Query psy12019
Match_columns 87
No_of_seqs 122 out of 1610
Neff 11.7
Searched_HMMs 46136
Date Fri Aug 16 16:34:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12019.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12019hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 2.9E-23 6.4E-28 111.2 3.6 83 2-85 144-238 (279)
2 KOG2462|consensus 99.9 5E-23 1.1E-27 110.3 2.5 78 3-83 176-264 (279)
3 KOG1074|consensus 99.7 8.8E-19 1.9E-23 105.1 2.1 53 32-85 604-656 (958)
4 KOG3623|consensus 99.7 2.3E-17 5E-22 98.4 1.5 70 13-83 891-971 (1007)
5 KOG1074|consensus 99.7 5E-17 1.1E-21 97.8 2.3 53 34-87 880-932 (958)
6 KOG3623|consensus 99.5 1.7E-15 3.6E-20 90.7 1.5 70 13-83 237-330 (1007)
7 KOG3576|consensus 99.5 9.7E-16 2.1E-20 79.9 0.4 75 12-87 113-198 (267)
8 PHA00733 hypothetical protein 99.5 2.1E-14 4.6E-19 71.1 2.4 73 12-87 36-124 (128)
9 PHA02768 hypothetical protein; 99.4 8.8E-14 1.9E-18 58.7 2.0 44 33-79 5-48 (55)
10 KOG3608|consensus 99.4 3E-13 6.5E-18 75.7 1.9 83 2-85 193-315 (467)
11 KOG3576|consensus 99.2 5.8E-12 1.2E-16 66.0 0.2 82 4-86 133-236 (267)
12 PF13465 zf-H2C2_2: Zinc-finge 99.1 4E-11 8.6E-16 43.8 1.9 26 48-74 1-26 (26)
13 PF13465 zf-H2C2_2: Zinc-finge 99.1 7.7E-12 1.7E-16 45.8 -1.3 25 3-27 1-25 (26)
14 KOG3608|consensus 98.9 5E-10 1.1E-14 63.1 2.0 85 2-86 277-376 (467)
15 PHA00732 hypothetical protein 98.9 2.2E-09 4.8E-14 49.1 2.6 45 33-84 1-46 (79)
16 PHA00616 hypothetical protein 98.8 2.9E-09 6.2E-14 43.1 0.9 26 62-87 1-26 (44)
17 PHA00616 hypothetical protein 98.7 5E-09 1.1E-13 42.4 1.5 34 33-67 1-34 (44)
18 KOG3993|consensus 98.7 1.7E-09 3.6E-14 62.2 -0.2 71 16-86 267-380 (500)
19 PHA02768 hypothetical protein; 98.6 3.1E-08 6.7E-13 42.0 1.5 24 63-86 6-29 (55)
20 PLN03086 PRLI-interacting fact 98.5 5.8E-08 1.3E-12 58.3 2.6 37 33-72 478-514 (567)
21 PF00096 zf-C2H2: Zinc finger, 98.5 3.3E-08 7.2E-13 34.9 0.9 22 63-84 1-22 (23)
22 PF05605 zf-Di19: Drought indu 98.5 2.9E-07 6.3E-12 39.2 3.8 52 33-87 2-54 (54)
23 PHA00733 hypothetical protein 98.5 1E-07 2.2E-12 47.5 2.6 54 4-58 62-124 (128)
24 PF13894 zf-C2H2_4: C2H2-type 98.5 7E-08 1.5E-12 34.2 1.3 24 63-86 1-24 (24)
25 PF13912 zf-C2H2_6: C2H2-type 98.4 1.5E-07 3.2E-12 34.5 1.2 24 63-86 2-25 (27)
26 PF00096 zf-C2H2: Zinc finger, 98.4 3.5E-07 7.5E-12 32.2 1.9 23 34-56 1-23 (23)
27 PLN03086 PRLI-interacting fact 98.3 9.1E-07 2E-11 53.4 4.3 77 4-86 468-564 (567)
28 PF13912 zf-C2H2_6: C2H2-type 98.1 1.9E-06 4.1E-11 31.4 1.6 25 33-57 1-25 (27)
29 smart00355 ZnF_C2H2 zinc finge 98.1 2.8E-06 6.1E-11 30.3 1.7 23 63-85 1-23 (26)
30 PF09237 GAGA: GAGA factor; I 98.0 2.8E-06 6.2E-11 35.3 1.0 26 62-87 24-49 (54)
31 PF13894 zf-C2H2_4: C2H2-type 97.9 1.4E-05 3E-10 27.9 2.0 23 34-56 1-23 (24)
32 COG5189 SFP1 Putative transcri 97.9 2.9E-06 6.4E-11 47.8 0.2 26 60-86 397-422 (423)
33 PRK04860 hypothetical protein; 97.7 3.2E-05 6.9E-10 40.0 2.5 39 32-75 118-156 (160)
34 PF12756 zf-C2H2_2: C2H2 type 97.7 3E-05 6.5E-10 36.7 1.7 22 63-84 51-72 (100)
35 smart00355 ZnF_C2H2 zinc finge 97.7 4.8E-05 1E-09 26.9 1.9 24 34-57 1-24 (26)
36 PF13909 zf-H2C2_5: C2H2-type 97.6 2.4E-05 5.1E-10 27.7 0.9 24 63-87 1-24 (24)
37 PF12874 zf-met: Zinc-finger o 97.5 0.00011 2.4E-09 26.1 1.6 22 34-55 1-22 (25)
38 PF12874 zf-met: Zinc-finger o 97.4 7E-05 1.5E-09 26.6 0.8 22 63-84 1-22 (25)
39 PHA00732 hypothetical protein 97.4 9E-05 1.9E-09 34.0 1.3 38 16-56 1-47 (79)
40 PF05605 zf-Di19: Drought indu 97.2 0.00034 7.4E-09 29.7 2.0 40 16-57 2-53 (54)
41 PF12171 zf-C2H2_jaz: Zinc-fin 97.2 0.00023 4.9E-09 25.8 1.2 21 63-83 2-22 (27)
42 PF12171 zf-C2H2_jaz: Zinc-fin 97.1 0.00027 5.9E-09 25.6 1.0 22 34-55 2-23 (27)
43 KOG3993|consensus 97.1 8.7E-05 1.9E-09 43.5 -0.7 52 33-85 267-318 (500)
44 PF09237 GAGA: GAGA factor; I 97.0 0.0015 3.2E-08 27.4 2.6 31 31-61 22-52 (54)
45 PF13913 zf-C2HC_2: zinc-finge 96.9 0.001 2.3E-08 23.7 1.6 20 63-83 3-22 (25)
46 PF12756 zf-C2H2_2: C2H2 type 96.8 0.0014 3.1E-08 30.9 2.2 25 33-57 50-74 (100)
47 COG2888 Predicted Zn-ribbon RN 96.4 0.0047 1E-07 26.6 2.3 49 16-70 9-58 (61)
48 PF09538 FYDLN_acid: Protein o 96.4 0.0023 4.9E-08 31.2 1.5 30 17-46 10-39 (108)
49 smart00451 ZnF_U1 U1-like zinc 96.1 0.0043 9.4E-08 23.6 1.3 21 63-83 4-24 (35)
50 PRK14890 putative Zn-ribbon RN 96.0 0.014 3E-07 25.2 2.8 50 15-70 6-56 (59)
51 cd00350 rubredoxin_like Rubred 95.8 0.009 2E-07 22.7 1.7 8 63-70 18-25 (33)
52 smart00659 RPOLCX RNA polymera 95.4 0.01 2.2E-07 24.2 1.1 24 17-40 3-26 (44)
53 PF03604 DNA_RNApol_7kD: DNA d 95.3 0.011 2.5E-07 22.4 1.1 8 63-70 18-25 (32)
54 PRK04860 hypothetical protein; 95.3 0.0029 6.3E-08 32.9 -0.7 30 16-46 119-156 (160)
55 TIGR02300 FYDLN_acid conserved 95.3 0.012 2.6E-07 29.4 1.4 32 17-48 10-41 (129)
56 PRK00398 rpoP DNA-directed RNA 95.1 0.014 3.1E-07 23.8 1.1 27 16-42 3-30 (46)
57 KOG2893|consensus 95.0 0.0073 1.6E-07 33.4 0.1 41 36-81 13-53 (341)
58 COG4049 Uncharacterized protei 94.9 0.0098 2.1E-07 25.3 0.4 29 30-58 14-42 (65)
59 PF09986 DUF2225: Uncharacteri 94.7 0.022 4.7E-07 31.1 1.6 16 14-29 3-18 (214)
60 cd00729 rubredoxin_SM Rubredox 94.7 0.027 5.9E-07 21.6 1.4 9 34-42 3-11 (34)
61 COG5048 FOG: Zn-finger [Genera 94.3 0.013 2.7E-07 34.3 0.0 53 33-86 289-347 (467)
62 PF15135 UPF0515: Uncharacteri 93.8 0.023 5.1E-07 31.6 0.5 57 13-75 109-168 (278)
63 TIGR02098 MJ0042_CXXC MJ0042 f 93.5 0.057 1.2E-06 21.0 1.3 33 34-72 3-35 (38)
64 PF13719 zinc_ribbon_5: zinc-r 93.4 0.073 1.6E-06 20.7 1.5 32 35-72 4-35 (37)
65 COG1592 Rubrerythrin [Energy p 93.2 0.046 1E-06 28.7 1.0 23 33-69 134-156 (166)
66 TIGR00373 conserved hypothetic 93.1 0.082 1.8E-06 27.6 1.8 33 31-73 107-139 (158)
67 PF13717 zinc_ribbon_4: zinc-r 93.1 0.086 1.9E-06 20.5 1.4 32 35-72 4-35 (36)
68 KOG1146|consensus 93.0 0.078 1.7E-06 36.1 2.0 51 32-83 464-539 (1406)
69 COG4530 Uncharacterized protei 92.9 0.062 1.4E-06 26.2 1.1 28 18-45 11-38 (129)
70 COG1997 RPL43A Ribosomal prote 92.8 0.081 1.8E-06 24.8 1.4 28 16-43 35-63 (89)
71 PRK06266 transcription initiat 92.6 0.088 1.9E-06 28.0 1.5 32 32-73 116-147 (178)
72 COG1571 Predicted DNA-binding 92.6 0.081 1.8E-06 31.8 1.5 33 16-48 350-382 (421)
73 PF07754 DUF1610: Domain of un 92.6 0.11 2.3E-06 18.4 1.2 7 63-69 17-23 (24)
74 PF14353 CpXC: CpXC protein 92.4 0.056 1.2E-06 27.0 0.6 11 18-28 3-13 (128)
75 PF09723 Zn-ribbon_8: Zinc rib 92.4 0.059 1.3E-06 21.6 0.6 13 34-46 6-18 (42)
76 PF08274 PhnA_Zn_Ribbon: PhnA 92.4 0.083 1.8E-06 19.7 0.9 24 18-41 4-27 (30)
77 TIGR00686 phnA alkylphosphonat 92.4 0.095 2.1E-06 25.5 1.3 31 17-47 3-33 (109)
78 KOG2186|consensus 92.3 0.11 2.3E-06 29.2 1.6 38 34-74 4-41 (276)
79 smart00734 ZnF_Rad18 Rad18-lik 92.3 0.15 3.2E-06 18.3 1.5 19 64-83 3-21 (26)
80 PTZ00255 60S ribosomal protein 92.2 0.081 1.7E-06 25.0 1.0 29 16-44 36-65 (90)
81 PF12013 DUF3505: Protein of u 92.1 0.12 2.6E-06 25.1 1.5 25 63-87 81-109 (109)
82 PRK00464 nrdR transcriptional 92.0 0.024 5.3E-07 29.4 -0.9 12 34-45 29-40 (154)
83 PRK10220 hypothetical protein; 92.0 0.13 2.9E-06 25.1 1.6 31 17-47 4-34 (111)
84 smart00834 CxxC_CXXC_SSSS Puta 91.9 0.08 1.7E-06 20.8 0.7 13 34-46 6-18 (41)
85 TIGR00280 L37a ribosomal prote 91.8 0.084 1.8E-06 25.0 0.8 29 16-44 35-64 (91)
86 TIGR02605 CxxC_CxxC_SSSS putat 91.8 0.073 1.6E-06 22.2 0.5 12 34-45 6-17 (52)
87 PF05443 ROS_MUCR: ROS/MUCR tr 91.8 0.095 2.1E-06 26.6 1.0 26 58-87 69-94 (132)
88 COG1996 RPC10 DNA-directed RNA 91.1 0.1 2.2E-06 21.8 0.6 25 16-40 6-31 (49)
89 smart00531 TFIIE Transcription 90.3 0.24 5.2E-06 25.5 1.7 38 31-73 97-134 (147)
90 PRK03976 rpl37ae 50S ribosomal 90.3 0.14 3E-06 24.2 0.7 29 16-44 36-65 (90)
91 PF04959 ARS2: Arsenite-resist 90.2 0.1 2.3E-06 28.6 0.3 24 63-86 78-101 (214)
92 PF02892 zf-BED: BED zinc fing 90.1 0.28 6.1E-06 19.7 1.5 22 63-84 17-42 (45)
93 COG4957 Predicted transcriptio 89.4 0.23 5E-06 25.3 1.1 22 63-87 77-98 (148)
94 smart00614 ZnF_BED BED zinc fi 89.4 0.31 6.8E-06 20.2 1.4 21 63-83 19-44 (50)
95 PF01780 Ribosomal_L37ae: Ribo 89.2 0.16 3.4E-06 24.0 0.5 28 16-43 35-63 (90)
96 PF09845 DUF2072: Zn-ribbon co 89.0 0.16 3.5E-06 25.7 0.4 25 16-40 1-26 (131)
97 PRK09678 DNA-binding transcrip 88.7 0.18 3.9E-06 22.9 0.4 12 63-74 28-41 (72)
98 COG3357 Predicted transcriptio 87.9 0.32 6.9E-06 23.0 1.0 12 33-44 58-69 (97)
99 COG5189 SFP1 Putative transcri 87.1 0.18 3.8E-06 29.4 -0.1 42 13-54 346-419 (423)
100 TIGR00622 ssl1 transcription f 86.9 0.89 1.9E-05 22.5 2.2 47 36-85 58-104 (112)
101 PF11781 RRN7: RNA polymerase 86.7 0.5 1.1E-05 18.3 1.1 26 16-41 8-33 (36)
102 PF01363 FYVE: FYVE zinc finge 86.1 0.56 1.2E-05 20.7 1.3 30 16-46 9-38 (69)
103 COG5152 Uncharacterized conser 85.8 0.31 6.8E-06 26.5 0.4 46 15-72 195-240 (259)
104 KOG1146|consensus 85.8 0.33 7.1E-06 33.4 0.6 69 17-86 1261-1352(1406)
105 COG1198 PriA Primosomal protei 85.5 0.9 1.9E-05 29.7 2.3 14 57-71 471-484 (730)
106 PRK00432 30S ribosomal protein 85.4 0.77 1.7E-05 19.2 1.4 10 63-72 38-47 (50)
107 PRK00420 hypothetical protein; 85.3 0.69 1.5E-05 22.9 1.4 28 17-44 24-51 (112)
108 PF06524 NOA36: NOA36 protein; 84.5 0.93 2E-05 25.9 1.9 24 18-41 127-150 (314)
109 PF10571 UPF0547: Uncharacteri 83.9 0.67 1.4E-05 16.6 0.8 10 64-73 16-25 (26)
110 KOG3507|consensus 83.8 0.62 1.3E-05 20.2 0.8 25 17-41 21-45 (62)
111 KOG3408|consensus 83.7 0.8 1.7E-05 22.9 1.3 26 30-55 54-79 (129)
112 cd00730 rubredoxin Rubredoxin; 83.3 0.83 1.8E-05 19.2 1.1 7 63-69 35-41 (50)
113 PF11789 zf-Nse: Zinc-finger o 82.9 1.3 2.8E-05 19.0 1.7 47 13-68 8-54 (57)
114 PRK03824 hypA hydrogenase nick 82.7 0.59 1.3E-05 23.8 0.6 15 32-46 69-83 (135)
115 PF08790 zf-LYAR: LYAR-type C2 82.4 0.46 1E-05 17.4 0.1 9 35-43 2-10 (28)
116 KOG2593|consensus 82.2 0.7 1.5E-05 28.1 0.9 28 14-41 126-161 (436)
117 PF00301 Rubredoxin: Rubredoxi 81.8 0.67 1.5E-05 19.2 0.5 7 63-69 35-41 (47)
118 PRK03681 hypA hydrogenase nick 81.8 0.67 1.5E-05 22.9 0.6 10 34-43 71-80 (114)
119 PF13453 zf-TFIIB: Transcripti 81.8 2.2 4.8E-05 16.8 2.1 16 34-49 20-35 (41)
120 PF06524 NOA36: NOA36 protein; 81.7 0.66 1.4E-05 26.4 0.6 23 60-83 208-230 (314)
121 PRK00564 hypA hydrogenase nick 81.2 0.74 1.6E-05 22.9 0.7 10 34-43 72-81 (117)
122 PF07282 OrfB_Zn_ribbon: Putat 81.1 2.4 5.3E-05 18.6 2.3 9 63-71 47-55 (69)
123 COG4888 Uncharacterized Zn rib 81.0 0.84 1.8E-05 22.1 0.8 30 14-43 20-56 (104)
124 PF14446 Prok-RING_1: Prokaryo 81.0 1.1 2.4E-05 19.1 1.1 26 17-43 6-31 (54)
125 PHA00626 hypothetical protein 80.5 0.88 1.9E-05 19.6 0.7 13 63-75 24-36 (59)
126 COG4391 Uncharacterized protei 80.2 1.4 3.1E-05 19.3 1.3 15 7-21 15-29 (62)
127 COG1773 Rubredoxin [Energy pro 80.1 1.1 2.4E-05 19.2 0.9 14 16-29 3-16 (55)
128 PF08271 TF_Zn_Ribbon: TFIIB z 79.3 1.1 2.5E-05 17.9 0.8 26 17-42 1-28 (43)
129 TIGR00416 sms DNA repair prote 79.2 1.1 2.3E-05 27.6 1.0 24 16-42 7-30 (454)
130 PRK14873 primosome assembly pr 79.1 2.2 4.8E-05 27.7 2.3 9 63-71 423-431 (665)
131 COG5048 FOG: Zn-finger [Genera 79.0 2 4.2E-05 25.4 2.0 54 32-86 32-87 (467)
132 KOG2893|consensus 78.6 1.1 2.3E-05 25.3 0.8 26 60-87 10-35 (341)
