SEEEE-TTTEEEE-
T ss_pred CcceeEe-cCCCeeee
Confidence 3444577 77776543
No 251
>KOG2906|consensus
Probab=31.56 E-value=12 Score=20.68 Aligned_cols=15 Identities=0% Similarity=0.044 Sum_probs=9.7
Q ss_pred ceeEEeecceehhhh
Q psy64 87 KYIFIVVKKIIVVIY 101 (115)
Q Consensus 87 ~~~C~~C~~~~~~~~ 101 (115)
.|.|..|++.|....
T Consensus 21 rf~C~tCpY~~~I~~ 35 (105)
T KOG2906|consen 21 RFSCRTCPYVFPISR 35 (105)
T ss_pred eEEcCCCCceeeEee
Confidence 467777777766553
No 252
>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=31.37 E-value=6.3 Score=17.39 Aligned_cols=30 Identities=17% Similarity=0.359 Sum_probs=17.3
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEee
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVV 93 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C 93 (115)
..||.|+..- ....|-....|...|.|-.|
T Consensus 6 v~CP~C~s~~----~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQSTE----GVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCCC----cceeCCCCCCCCEeEecCcC
Confidence 4677776322 13344445566677888776
No 253
>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=31.30 E-value=23 Score=16.75 Aligned_cols=11 Identities=36% Similarity=1.053 Sum_probs=4.9
Q ss_pred eeccccccccc
Q psy64 60 FQCKVCDRAFF 70 (115)
Q Consensus 60 ~~C~~c~~~~~ 70 (115)
+.|..||+.|-
T Consensus 19 ~~Cr~Cg~~~C 29 (57)
T cd00065 19 HHCRNCGRIFC 29 (57)
T ss_pred cccCcCcCCcC
Confidence 34444444443
No 254
>KOG1088|consensus
Probab=31.28 E-value=21 Score=20.37 Aligned_cols=25 Identities=8% Similarity=0.074 Sum_probs=19.3
Q ss_pred HHHhcCCCceeEEeecceehhhhhh
Q psy64 79 MRIHTGEKKYIFIVVKKIIVVIYAK 103 (115)
Q Consensus 79 ~~~h~~~~~~~C~~C~~~~~~~~~~ 103 (115)
..++..|..-+|+.||..|+-+.++
T Consensus 90 le~~v~EG~l~CpetG~vfpI~~GI 114 (124)
T KOG1088|consen 90 LEIDVIEGELVCPETGRVFPISDGI 114 (124)
T ss_pred hhhhhccceEecCCCCcEeecccCC
Confidence 4456677788999999999877654
No 255
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=30.74 E-value=12 Score=28.18 Aligned_cols=11 Identities=18% Similarity=0.628 Sum_probs=8.4
Q ss_pred Cceeccccccc
Q psy64 58 RDFQCKVCDRA 68 (115)
Q Consensus 58 ~~~~C~~c~~~ 68 (115)
.|..|+.||-.
T Consensus 172 Qp~aCp~CGP~ 182 (750)
T COG0068 172 QPIACPKCGPH 182 (750)
T ss_pred ccccCcccCCC
Confidence 36789999963
No 256
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=30.23 E-value=22 Score=23.80 Aligned_cols=16 Identities=13% Similarity=0.125 Sum_probs=10.5
Q ss_pred ceecccccccccChhh
Q psy64 59 DFQCKVCDRAFFDVYN 74 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~ 74 (115)
-+.|+.||..|.-...
T Consensus 57 ~~vcp~c~~h~rltAr 72 (296)
T CHL00174 57 MNICEQCGYHLKMSSS 72 (296)
T ss_pred CCCCCCCCCCcCCCHH
Confidence 3578888876665543
No 257
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=30.19 E-value=24 Score=14.99 Aligned_cols=11 Identities=27% Similarity=0.326 Sum_probs=6.5
Q ss_pred ceeEEeeccee
Q psy64 87 KYIFIVVKKII 97 (115)
Q Consensus 87 ~~~C~~C~~~~ 97 (115)
-|+|..|+...