133 TIGR01206 lysW lysine biosynth 78.4 1.6 3.5E-05 18.6 1.2 9 63-71 23-31 (54)
134 smart00661 RPOL9 RNA polymeras 77.9 1.9 4.1E-05 17.7 1.4 9 63-71 21-29 (52)
135 KOG0978|consensus 77.7 0.7 1.5E-05 29.9 -0.0 52 17-79 644-695 (698)
136 PRK11823 DNA repair protein Ra 77.6 1.3 2.8E-05 27.2 1.0 25 15-42 6-30 (446)
137 PF05290 Baculo_IE-1: Baculovi 77.1 2 4.3E-05 22.0 1.4 60 12-77 76-136 (140)
138 COG2824 PhnA Uncharacterized Z 77.1 1.7 3.6E-05 21.3 1.1 29 18-46 5-33 (112)
139 cd01121 Sms Sms (bacterial rad 76.3 1.7 3.7E-05 26.1 1.2 23 17-42 1-23 (372)
140 PF05191 ADK_lid: Adenylate ki 75.9 2.5 5.5E-05 16.4 1.3 10 35-44 3-12 (36)
141 COG4306 Uncharacterized protei 75.9 1 2.2E-05 22.7 0.2 10 36-45 71-80 (160)
142 KOG4167|consensus 75.4 0.42 9.2E-06 31.0 -1.4 24 62-85 792-815 (907)
143 COG2331 Uncharacterized protei 75.2 1.7 3.7E-05 19.9 0.8 10 34-43 13-22 (82)
144 PF01155 HypA: Hydrogenase exp 74.9 0.54 1.2E-05 23.2 -0.9 12 34-45 71-82 (113)
145 KOG4167|consensus 74.3 0.78 1.7E-05 29.9 -0.4 27 32-58 791-817 (907)
146 COG3364 Zn-ribbon containing p 74.0 0.97 2.1E-05 21.9 -0.1 25 16-40 2-27 (112)
147 smart00440 ZnF_C2C2 C2C2 Zinc 73.7 0.3 6.5E-06 19.4 -1.6 10 63-72 29-38 (40)
148 PF13451 zf-trcl: Probable zin 73.4 2.5 5.4E-05 17.7 1.1 16 32-47 3-18 (49)
149 PF04810 zf-Sec23_Sec24: Sec23 72.9 3 6.6E-05 16.4 1.2 10 32-41 23-32 (40)
150 PF07649 C1_3: C1-like domain; 72.8 2.3 5.1E-05 15.4 0.9 8 33-40 15-22 (30)
151 PF14803 Nudix_N_2: Nudix N-te 72.1 2.3 5E-05 16.3 0.8 7 34-40 23-29 (34)
152 PRK12496 hypothetical protein; 72.0 2.5 5.4E-05 22.3 1.1 11 33-43 127-137 (164)
153 PF08792 A2L_zn_ribbon: A2L zi 71.9 3.5 7.6E-05 15.6 1.3 8 64-71 23-30 (33)
154 PRK12380 hydrogenase nickel in 71.5 1.9 4.1E-05 21.3 0.6 10 34-43 71-80 (113)
155 PF12760 Zn_Tnp_IS1595: Transp 71.1 3.6 7.8E-05 16.7 1.3 8 63-70 38-45 (46)
156 PF00130 C1_1: Phorbol esters/ 71.0 3.8 8.2E-05 16.9 1.4 29 14-42 9-37 (53)
157 KOG2071|consensus 70.7 3 6.6E-05 26.6 1.4 25 60-85 417-441 (579)
158 PF13878 zf-C2H2_3: zinc-finge 69.5 5.6 0.00012 15.8 1.7 11 35-45 15-25 (41)
159 KOG0782|consensus 69.1 0.8 1.7E-05 29.2 -1.2 44 3-46 240-289 (1004)
160 PF09963 DUF2197: Uncharacteri 68.6 1.9 4E-05 18.6 0.2 8 63-70 32-39 (56)
161 KOG2636|consensus 68.5 4.2 9.2E-05 25.2 1.6 28 54-82 394-422 (497)
162 KOG4173|consensus 68.5 2.2 4.7E-05 23.6 0.4 51 35-86 108-170 (253)
163 cd00065 FYVE FYVE domain; Zinc 68.3 3.7 8E-05 17.2 1.1 28 18-46 4-31 (57)
164 PF01927 Mut7-C: Mut7-C RNAse 66.9 4.3 9.3E-05 20.9 1.3 19 63-81 125-143 (147)
165 TIGR00100 hypA hydrogenase nic 66.6 2.8 6.1E-05 20.7 0.6 12 34-45 71-82 (115)
166 PF07975 C1_4: TFIIH C1-like d 66.5 2 4.4E-05 18.1 0.1 16 33-48 21-36 (51)
167 KOG0320|consensus 66.4 2 4.4E-05 23.1 0.1 49 14-72 129-177 (187)
168 KOG2785|consensus 66.3 6.2 0.00014 23.9 2.0 21 63-83 69-89 (390)
169 PHA02942 putative transposase; 66.3 8.9 0.00019 23.3 2.7 8 63-70 343-350 (383)
170 PF13445 zf-RING_UBOX: RING-ty 65.5 9 0.00019 15.4 1.9 28 19-48 1-28 (43)
171 cd00029 C1 Protein kinase C co 65.3 5.2 0.00011 16.0 1.3 26 16-41 11-36 (50)
172 PF05129 Elf1: Transcription e 65.3 3.2 7E-05 19.2 0.6 31 15-45 21-58 (81)
173 KOG0317|consensus 65.0 6.2 0.00013 23.0 1.8 48 15-74 238-285 (293)
174 smart00154 ZnF_AN1 AN1-like Zi 64.1 3.7 7.9E-05 16.2 0.6 11 63-73 13-23 (39)
175 PF14311 DUF4379: Domain of un 64.0 8.4 0.00018 16.2 1.8 14 33-46 28-41 (55)
176 KOG2907|consensus 63.9 3 6.5E-05 20.7 0.4 40 34-75 75-115 (116)
177 PF08646 Rep_fac-A_C: Replicat 63.4 4.5 9.8E-05 20.7 1.0 26 18-43 20-47 (146)
178 PF00628 PHD: PHD-finger; Int 63.3 6.9 0.00015 15.9 1.4 12 32-43 13-24 (51)
179 PF03107 C1_2: C1 domain; Int 62.8 5.4 0.00012 14.5 1.0 6 34-39 16-21 (30)
180 KOG2231|consensus 61.7 9.8 0.00021 25.0 2.4 51 35-87 184-237 (669)
181 KOG0402|consensus 61.7 4.1 8.9E-05 19.1 0.6 26 17-42 37-63 (92)
182 PF14634 zf-RING_5: zinc-RING 61.3 11 0.00023 14.9 2.3 43 19-70 2-44 (44)
183 cd04476 RPA1_DBD_C RPA1_DBD_C: 60.8 6.1 0.00013 20.7 1.3 25 18-42 36-60 (166)
184 TIGR00570 cdk7 CDK-activating 60.0 20 0.00044 21.3 3.3 52 17-75 4-56 (309)
185 PRK00762 hypA hydrogenase nick 59.7 4.4 9.6E-05 20.4 0.6 13 33-46 70-82 (124)
186 PF10013 DUF2256: Uncharacteri 59.5 6.4 0.00014 15.9 0.9 16 35-50 10-25 (42)
187 KOG2482|consensus 59.3 5.3 0.00012 23.9 0.9 22 63-84 196-217 (423)
188 COG1675 TFA1 Transcription ini 59.2 9.7 0.00021 20.6 1.8 32 31-72 111-142 (176)
189 PF04423 Rad50_zn_hook: Rad50 59.1 4.1 8.9E-05 17.1 0.4 11 64-74 22-32 (54)
190 KOG0717|consensus 58.8 5 0.00011 25.0 0.8 21 63-83 293-313 (508)
191 TIGR00595 priA primosomal prot 58.5 7.3 0.00016 24.5 1.5 8 63-70 254-261 (505)
192 KOG1729|consensus 58.3 0.94 2E-05 26.2 -2.1 30 16-45 168-197 (288)
193 PF09297 zf-NADH-PPase: NADH p 57.8 6.5 0.00014 14.5 0.8 8 33-40 21-28 (32)
194 PF10083 DUF2321: Uncharacteri 57.7 7.2 0.00015 20.6 1.1 12 63-74 69-80 (158)
195 PF01428 zf-AN1: AN1-like Zinc 57.6 4.5 9.8E-05 16.1 0.4 15 32-46 12-26 (43)
196 PF11672 DUF3268: Protein of u 57.6 4.9 0.00011 19.6 0.5 9 16-24 2-10 (102)
197 PLN02294 cytochrome c oxidase 57.6 6.2 0.00013 21.2 0.9 20 52-73 133-152 (174)
198 smart00064 FYVE Protein presen 57.4 11 0.00025 16.4 1.7 29 17-46 11-39 (68)
199 PF02176 zf-TRAF: TRAF-type zi 57.3 9 0.0002 16.1 1.3 40 33-73 9-53 (60)
200 PF11023 DUF2614: Protein of u 56.8 7.7 0.00017 19.3 1.1 29 15-44 68-96 (114)
201 PRK04023 DNA polymerase II lar 56.6 9.9 0.00021 26.3 1.8 22 16-42 626-647 (1121)
202 PF01286 XPA_N: XPA protein N- 55.8 5.9 0.00013 15.2 0.5 12 64-75 5-16 (34)
203 CHL00174 accD acetyl-CoA carbo 55.8 4.5 9.7E-05 23.7 0.3 11 34-44 58-68 (296)
204 TIGR00244 transcriptional regu 55.4 6 0.00013 20.7 0.7 14 63-76 29-42 (147)
205 PF10537 WAC_Acf1_DNA_bd: ATP- 55.4 21 0.00046 17.4 2.5 36 33-70 3-38 (102)
206 TIGR00515 accD acetyl-CoA carb 55.2 4.6 9.9E-05 23.5 0.2 28 18-45 28-57 (285)
207 PLN03208 E3 ubiquitin-protein 54.6 26 0.00057 19.3 3.0 53 15-73 17-79 (193)
208 PF13824 zf-Mss51: Zinc-finger 54.5 14 0.00031 15.9 1.6 9 33-41 14-22 (55)
209 PHA02998 RNA polymerase subuni 54.3 1.9 4.1E-05 23.2 -1.2 11 63-73 172-182 (195)
210 COG1594 RPB9 DNA-directed RNA 54.0 2.4 5.1E-05 21.0 -0.9 11 63-73 101-111 (113)
211 cd00924 Cyt_c_Oxidase_Vb Cytoc 53.4 8.8 0.00019 18.6 1.0 15 30-44 76-90 (97)
212 PF04780 DUF629: Protein of un 53.0 9.6 0.00021 23.9 1.3 22 63-84 58-79 (466)
213 TIGR03830 CxxCG_CxxCG_HTH puta 52.6 18 0.00039 17.8 2.1 17 33-49 31-47 (127)
214 TIGR00627 tfb4 transcription f 52.5 8.2 0.00018 22.4 1.0 25 33-72 255-279 (279)
215 PF12773 DZR: Double zinc ribb 52.2 8.3 0.00018 15.7 0.8 10 63-72 30-39 (50)
216 PF02891 zf-MIZ: MIZ/SP-RING z 51.9 10 0.00022 15.8 1.0 23 43-70 27-49 (50)
217 PF15616 TerY-C: TerY-C metal 51.8 12 0.00026 19.2 1.4 9 63-71 106-114 (131)
218 PRK05654 acetyl-CoA carboxylas 51.6 5.4 0.00012 23.3 0.2 28 18-45 29-58 (292)
219 PF07191 zinc-ribbons_6: zinc- 51.3 8 0.00017 17.5 0.6 24 19-43 4-27 (70)
220 PF07503 zf-HYPF: HypF finger; 51.1 5.8 0.00012 15.3 0.2 10 63-72 22-31 (35)
221 PRK07591 threonine synthase; V 51.1 8.4 0.00018 23.6 0.9 27 16-44 18-44 (421)
222 KOG1813|consensus 50.9 5.8 0.00012 23.2 0.2 16 14-29 239-254 (313)
223 PF15269 zf-C2H2_7: Zinc-finge 50.5 11 0.00024 15.4 0.9 21 63-83 21-41 (54)
224 COG1998 RPS31 Ribosomal protei 50.2 13 0.00028 15.6 1.1 9 63-71 38-46 (51)
225 COG3677 Transposase and inacti 50.1 11 0.00023 19.2 1.1 14 59-73 51-64 (129)
226 PF02591 DUF164: Putative zinc 49.4 19 0.00041 15.2 1.7 32 35-71 24-55 (56)
227 PRK05452 anaerobic nitric oxid 49.4 10 0.00022 23.8 1.1 14 32-45 424-437 (479)
228 PF14787 zf-CCHC_5: GAG-polypr 48.9 10 0.00022 14.8 0.7 15 63-77 3-17 (36)
229 PF07295 DUF1451: Protein of u 48.6 5.1 0.00011 20.9 -0.2 31 30-71 109-139 (146)
230 COG5112 UFD2 U1-like Zn-finger 48.2 9.7 0.00021 18.8 0.7 26 30-55 52-77 (126)
231 smart00249 PHD PHD zinc finger 47.7 17 0.00037 13.9 1.4 11 33-43 14-24 (47)
232 PF11931 DUF3449: Domain of un 47.1 6.3 0.00014 21.6 0.0 26 55-81 95-121 (196)
233 PF04606 Ogr_Delta: Ogr/Delta- 46.8 4.1 8.9E-05 16.6 -0.6 13 63-75 26-40 (47)
234 COG4338 Uncharacterized protei 46.8 7.6 0.00017 16.2 0.2 16 35-50 14-29 (54)
235 smart00109 C1 Protein kinase C 46.6 18 0.0004 14.1 1.4 24 16-40 11-34 (49)
236 smart00132 LIM Zinc-binding do 46.5 3.8 8.2E-05 15.2 -0.7 10 63-72 28-37 (39)
237 KOG3362|consensus 46.0 6.8 0.00015 20.4 0.0 19 63-81 130-148 (156)
238 COG1327 Predicted transcriptio 45.9 9.7 0.00021 20.1 0.6 13 63-75 29-41 (156)
239 PRK06450 threonine synthase; V 45.7 11 0.00023 22.4 0.8 25 17-43 4-28 (338)
240 COG0675 Transposase and inacti 45.6 25 0.00054 20.4 2.2 24 18-45 311-334 (364)
241 PF07800 DUF1644: Protein of u 45.1 39 0.00084 18.1 2.6 52 33-86 80-132 (162)
242 KOG1842|consensus 45.0 11 0.00023 23.6 0.7 21 34-54 16-36 (505)
243 PRK04351 hypothetical protein; 45.0 14 0.0003 19.3 1.0 34 32-74 111-144 (149)
244 COG1779 C4-type Zn-finger prot 44.7 9.4 0.0002 21.0 0.4 28 17-44 15-54 (201)
245 COG1645 Uncharacterized Zn-fin 44.3 15 0.00033 18.9 1.1 23 18-41 30-52 (131)
246 PRK06260 threonine synthase; V 44.3 12 0.00027 22.6 0.9 26 17-43 4-29 (397)
247 TIGR03831 YgiT_finger YgiT-typ 44.1 10 0.00022 14.9 0.4 12 33-44 32-43 (46)
248 smart00504 Ubox Modified RING 44.1 28 0.00061 14.6 2.8 45 17-73 2-46 (63)
249 PF08209 Sgf11: Sgf11 (transcr 43.9 23 0.00049 13.5 2.0 21 33-54 4-24 (33)
250 COG1326 Uncharacterized archae 43.9 27 0.00058 19.3 2.0 10 34-43 31-40 (201)
251 COG4640 Predicted membrane pro 43.9 18 0.0004 22.3 1.5 15 34-48 16-30 (465)
252 COG1066 Sms Predicted ATP-depe 43.4 12 0.00027 23.2 0.8 24 15-41 6-29 (456)
253 PF10276 zf-CHCC: Zinc-finger 43.2 8.6 0.00019 15.3 0.1 10 63-72 30-39 (40)
254 PTZ00303 phosphatidylinositol 42.6 16 0.00035 24.9 1.2 31 17-47 461-495 (1374)
255 PRK05978 hypothetical protein; 42.1 16 0.00034 19.2 0.9 11 63-73 53-63 (148)
256 PF10263 SprT-like: SprT-like 41.2 13 0.00028 19.1 0.6 32 33-73 123-154 (157)
257 PRK12366 replication factor A; 41.1 14 0.00031 24.1 0.9 22 19-41 535-556 (637)
258 KOG1280|consensus 41.0 27 0.00058 21.2 1.8 24 63-86 80-103 (381)
259 PF02146 SIR2: Sir2 family; I 40.9 47 0.001 17.6 2.7 35 33-72 105-139 (178)
260 TIGR01384 TFS_arch transcripti 40.7 22 0.00048 17.0 1.3 10 63-72 63-72 (104)
261 PRK05580 primosome assembly pr 40.6 21 0.00044 23.6 1.5 24 17-40 391-415 (679)
262 PRK08402 replication factor A; 40.5 17 0.00038 21.9 1.1 23 18-40 214-237 (355)
263 COG5216 Uncharacterized conser 40.5 17 0.00038 15.8 0.8 6 63-68 45-50 (67)
264 COG5188 PRP9 Splicing factor 3 40.4 19 0.00041 21.9 1.2 28 53-81 366-394 (470)
265 PF01096 TFIIS_C: Transcriptio 40.3 9.5 0.00021 14.9 0.0 9 63-71 29-37 (39)
266 PF06677 Auto_anti-p27: Sjogre 40.0 23 0.0005 14.2 1.1 6 35-40 19-24 (41)
267 PF04641 Rtf2: Rtf2 RING-finge 39.8 19 0.00041 20.6 1.2 51 13-73 110-161 (260)
268 PRK14138 NAD-dependent deacety 39.7 42 0.0009 19.1 2.4 33 33-70 119-151 (244)
269 COG0846 SIR2 NAD-dependent pro 39.6 26 0.00057 20.1 1.6 33 33-70 122-154 (250)
270 PRK11827 hypothetical protein; 39.4 28 0.00061 15.3 1.4 30 17-46 9-39 (60)