T Consensus 7 ~ykC~~Cgniv 17 (34)
T TIGR00319 7 VYKCEVCGNIV 17 (34)
T ss_pred EEEcCCCCcEE
Confidence 46666666544
No 258
>PRK12722 transcriptional activator FlhC; Provisional
Probab=29.93 E-value=21 Score=22.25 Aligned_cols=28 Identities=11% Similarity=0.295 Sum_probs=18.9
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecc
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKK 95 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 95 (115)
..|..||-.|..... .....|.|+.|.-
T Consensus 135 ~~C~~Cgg~fv~~~~--------e~~~~f~CplC~~ 162 (187)
T PRK12722 135 SSCNCCGGHFVTHAH--------DPVGSFVCGLCQP 162 (187)
T ss_pred ccCCCCCCCeecccc--------ccCCCCcCCCCCC
Confidence 358888877774432 3345789999875
No 259
>PLN03239 histone acetyltransferase; Provisional
Probab=29.43 E-value=15 Score=25.12 Aligned_cols=24 Identities=4% Similarity=-0.205 Sum_probs=21.2
Q ss_pred CCceeEEeecceehhhhhhccCCc
Q psy64 85 EKKYIFIVVKKIIVVIYAKKFSLD 108 (115)
Q Consensus 85 ~~~~~C~~C~~~~~~~~~~~~h~~ 108 (115)
+..|.|+.|-+-|.+...+.+|+.
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHH
Confidence 568999999999999999988864
No 260
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=29.42 E-value=8.7 Score=19.02 Aligned_cols=14 Identities=0% Similarity=-0.005 Sum_probs=6.4
Q ss_pred CceeEEeecceehh
Q psy64 86 KKYIFIVVKKIIVV 99 (115)
Q Consensus 86 ~~~~C~~C~~~~~~ 99 (115)
..|.|..|++.+-.
T Consensus 10 ~lw~CL~Cg~~~C~ 23 (63)
T PF02148_consen 10 NLWLCLTCGYVGCG 23 (63)
T ss_dssp SEEEETTTS-EEET
T ss_pred ceEEeCCCCccccc
Confidence 34555555554444
No 261
>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=29.06 E-value=25 Score=14.93 Aligned_cols=11 Identities=18% Similarity=0.316 Sum_probs=6.7
Q ss_pred ceeEEeeccee
Q psy64 87 KYIFIVVKKII 97 (115)
Q Consensus 87 ~~~C~~C~~~~ 97 (115)
-|+|..|+...
T Consensus 4 ~ykC~~CGniv 14 (34)
T cd00974 4 VYKCEICGNIV 14 (34)
T ss_pred EEEcCCCCcEE
Confidence 46666666544
No 262
>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=28.38 E-value=14 Score=17.49 Aligned_cols=8 Identities=13% Similarity=0.239 Sum_probs=2.7
Q ss_pred eeEEeecc
Q psy64 88 YIFIVVKK 95 (115)
Q Consensus 88 ~~C~~C~~ 95 (115)
|.|++|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 66666654
No 263
>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=28.14 E-value=26 Score=23.34 Aligned_cols=15 Identities=20% Similarity=0.233 Sum_probs=10.3
Q ss_pred eecccccccccChhh
Q psy64 60 FQCKVCDRAFFDVYN 74 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~ 74 (115)
+.|+.||.-|.-...
T Consensus 46 ~vc~~c~~h~rl~ar 60 (285)
T TIGR00515 46 EVCPKCDHHMRMDAR 60 (285)
T ss_pred CCCCCCCCcCcCCHH
Confidence 578888877665443
No 264
>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=27.80 E-value=47 Score=20.81 Aligned_cols=41 Identities=15% Similarity=0.120 Sum_probs=23.2
Q ss_pred hhcCCCceecccccccccChhhHHHHHHHhcCCCceeEEeecce
Q psy64 53 VHEKIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKI 96 (115)
Q Consensus 53 ~h~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 96 (115)
.|..-....|..|+..+....... .....+..-.|+.|+..
T Consensus 89 lHG~~~~~~C~~C~~~~~~~~~~~---~~~~~~~~p~C~~Cgg~ 129 (206)
T cd01410 89 LHGNMFIEVCKSCGPEYVRDDVVE---TRGDKETGRRCHACGGI 129 (206)
T ss_pred ecCCcCcccCCCCCCccchHHHHH---HhhcCCCCCcCCCCcCc
Confidence 344455567999997765443221 11223334579999854
No 265
>PRK07218 replication factor A; Provisional
Probab=27.77 E-value=23 Score=25.03 Aligned_cols=21 Identities=14% Similarity=0.183 Sum_probs=14.9
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecce
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKI 96 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 96 (115)
..||.|++.... +.|+.||+.
T Consensus 298 ~rCP~C~r~v~~----------------~~C~~hG~v 318 (423)
T PRK07218 298 ERCPECGRVIQK----------------GQCRSHGAV 318 (423)
T ss_pred ecCcCccccccC----------------CcCCCCCCc
Confidence 479999876522 678777764
No 266
>KOG0696|consensus
Probab=27.47 E-value=11 Score=26.81 Aligned_cols=39 Identities=18% Similarity=0.170 Sum_probs=20.0
Q ss_pred ceecccccccccChhhHHHH-HHHhcCCCceeEEeeccee
Q psy64 59 DFQCKVCDRAFFDVYNLKLH-MRIHTGEKKYIFIVVKKII 97 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h-~~~h~~~~~~~C~~C~~~~ 97 (115)
.|.|+--++.+.....-..| ...|+-..|--|..||...
T Consensus 92 tF~CPGadkg~dtDdpr~kHkf~~~tYssPTFCDhCGsLL 131 (683)
T KOG0696|consen 92 TFSCPGADKGPDTDDPRSKHKFKIHTYSSPTFCDHCGSLL 131 (683)
T ss_pred EEECCCCCCCCCCCCcccccceeeeecCCCchhhhHHHHH
Confidence 35566555555554443334 3345555555566665443
No 267
>PHA02942 putative transposase; Provisional
Probab=26.99 E-value=37 Score=23.59 Aligned_cols=27 Identities=7% Similarity=0.139 Sum_probs=18.0
Q ss_pred ecccccccccChhhHHHHHHHhcCCCceeEEeecceeh
Q psy64 61 QCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIV 98 (115)
Q Consensus 61 ~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 98 (115)
.|+.||..-. ....+.|.|+.||....
T Consensus 327 ~Cs~CG~~~~-----------~l~~r~f~C~~CG~~~d 353 (383)
T PHA02942 327 SCPKCGHKMV-----------EIAHRYFHCPSCGYEND 353 (383)
T ss_pred cCCCCCCccC-----------cCCCCEEECCCCCCEeC
Confidence 5888885321 11346799999998653
No 268
>PTZ00064 histone acetyltransferase; Provisional
Probab=26.00 E-value=17 Score=26.26 Aligned_cols=25 Identities=4% Similarity=-0.217 Sum_probs=22.2
Q ss_pred CCCceeEEeecceehhhhhhccCCc
Q psy64 84 GEKKYIFIVVKKIIVVIYAKKFSLD 108 (115)
Q Consensus 84 ~~~~~~C~~C~~~~~~~~~~~~h~~ 108 (115)
-+..|.|+.|-+-|.....+.+|+.
T Consensus 277 ~d~LYICEfCLkY~~s~~~l~rH~~ 301 (552)
T PTZ00064 277 VDTLHFCEYCLDFFCFEDELIRHLS 301 (552)
T ss_pred CCeEEEccchhhhhCCHHHHHHHHh
Confidence 4567999999999999999999975
No 269
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=25.93 E-value=25 Score=23.49 Aligned_cols=16 Identities=13% Similarity=0.079 Sum_probs=11.7
Q ss_pred ceecccccccccChhh
Q psy64 59 DFQCKVCDRAFFDVYN 74 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~ 74 (115)
-+.|+.||.-|.-...
T Consensus 46 ~~vc~~c~~h~rl~ar 61 (292)
T PRK05654 46 LNVCPKCGHHMRISAR 61 (292)
T ss_pred CCCCCCCCCCeeCCHH
Confidence 3589999988875544
No 270
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=25.86 E-value=12 Score=25.66 Aligned_cols=44 Identities=14% Similarity=0.270 Sum_probs=21.1
Q ss_pred CCceecccccccccChhhHHHH----HHHhcCCCc-eeEEeecceehhh
Q psy64 57 IRDFQCKVCDRAFFDVYNLKLH----MRIHTGEKK-YIFIVVKKIIVVI 100 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~~~~l~~h----~~~h~~~~~-~~C~~C~~~~~~~ 100 (115)
.+.+.|..|.+........-.- +..+...+. |.|..|++....-
T Consensus 250 ~kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~sl 298 (344)
T PF09332_consen 250 CKAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTISL 298 (344)
T ss_dssp EEEEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEEES
T ss_pred EEEEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeeeec
Confidence 4578899998776666543211 112334444 7899999876543
No 271
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=25.81 E-value=16 Score=26.00 Aligned_cols=25 Identities=12% Similarity=0.001 Sum_probs=21.6
Q ss_pred CCCceeEEeecceehhhhhhccCCc
Q psy64 84 GEKKYIFIVVKKIIVVIYAKKFSLD 108 (115)
Q Consensus 84 ~~~~~~C~~C~~~~~~~~~~~~h~~ 108 (115)
.+..|.|+.|-+-|.....+.+|+.