271 PF12907 zf-met2: Zinc-binding 39.4 8.2 0.00018 15.4 -0.2 6 64-69 3-8 (40)
272 COG0068 HypF Hydrogenase matur 39.2 3.4 7.5E-05 27.1 -1.9 29 36-71 154-182 (750)
273 PF12230 PRP21_like_P: Pre-mRN 38.7 10 0.00022 21.1 0.0 22 63-85 169-190 (229)
274 PRK07218 replication factor A; 38.4 17 0.00036 22.6 0.8 9 18-26 299-307 (423)
275 PF01215 COX5B: Cytochrome c o 38.3 17 0.00037 18.8 0.7 17 30-46 109-125 (136)
276 PF06827 zf-FPG_IleRS: Zinc fi 37.9 17 0.00036 13.0 0.5 7 19-25 4-10 (30)
277 PF06397 Desulfoferrod_N: Desu 37.7 17 0.00037 14.1 0.5 11 33-43 6-16 (36)
278 smart00731 SprT SprT homologue 37.6 19 0.0004 18.6 0.8 34 32-73 111-144 (146)
279 PF02318 FYVE_2: FYVE-type zin 37.0 24 0.00052 17.5 1.1 49 16-70 54-102 (118)
280 PRK14892 putative transcriptio 35.9 26 0.00057 17.0 1.1 8 16-23 21-28 (99)
281 PRK11788 tetratricopeptide rep 35.9 24 0.00053 20.8 1.2 21 17-40 355-375 (389)
282 PF14445 Prok-RING_2: Prokaryo 35.9 3.7 8E-05 17.3 -1.5 12 17-28 8-19 (57)
283 PRK08222 hydrogenase 4 subunit 35.9 28 0.00062 18.7 1.4 17 63-79 115-131 (181)
284 cd01413 SIR2_Af2 SIR2_Af2: Arc 35.9 42 0.00091 18.7 2.1 32 33-70 113-144 (222)
285 COG1656 Uncharacterized conser 35.7 28 0.0006 18.7 1.3 18 63-80 131-148 (165)
286 TIGR03826 YvyF flagellar opero 35.7 14 0.0003 19.1 0.2 23 17-41 4-26 (137)
287 KOG3214|consensus 35.3 21 0.00046 17.4 0.7 12 34-45 48-59 (109)
288 PF06689 zf-C4_ClpX: ClpX C4-t 35.0 9.7 0.00021 15.1 -0.4 10 18-27 3-12 (41)
289 COG5236 Uncharacterized conser 35.0 46 0.001 20.4 2.2 51 35-87 222-276 (493)
290 COG3091 SprT Zn-dependent meta 34.4 20 0.00043 19.0 0.6 34 33-72 117-150 (156)
291 PTZ00043 cytochrome c oxidase 34.4 20 0.00043 20.4 0.7 16 14-29 179-194 (268)
292 KOG2923|consensus 34.2 28 0.00061 15.5 1.0 7 63-69 45-51 (67)
293 PF15227 zf-C3HC4_4: zinc fing 34.1 24 0.00053 13.9 0.8 10 38-47 15-24 (42)
294 COG2956 Predicted N-acetylgluc 34.0 25 0.00053 21.4 1.0 9 16-24 354-362 (389)
295 COG1379 PHP family phosphoeste 33.9 12 0.00025 22.6 -0.3 28 18-45 248-277 (403)
296 PF00412 LIM: LIM domain; Int 33.6 4.8 0.00011 16.7 -1.4 10 63-72 27-36 (58)
297 KOG4215|consensus 33.6 17 0.00037 22.2 0.3 37 17-54 20-56 (432)
298 PRK12387 formate hydrogenlyase 33.1 28 0.0006 18.6 1.1 18 62-79 114-131 (180)
299 PRK11088 rrmA 23S rRNA methylt 32.7 37 0.0008 19.4 1.6 21 17-38 3-23 (272)
300 PRK12286 rpmF 50S ribosomal pr 32.7 36 0.00078 14.7 1.2 7 34-40 41-47 (57)
301 PF03966 Trm112p: Trm112p-like 32.6 17 0.00036 16.1 0.2 11 63-73 54-64 (68)
302 PF03563 Bunya_G2: Bunyavirus 32.0 46 0.00099 19.5 1.8 17 38-54 255-271 (285)
303 KOG0823|consensus 32.0 43 0.00093 19.1 1.7 46 15-69 46-91 (230)
304 PF11494 Ta0938: Ta0938; Inte 31.4 35 0.00076 16.6 1.1 35 12-46 10-50 (105)
305 KOG2164|consensus 31.2 67 0.0014 20.7 2.5 50 16-72 186-235 (513)
306 PRK01343 zinc-binding protein; 31.1 28 0.0006 15.1 0.7 12 62-73 9-20 (57)
307 PLN02748 tRNA dimethylallyltra 31.0 44 0.00095 21.2 1.8 23 60-83 417-440 (468)
308 TIGR03844 cysteate_syn cysteat 30.5 28 0.0006 21.4 0.9 22 17-40 3-24 (398)
309 PF14369 zf-RING_3: zinc-finge 30.4 29 0.00063 13.2 0.7 10 64-73 23-32 (35)
310 PF09855 DUF2082: Nucleic-acid 30.1 30 0.00065 15.4 0.7 7 63-69 1-7 (64)
311 PF09889 DUF2116: Uncharacteri 30.0 32 0.00069 15.0 0.8 6 19-24 6-11 (59)
312 PTZ00448 hypothetical protein; 30.0 42 0.0009 20.6 1.5 21 63-83 315-335 (373)
313 PF09862 DUF2089: Protein of u 30.0 30 0.00066 17.3 0.8 8 34-41 13-20 (113)
314 KOG1409|consensus 29.8 14 0.0003 22.4 -0.4 41 33-75 282-322 (404)
315 KOG1088|consensus 29.3 26 0.00056 17.7 0.5 18 56-74 93-110 (124)
316 COG1439 Predicted nucleic acid 29.1 26 0.00055 19.1 0.5 13 32-44 138-150 (177)
317 TIGR00319 desulf_FeS4 desulfof 28.9 31 0.00066 12.8 0.6 11 33-43 7-17 (34)
318 cd00974 DSRD Desulforedoxin (D 28.8 31 0.00067 12.8 0.6 11 33-43 4-14 (34)
319 TIGR03829 YokU_near_AblA uncha 28.7 40 0.00087 16.1 1.1 21 34-54 36-56 (89)
320 KOG3352|consensus 28.6 36 0.00077 18.0 1.0 19 53-73 126-144 (153)
321 cd01407 SIR2-fam SIR2 family o 28.0 82 0.0018 17.4 2.4 34 33-71 109-142 (218)
322 PF10080 DUF2318: Predicted me 27.9 27 0.00059 17.1 0.5 30 18-47 37-66 (102)
323 PF02148 zf-UBP: Zn-finger in 27.2 33 0.00072 14.8 0.7 16 31-46 9-24 (63)
324 cd01675 RNR_III Class III ribo 27.2 43 0.00093 21.6 1.3 9 63-71 533-541 (555)
325 KOG0801|consensus 27.0 18 0.00038 19.4 -0.3 11 63-73 139-149 (205)
326 COG0777 AccD Acetyl-CoA carbox 26.9 22 0.00049 20.8 0.1 31 17-47 29-61 (294)
327 COG5533 UBP5 Ubiquitin C-termi 26.8 27 0.00059 21.0 0.4 10 17-26 236-245 (415)
328 PLN03238 probable histone acet 26.7 97 0.0021 18.4 2.5 27 31-57 46-72 (290)
329 COG1096 Predicted RNA-binding 26.6 43 0.00094 18.4 1.1 23 18-41 151-173 (188)
330 KOG1818|consensus 26.3 19 0.00042 23.6 -0.2 50 18-68 167-217 (634)
331 PF01844 HNH: HNH endonuclease 26.2 10 0.00022 14.9 -1.0 9 65-73 1-9 (47)
332 cd02249 ZZ Zinc finger, ZZ typ 26.2 60 0.0013 13.0 1.5 7 18-24 2-8 (46)
333 PF06170 DUF983: Protein of un 25.3 34 0.00073 16.2 0.5 11 35-45 10-20 (86)
334 PRK08270 anaerobic ribonucleos 25.2 42 0.00091 22.2 1.1 9 63-71 640-648 (656)
335 PF13639 zf-RING_2: Ring finge 25.2 52 0.0011 12.8 1.0 28 18-47 2-29 (44)
336 PF09082 DUF1922: Domain of un 25.1 30 0.00064 15.7 0.3 24 17-42 4-28 (68)
337 PF14354 Lar_restr_allev: Rest 25.1 44 0.00095 14.1 0.8 11 16-26 3-13 (61)
338 TIGR01031 rpmF_bact ribosomal 25.0 55 0.0012 14.0 1.1 19 18-40 28-46 (55)
339 COG5222 Uncharacterized conser 24.9 1.4E+02 0.0031 18.0 2.9 46 15-70 273-318 (427)
340 PRK08329 threonine synthase; V 24.9 49 0.0011 19.8 1.2 24 17-43 2-25 (347)
341 PRK00423 tfb transcription ini 24.9 59 0.0013 19.2 1.5 31 13-43 8-40 (310)
342 PRK05638 threonine synthase; V 24.7 43 0.00094 20.8 1.0 24 17-43 2-25 (442)
343 PF14447 Prok-RING_4: Prokaryo 24.7 40 0.00087 14.6 0.6 13 34-46 40-52 (55)
344 PF03884 DUF329: Domain of unk 24.6 32 0.00068 14.9 0.3 12 63-74 3-14 (57)
345 PF10367 Vps39_2: Vacuolar sor 24.6 45 0.00097 15.7 0.9 12 63-74 79-90 (109)
346 TIGR01385 TFSII transcription 24.5 14 0.00031 21.7 -0.9 10 63-72 287-296 (299)
347 PF14122 YokU: YokU-like prote 24.3 82 0.0018 15.0 1.6 16 34-49 36-51 (87)
348 PF13597 NRDD: Anaerobic ribon 24.3 41 0.00089 21.7 0.9 9 33-41 504-512 (546)
349 PRK08359 transcription factor; 24.3 24 0.00052 19.1 -0.1 30 15-44 5-41 (176)
350 PRK09710 lar restriction allev 24.2 49 0.0011 14.8 0.9 25 18-42 8-36 (64)
351 PRK11032 hypothetical protein; 23.9 68 0.0015 17.2 1.5 31 30-71 121-151 (160)
352 cd00162 RING RING-finger (Real 23.7 58 0.0013 12.0 3.0 8 63-70 36-43 (45)
353 TIGR00155 pqiA_fam integral me 23.6 80 0.0017 19.6 1.9 29 14-42 11-42 (403)
354 PF14255 Cys_rich_CPXG: Cystei 23.5 51 0.0011 14.0 0.8 9 64-72 2-10 (52)
355 PF14375 Cys_rich_CWC: Cystein 23.3 46 0.001 13.7 0.7 7 66-72 2-8 (50)
356 PF04438 zf-HIT: HIT zinc fing 23.1 36 0.00077 12.5 0.3 8 63-70 14-21 (30)
357 PRK02935 hypothetical protein; 23.1 50 0.0011 16.4 0.9 27 16-43 70-96 (110)
358 KOG4727|consensus 23.0 65 0.0014 17.6 1.3 24 31-54 73-96 (193)
359 COG1631 RPL42A Ribosomal prote 22.6 26 0.00056 16.8 -0.1 10 63-72 69-78 (94)
360 KOG0562|consensus 22.5 42 0.00091 18.2 0.6 23 63-85 154-176 (184)
361 PRK08197 threonine synthase; V 22.4 48 0.001 20.2 0.9 26 16-43 7-32 (394)
362 smart00391 MBD Methyl-CpG bind 22.3 66 0.0014 14.8 1.2 16 68-83 36-51 (77)
363 cd01410 SIRT7 SIRT7: Eukaryoti 22.3 1.5E+02 0.0033 16.4 2.7 35 33-71 95-129 (206)
364 PF04161 Arv1: Arv1-like famil 22.2 43 0.00093 18.5 0.6 8 34-41 25-32 (208)
365 cd02337 ZZ_CBP Zinc finger, ZZ 22.1 74 0.0016 12.6 1.4 7 33-39 13-19 (41)
366 COG3024 Uncharacterized protei 22.0 49 0.0011 14.8 0.7 12 63-74 8-19 (65)
367 COG5574 PEX10 RING-finger-cont 21.9 61 0.0013 19.0 1.2 45 14-69 213-258 (271)
368 COG1655 Uncharacterized protei 21.9 18 0.00039 20.6 -0.8 8 63-70 63-70 (267)
369 KOG3268|consensus 21.8 1.6E+02 0.0035 16.3 2.7 13 16-28 148-160 (234)
370 PRK00481 NAD-dependent deacety 21.7 91 0.002 17.6 1.8 29 33-70 122-150 (242)
371 PTZ00409 Sir2 (Silent Informat 21.6 1.4E+02 0.0031 17.4 2.6 15 33-47 137-151 (271)
372 PRK07111 anaerobic ribonucleos 21.6 56 0.0012 22.1 1.1 7 34-40 694-700 (735)
373 cd00122 MBD MeCP2, MBD1, MBD2, 21.5 75 0.0016 13.7 1.2 16 68-83 33-48 (62)
374 COG1579 Zn-ribbon protein, pos 21.4 77 0.0017 18.2 1.5 35 35-74 199-233 (239)
375 COG1885 Uncharacterized protei 20.7 62 0.0013 16.0 0.9 10 63-72 50-59 (115)
376 PF06957 COPI_C: Coatomer (COP 20.5 50 0.0011 20.7 0.7 25 20-44 365-391 (422)
377 KOG4602|consensus 20.4 47 0.001 19.4 0.6 11 32-42 267-277 (318)
378 smart00647 IBR In Between Ring 20.4 76 0.0016 13.2 1.1 10 63-72 41-50 (64)
379 PF03833 PolC_DP2: DNA polymer 20.4 34 0.00073 23.5 0.0 9 17-25 656-664 (900)
380 TIGR00382 clpX endopeptidase C 20.1 62 0.0013 20.2 1.0 26 18-43 9-39 (413)
No 1
>KOG2462|consensus
Probab=99.88 E-value=2.9e-23 Score=111.15 Aligned_cols=83 Identities=24% Similarity=0.442 Sum_probs=54.1
Q ss_pred ccceeeccccCC---CCcccccccchhhhcc---------CCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCC
Q psy12019 2 LNVIVKPRTHRE---PKHNKCLINWSAVQQN---------HAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCP 69 (87)
Q Consensus 2 ~~l~~h~~~h~~---~~~~~c~~c~~~~~~~---------~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~ 69 (87)
++|..|..+|.. .+.+.|..|++.+.+. ..-+++|..||+.|...=.|+.|+|+|+||+| |.|..|+
T Consensus 144 snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKP-F~C~hC~ 222 (279)
T KOG2462|consen 144 SNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKP-FSCPHCG 222 (279)
T ss_pred cccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCC-ccCCccc
Confidence 456666666642 3456677777776653 23356677777777666667777777777666 7777777
Q ss_pred cccccchHHHhhhhhc
Q psy12019 70 YRAKQNAHLTTHMAIK 85 (87)
Q Consensus 70 ~~f~~~~~l~~h~~~~ 85 (87)
|+|..+++|..|+++|
T Consensus 223 kAFADRSNLRAHmQTH 238 (279)
T KOG2462|consen 223 KAFADRSNLRAHMQTH 238 (279)
T ss_pred chhcchHHHHHHHHhh
Confidence 7777777777776665
No 2
>KOG2462|consensus
Probab=99.87 E-value=5e-23 Score=110.28 Aligned_cols=78 Identities=23% Similarity=0.392 Sum_probs=72.3
Q ss_pred cceeeccccCCCCcccccccchhhhcc-----------CCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcc
Q psy12019 3 NVIVKPRTHREPKHNKCLINWSAVQQN-----------HAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYR 71 (87)
Q Consensus 3 ~l~~h~~~h~~~~~~~c~~c~~~~~~~-----------~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~ 71 (87)
.|..|+|+|. -+.+|.+|++.|+.. |++||.|..|+++|.+.++|..|+++|.+.++ |+|..|+|+
T Consensus 176 ALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~-~qC~~C~Ks 252 (279)
T KOG2462|consen 176 ALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKK-HQCPRCGKS 252 (279)
T ss_pred HHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCcc-ccCcchhhH
Confidence 4778888887 689999999999864 89999999999999999999999999999998 999999999
Q ss_pred cccchHHHhhhh
Q psy12019 72 AKQNAHLTTHMA 83 (87)
Q Consensus 72 f~~~~~l~~h~~ 83 (87)
|...+-|++|..