T Consensus 195 ~~~lyiCe~Cl~y~~~~~~~~~H~~ 219 (450)
T PLN00104 195 CSKLYFCEFCLKFMKRKEQLQRHMK 219 (450)
T ss_pred CCeEEEchhhhhhhcCHHHHHHHHh
Confidence 4567999999999999999999875
No 272
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=25.64 E-value=34 Score=15.45 Aligned_cols=10 Identities=40% Similarity=0.776 Sum_probs=7.1
Q ss_pred CeecCCChhh
Q psy64 17 PFVCNMCPST 26 (115)
Q Consensus 17 ~~~C~~C~~~ 26 (115)
|..|+.||..
T Consensus 2 ~~~Cp~Cg~~ 11 (47)
T PF14690_consen 2 PPRCPHCGSP 11 (47)
T ss_pred CccCCCcCCC
Confidence 5678888843
No 273
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=25.18 E-value=27 Score=21.41 Aligned_cols=19 Identities=0% Similarity=-0.323 Sum_probs=14.7
Q ss_pred CCceeEEeecceehhhhhh
Q psy64 85 EKKYIFIVVKKIIVVIYAK 103 (115)
Q Consensus 85 ~~~~~C~~C~~~~~~~~~~ 103 (115)
.....|..||+.|.....+
T Consensus 112 ~~~~~C~~Cg~~f~~~k~i 130 (181)
T PRK08222 112 FHLQRCSRCERPFAPQKTV 130 (181)
T ss_pred cccCcCcccCCccCcHhHH
Confidence 4578899999999865544
No 274
>PRK06450 threonine synthase; Validated
Probab=25.08 E-value=33 Score=23.31 Aligned_cols=30 Identities=7% Similarity=-0.013 Sum_probs=18.3
Q ss_pred eecccccccccChhhHHHHHHHhcCCCceeEEeecceehhhhh
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVVIYA 102 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~ 102 (115)
++|..||+.|.. +-.|.|+.|+..+.-..+
T Consensus 4 ~~C~~Cg~~~~~-------------~~~~~C~~cg~~l~~~~d 33 (338)
T PRK06450 4 EVCMKCGKERES-------------IYEIRCKKCGGPFEILID 33 (338)
T ss_pred eEECCcCCcCCC-------------cccccCCcCCCEeEEeec
Confidence 678888876521 223678778765555443
No 275
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=24.85 E-value=52 Score=20.07 Aligned_cols=22 Identities=9% Similarity=0.398 Sum_probs=16.2
Q ss_pred CCceecccccccccChhhHHHH
Q psy64 57 IRDFQCKVCDRAFFDVYNLKLH 78 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~~~~l~~h 78 (115)
..-+.|+.||+.|..-+.+..-
T Consensus 128 ~~f~~C~~CgkiYW~GsHw~~m 149 (165)
T COG1656 128 EEFYRCPKCGKIYWKGSHWRRM 149 (165)
T ss_pred cceeECCCCcccccCchHHHHH
Confidence 3456899999999887665433
No 276
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.66 E-value=34 Score=22.74 Aligned_cols=10 Identities=10% Similarity=0.431 Sum_probs=4.5
Q ss_pred eeEEeeccee
Q psy64 88 YIFIVVKKII 97 (115)
Q Consensus 88 ~~C~~C~~~~ 97 (115)
|.|++|.-.|
T Consensus 256 yvCs~Clsi~ 265 (279)
T TIGR00627 256 FVCSVCLSVL 265 (279)
T ss_pred EECCCccCCc
Confidence 4444444433
No 277
>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=24.58 E-value=6.7 Score=17.75 Aligned_cols=30 Identities=27% Similarity=0.406 Sum_probs=14.1
Q ss_pred ecccccccccChhhHHHHHHHhcCC-CceeEEeecce
Q psy64 61 QCKVCDRAFFDVYNLKLHMRIHTGE-KKYIFIVVKKI 96 (115)
Q Consensus 61 ~C~~c~~~~~~~~~l~~h~~~h~~~-~~~~C~~C~~~ 96 (115)
.|..||+.-.....|. .|. ..|.|+.|-..
T Consensus 3 ~CSFCgr~~~~v~~li------~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLI------SGPNGAYICDECVEQ 33 (41)
T ss_dssp B-TTT--BTTTSSSEE------EES-SEEEEHHHHHH
T ss_pred CccCCCCCHHHHhcee------cCCCCcEECHHHHHH
Confidence 4666776555443331 233 46777776543
No 278
>PF12907 zf-met2: Zinc-binding
Probab=24.47 E-value=39 Score=15.32 Aligned_cols=22 Identities=32% Similarity=0.647 Sum_probs=12.9
Q ss_pred eecccccccccC---hhhHHHHHHH
Q psy64 60 FQCKVCDRAFFD---VYNLKLHMRI 81 (115)
Q Consensus 60 ~~C~~c~~~~~~---~~~l~~h~~~ 81 (115)
+.|..|-..|.. ...|..|...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~en 26 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAEN 26 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHc
Confidence 467777744443 3457777654
No 279
>PRK07591 threonine synthase; Validated
Probab=24.16 E-value=47 Score=23.35 Aligned_cols=12 Identities=17% Similarity=0.717 Sum_probs=9.7
Q ss_pred CeecCCChhhcc
Q psy64 17 PFVCNMCPSTFK 28 (115)
Q Consensus 17 ~~~C~~C~~~~~ 28 (115)
-++|..||..|.
T Consensus 18 ~l~C~~Cg~~~~ 29 (421)
T PRK07591 18 ALKCRECGAEYP 29 (421)
T ss_pred EEEeCCCCCcCC
Confidence 478999998875
No 280
>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=24.13 E-value=52 Score=20.87 Aligned_cols=38 Identities=11% Similarity=0.049 Sum_probs=21.4
Q ss_pred hcCCCceecccccccccChhhHHHHHHHhcCCCceeEEeecce
Q psy64 54 HEKIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKI 96 (115)
Q Consensus 54 h~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 96 (115)
|..-....|..|+..+..... .....+..-.|+.|+..
T Consensus 108 HG~l~~~~C~~C~~~~~~~~~-----~~~~~~~~p~C~~Cgg~ 145 (222)
T cd01413 108 HGTLQTAYCVNCGSKYDLEEV-----KYAKKHEVPRCPKCGGI 145 (222)
T ss_pred cCCcCcceECCCCCCcchhHH-----HHhccCCCCcCCCCCCc
Confidence 444445679889887665432 11111234478888753
No 281
>KOG1984|consensus
Probab=24.03 E-value=24 Score=27.40 Aligned_cols=45 Identities=18% Similarity=0.191 Sum_probs=28.8
Q ss_pred CCceecccccccccChhhHHHHHHHhcCCCceeEEeecceehhhhhhccCC
Q psy64 57 IRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVVIYAKKFSL 107 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~~~~h~ 107 (115)
..|.+|.-|. ++..--++.-.+.+.|.|+.|+..-....+...|+
T Consensus 336 sgPvRC~RCk------aYinPFmqF~~~gr~f~Cn~C~~~n~vp~~yf~~L 380 (1007)
T KOG1984|consen 336 SGPVRCNRCK------AYINPFMQFIDGGRKFICNFCGSKNQVPDDYFNHL 380 (1007)
T ss_pred CCCcchhhhh------hhcCcceEEecCCceEEecCCCccccCChhhcccC
Confidence 3466677662 22222344556677899999998877776665555
No 282
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=23.75 E-value=39 Score=16.22 Aligned_cols=38 Identities=11% Similarity=0.079 Sum_probs=24.4
Q ss_pred ecc--cccccccChhhHHHHHHHhcCCCceeEEeecceehhhhhhccC
Q psy64 61 QCK--VCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKIIVVIYAKKFS 106 (115)
Q Consensus 61 ~C~--~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~~~~h 106 (115)
.|+ .|+....... ..+.....|+.|+..|-..-....|
T Consensus 20 ~CP~~~C~~~~~~~~--------~~~~~~v~C~~C~~~fC~~C~~~~H 59 (64)
T smart00647 20 WCPAPDCSAAIIVTE--------EEGCNRVTCPKCGFSFCFRCKVPWH 59 (64)
T ss_pred CCCCCCCcceEEecC--------CCCCCeeECCCCCCeECCCCCCcCC
Confidence 477 7876655432 2345567888899888766554444
No 283
>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=23.65 E-value=14 Score=26.88 Aligned_cols=42 Identities=17% Similarity=0.082 Sum_probs=23.7
Q ss_pred ceecccccccccCh-hhHHHHHHHhcCCCceeEEeecceehhh
Q psy64 59 DFQCKVCDRAFFDV-YNLKLHMRIHTGEKKYIFIVVKKIIVVI 100 (115)
Q Consensus 59 ~~~C~~c~~~~~~~-~~l~~h~~~h~~~~~~~C~~C~~~~~~~ 100 (115)
-.+||.||..+.-. ..+.-....-...-.|+|+.||......