T Consensus 253 Fsl~SyLnKH~E 264 (279)
T KOG2462|consen 253 FALKSYLNKHSE 264 (279)
T ss_pred HHHHHHHHHhhh
Confidence 999999999964
No 3
>KOG1074|consensus
Probab=99.73 E-value=8.8e-19 Score=105.10 Aligned_cols=53 Identities=19% Similarity=0.469 Sum_probs=50.0
Q ss_pred cceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccccchHHHhhhhhc
Q psy12019 32 GMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMAIK 85 (87)
Q Consensus 32 ~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 85 (87)
.|.+|..|.+..+-.++|+.|.+.|+||+| |+|.+||++|....+|+.|+.+|
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERP-FkCKiCgRAFtTkGNLkaH~~vH 656 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERP-FKCKICGRAFTTKGNLKAHMSVH 656 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCc-cccccccchhccccchhhccccc
Confidence 367899999999999999999999999999 99999999999999999998775
No 4
>KOG3623|consensus
Probab=99.66 E-value=2.3e-17 Score=98.36 Aligned_cols=70 Identities=27% Similarity=0.545 Sum_probs=64.5
Q ss_pred CCCcccccccchhhhcc-----------CCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccccchHHHhh
Q psy12019 13 EPKHNKCLINWSAVQQN-----------HAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTH 81 (87)
Q Consensus 13 ~~~~~~c~~c~~~~~~~-----------~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h 81 (87)
.+-.|.|..|+++|... |.+||+|..|.++|...-.|..|.|.|.|++| |+|..|+|+|+++.+...|
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKP-fQCdKClKRFSHSGSYSQH 969 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKP-FQCDKCLKRFSHSGSYSQH 969 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCc-chhhhhhhhcccccchHhh
Confidence 34579999999999753 88899999999999999999999999999999 9999999999999999998
Q ss_pred hh
Q psy12019 82 MA 83 (87)
Q Consensus 82 ~~ 83 (87)
+-
T Consensus 970 MN 971 (1007)
T KOG3623|consen 970 MN 971 (1007)
T ss_pred hc
Confidence 73
No 5
>KOG1074|consensus
Probab=99.65 E-value=5e-17 Score=97.77 Aligned_cols=53 Identities=25% Similarity=0.604 Sum_probs=50.4
Q ss_pred eecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccccchHHHhhhhhcCC
Q psy12019 34 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMAIKHY 87 (87)
Q Consensus 34 ~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~h~ 87 (87)
..|..||+.|...++|+.|+++|++++| |.|..|++.|.....|+.|+.+|+.
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KP-F~C~fC~~aFttrgnLKvHMgtH~w 932 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKP-FFCHFCEEAFTTRGNLKVHMGTHMW 932 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCC-ccchhhhhhhhhhhhhhhhhccccc
Confidence 5799999999999999999999999999 9999999999999999999998863
No 6
>KOG3623|consensus
Probab=99.54 E-value=1.7e-15 Score=90.65 Aligned_cols=70 Identities=24% Similarity=0.648 Sum_probs=61.7
Q ss_pred CCCcccccccchhhhcc------------------------CCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCC
Q psy12019 13 EPKHNKCLINWSAVQQN------------------------HAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQC 68 (87)
Q Consensus 13 ~~~~~~c~~c~~~~~~~------------------------~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c 68 (87)
.+..|.|..|..+|-.. ..+.|.|.+||++|...-.|..|+|+|.|++| |+|+.|
T Consensus 237 ne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKP-feCpnC 315 (1007)
T KOG3623|consen 237 NEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKP-FECPNC 315 (1007)
T ss_pred CCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCC-cCCccc
Confidence 34568999999998652 23469999999999999999999999999999 999999
Q ss_pred CcccccchHHHhhhh
Q psy12019 69 PYRAKQNAHLTTHMA 83 (87)
Q Consensus 69 ~~~f~~~~~l~~h~~ 83 (87)
+|+|+++.+...|+.
T Consensus 316 kKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 316 KKRFSHSGSYSSHMS 330 (1007)
T ss_pred ccccccCCccccccc
Confidence 999999999998874
No 7
>KOG3576|consensus
Probab=99.54 E-value=9.7e-16 Score=79.88 Aligned_cols=75 Identities=23% Similarity=0.491 Sum_probs=64.7
Q ss_pred CCCCcccccccchhhhcc-----------CCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccccchHHHh
Q psy12019 12 REPKHNKCLINWSAVQQN-----------HAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTT 80 (87)
Q Consensus 12 ~~~~~~~c~~c~~~~~~~-----------~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~ 80 (87)
.+...|.|.+|++.|... ..+.+-|..||+.|...-.|..|.++|+|.+| |.|+.|+|+|.+.-+|..
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrp-ykc~~c~kaftqrcsles 191 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRP-YKCSLCEKAFTQRCSLES 191 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccc-cchhhhhHHHHhhccHHH
Confidence 344568999999999753 33457799999999999999999999999998 999999999999999999
Q ss_pred hhhhcCC
Q psy12019 81 HMAIKHY 87 (87)
Q Consensus 81 h~~~~h~ 87 (87)
|.+.-|+
T Consensus 192 hl~kvhg 198 (267)
T KOG3576|consen 192 HLKKVHG 198 (267)
T ss_pred HHHHHcC
Confidence 9876554
No 8
>PHA00733 hypothetical protein
Probab=99.48 E-value=2.1e-14 Score=71.11 Aligned_cols=73 Identities=15% Similarity=0.320 Sum_probs=61.8
Q ss_pred CCCCcccccccchhhhcc----------------CCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccccc
Q psy12019 12 REPKHNKCLINWSAVQQN----------------HAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQN 75 (87)
Q Consensus 12 ~~~~~~~c~~c~~~~~~~----------------~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~~ 75 (87)
...+++.|.+|...+... +.++|.|+.||+.|.....|..|++.+ +.+ +.|.+|++.|...
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~-~~C~~CgK~F~~~ 112 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHS-KVCPVCGKEFRNT 112 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcC-ccCCCCCCccCCH
Confidence 345678898888777543 456899999999999999999999976 355 9999999999999
Q ss_pred hHHHhhhhhcCC
Q psy12019 76 AHLTTHMAIKHY 87 (87)
Q Consensus 76 ~~l~~h~~~~h~ 87 (87)
..|..|+...|.
T Consensus 113 ~sL~~H~~~~h~ 124 (128)
T PHA00733 113 DSTLDHVCKKHN 124 (128)
T ss_pred HHHHHHHHHhcC
Confidence 999999988774
No 9
>PHA02768 hypothetical protein; Provisional
Probab=99.43 E-value=8.8e-14 Score=58.73 Aligned_cols=44 Identities=14% Similarity=0.360 Sum_probs=39.6
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccccchHHH
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLT 79 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~ 79 (87)
.|+|+.||+.|...++|..|++.|+ ++ +.|..|++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~-~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TN-LKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--Cc-ccCCcccceecccceeE
Confidence 4799999999999999999999998 56 99999999999877653
No 10
>KOG3608|consensus
Probab=99.36 E-value=3e-13 Score=75.68 Aligned_cols=83 Identities=18% Similarity=0.454 Sum_probs=64.9
Q ss_pred ccceeeccccCCCCcccccccchhhhcc---------------------------------------CCcceecCccccc
Q psy12019 2 LNVIVKPRTHREPKHNKCLINWSAVQQN---------------------------------------HAGMFMCDVCGKG 42 (87)
Q Consensus 2 ~~l~~h~~~h~~~~~~~c~~c~~~~~~~---------------------------------------~~~~~~c~~c~~~ 42 (87)
.+|+.|.+.|+++|...|+.|+..|... ....|.|+.|+..
T Consensus 193 ~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmt 272 (467)
T KOG3608|consen 193 YRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMT 272 (467)
T ss_pred HHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccC
Confidence 5788999999999999999999999763 1224677777777
Q ss_pred ccchhhHHHHhhhh-cCCCCCccCCCCCcccccchHHHhhhhhc
Q psy12019 43 YKYKNGIYRHKKFE-CGQEPKYQCPQCPYRAKQNAHLTTHMAIK 85 (87)
Q Consensus 43 ~~~~~~~~~h~~~~-~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 85 (87)
....+.|..|++.- ..++| |+|..|.+.+...+.|.+|...|
T Consensus 273 c~~~ssL~~H~r~rHs~dkp-fKCd~Cd~~c~~esdL~kH~~~H 315 (467)
T KOG3608|consen 273 CSSASSLTTHIRYRHSKDKP-FKCDECDTRCVRESDLAKHVQVH 315 (467)
T ss_pred CCChHHHHHHHHhhhccCCC-ccccchhhhhccHHHHHHHHHhc
Confidence 77778888887753 34455 88888888888888888887754
No 11
>KOG3576|consensus
Probab=99.15 E-value=5.8e-12 Score=66.05 Aligned_cols=82 Identities=18% Similarity=0.425 Sum_probs=63.5
Q ss_pred ceeeccccCCCCcccccccchhhhcc-----------CCcceecCcccccccchhhHHHHhhhhcC-----------CCC
Q psy12019 4 VIVKPRTHREPKHNKCLINWSAVQQN-----------HAGMFMCDVCGKGYKYKNGIYRHKKFECG-----------QEP 61 (87)
Q Consensus 4 l~~h~~~h~~~~~~~c~~c~~~~~~~-----------~~~~~~c~~c~~~~~~~~~~~~h~~~~~~-----------~~~ 61 (87)
|..|++-|...+-+.|..|++.|... +.+||.|..|+++|.....|..|.+.-.| .+.
T Consensus 133 lnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl 212 (267)
T KOG3576|consen 133 LNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKL 212 (267)
T ss_pred HHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhhe
Confidence 45677778888888888888888764 66788899999999888888888774333 244
Q ss_pred CccCCCCCcccccchHHHhhhhhcC
Q psy12019 62 KYQCPQCPYRAKQNAHLTTHMAIKH 86 (87)
Q Consensus 62 ~~~c~~c~~~f~~~~~l~~h~~~~h 86 (87)
|.|..||.+-.....+..|+..+|
T Consensus 213 -~vcedcg~t~~~~e~~~~h~~~~h 236 (267)
T KOG3576|consen 213 -YVCEDCGYTSERPEVYYLHLKLHH 236 (267)
T ss_pred -eeecccCCCCCChhHHHHHHHhcC
Confidence 888899988877777777877765
No 12
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.13 E-value=4e-11 Score=43.83 Aligned_cols=26 Identities=31% Similarity=0.782 Sum_probs=23.5
Q ss_pred hHHHHhhhhcCCCCCccCCCCCccccc
Q psy12019 48 GIYRHKKFECGQEPKYQCPQCPYRAKQ 74 (87)
Q Consensus 48 ~~~~h~~~~~~~~~~~~c~~c~~~f~~ 74 (87)
+|..|++.|++++| |.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~-~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKP-YKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSS-EEESSSSEEESS
T ss_pred CHHHHhhhcCCCCC-CCCCCCcCeeCc
Confidence 47899999999998 999999999963
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=99.06 E-value=7.7e-12 Score=45.76 Aligned_cols=25 Identities=28% Similarity=0.258 Sum_probs=22.5
Q ss_pred cceeeccccCCCCcccccccchhhh
Q psy12019 3 NVIVKPRTHREPKHNKCLINWSAVQ 27 (87)
Q Consensus 3 ~l~~h~~~h~~~~~~~c~~c~~~~~ 27 (87)
+|..|+++|++++||.|+.|++.|.
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 4788999999999999999998875
No 14
>KOG3608|consensus
Probab=98.93 E-value=5e-10 Score=63.14 Aligned_cols=85 Identities=20% Similarity=0.296 Sum_probs=65.0
Q ss_pred ccceeecc-ccCCCCcccccccchhhhcc----------CCcceecCc--ccccccchhhHHHHhhhhc-CCC-CCccCC
Q psy12019 2 LNVIVKPR-THREPKHNKCLINWSAVQQN----------HAGMFMCDV--CGKGYKYKNGIYRHKKFEC-GQE-PKYQCP 66 (87)
Q Consensus 2 ~~l~~h~~-~h~~~~~~~c~~c~~~~~~~----------~~~~~~c~~--c~~~~~~~~~~~~h~~~~~-~~~-~~~~c~ 66 (87)
+.|..|++ .|+..+||+|..|+..+..+ .+..|.|.. |..++++...+..|.+-+. |.. ++|.|-
T Consensus 277 ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH 356 (467)
T KOG3608|consen 277 SSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACH 356 (467)
T ss_pred HHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeee
Confidence 45677776 47788899999999888664 344678877 8888888888888887444 433 348999
Q ss_pred CCCcccccchHHHhhhhhcC
Q psy12019 67 QCPYRAKQNAHLTTHMAIKH 86 (87)
Q Consensus 67 ~c~~~f~~~~~l~~h~~~~h 86 (87)
.|.+.|..-.+|..|+.-.|
T Consensus 357 ~Cdr~ft~G~~L~~HL~kkH 376 (467)
T KOG3608|consen 357 CCDRFFTSGKSLSAHLMKKH 376 (467)
T ss_pred cchhhhccchhHHHHHHHhh
Confidence 99999999999999987555
No 15
>PHA00732 hypothetical protein
Probab=98.87 E-value=2.2e-09 Score=49.09 Aligned_cols=45 Identities=24% Similarity=0.496 Sum_probs=37.1
Q ss_pred ceecCcccccccchhhHHHHhhh-hcCCCCCccCCCCCcccccchHHHhhhhh
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKF-ECGQEPKYQCPQCPYRAKQNAHLTTHMAI 84 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~-~~~~~~~~~c~~c~~~f~~~~~l~~h~~~ 84 (87)
||.|+.||+.|.....|..|++. |. + +.|++|++.|. .+..|.+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~-~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---L-TKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---C-CccCCCCCEeC---Chhhhhcc
Confidence 57899999999999999999984 54 3 78999999997 46677643
No 16
>PHA00616 hypothetical protein
Probab=98.76 E-value=2.9e-09 Score=43.12 Aligned_cols=26 Identities=23% Similarity=0.451 Sum_probs=20.2
Q ss_pred CccCCCCCcccccchHHHhhhhhcCC
Q psy12019 62 KYQCPQCPYRAKQNAHLTTHMAIKHY 87 (87)
Q Consensus 62 ~~~c~~c~~~f~~~~~l~~h~~~~h~ 87 (87)
||+|+.||+.|.+.++|..|++.+|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg 26 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHK 26 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcC
Confidence 37788888888888888888877764
No 17
>PHA00616 hypothetical protein
Probab=98.75 E-value=5e-09 Score=42.43 Aligned_cols=34 Identities=21% Similarity=0.316 Sum_probs=30.8
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCC
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQ 67 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~ 67 (87)
||+|..||+.|...+.+..|++.++++++ +.|..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~-~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK-LTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc-cceeE
Confidence 58999999999999999999999999988 87653
No 18
>KOG3993|consensus
Probab=98.73 E-value=1.7e-09 Score=62.17 Aligned_cols=71 Identities=14% Similarity=0.338 Sum_probs=57.4
Q ss_pred cccccccchhhhcc-----------CCcceecCcccccccchhhHHHHhhhhcCC--------C----------------
Q psy12019 16 HNKCLINWSAVQQN-----------HAGMFMCDVCGKGYKYKNGIYRHKKFECGQ--------E---------------- 60 (87)
Q Consensus 16 ~~~c~~c~~~~~~~-----------~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~--------~---------------- 60 (87)
.|.|+.|...|.+. -..-|.|++|+|.|+-..+|..|+|+|.-. .
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 47888888887664 223589999999999999999999997521 1
Q ss_pred --------CCccCCCCCcccccchHHHhhhhhcC
Q psy12019 61 --------PKYQCPQCPYRAKQNAHLTTHMAIKH 86 (87)
Q Consensus 61 --------~~~~c~~c~~~f~~~~~l~~h~~~~h 86 (87)
..|.|..|+|.|+...-|..|+-.||
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 13789999999999999999987775
No 19
>PHA02768 hypothetical protein; Provisional
Probab=98.58 E-value=3.1e-08 Score=42.01 Aligned_cols=24 Identities=25% Similarity=0.570 Sum_probs=23.0
Q ss_pred ccCCCCCcccccchHHHhhhhhcC
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMAIKH 86 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~~h 86 (87)
|+|++||+.|...+.|..|+++|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC
Confidence 899999999999999999999975
No 20
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.54 E-value=5.8e-08 Score=58.29 Aligned_cols=37 Identities=22% Similarity=0.444 Sum_probs=18.6
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCccc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRA 72 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f 72 (87)
++.|+ ||+.+ ....|..|+..+...++ +.|..|++.|
T Consensus 478 pv~Cp-Cg~~~-~R~~L~~H~~thCp~Kp-i~C~fC~~~v 514 (567)
T PLN03086 478 PLQCP-CGVVL-EKEQMVQHQASTCPLRL-ITCRFCGDMV 514 (567)
T ss_pred CccCC-CCCCc-chhHHHhhhhccCCCCc-eeCCCCCCcc
Confidence 44555 55433 33455555555555444 5555555555
No 21
>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=98.53 E-value=3.3e-08 Score=34.88 Aligned_cols=22 Identities=32% Similarity=0.703 Sum_probs=14.0
Q ss_pred ccCCCCCcccccchHHHhhhhh
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMAI 84 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~ 84 (87)
|.|+.|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4566666666666666666655
No 22
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.52 E-value=2.9e-07 Score=39.25 Aligned_cols=52 Identities=27% Similarity=0.572 Sum_probs=39.2
Q ss_pred ceecCcccccccchhhHHHHhh-hhcCCCCCccCCCCCcccccchHHHhhhhhcCC
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKK-FECGQEPKYQCPQCPYRAKQNAHLTTHMAIKHY 87 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~-~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~h~ 87 (87)
.|.|+.|++. .....|..|.. .|..+...+.|++|...+. .+|..|+.+.|.
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 4789999995 45667888866 4555443499999998655 488999998874
No 23
>PHA00733 hypothetical protein
Probab=98.51 E-value=1e-07 Score=47.47 Aligned_cols=54 Identities=13% Similarity=0.233 Sum_probs=42.0
Q ss_pred ceeeccccCCCCcccccccchhhhcc---------CCcceecCcccccccchhhHHHHhhhhcC
Q psy12019 4 VIVKPRTHREPKHNKCLINWSAVQQN---------HAGMFMCDVCGKGYKYKNGIYRHKKFECG 58 (87)
Q Consensus 4 l~~h~~~h~~~~~~~c~~c~~~~~~~---------~~~~~~c~~c~~~~~~~~~~~~h~~~~~~ 58 (87)
|..++..+ +++||.|..|++.|... ...++.|+.|++.|.....|..|+....+
T Consensus 62 l~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 62 LYKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred HHhhcccC-CCCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 34444443 47899999999999764 14578999999999999999999876543
No 24
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.49 E-value=7e-08 Score=34.15 Aligned_cols=24 Identities=33% Similarity=0.764 Sum_probs=17.2
Q ss_pred ccCCCCCcccccchHHHhhhhhcC
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMAIKH 86 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~~h 86 (87)
|.|+.|++.|.+...|..|+..+|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 467788888888888888887766
No 25
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.40 E-value=1.5e-07 Score=34.48 Aligned_cols=24 Identities=17% Similarity=0.382 Sum_probs=16.3
Q ss_pred ccCCCCCcccccchHHHhhhhhcC
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMAIKH 86 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~~h 86 (87)
|.|..|++.|.....|..|++.|+
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 666777777777777777766654
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.38 E-value=3.5e-07 Score=32.17 Aligned_cols=23 Identities=30% Similarity=0.826 Sum_probs=21.0
Q ss_pred eecCcccccccchhhHHHHhhhh
Q psy12019 34 FMCDVCGKGYKYKNGIYRHKKFE 56 (87)
Q Consensus 34 ~~c~~c~~~~~~~~~~~~h~~~~ 56 (87)
|.|+.|++.|.....|..|++.|
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 68999999999999999999864
No 27
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.35 E-value=9.1e-07 Score=53.38 Aligned_cols=77 Identities=14% Similarity=0.318 Sum_probs=45.3
Q ss_pred ceeeccccCCCCcccccccchhhhcc----------CCcceecCcccccccc----------hhhHHHHhhhhcCCCCCc
Q psy12019 4 VIVKPRTHREPKHNKCLINWSAVQQN----------HAGMFMCDVCGKGYKY----------KNGIYRHKKFECGQEPKY 63 (87)
Q Consensus 4 l~~h~~~h~~~~~~~c~~c~~~~~~~----------~~~~~~c~~c~~~~~~----------~~~~~~h~~~~~~~~~~~ 63 (87)
|..|..++. +++.|+ |+..+... ..+++.|..|+..+.. .+.|..|.... |.++ +
T Consensus 468 LekH~~~~H--kpv~Cp-Cg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt-~ 542 (567)
T PLN03086 468 MEKHMKVFH--EPLQCP-CGVVLEKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRT-A 542 (567)
T ss_pred HHHHHHhcC--CCccCC-CCCCcchhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcc-e
Confidence 445555542 567776 76544321 3456777777776642 23566776664 5566 7
Q ss_pred cCCCCCcccccchHHHhhhhhcC
Q psy12019 64 QCPQCPYRAKQNAHLTTHMAIKH 86 (87)
Q Consensus 64 ~c~~c~~~f~~~~~l~~h~~~~h 86 (87)
.|..||+.+... .+..|+..-|
T Consensus 543 ~C~~Cgk~Vrlr-dm~~H~~~~h 564 (567)
T PLN03086 543 PCDSCGRSVMLK-EMDIHQIAVH 564 (567)
T ss_pred EccccCCeeeeh-hHHHHHHHhh
Confidence 777777776644 4566655443
No 28
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.13 E-value=1.9e-06 Score=31.42 Aligned_cols=25 Identities=36% Similarity=0.828 Sum_probs=22.7
Q ss_pred ceecCcccccccchhhHHHHhhhhc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFEC 57 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~ 57 (87)
+|.|+.|++.|.....|..|++.|.
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 5889999999999999999998764
No 29
>smart00355 ZnF_C2H2 zinc finger.
Probab=98.08 E-value=2.8e-06 Score=30.29 Aligned_cols=23 Identities=35% Similarity=0.751 Sum_probs=18.1
Q ss_pred ccCCCCCcccccchHHHhhhhhc
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMAIK 85 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~~ 85 (87)
|.|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 46788888888888888888754
No 30
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=98.00 E-value=2.8e-06 Score=35.29 Aligned_cols=26 Identities=31% Similarity=0.723 Sum_probs=18.4
Q ss_pred CccCCCCCcccccchHHHhhhhhcCC
Q psy12019 62 KYQCPQCPYRAKQNAHLTTHMAIKHY 87 (87)
Q Consensus 62 ~~~c~~c~~~f~~~~~l~~h~~~~h~ 87 (87)
|-.|++|+..+++..+|.+|+.+.|+
T Consensus 24 PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred CCCCCcchhhccchhhHHHHHHHHhc
Confidence 38888888888888888888888775
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=97.89 E-value=1.4e-05 Score=27.93 Aligned_cols=23 Identities=30% Similarity=0.852 Sum_probs=19.0
Q ss_pred eecCcccccccchhhHHHHhhhh
Q psy12019 34 FMCDVCGKGYKYKNGIYRHKKFE 56 (87)
Q Consensus 34 ~~c~~c~~~~~~~~~~~~h~~~~ 56 (87)
|.|+.|++.|.....+..|+..+
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 67999999999999999999865
No 32
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.88 E-value=2.9e-06 Score=47.83 Aligned_cols=26 Identities=35% Similarity=0.616 Sum_probs=21.9
Q ss_pred CCCccCCCCCcccccchHHHhhhhhcC
Q psy12019 60 EPKYQCPQCPYRAKQNAHLTTHMAIKH 86 (87)
Q Consensus 60 ~~~~~c~~c~~~f~~~~~l~~h~~~~h 86 (87)
+| |.|++|+|++.....|+-|..-.|
T Consensus 397 KP-YrCevC~KRYKNlNGLKYHr~Hsh 422 (423)
T COG5189 397 KP-YRCEVCDKRYKNLNGLKYHRKHSH 422 (423)
T ss_pred Cc-eeccccchhhccCccceecccccC
Confidence 55 999999999999999988876543
No 33
>PRK04860 hypothetical protein; Provisional
Probab=97.73 E-value=3.2e-05 Score=40.04 Aligned_cols=39 Identities=21% Similarity=0.483 Sum_probs=33.2
Q ss_pred cceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccccc
Q psy12019 32 GMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQN 75 (87)
Q Consensus 32 ~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~~ 75 (87)
-+|.|. |+. ....+..|.++++++++ |.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~-YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAV-YRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCcc-EECCCCCceeEEe
Confidence 368997 987 66778899999999998 9999999988654
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.67 E-value=3e-05 Score=36.68 Aligned_cols=22 Identities=27% Similarity=0.670 Sum_probs=16.4
Q ss_pred ccCCCCCcccccchHHHhhhhh
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMAI 84 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~ 84 (87)
+.|..|++.|.....|..|++.
T Consensus 51 ~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 51 FRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp EEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCccCCCCcCHHHHHHHHcC
Confidence 7788888888888888888764
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.67 E-value=4.8e-05 Score=26.89 Aligned_cols=24 Identities=29% Similarity=0.663 Sum_probs=21.1
Q ss_pred eecCcccccccchhhHHHHhhhhc
Q psy12019 34 FMCDVCGKGYKYKNGIYRHKKFEC 57 (87)
Q Consensus 34 ~~c~~c~~~~~~~~~~~~h~~~~~ 57 (87)
+.|..|++.|.....+..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 478999999999999999998664
No 36
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.64 E-value=2.4e-05 Score=27.66 Aligned_cols=24 Identities=33% Similarity=0.920 Sum_probs=16.3
Q ss_pred ccCCCCCcccccchHHHhhhhhcCC
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMAIKHY 87 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~~h~ 87 (87)
|.|+.|+.... ...|..|++.+|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 46778887776 7788888877763
No 37
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.46 E-value=0.00011 Score=26.09 Aligned_cols=22 Identities=32% Similarity=0.857 Sum_probs=11.8
Q ss_pred eecCcccccccchhhHHHHhhh
Q psy12019 34 FMCDVCGKGYKYKNGIYRHKKF 55 (87)
Q Consensus 34 ~~c~~c~~~~~~~~~~~~h~~~ 55 (87)
|.|+.|++.|.....+.+|++.
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 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.41 E-value=7e-05 Score=26.59 Aligned_cols=22 Identities=18% Similarity=0.443 Sum_probs=19.9
Q ss_pred ccCCCCCcccccchHHHhhhhh
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMAI 84 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~ 84 (87)
|.|..|++.|.....+..|++.
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 5689999999999999999875
No 39
>PHA00732 hypothetical protein
Probab=97.40 E-value=9e-05 Score=34.03 Aligned_cols=38 Identities=24% Similarity=0.349 Sum_probs=28.2
Q ss_pred cccccccchhhhcc---------CCcceecCcccccccchhhHHHHhhhh
Q psy12019 16 HNKCLINWSAVQQN---------HAGMFMCDVCGKGYKYKNGIYRHKKFE 56 (87)
Q Consensus 16 ~~~c~~c~~~~~~~---------~~~~~~c~~c~~~~~~~~~~~~h~~~~ 56 (87)
||.|..|++.|... ...++.|+.||+.|. .+..|....
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeC---Chhhhhccc
Confidence 68899999999764 123578999999997 466676543
No 40
>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=97.22 E-value=0.00034 Score=29.73 Aligned_cols=40 Identities=13% Similarity=0.322 Sum_probs=28.4
Q ss_pred cccccccchhhhcc------------CCcceecCcccccccchhhHHHHhhhhc
Q psy12019 16 HNKCLINWSAVQQN------------HAGMFMCDVCGKGYKYKNGIYRHKKFEC 57 (87)
Q Consensus 16 ~~~c~~c~~~~~~~------------~~~~~~c~~c~~~~~~~~~~~~h~~~~~ 57 (87)
.|.|+.|++.|... ..+.+.|+.|...+. .++..|+..+.
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 58899999966532 334688999997644 47888877643
No 41
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.20 E-value=0.00023 Score=25.84 Aligned_cols=21 Identities=24% Similarity=0.551 Sum_probs=14.1
Q ss_pred ccCCCCCcccccchHHHhhhh
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMA 83 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~ 83 (87)
|-|..|++.|.....+..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 556677777777777766664
No 42
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.09 E-value=0.00027 Score=25.62 Aligned_cols=22 Identities=36% Similarity=0.733 Sum_probs=19.8
Q ss_pred eecCcccccccchhhHHHHhhh
Q psy12019 34 FMCDVCGKGYKYKNGIYRHKKF 55 (87)
Q Consensus 34 ~~c~~c~~~~~~~~~~~~h~~~ 55 (87)
|.|..|++.|.....+..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6799999999999999999875
No 43
>KOG3993|consensus
Probab=97.08 E-value=8.7e-05 Score=43.55 Aligned_cols=52 Identities=21% Similarity=0.482 Sum_probs=45.2
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccccchHHHhhhhhc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMAIK 85 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 85 (87)
.|.|..|...|...-.|.+|.-.-+...- |.|++|+|.|+=..+|-.|.|-|
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vE-YrCPEC~KVFsCPANLASHRRWH 318 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVE-YRCPECDKVFSCPANLASHRRWH 318 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEee-ecCCcccccccCchhhhhhhccc
Confidence 58899999999999999999876666555 99999999999999999998754
No 44
>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=96.97 E-value=0.0015 Score=27.36 Aligned_cols=31 Identities=19% Similarity=0.421 Sum_probs=21.9
Q ss_pred CcceecCcccccccchhhHHHHhhhhcCCCC
Q psy12019 31 AGMFMCDVCGKGYKYKNGIYRHKKFECGQEP 61 (87)
Q Consensus 31 ~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~ 61 (87)
..|-.|+.|+..++...+|..|+....+.+|
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 3577899999999999999999988777554
No 45
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.87 E-value=0.001 Score=23.74 Aligned_cols=20 Identities=25% Similarity=0.536 Sum_probs=11.8
Q ss_pred ccCCCCCcccccchHHHhhhh
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMA 83 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~ 83 (87)
..|+.||+.| ....|..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3566677777 3445566654
No 46
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.77 E-value=0.0014 Score=30.88 Aligned_cols=25 Identities=20% Similarity=0.580 Sum_probs=21.7
Q ss_pred ceecCcccccccchhhHHHHhhhhc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFEC 57 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~ 57 (87)
.+.|..|++.|.....|..|++.+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 5899999999999999999999753
No 47
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=96.42 E-value=0.0047 Score=26.64 Aligned_cols=49 Identities=27% Similarity=0.548 Sum_probs=31.5
Q ss_pred cccccccchhh-hccCCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCc
Q psy12019 16 HNKCLINWSAV-QQNHAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 70 (87)
Q Consensus 16 ~~~c~~c~~~~-~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~ 70 (87)
+-.|..|+... ..++...|.|+.||+..-.... +--....+ |.|+.||-
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~-----~CRk~g~~-Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCA-----KCRKLGNP-YRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhh-----hHHHcCCc-eECCCcCc
Confidence 45677787776 3334557899999966544432 22223366 99999984
No 48
>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=96.41 E-value=0.0023 Score=31.18 Aligned_cols=30 Identities=13% Similarity=0.326 Sum_probs=23.7
Q ss_pred ccccccchhhhccCCcceecCcccccccch
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGKGYKYK 46 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~ 46 (87)
-.|+.|+..|-..+..|..|+.||..|...
T Consensus 10 R~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 368888888888877888888888877665
No 49
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=96.08 E-value=0.0043 Score=23.62 Aligned_cols=21 Identities=14% Similarity=0.498 Sum_probs=13.8
Q ss_pred ccCCCCCcccccchHHHhhhh
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMA 83 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~ 83 (87)
|.|..|++.|.....+..|+.
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEccccCCccCCHHHHHHHHC
Confidence 567777777776666666653
No 50
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=96.02 E-value=0.014 Score=25.22 Aligned_cols=50 Identities=28% Similarity=0.633 Sum_probs=31.5
Q ss_pred CcccccccchhhhccC-CcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCc
Q psy12019 15 KHNKCLINWSAVQQNH-AGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 70 (87)
Q Consensus 15 ~~~~c~~c~~~~~~~~-~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~ 70 (87)
.+..|..|+......+ ...|.|+.||+.....-. +--....+ |.|+.||.
T Consensus 6 ~~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~-----~CRk~~~~-Y~CP~CGF 56 (59)
T PRK14890 6 EPPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCE-----KCRKQSNP-YTCPKCGF 56 (59)
T ss_pred cCccccCCCCcccCCCccCEeeCCCCCCeeEeech-----hHHhcCCc-eECCCCCC
Confidence 3557888887766443 457899999986333321 11122255 99999984
No 51
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=95.84 E-value=0.009 Score=22.72 Aligned_cols=8 Identities=38% Similarity=1.161 Sum_probs=5.2
Q ss_pred ccCCCCCc
Q psy12019 63 YQCPQCPY 70 (87)
Q Consensus 63 ~~c~~c~~ 70 (87)
+.|++||.