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~ 242 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEH 242 (557)
T ss_pred EccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHH
Confidence 34899999877644 2222100001112349999999877653
No 284
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=23.54 E-value=43 Score=16.03 Aligned_cols=11 Identities=0% Similarity=-0.224 Sum_probs=9.3
Q ss_pred ceeEEeeccee
Q psy64 87 KYIFIVVKKII 97 (115)
Q Consensus 87 ~~~C~~C~~~~ 97 (115)
.|.|..||++-
T Consensus 37 R~~CGkCgyTe 47 (51)
T COG1998 37 RWACGKCGYTE 47 (51)
T ss_pred eeEeccccceE
Confidence 78999999874
No 285
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=23.11 E-value=32 Score=16.57 Aligned_cols=12 Identities=25% Similarity=0.553 Sum_probs=8.3
Q ss_pred ecccccccccCh
Q psy64 61 QCKVCDRAFFDV 72 (115)
Q Consensus 61 ~C~~c~~~~~~~ 72 (115)
.||.||..+...
T Consensus 2 ~CPyCge~~~~~ 13 (52)
T PF14255_consen 2 QCPYCGEPIEIL 13 (52)
T ss_pred CCCCCCCeeEEE
Confidence 588888766543
No 286
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.06 E-value=64 Score=16.19 Aligned_cols=8 Identities=13% Similarity=0.285 Sum_probs=4.2
Q ss_pred eeEEeecc
Q psy64 88 YIFIVVKK 95 (115)
Q Consensus 88 ~~C~~C~~ 95 (115)
|.|+.|.-
T Consensus 32 ymC~eC~~ 39 (68)
T COG4896 32 YMCPECEH 39 (68)
T ss_pred EechhhHh
Confidence 55555544
No 287
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=22.80 E-value=55 Score=15.18 Aligned_cols=30 Identities=17% Similarity=0.382 Sum_probs=17.3
Q ss_pred CCceecccccccccChhhHHHHHHHhcCCCceeEEeeccee
Q psy64 57 IRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKII 97 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~ 97 (115)
.+|-.|..|++.... .+...|.|..|+...
T Consensus 9 ~~~~~C~~C~~~i~g-----------~~~~g~~C~~C~~~~ 38 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWG-----------LGKQGYRCSWCGLVC 38 (53)
T ss_dssp SSTEB-TTSSSBECS-----------SSSCEEEETTTT-EE
T ss_pred CCCCCCcccCcccCC-----------CCCCeEEECCCCChH
Confidence 456678888876511 234457888877654
No 288
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=22.79 E-value=29 Score=14.53 Aligned_cols=11 Identities=18% Similarity=-0.040 Sum_probs=4.0
Q ss_pred ceeEEeeccee
Q psy64 87 KYIFIVVKKII 97 (115)
Q Consensus 87 ~~~C~~C~~~~ 97 (115)
.|.|+.|+..+
T Consensus 13 kY~Cp~C~~~~ 23 (30)
T PF04438_consen 13 KYRCPRCGARY 23 (30)
T ss_dssp SEE-TTT--EE
T ss_pred EEECCCcCCce
Confidence 35555555443
No 289
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=22.42 E-value=63 Score=20.88 Aligned_cols=40 Identities=8% Similarity=0.157 Sum_probs=22.4
Q ss_pred hhcCCCceecccccccccChhhHHHHHHHhcCCCceeEEeecce
Q psy64 53 VHEKIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKI 96 (115)
Q Consensus 53 ~h~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 96 (115)
.|..-....|..|++.+....... .-.....-.|+.|+..
T Consensus 113 lHG~~~~~~C~~C~~~~~~~~~~~----~~~~~~~p~Cp~Cgg~ 152 (244)
T PRK14138 113 LHGNVEEYYCVRCGKRYTVEDVIE----KLEKSDVPRCDDCSGL 152 (244)
T ss_pred ccCCcCeeEECCCCCcccHHHHHH----HHhcCCCCCCCCCCCe
Confidence 344445567989998776543332 1111223468888753
No 290
>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=22.21 E-value=26 Score=20.88 Aligned_cols=12 Identities=0% Similarity=-0.108 Sum_probs=8.7
Q ss_pred eeEEeecceehh
Q psy64 88 YIFIVVKKIIVV 99 (115)
Q Consensus 88 ~~C~~C~~~~~~ 99 (115)
-.|..|++.|+.
T Consensus 29 ReC~~C~~RFTT 40 (147)
T TIGR00244 29 RECLECHERFTT 40 (147)
T ss_pred ccCCccCCccce
Confidence 467788887765
No 291
>KOG3352|consensus
Probab=21.99 E-value=41 Score=20.15 Aligned_cols=14 Identities=21% Similarity=0.418 Sum_probs=9.8
Q ss_pred CCceeccccccccc
Q psy64 57 IRDFQCKVCDRAFF 70 (115)
Q Consensus 57 ~~~~~C~~c~~~~~ 70 (115)
.+..+|++||..|.