T Consensus 18 ~~CP~Cg~ 25 (33)
T cd00350 18 WVCPVCGA 25 (33)
T ss_pred CcCcCCCC
Confidence 66777653
No 52
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=95.35 E-value=0.01 Score=24.17 Aligned_cols=24 Identities=17% Similarity=0.282 Sum_probs=10.7
Q ss_pred ccccccchhhhccCCcceecCccc
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCG 40 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~ 40 (87)
|.|..|+..+......+..|+.||
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG 26 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECG 26 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCC
Confidence 444444444443333344444444
No 53
>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=95.34 E-value=0.011 Score=22.37 Aligned_cols=8 Identities=38% Similarity=1.219 Sum_probs=3.5
Q ss_pred ccCCCCCc
Q psy12019 63 YQCPQCPY 70 (87)
Q Consensus 63 ~~c~~c~~ 70 (87)
..|+.||.
T Consensus 18 irC~~CG~ 25 (32)
T PF03604_consen 18 IRCPECGH 25 (32)
T ss_dssp SSBSSSS-
T ss_pred EECCcCCC
Confidence 45555543
No 54
>PRK04860 hypothetical protein; Provisional
Probab=95.32 E-value=0.0029 Score=32.93 Aligned_cols=30 Identities=17% Similarity=0.416 Sum_probs=18.9
Q ss_pred cccccccchhhhcc--------CCcceecCcccccccch
Q psy12019 16 HNKCLINWSAVQQN--------HAGMFMCDVCGKGYKYK 46 (87)
Q Consensus 16 ~~~c~~c~~~~~~~--------~~~~~~c~~c~~~~~~~ 46 (87)
+|.|. |+....+. +.++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 67786 76633221 45678888888776543
No 55
>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=95.29 E-value=0.012 Score=29.38 Aligned_cols=32 Identities=9% Similarity=0.047 Sum_probs=24.8
Q ss_pred ccccccchhhhccCCcceecCcccccccchhh
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGKGYKYKNG 48 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~ 48 (87)
..|+.|+..|-..+..|..|+.||..|.....
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~~~ 41 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQFPPEEA 41 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCccCcchh
Confidence 46888888888887788888888887765533
No 56
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=95.07 E-value=0.014 Score=23.84 Aligned_cols=27 Identities=26% Similarity=0.423 Sum_probs=14.2
Q ss_pred cccccccchhhhccCCc-ceecCccccc
Q psy12019 16 HNKCLINWSAVQQNHAG-MFMCDVCGKG 42 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~-~~~c~~c~~~ 42 (87)
.|.|+.|+..+...... ...|+.||..
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCe
Confidence 45666666655443221 4566666643
No 57
>KOG2893|consensus
Probab=94.96 E-value=0.0073 Score=33.41 Aligned_cols=41 Identities=20% Similarity=0.516 Sum_probs=30.8
Q ss_pred cCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccccchHHHhh
Q psy12019 36 CDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTH 81 (87)
Q Consensus 36 c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h 81 (87)
|=.|++.|.....|.+|++. +. |+|-+|.|.+-+-..|..|
T Consensus 13 cwycnrefddekiliqhqka----kh-fkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KH-FKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhh----cc-ceeeeehhhhccCCCceee
Confidence 33688899999999999875 66 8999998765555555555
No 58
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.91 E-value=0.0098 Score=25.34 Aligned_cols=29 Identities=21% Similarity=0.482 Sum_probs=17.9
Q ss_pred CCcceecCcccccccchhhHHHHhhhhcC
Q psy12019 30 HAGMFMCDVCGKGYKYKNGIYRHKKFECG 58 (87)
Q Consensus 30 ~~~~~~c~~c~~~~~~~~~~~~h~~~~~~ 58 (87)
++.-+.|+.||..|........|.....+
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 34456677777777776666666654444
No 59
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=94.72 E-value=0.022 Score=31.12 Aligned_cols=16 Identities=13% Similarity=0.198 Sum_probs=12.3
Q ss_pred CCcccccccchhhhcc
Q psy12019 14 PKHNKCLINWSAVQQN 29 (87)
Q Consensus 14 ~~~~~c~~c~~~~~~~ 29 (87)
++...|++|+..|...
T Consensus 3 ~k~~~CPvC~~~F~~~ 18 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTK 18 (214)
T ss_pred CCceECCCCCCeeeee
Confidence 3567899999998754
No 60
>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=94.67 E-value=0.027 Score=21.59 Aligned_cols=9 Identities=44% Similarity=1.143 Sum_probs=5.5
Q ss_pred eecCccccc
Q psy12019 34 FMCDVCGKG 42 (87)
Q Consensus 34 ~~c~~c~~~ 42 (87)
|.|..||..
T Consensus 3 ~~C~~CG~i 11 (34)
T cd00729 3 WVCPVCGYI 11 (34)
T ss_pred EECCCCCCE
Confidence 566666654
No 61
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.25 E-value=0.013 Score=34.34 Aligned_cols=53 Identities=21% Similarity=0.508 Sum_probs=46.4
Q ss_pred ceecCcccccccchhhHHHHhh--hhcCC--CCCccCC--CCCcccccchHHHhhhhhcC
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKK--FECGQ--EPKYQCP--QCPYRAKQNAHLTTHMAIKH 86 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~--~~~~~--~~~~~c~--~c~~~f~~~~~l~~h~~~~h 86 (87)
++.|..|...|.....+..|.+ .|.++ ++ +.|+ .|++.|.....+..|..++.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~-~~~p~~~~~~~~~~~~~~~~~~~~~~ 347 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKP-FSCPYSLCGKLFSRNDALKRHILLHT 347 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCc-eeeeccCCCccccccccccCCccccc
Confidence 5788889999999999999999 89998 77 9999 79999999998888876653
No 62
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=93.83 E-value=0.023 Score=31.60 Aligned_cols=57 Identities=16% Similarity=0.257 Sum_probs=28.6
Q ss_pred CCCcccccccchhhhcc---CCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccccc
Q psy12019 13 EPKHNKCLINWSAVQQN---HAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQN 75 (87)
Q Consensus 13 ~~~~~~c~~c~~~~~~~---~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~~ 75 (87)
..+.|.|..|....... ....-.|..|.+.|..-.. ....|-.. |.|+.|+..|...
T Consensus 109 ~drqFaC~~Cd~~WwRrvp~rKeVSRCr~C~~rYDPVP~-----dkmwG~ae-f~C~~C~h~F~G~ 168 (278)
T PF15135_consen 109 VDRQFACSSCDHMWWRRVPQRKEVSRCRKCRKRYDPVPC-----DKMWGIAE-FHCPKCRHNFRGF 168 (278)
T ss_pred cceeeeccccchHHHhccCcccccccccccccccCCCcc-----ccccceee-eecccccccchhh
Confidence 34678888887665432 2223346666555433221 01123233 6666666666544
No 63
>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=93.52 E-value=0.057 Score=20.99 Aligned_cols=33 Identities=12% Similarity=0.373 Sum_probs=16.6
Q ss_pred eecCcccccccchhhHHHHhhhhcCCCCCccCCCCCccc
Q psy12019 34 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRA 72 (87)
Q Consensus 34 ~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f 72 (87)
..|+.|+..|.-..... ...... ..|+.|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~-----~~~~~~-v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-----GANGGK-VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHc-----CCCCCE-EECCCCCCEE
Confidence 35667776655444321 111123 5677777655
No 64
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.37 E-value=0.073 Score=20.75 Aligned_cols=32 Identities=22% Similarity=0.636 Sum_probs=16.5
Q ss_pred ecCcccccccchhhHHHHhhhhcCCCCCccCCCCCccc
Q psy12019 35 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRA 72 (87)
Q Consensus 35 ~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f 72 (87)
+|+.|+..|.-... +.-.+... ..|+.|+..|
T Consensus 4 ~CP~C~~~f~v~~~-----~l~~~~~~-vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD-----KLPAGGRK-VRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHH-----HcccCCcE-EECCCCCcEe
Confidence 56666666654443 11122234 5677776655
No 65
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=93.24 E-value=0.046 Score=28.75 Aligned_cols=23 Identities=39% Similarity=1.044 Sum_probs=15.6
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCC
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCP 69 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~ 69 (87)
.|.|..||.. +.++.| ..|++||
T Consensus 134 ~~vC~vCGy~-------------~~ge~P-~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAP-EVCPICG 156 (166)
T ss_pred EEEcCCCCCc-------------ccCCCC-CcCCCCC
Confidence 5788888754 345344 8888887
No 66
>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=93.14 E-value=0.082 Score=27.58 Aligned_cols=33 Identities=15% Similarity=0.505 Sum_probs=25.5
Q ss_pred CcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccc
Q psy12019 31 AGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 73 (87)
Q Consensus 31 ~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~ 73 (87)
..-|.|+.|+..|+...++. .. |.|+.||..+.
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~---------~~-F~Cp~Cg~~L~ 139 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME---------LN-FTCPRCGAMLD 139 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH---------cC-CcCCCCCCEee
Confidence 34688999998888887764 24 99999997654
No 67
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=93.08 E-value=0.086 Score=20.45 Aligned_cols=32 Identities=16% Similarity=0.373 Sum_probs=16.4
Q ss_pred ecCcccccccchhhHHHHhhhhcCCCCCccCCCCCccc
Q psy12019 35 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRA 72 (87)
Q Consensus 35 ~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f 72 (87)
+|+.|+..|.-..... -..... ..|+.|+..|
T Consensus 4 ~Cp~C~~~y~i~d~~i-----p~~g~~-v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKI-----PPKGRK-VRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHC-----CCCCcE-EECCCCCCEe
Confidence 5666666665544321 112233 5677776655
No 68
>KOG1146|consensus
Probab=93.04 E-value=0.078 Score=36.06 Aligned_cols=51 Identities=25% Similarity=0.578 Sum_probs=41.9
Q ss_pred cceecCcccccccchhhHHHHhhhh-----------------c--------CCCCCccCCCCCcccccchHHHhhhh
Q psy12019 32 GMFMCDVCGKGYKYKNGIYRHKKFE-----------------C--------GQEPKYQCPQCPYRAKQNAHLTTHMA 83 (87)
Q Consensus 32 ~~~~c~~c~~~~~~~~~~~~h~~~~-----------------~--------~~~~~~~c~~c~~~f~~~~~l~~h~~ 83 (87)
+.+.|+.|+..+.....|..|+|.- . +.++ |.|..|...+.....|.+|+.
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p-~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKP-YPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCc-ccceeeeeeeecchHHHHHHH
Confidence 5678999999999999999999870 0 1134 899999999999999999975
No 69
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.90 E-value=0.062 Score=26.22 Aligned_cols=28 Identities=11% Similarity=-0.039 Sum_probs=21.4
Q ss_pred cccccchhhhccCCcceecCcccccccc
Q psy12019 18 KCLINWSAVQQNHAGMFMCDVCGKGYKY 45 (87)
Q Consensus 18 ~c~~c~~~~~~~~~~~~~c~~c~~~~~~ 45 (87)
.|+.|++.|-..+..|..|+.||++|..
T Consensus 11 idPetg~KFYDLNrdPiVsPytG~s~P~ 38 (129)
T COG4530 11 IDPETGKKFYDLNRDPIVSPYTGKSYPR 38 (129)
T ss_pred cCccccchhhccCCCccccCcccccchH
Confidence 4677888887777778888888888733
No 70
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=92.85 E-value=0.081 Score=24.75 Aligned_cols=28 Identities=18% Similarity=0.529 Sum_probs=11.9
Q ss_pred cccccccchhhhc-cCCcceecCcccccc
Q psy12019 16 HNKCLINWSAVQQ-NHAGMFMCDVCGKGY 43 (87)
Q Consensus 16 ~~~c~~c~~~~~~-~~~~~~~c~~c~~~~ 43 (87)
.|.|+.|++.-.. ....-|.|..||..|
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 3455555544211 122334555555444
No 71
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=92.63 E-value=0.088 Score=28.03 Aligned_cols=32 Identities=22% Similarity=0.666 Sum_probs=24.4
Q ss_pred cceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccc
Q psy12019 32 GMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 73 (87)
Q Consensus 32 ~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~ 73 (87)
.-|.|+.|+..|....++. .. |.|+.||-.+.
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~---------~~-F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME---------YG-FRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHhh---------cC-CcCCCCCCCCe
Confidence 4688999998887777652 34 99999997654
No 72
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=92.59 E-value=0.081 Score=31.80 Aligned_cols=33 Identities=15% Similarity=0.209 Sum_probs=27.0
Q ss_pred cccccccchhhhccCCcceecCcccccccchhh
Q psy12019 16 HNKCLINWSAVQQNHAGMFMCDVCGKGYKYKNG 48 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~ 48 (87)
.-.|+.|+..+.+.+.+.|.|..||..++....
T Consensus 350 ~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~~ 382 (421)
T COG1571 350 NPVCPRCGGRMKSAGRNGFRCKKCGTRARETLI 382 (421)
T ss_pred CCCCCccCCchhhcCCCCcccccccccCCcccc
Confidence 347999999999988778999999988766544
No 73
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=92.57 E-value=0.11 Score=18.38 Aligned_cols=7 Identities=43% Similarity=1.644 Sum_probs=2.9
Q ss_pred ccCCCCC
Q psy12019 63 YQCPQCP 69 (87)
Q Consensus 63 ~~c~~c~ 69 (87)
|.|+.||
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 4444443
No 74
>PF14353 CpXC: CpXC protein
Probab=92.42 E-value=0.056 Score=27.02 Aligned_cols=11 Identities=9% Similarity=0.012 Sum_probs=6.3
Q ss_pred cccccchhhhc
Q psy12019 18 KCLINWSAVQQ 28 (87)
Q Consensus 18 ~c~~c~~~~~~ 28 (87)
.|+.|+..|..
T Consensus 3 tCP~C~~~~~~ 13 (128)
T PF14353_consen 3 TCPHCGHEFEF 13 (128)
T ss_pred CCCCCCCeeEE
Confidence 46666666543
No 75
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=92.41 E-value=0.059 Score=21.62 Aligned_cols=13 Identities=23% Similarity=0.940 Sum_probs=7.4
Q ss_pred eecCcccccccch
Q psy12019 34 FMCDVCGKGYKYK 46 (87)
Q Consensus 34 ~~c~~c~~~~~~~ 46 (87)
|.|..||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 6 YRCEECGHEFEVL 18 (42)
T ss_pred EEeCCCCCEEEEE
Confidence 5566666655443
No 76
>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=92.37 E-value=0.083 Score=19.71 Aligned_cols=24 Identities=25% Similarity=0.609 Sum_probs=9.9
Q ss_pred cccccchhhhccCCcceecCcccc
Q psy12019 18 KCLINWSAVQQNHAGMFMCDVCGK 41 (87)
Q Consensus 18 ~c~~c~~~~~~~~~~~~~c~~c~~ 41 (87)
+|+.|+..+.......+.|+.|+.
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----EE-SSSEEETTTTE
T ss_pred CCCCCCCcceeccCCEEeCCcccc
Confidence 466666666555555666666654
No 77
>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=92.37 E-value=0.095 Score=25.52 Aligned_cols=31 Identities=13% Similarity=0.238 Sum_probs=24.8
Q ss_pred ccccccchhhhccCCcceecCcccccccchh
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGKGYKYKN 47 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~ 47 (87)
-.|+.|...+.......|.|++|+..+....
T Consensus 3 p~CP~C~seytY~dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQLICPSCLYEWNENE 33 (109)
T ss_pred CcCCcCCCcceEecCCeeECccccccccccc
Confidence 3689999888888777899999998776553
No 78
>KOG2186|consensus
Probab=92.28 E-value=0.11 Score=29.19 Aligned_cols=38 Identities=24% Similarity=0.554 Sum_probs=17.5
Q ss_pred eecCcccccccchhhHHHHhhhhcCCCCCccCCCCCccccc
Q psy12019 34 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQ 74 (87)
Q Consensus 34 ~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~ 74 (87)
|.|..||....... +..|+-...+ .. |.|--|++.|..
T Consensus 4 FtCnvCgEsvKKp~-vekH~srCrn-~~-fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKHMSRCRN-AY-FSCIDCGKTFER 41 (276)
T ss_pred Eehhhhhhhccccc-hHHHHHhccC-Ce-eEEeeccccccc
Confidence 44555554443332 3334444444 33 555555555544
No 79
>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=92.27 E-value=0.15 Score=18.26 Aligned_cols=19 Identities=26% Similarity=0.676 Sum_probs=12.9
Q ss_pred cCCCCCcccccchHHHhhhh
Q psy12019 64 QCPQCPYRAKQNAHLTTHMA 83 (87)
Q Consensus 64 ~c~~c~~~f~~~~~l~~h~~ 83 (87)
.|++|++.+ ....++.|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577887777 4556677764
No 80
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=92.22 E-value=0.081 Score=24.99 Aligned_cols=29 Identities=21% Similarity=0.423 Sum_probs=14.9
Q ss_pred cccccccchh-hhccCCcceecCccccccc
Q psy12019 16 HNKCLINWSA-VQQNHAGMFMCDVCGKGYK 44 (87)
Q Consensus 16 ~~~c~~c~~~-~~~~~~~~~~c~~c~~~~~ 44 (87)
.|.|+.|++. +.......|.|..|++.|.