T Consensus 131 ge~~rc~eCG~~fk 144 (153)
T KOG3352|consen 131 GETQRCPECGHYFK 144 (153)
T ss_pred CCcccCCcccceEE
Confidence 34567888887665
No 292
>KOG2747|consensus
Probab=21.73 E-value=20 Score=25.03 Aligned_cols=27 Identities=19% Similarity=0.043 Sum_probs=19.9
Q ss_pred cCCCceeEEeecceehhhhhhccCCcc
Q psy64 83 TGEKKYIFIVVKKIIVVIYAKKFSLDI 109 (115)
Q Consensus 83 ~~~~~~~C~~C~~~~~~~~~~~~h~~~ 109 (115)
...+.|.|+.|-+-+.++..|.+|++.
T Consensus 154 ~~~~lYiCEfCLkY~~s~~~l~rH~~k 180 (396)
T KOG2747|consen 154 KLDKLYICEFCLKYMKSRTSLQRHLKK 180 (396)
T ss_pred cCCeEEEehHHHhHhchHHHHHHHHHh
Confidence 345668888888888888888877653
No 293
>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=21.54 E-value=16 Score=24.52 Aligned_cols=37 Identities=19% Similarity=0.238 Sum_probs=20.5
Q ss_pred ceecccccccccChhhHHHHHHHhcCCCc---eeEEeecceeh
Q psy64 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKK---YIFIVVKKIIV 98 (115)
Q Consensus 59 ~~~C~~c~~~~~~~~~l~~h~~~h~~~~~---~~C~~C~~~~~ 98 (115)
.+.|+.||..=.....+ ..+ ...|.+ |.|..|+..+.
T Consensus 258 ~~~C~~C~~~~~~~~q~--Qtr-saDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQL--QTR-SADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccCCCCCCccceEEEe--ccc-CCCCCCeEEEEcCCCCCeee
Confidence 48999998433322221 111 222322 79999997654
No 294
>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=21.44 E-value=72 Score=17.32 Aligned_cols=19 Identities=16% Similarity=0.429 Sum_probs=14.1
Q ss_pred CCceecccccccccChhhH
Q psy64 57 IRDFQCKVCDRAFFDVYNL 75 (115)
Q Consensus 57 ~~~~~C~~c~~~~~~~~~l 75 (115)
.....|+.||..|....-.
T Consensus 33 VPa~~C~~CGe~y~~dev~ 51 (89)
T TIGR03829 33 TPSISCSHCGMEYQDDTTV 51 (89)
T ss_pred CCcccccCCCcEeecHHHH
Confidence 4456899999988876544
No 295
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=21.39 E-value=34 Score=20.86 Aligned_cols=19 Identities=11% Similarity=-0.209 Sum_probs=14.5
Q ss_pred CCceeEEeecceehhhhhh
Q psy64 85 EKKYIFIVVKKIIVVIYAK 103 (115)
Q Consensus 85 ~~~~~C~~C~~~~~~~~~~ 103 (115)
..++.|..||+.|.....+
T Consensus 112 ~~~~~C~~CG~~f~~~~~i 130 (180)
T PRK12387 112 FALCNCRVCGRPFAVQKEI 130 (180)
T ss_pred eCcccchhhCCccccHHHH
Confidence 3578999999999766543
No 296
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=20.93 E-value=42 Score=18.30 Aligned_cols=13 Identities=8% Similarity=-0.187 Sum_probs=9.5
Q ss_pred ceeEEeecceehh
Q psy64 87 KYIFIVVKKIIVV 99 (115)
Q Consensus 87 ~~~C~~C~~~~~~ 99 (115)
.|.|+.|++.-..
T Consensus 68 r~~Ct~Cgkah~~ 80 (94)
T COG1631 68 RLRCTECGKAHQR 80 (94)
T ss_pred EEEehhhcccccc
Confidence 3789999976543
No 297
>PF14369 zf-RING_3: zinc-finger
Probab=20.82 E-value=43 Score=14.53 Aligned_cols=10 Identities=30% Similarity=0.800 Sum_probs=8.2
Q ss_pred ecCCChhhcc
Q psy64 19 VCNMCPSTFK 28 (115)
Q Consensus 19 ~C~~C~~~~~ 28 (115)
.|+.|+..|-
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 5999998875
No 298
>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=20.81 E-value=38 Score=20.49 Aligned_cols=40 Identities=13% Similarity=0.233 Sum_probs=23.3
Q ss_pred hcCCCceecccccccccChhhHHHHHHHhcCCCceeEEeeccee
Q psy64 54 HEKIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVVKKII 97 (115)
Q Consensus 54 h~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~~ 97 (115)
|..-....|..|++.+....... ... .+.+-.|+.|+...