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 36 KYFCPFCGKHAVKRQAVGIWRCKGCKKTVA 65 (90)
T ss_pred CccCCCCCCCceeeeeeEEEEcCCCCCEEe
Confidence 5666666543 2222334566666665543
No 81
>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=92.10 E-value=0.12 Score=25.13 Aligned_cols=25 Identities=28% Similarity=0.756 Sum_probs=23.3
Q ss_pred ccC----CCCCcccccchHHHhhhhhcCC
Q psy12019 63 YQC----PQCPYRAKQNAHLTTHMAIKHY 87 (87)
Q Consensus 63 ~~c----~~c~~~f~~~~~l~~h~~~~h~ 87 (87)
|.| ..|++.......+..|.+..|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 9999999999999999999886
No 82
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=92.05 E-value=0.024 Score=29.40 Aligned_cols=12 Identities=33% Similarity=0.722 Sum_probs=5.9
Q ss_pred eecCcccccccc
Q psy12019 34 FMCDVCGKGYKY 45 (87)
Q Consensus 34 ~~c~~c~~~~~~ 45 (87)
++|+.||..|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 445555555443
No 83
>PRK10220 hypothetical protein; Provisional
Probab=92.02 E-value=0.13 Score=25.07 Aligned_cols=31 Identities=19% Similarity=0.470 Sum_probs=25.0
Q ss_pred ccccccchhhhccCCcceecCcccccccchh
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGKGYKYKN 47 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~ 47 (87)
-.|+.|...+.......|.|++|+.-+....
T Consensus 4 P~CP~C~seytY~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 4 PHCPKCNSEYTYEDNGMYICPECAHEWNDAE 34 (111)
T ss_pred CcCCCCCCcceEcCCCeEECCcccCcCCccc
Confidence 3689999988888777899999998776554
No 84
>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=91.85 E-value=0.08 Score=20.79 Aligned_cols=13 Identities=23% Similarity=0.907 Sum_probs=7.5
Q ss_pred eecCcccccccch
Q psy12019 34 FMCDVCGKGYKYK 46 (87)
Q Consensus 34 ~~c~~c~~~~~~~ 46 (87)
|.|..||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (41)
T smart00834 6 YRCEDCGHTFEVL 18 (41)
T ss_pred EEcCCCCCEEEEE
Confidence 5666666655433
No 85
>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=91.81 E-value=0.084 Score=24.97 Aligned_cols=29 Identities=21% Similarity=0.595 Sum_probs=15.6
Q ss_pred cccccccchh-hhccCCcceecCccccccc
Q psy12019 16 HNKCLINWSA-VQQNHAGMFMCDVCGKGYK 44 (87)
Q Consensus 16 ~~~c~~c~~~-~~~~~~~~~~c~~c~~~~~ 44 (87)
.|.|+.|++. +.......|.|..|++.|.
T Consensus 35 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 35 KYVCPFCGKKTVKRGSTGIWTCRKCGAKFA 64 (91)
T ss_pred CccCCCCCCCceEEEeeEEEEcCCCCCEEe
Confidence 5666666543 2222344566666666553
No 86
>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=91.80 E-value=0.073 Score=22.21 Aligned_cols=12 Identities=25% Similarity=1.052 Sum_probs=6.8
Q ss_pred eecCcccccccc
Q psy12019 34 FMCDVCGKGYKY 45 (87)
Q Consensus 34 ~~c~~c~~~~~~ 45 (87)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCTACGHRFEV 17 (52)
T ss_pred EEeCCCCCEeEE
Confidence 456666665543
No 87
>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=91.80 E-value=0.095 Score=26.57 Aligned_cols=26 Identities=23% Similarity=0.413 Sum_probs=15.0
Q ss_pred CCCCCccCCCCCcccccchHHHhhhhhcCC
Q psy12019 58 GQEPKYQCPQCPYRAKQNAHLTTHMAIKHY 87 (87)
Q Consensus 58 ~~~~~~~c~~c~~~f~~~~~l~~h~~~~h~ 87 (87)
.+.. ..|-+||+.|.. |.+|++.|||
T Consensus 69 ~~d~-i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 69 TPDY-IICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp -SS--EE-TBT--EESB---HHHHHHHTT-
T ss_pred ccCe-eEEccCCcccch---HHHHHHHccC
Confidence 3344 678889998864 4789888875
No 88
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=91.12 E-value=0.1 Score=21.80 Aligned_cols=25 Identities=24% Similarity=0.446 Sum_probs=11.9
Q ss_pred cccccccchhhhcc-CCcceecCccc
Q psy12019 16 HNKCLINWSAVQQN-HAGMFMCDVCG 40 (87)
Q Consensus 16 ~~~c~~c~~~~~~~-~~~~~~c~~c~ 40 (87)
.|.|..|++.+... ......|+.||
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg 31 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCG 31 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCC
Confidence 35555555555422 22344555555
No 89
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=90.32 E-value=0.24 Score=25.49 Aligned_cols=38 Identities=16% Similarity=0.534 Sum_probs=25.2
Q ss_pred CcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccc
Q psy12019 31 AGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 73 (87)
Q Consensus 31 ~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~ 73 (87)
..-|.|+.|+..|....++..- .. +.. |.|+.||....
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~---d~-~~~-f~Cp~Cg~~l~ 134 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLL---DM-DGT-FTCPRCGEELE 134 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhc---CC-CCc-EECCCCCCEEE
Confidence 3468899999888765543321 11 344 89999997653
No 90
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=90.29 E-value=0.14 Score=24.23 Aligned_cols=29 Identities=21% Similarity=0.594 Sum_probs=15.7
Q ss_pred cccccccchh-hhccCCcceecCccccccc
Q psy12019 16 HNKCLINWSA-VQQNHAGMFMCDVCGKGYK 44 (87)
Q Consensus 16 ~~~c~~c~~~-~~~~~~~~~~c~~c~~~~~ 44 (87)
.|.|+.|++. +.......|.|..|++.|.
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 36 KHVCPVCGRPKVKRVGTGIWECRKCGAKFA 65 (90)
T ss_pred CccCCCCCCCceEEEEEEEEEcCCCCCEEe
Confidence 5667776543 2222344566766666553
No 91
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=90.17 E-value=0.1 Score=28.60 Aligned_cols=24 Identities=29% Similarity=0.582 Sum_probs=13.6
Q ss_pred ccCCCCCcccccchHHHhhhhhcC
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMAIKH 86 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~~h 86 (87)
|.|..|+|.|....-+..|+...|
T Consensus 78 ~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp EEE-SSS-EESSHHHHHHHHHHH-
T ss_pred ECCCCCCcccCChHHHHHHHhhcC
Confidence 666666666666666666665444
No 92
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=90.13 E-value=0.28 Score=19.65 Aligned_cols=22 Identities=23% Similarity=0.425 Sum_probs=11.8
Q ss_pred ccCCCCCccccc----chHHHhhhhh
Q psy12019 63 YQCPQCPYRAKQ----NAHLTTHMAI 84 (87)
Q Consensus 63 ~~c~~c~~~f~~----~~~l~~h~~~ 84 (87)
..|..|++.+.. .+.|.+|++.
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHHHH
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 566777766554 3566666643
No 93
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=89.39 E-value=0.23 Score=25.26 Aligned_cols=22 Identities=18% Similarity=0.182 Sum_probs=15.8
Q ss_pred ccCCCCCcccccchHHHhhhhhcCC
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMAIKHY 87 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~~h~ 87 (87)
..|-++||.|. +|.+|+.+|++
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccC
Confidence 46777788775 57888887764
No 94
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=89.38 E-value=0.31 Score=20.19 Aligned_cols=21 Identities=19% Similarity=0.547 Sum_probs=13.8
Q ss_pred ccCCCCCcccccc-----hHHHhhhh
Q psy12019 63 YQCPQCPYRAKQN-----AHLTTHMA 83 (87)
Q Consensus 63 ~~c~~c~~~f~~~-----~~l~~h~~ 83 (87)
-.|..|++.+... +.|.+|+.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 4667777666443 57777776
No 95
>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=89.22 E-value=0.16 Score=24.04 Aligned_cols=28 Identities=21% Similarity=0.571 Sum_probs=12.2
Q ss_pred cccccccchhhhc-cCCcceecCcccccc
Q psy12019 16 HNKCLINWSAVQQ-NHAGMFMCDVCGKGY 43 (87)
Q Consensus 16 ~~~c~~c~~~~~~-~~~~~~~c~~c~~~~ 43 (87)
.|.|+.|++.-.. ....-|.|..|++.|
T Consensus 35 ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp -BEESSSSSSEEEEEETTEEEETTTTEEE
T ss_pred CCcCCCCCCceeEEeeeEEeecCCCCCEE
Confidence 4555555544321 122235555555544
No 96
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=88.95 E-value=0.16 Score=25.66 Aligned_cols=25 Identities=16% Similarity=0.388 Sum_probs=14.8
Q ss_pred cccccccchhhhccCCc-ceecCccc
Q psy12019 16 HNKCLINWSAVQQNHAG-MFMCDVCG 40 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~-~~~c~~c~ 40 (87)
|++|..|++.|...... .-=|+.||
T Consensus 1 PH~Ct~Cg~~f~dgs~eil~GCP~CG 26 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEILSGCPECG 26 (131)
T ss_pred CcccCcCCCCcCCCcHHHHccCcccC
Confidence 56777777777764211 22366666
No 97
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=88.68 E-value=0.18 Score=22.86 Aligned_cols=12 Identities=25% Similarity=0.490 Sum_probs=6.5
Q ss_pred ccCC--CCCccccc
Q psy12019 63 YQCP--QCPYRAKQ 74 (87)
Q Consensus 63 ~~c~--~c~~~f~~ 74 (87)
++|. +||.+|..
T Consensus 28 ~qC~N~eCg~tF~t 41 (72)
T PRK09678 28 HQCQNVNCSATFIT 41 (72)
T ss_pred eecCCCCCCCEEEE
Confidence 5554 56655543
No 98
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=87.94 E-value=0.32 Score=23.03 Aligned_cols=12 Identities=25% Similarity=0.714 Sum_probs=5.7
Q ss_pred ceecCccccccc
Q psy12019 33 MFMCDVCGKGYK 44 (87)
Q Consensus 33 ~~~c~~c~~~~~ 44 (87)
|-.|..||..|.
T Consensus 58 Pa~CkkCGfef~ 69 (97)
T COG3357 58 PARCKKCGFEFR 69 (97)
T ss_pred ChhhcccCcccc
Confidence 334555555443
No 99
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=87.14 E-value=0.18 Score=29.43 Aligned_cols=42 Identities=31% Similarity=0.585 Sum_probs=34.1
Q ss_pred CCCcccccc--cchhhhcc------------------------------CCcceecCcccccccchhhHHHHhh
Q psy12019 13 EPKHNKCLI--NWSAVQQN------------------------------HAGMFMCDVCGKGYKYKNGIYRHKK 54 (87)
Q Consensus 13 ~~~~~~c~~--c~~~~~~~------------------------------~~~~~~c~~c~~~~~~~~~~~~h~~ 54 (87)
+++||+|++ |.+.+... ..+||.|..|++.+.....|.-|+.
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 358999987 88888653 4579999999999999888877654
No 100
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=86.93 E-value=0.89 Score=22.50 Aligned_cols=47 Identities=13% Similarity=0.147 Sum_probs=27.3
Q ss_pred cCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccccchHHHhhhhhc
Q psy12019 36 CDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMAIK 85 (87)
Q Consensus 36 c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 85 (87)
|-.|...|........ ..-..... |+|+.|...|--.-++-.|..+|
T Consensus 58 C~~C~~~f~~~~~~~~--~~~~~~~~-y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 58 CFGCQGPFPKPPVSPF--DELKDSHR-YVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred ccCcCCCCCCcccccc--cccccccc-eeCCCCCCccccccchhhhhhcc
Confidence 6667777655431110 00111234 88888888887777777776655
No 101
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=86.72 E-value=0.5 Score=18.35 Aligned_cols=26 Identities=27% Similarity=0.637 Sum_probs=17.2
Q ss_pred cccccccchhhhccCCcceecCcccc
Q psy12019 16 HNKCLINWSAVQQNHAGMFMCDVCGK 41 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~~~~c~~c~~ 41 (87)
...|..|+..+-......+.|..||.
T Consensus 8 ~~~C~~C~~~~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 8 NEPCPVCGSRWFYSDDGFYYCDRCGH 33 (36)
T ss_pred CCcCCCCCCeEeEccCCEEEhhhCce
Confidence 35577777775555666677777764
No 102
>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=86.08 E-value=0.56 Score=20.67 Aligned_cols=30 Identities=17% Similarity=0.310 Sum_probs=13.3
Q ss_pred cccccccchhhhccCCcceecCcccccccch
Q psy12019 16 HNKCLINWSAVQQNHAGMFMCDVCGKGYKYK 46 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~ 46 (87)
.-.|..|.+.|.- ..+.+.|..||..|-..
T Consensus 9 ~~~C~~C~~~F~~-~~rrhhCr~CG~~vC~~ 38 (69)
T PF01363_consen 9 ASNCMICGKKFSL-FRRRHHCRNCGRVVCSS 38 (69)
T ss_dssp -SB-TTT--B-BS-SS-EEE-TTT--EEECC
T ss_pred CCcCcCcCCcCCC-ceeeEccCCCCCEECCc
Confidence 3467788888844 34456788887766544
No 103
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=85.83 E-value=0.31 Score=26.50 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=29.3
Q ss_pred CcccccccchhhhccCCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCccc
Q psy12019 15 KHNKCLINWSAVQQNHAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRA 72 (87)
Q Consensus 15 ~~~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f 72 (87)
.||.|.+|.+.|.+. .-..||..|....+....+. . -.|-+||+.-
T Consensus 195 IPF~C~iCKkdy~sp-----vvt~CGH~FC~~Cai~~y~k------g-~~C~~Cgk~t 240 (259)
T COG5152 195 IPFLCGICKKDYESP-----VVTECGHSFCSLCAIRKYQK------G-DECGVCGKAT 240 (259)
T ss_pred Cceeehhchhhccch-----hhhhcchhHHHHHHHHHhcc------C-Ccceecchhh
Confidence 488999998887664 23357777766665543322 2 4777788643
No 104
>KOG1146|consensus
Probab=85.80 E-value=0.33 Score=33.39 Aligned_cols=69 Identities=14% Similarity=0.277 Sum_probs=48.3
Q ss_pred ccccccchhhhcc-------CCcceecCcccccccchhhHHHHhhhhc----------------CCCCCccCCCCCcccc
Q psy12019 17 NKCLINWSAVQQN-------HAGMFMCDVCGKGYKYKNGIYRHKKFEC----------------GQEPKYQCPQCPYRAK 73 (87)
Q Consensus 17 ~~c~~c~~~~~~~-------~~~~~~c~~c~~~~~~~~~~~~h~~~~~----------------~~~~~~~c~~c~~~f~ 73 (87)
+.|..|...+... ...+|.|..|...|.....+..|++.-. -+..+| |..|...|+
T Consensus 1261 ~~c~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~ 1339 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGISTLDVTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLS 1339 (1406)
T ss_pred chhhhccccccCccceeecccchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhcc
Confidence 4566666555432 3446788888888888888888875311 112336 999999999
Q ss_pred cchHHHhhhhhcC
Q psy12019 74 QNAHLTTHMAIKH 86 (87)
Q Consensus 74 ~~~~l~~h~~~~h 86 (87)
+...|..|+++-+
T Consensus 1340 ~~~alqihm~~~~ 1352 (1406)
T KOG1146|consen 1340 GREALQIHMRSSA 1352 (1406)
T ss_pred hhHHHHHHHHHhh
Confidence 9999999998643
No 105
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=85.55 E-value=0.9 Score=29.65 Aligned_cols=14 Identities=29% Similarity=0.695 Sum_probs=9.5
Q ss_pred cCCCCCccCCCCCcc
Q psy12019 57 CGQEPKYQCPQCPYR 71 (87)
Q Consensus 57 ~~~~~~~~c~~c~~~ 71 (87)
....| ..|+.||..
T Consensus 471 ~~~~p-~~Cp~Cgs~ 484 (730)
T COG1198 471 QEPIP-QSCPECGSE 484 (730)
T ss_pred CCCCC-CCCCCCCCC
Confidence 33345 899999854
No 106
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=85.38 E-value=0.77 Score=19.23 Aligned_cols=10 Identities=30% Similarity=1.138 Sum_probs=5.9
Q ss_pred ccCCCCCccc
Q psy12019 63 YQCPQCPYRA 72 (87)
Q Consensus 63 ~~c~~c~~~f 72 (87)
+.|..||..+
T Consensus 38 ~~C~~Cgyt~ 47 (50)
T PRK00432 38 WHCGKCGYTE 47 (50)
T ss_pred EECCCcCCEE
Confidence 5666666543
No 107
>PRK00420 hypothetical protein; Validated
Probab=85.31 E-value=0.69 Score=22.88 Aligned_cols=28 Identities=25% Similarity=0.426 Sum_probs=18.6
Q ss_pred ccccccchhhhccCCcceecCccccccc
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGKGYK 44 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~~~~ 44 (87)
-.|+.|+..+.........|+.||....