T Consensus 100 HG~l~~~~C~~C~~~~~~~~~~~---~~~-~~~~~~C~~C~~~l 139 (178)
T PF02146_consen 100 HGSLFRLRCSKCGKEYDREDIVD---SID-EEEPPRCPKCGGLL 139 (178)
T ss_dssp TEEEEEEEETTTSBEEEGHHHHH---HHH-TTSSCBCTTTSCBE
T ss_pred HhhhceeeecCCCccccchhhcc---ccc-ccccccccccCccC
Confidence 44444568999998877543221 122 22333888888743
No 299
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.71 E-value=41 Score=19.94 Aligned_cols=12 Identities=8% Similarity=-0.222 Sum_probs=7.7
Q ss_pred ceeEEeecceeh
Q psy64 87 KYIFIVVKKIIV 98 (115)
Q Consensus 87 ~~~C~~C~~~~~ 98 (115)
.|.|..|+.+..
T Consensus 13 IYrC~~C~~TwN 24 (142)
T PF06353_consen 13 IYRCEKCDYTWN 24 (142)
T ss_pred EEEcccCcCccc
Confidence 367777776543
No 300
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=20.32 E-value=65 Score=21.70 Aligned_cols=10 Identities=20% Similarity=0.703 Sum_probs=6.7
Q ss_pred CCceeccccc
Q psy64 57 IRDFQCKVCD 66 (115)
Q Consensus 57 ~~~~~C~~c~ 66 (115)
.+.+.||.|+
T Consensus 366 ~~~~~c~~c~ 375 (389)
T PRK11788 366 TLYWHCPSCK 375 (389)
T ss_pred cceeECcCCC
Confidence 4556777776
No 301
>KOG4602|consensus
Probab=20.28 E-value=31 Score=22.67 Aligned_cols=48 Identities=10% Similarity=0.078 Sum_probs=25.3
Q ss_pred eecccccccccChhhHHHHHHHhcC-------CCceeEEeecceehhhhhhccCC
Q psy64 60 FQCKVCDRAFFDVYNLKLHMRIHTG-------EKKYIFIVVKKIIVVIYAKKFSL 107 (115)
Q Consensus 60 ~~C~~c~~~~~~~~~l~~h~~~h~~-------~~~~~C~~C~~~~~~~~~~~~h~ 107 (115)
..|..|...-.....+..|.-.-.. -+.|+|++||.+-.+.-....+.
T Consensus 234 l~CvFC~nN~E~~A~y~tH~lkd~dgRVLCPkLR~YVCPiCGATgDnAHTiKyCP 288 (318)
T KOG4602|consen 234 LCCVFCFNNAEEFARYHTHPLKDKDGRVLCPKLRSYVCPICGATGDNAHTIKYCP 288 (318)
T ss_pred eeEEeecCCCchhhheecccccCCCCcEechhHhhhcCccccccCCcccceeccc
Confidence 3455564444444444444222211 14589999998776665544443
No 302
>KOG2857|consensus
Probab=20.24 E-value=32 Score=20.42 Aligned_cols=20 Identities=10% Similarity=-0.106 Sum_probs=11.0
Q ss_pred eeEEeecceehhhhhhccCC
Q psy64 88 YIFIVVKKIIVVIYAKKFSL 107 (115)
Q Consensus 88 ~~C~~C~~~~~~~~~~~~h~ 107 (115)
|+|+.|...+-+..-+..|.
T Consensus 18 YKCpkC~vPYCSl~CfKiHk 37 (157)
T KOG2857|consen 18 YKCPKCSVPYCSLPCFKIHK 37 (157)
T ss_pred ccCCCCCCccccchhhhhcc
Confidence 55666665555555554443
No 303
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=20.04 E-value=47 Score=21.01 Aligned_cols=16 Identities=25% Similarity=0.906 Sum_probs=13.4
Q ss_pred CCCeecCCChhhccCh
Q psy64 15 DRPFVCNMCPSTFKLK 30 (115)
Q Consensus 15 ~~~~~C~~C~~~~~~~ 30 (115)
..||.|.+|-+.|.++
T Consensus 194 ~IPF~C~iCKkdy~sp 209 (259)
T COG5152 194 KIPFLCGICKKDYESP 209 (259)
T ss_pred CCceeehhchhhccch
Confidence 4689999999988765
Done!