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeee
Confidence 4677888776654445667888887543
No 108
>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=84.51 E-value=0.93 Score=25.85 Aligned_cols=24 Identities=21% Similarity=0.523 Sum_probs=12.6
Q ss_pred cccccchhhhccCCcceecCcccc
Q psy12019 18 KCLINWSAVQQNHAGMFMCDVCGK 41 (87)
Q Consensus 18 ~c~~c~~~~~~~~~~~~~c~~c~~ 41 (87)
.|.+|.+.....+.+.|.|..|..
T Consensus 127 ~C~EC~R~vw~hGGrif~CsfC~~ 150 (314)
T PF06524_consen 127 VCIECERGVWDHGGRIFKCSFCDN 150 (314)
T ss_pred EeeeeecccccCCCeEEEeecCCC
Confidence 455565555555555555555543
No 109
>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=83.86 E-value=0.67 Score=16.60 Aligned_cols=10 Identities=40% Similarity=1.132 Sum_probs=5.7
Q ss_pred cCCCCCcccc
Q psy12019 64 QCPQCPYRAK 73 (87)
Q Consensus 64 ~c~~c~~~f~ 73 (87)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5566666553
No 110
>KOG3507|consensus
Probab=83.77 E-value=0.62 Score=20.19 Aligned_cols=25 Identities=16% Similarity=0.250 Sum_probs=10.8
Q ss_pred ccccccchhhhccCCcceecCcccc
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGK 41 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~ 41 (87)
|.|..|+..-.-.....+.|.+||.
T Consensus 21 YiCgdC~~en~lk~~D~irCReCG~ 45 (62)
T KOG3507|consen 21 YICGDCGQENTLKRGDVIRCRECGY 45 (62)
T ss_pred EEeccccccccccCCCcEehhhcch
Confidence 4444444433333333444555543
No 111
>KOG3408|consensus
Probab=83.65 E-value=0.8 Score=22.93 Aligned_cols=26 Identities=23% Similarity=0.428 Sum_probs=23.0
Q ss_pred CCcceecCcccccccchhhHHHHhhh
Q psy12019 30 HAGMFMCDVCGKGYKYKNGIYRHKKF 55 (87)
Q Consensus 30 ~~~~~~c~~c~~~~~~~~~~~~h~~~ 55 (87)
+...|-|..|.+-|....++..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 56679999999999999999999875
No 112
>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=83.25 E-value=0.83 Score=19.15 Aligned_cols=7 Identities=43% Similarity=1.431 Sum_probs=4.7
Q ss_pred ccCCCCC
Q psy12019 63 YQCPQCP 69 (87)
Q Consensus 63 ~~c~~c~ 69 (87)
|.|+.|+
T Consensus 35 w~CP~C~ 41 (50)
T cd00730 35 WVCPVCG 41 (50)
T ss_pred CCCCCCC
Confidence 6677765
No 113
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=82.91 E-value=1.3 Score=19.04 Aligned_cols=47 Identities=15% Similarity=0.294 Sum_probs=24.3
Q ss_pred CCCcccccccchhhhccCCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCC
Q psy12019 13 EPKHNKCLINWSAVQQNHAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQC 68 (87)
Q Consensus 13 ~~~~~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c 68 (87)
+...+.|++..+.|.. |.....|+-.|...+.+ .+. ..... ..|++.
T Consensus 8 ~~~~~~CPiT~~~~~~----PV~s~~C~H~fek~aI~-~~i---~~~~~-~~CPv~ 54 (57)
T PF11789_consen 8 GTISLKCPITLQPFED----PVKSKKCGHTFEKEAIL-QYI---QRNGS-KRCPVA 54 (57)
T ss_dssp SB--SB-TTTSSB-SS----EEEESSS--EEEHHHHH-HHC---TTTS--EE-SCC
T ss_pred cEeccCCCCcCChhhC----CcCcCCCCCeecHHHHH-HHH---HhcCC-CCCCCC
Confidence 4456788887777554 67777898888766544 333 12233 777763
No 114
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=82.74 E-value=0.59 Score=23.82 Aligned_cols=15 Identities=27% Similarity=0.826 Sum_probs=9.6
Q ss_pred cceecCcccccccch
Q psy12019 32 GMFMCDVCGKGYKYK 46 (87)
Q Consensus 32 ~~~~c~~c~~~~~~~ 46 (87)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 356788888666543
No 115
>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=82.35 E-value=0.46 Score=17.42 Aligned_cols=9 Identities=33% Similarity=0.877 Sum_probs=5.4
Q ss_pred ecCcccccc
Q psy12019 35 MCDVCGKGY 43 (87)
Q Consensus 35 ~c~~c~~~~ 43 (87)
.|..|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 455666666
No 116
>KOG2593|consensus
Probab=82.18 E-value=0.7 Score=28.08 Aligned_cols=28 Identities=21% Similarity=0.374 Sum_probs=16.6
Q ss_pred CCcccccccchhhhcc--------CCcceecCcccc
Q psy12019 14 PKHNKCLINWSAVQQN--------HAGMFMCDVCGK 41 (87)
Q Consensus 14 ~~~~~c~~c~~~~~~~--------~~~~~~c~~c~~ 41 (87)
..-|.|+.|.+.|... ....|.|..|+-
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGG 161 (436)
T ss_pred cccccCCccccchhhhHHHHhhcccCceEEEecCCC
Confidence 3456777777776654 234566666664
No 117
>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=81.85 E-value=0.67 Score=19.17 Aligned_cols=7 Identities=43% Similarity=1.431 Sum_probs=3.3
Q ss_pred ccCCCCC
Q psy12019 63 YQCPQCP 69 (87)
Q Consensus 63 ~~c~~c~ 69 (87)
|.|+.|+
T Consensus 35 w~CP~C~ 41 (47)
T PF00301_consen 35 WVCPVCG 41 (47)
T ss_dssp -B-TTTS
T ss_pred CcCcCCC
Confidence 6666665
No 118
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=81.84 E-value=0.67 Score=22.89 Aligned_cols=10 Identities=20% Similarity=0.644 Sum_probs=5.3
Q ss_pred eecCcccccc
Q psy12019 34 FMCDVCGKGY 43 (87)
Q Consensus 34 ~~c~~c~~~~ 43 (87)
..|..||..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 4566666433
No 119
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=81.84 E-value=2.2 Score=16.81 Aligned_cols=16 Identities=19% Similarity=0.405 Sum_probs=7.8
Q ss_pred eecCcccccccchhhH
Q psy12019 34 FMCDVCGKGYKYKNGI 49 (87)
Q Consensus 34 ~~c~~c~~~~~~~~~~ 49 (87)
..|+.|+-.+.....+
T Consensus 20 d~C~~C~G~W~d~~el 35 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGEL 35 (41)
T ss_pred EECCCCCeEEccHHHH
Confidence 3455555554444433
No 120
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=81.70 E-value=0.66 Score=26.41 Aligned_cols=23 Identities=26% Similarity=0.788 Sum_probs=15.4
Q ss_pred CCCccCCCCCcccccchHHHhhhh
Q psy12019 60 EPKYQCPQCPYRAKQNAHLTTHMA 83 (87)
Q Consensus 60 ~~~~~c~~c~~~f~~~~~l~~h~~ 83 (87)
++ +.|+.||........|.--.|
T Consensus 208 k~-~PCPKCg~et~eTkdLSmStR 230 (314)
T PF06524_consen 208 KP-IPCPKCGYETQETKDLSMSTR 230 (314)
T ss_pred CC-CCCCCCCCcccccccceeeee
Confidence 55 889999987766655544333
No 121
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=81.25 E-value=0.74 Score=22.86 Aligned_cols=10 Identities=20% Similarity=0.780 Sum_probs=5.3
Q ss_pred eecCcccccc
Q psy12019 34 FMCDVCGKGY 43 (87)
Q Consensus 34 ~~c~~c~~~~ 43 (87)
+.|..||..|
T Consensus 72 ~~C~~Cg~~~ 81 (117)
T PRK00564 72 LECKDCSHVF 81 (117)
T ss_pred EEhhhCCCcc
Confidence 4566666444
No 122
>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=81.15 E-value=2.4 Score=18.62 Aligned_cols=9 Identities=33% Similarity=1.490 Sum_probs=4.5
Q ss_pred ccCCCCCcc
Q psy12019 63 YQCPQCPYR 71 (87)
Q Consensus 63 ~~c~~c~~~ 71 (87)
+.|+.||..
T Consensus 47 ~~C~~Cg~~ 55 (69)
T PF07282_consen 47 FTCPNCGFE 55 (69)
T ss_pred EEcCCCCCE
Confidence 555555543
No 123
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=80.98 E-value=0.84 Score=22.07 Aligned_cols=30 Identities=23% Similarity=0.476 Sum_probs=19.0
Q ss_pred CCcccccccchhhhcc-------CCcceecCcccccc
Q psy12019 14 PKHNKCLINWSAVQQN-------HAGMFMCDVCGKGY 43 (87)
Q Consensus 14 ~~~~~c~~c~~~~~~~-------~~~~~~c~~c~~~~ 43 (87)
++.|.|+.|+..-... ......|..||.+|
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSF 56 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcceE
Confidence 4567888888775542 22345677777655
No 124
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=80.98 E-value=1.1 Score=19.13 Aligned_cols=26 Identities=23% Similarity=0.611 Sum_probs=17.2
Q ss_pred ccccccchhhhccCCcceecCcccccc
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGKGY 43 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~~~ 43 (87)
..|..|++.|..... ...|+.||..+
T Consensus 6 ~~C~~Cg~~~~~~dD-iVvCp~Cgapy 31 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDD-IVVCPECGAPY 31 (54)
T ss_pred ccChhhCCcccCCCC-EEECCCCCCcc
Confidence 468888888865333 34788887653
No 125
>PHA00626 hypothetical protein
Probab=80.46 E-value=0.88 Score=19.56 Aligned_cols=13 Identities=31% Similarity=0.950 Sum_probs=10.7
Q ss_pred ccCCCCCcccccc
Q psy12019 63 YQCPQCPYRAKQN 75 (87)
Q Consensus 63 ~~c~~c~~~f~~~ 75 (87)
|.|+.||..|...
T Consensus 24 YkCkdCGY~ft~~ 36 (59)
T PHA00626 24 YVCCDCGYNDSKD 36 (59)
T ss_pred eEcCCCCCeechh
Confidence 9999999888643
No 126
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.22 E-value=1.4 Score=19.28 Aligned_cols=15 Identities=7% Similarity=-0.155 Sum_probs=7.2
Q ss_pred eccccCCCCcccccc
Q psy12019 7 KPRTHREPKHNKCLI 21 (87)
Q Consensus 7 h~~~h~~~~~~~c~~ 21 (87)
+..++.+..++-|+-
T Consensus 15 ~~~I~~~~~~l~C~g 29 (62)
T COG4391 15 HETIEIGDLPLMCPG 29 (62)
T ss_pred ceEEEeCCeeEEcCC
Confidence 334455555555543
No 127
>COG1773 Rubredoxin [Energy production and conversion]
Probab=80.09 E-value=1.1 Score=19.20 Aligned_cols=14 Identities=7% Similarity=0.124 Sum_probs=8.2
Q ss_pred cccccccchhhhcc
Q psy12019 16 HNKCLINWSAVQQN 29 (87)
Q Consensus 16 ~~~c~~c~~~~~~~ 29 (87)
-++|..|+..|...
T Consensus 3 ~~~C~~CG~vYd~e 16 (55)
T COG1773 3 RWRCSVCGYVYDPE 16 (55)
T ss_pred ceEecCCceEeccc
Confidence 35666666666543
No 128
>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=79.31 E-value=1.1 Score=17.85 Aligned_cols=26 Identities=27% Similarity=0.372 Sum_probs=12.8
Q ss_pred ccccccchhhh--ccCCcceecCccccc
Q psy12019 17 NKCLINWSAVQ--QNHAGMFMCDVCGKG 42 (87)
Q Consensus 17 ~~c~~c~~~~~--~~~~~~~~c~~c~~~ 42 (87)
+.|+.|+.... ......+.|..||..
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLV 28 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BB
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCE
Confidence 35666665431 113344567777654
No 129
>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=79.21 E-value=1.1 Score=27.59 Aligned_cols=24 Identities=13% Similarity=0.055 Sum_probs=18.9
Q ss_pred cccccccchhhhccCCcceecCccccc
Q psy12019 16 HNKCLINWSAVQQNHAGMFMCDVCGKG 42 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~~~~c~~c~~~ 42 (87)
.|.|..|+..... +.+.|+.|+.+
T Consensus 7 ~y~C~~Cg~~~~~---~~g~Cp~C~~w 30 (454)
T TIGR00416 7 KFVCQHCGADSPK---WQGKCPACHAW 30 (454)
T ss_pred eEECCcCCCCCcc---ccEECcCCCCc
Confidence 5999999977544 57899999853
No 130
>PRK14873 primosome assembly protein PriA; Provisional
Probab=79.08 E-value=2.2 Score=27.67 Aligned_cols=9 Identities=33% Similarity=1.254 Sum_probs=6.9
Q ss_pred ccCCCCCcc
Q psy12019 63 YQCPQCPYR 71 (87)
Q Consensus 63 ~~c~~c~~~ 71 (87)
+.|+.||..
T Consensus 423 ~~Cp~Cgs~ 431 (665)
T PRK14873 423 WRCPRCGSD 431 (665)
T ss_pred ccCCCCcCC
Confidence 888888754
No 131
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=79.03 E-value=2 Score=25.37 Aligned_cols=54 Identities=22% Similarity=0.460 Sum_probs=41.8
Q ss_pred cceecCcccccccchhhHHHHhhhhcCCCCCccCCC--CCcccccchHHHhhhhhcC
Q psy12019 32 GMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQ--CPYRAKQNAHLTTHMAIKH 86 (87)
Q Consensus 32 ~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~--c~~~f~~~~~l~~h~~~~h 86 (87)
..+.|+.|...|........+.+.+.++++ +.|.. |...+.....+..+...++
T Consensus 32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (467)
T COG5048 32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKP-SQCSYSGCDKSFSRPLELSRHLRTHH 87 (467)
T ss_pred chhhcccccccccccchhhhhcccccccCC-ccccccccccccCCcchhhhhccccc
Confidence 457788999999999999999999999888 88865 4566666666666665544
No 132
>KOG2893|consensus
Probab=78.62 E-value=1.1 Score=25.32 Aligned_cols=26 Identities=27% Similarity=0.588 Sum_probs=22.2
Q ss_pred CCCccCCCCCcccccchHHHhhhhhcCC
Q psy12019 60 EPKYQCPQCPYRAKQNAHLTTHMAIKHY 87 (87)
Q Consensus 60 ~~~~~c~~c~~~f~~~~~l~~h~~~~h~ 87 (87)
++ | |..|++.|-...-|..|++..||
T Consensus 10 kp-w-cwycnrefddekiliqhqkakhf 35 (341)
T KOG2893|consen 10 KP-W-CWYCNREFDDEKILIQHQKAKHF 35 (341)
T ss_pred Cc-e-eeecccccchhhhhhhhhhhccc
Confidence 44 4 78899999999999999998876
No 133
>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=78.36 E-value=1.6 Score=18.62 Aligned_cols=9 Identities=22% Similarity=0.652 Sum_probs=4.6
Q ss_pred ccCCCCCcc
Q psy12019 63 YQCPQCPYR 71 (87)
Q Consensus 63 ~~c~~c~~~ 71 (87)
..|+.||..
T Consensus 23 V~Cp~CGae 31 (54)
T TIGR01206 23 VICDECGAE 31 (54)
T ss_pred EeCCCCCCE
Confidence 455555543
No 134
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=77.95 E-value=1.9 Score=17.72 Aligned_cols=9 Identities=33% Similarity=1.250 Sum_probs=4.0
Q ss_pred ccCCCCCcc
Q psy12019 63 YQCPQCPYR 71 (87)
Q Consensus 63 ~~c~~c~~~ 71 (87)
+.|+.||..
T Consensus 21 ~vC~~Cg~~ 29 (52)
T smart00661 21 FVCRKCGYE 29 (52)
T ss_pred EECCcCCCe
Confidence 444444433
No 135
>KOG0978|consensus
Probab=77.66 E-value=0.7 Score=29.86 Aligned_cols=52 Identities=15% Similarity=0.259 Sum_probs=27.3
Q ss_pred ccccccchhhhccCCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccccchHHH
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLT 79 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~ 79 (87)
..|+.|...+... .-..|+-.|..... +.-...+. -.||.|+.+|...--+.
T Consensus 644 LkCs~Cn~R~Kd~-----vI~kC~H~FC~~Cv-----q~r~etRq-RKCP~Cn~aFganDv~~ 695 (698)
T KOG0978|consen 644 LKCSVCNTRWKDA-----VITKCGHVFCEECV-----QTRYETRQ-RKCPKCNAAFGANDVHR 695 (698)
T ss_pred eeCCCccCchhhH-----HHHhcchHHHHHHH-----HHHHHHhc-CCCCCCCCCCCcccccc
Confidence 3577776443332 22345555544432 22222244 58889999987664433
No 136
>PRK11823 DNA repair protein RadA; Provisional
Probab=77.64 E-value=1.3 Score=27.18 Aligned_cols=25 Identities=16% Similarity=0.182 Sum_probs=19.1
Q ss_pred CcccccccchhhhccCCcceecCccccc
Q psy12019 15 KHNKCLINWSAVQQNHAGMFMCDVCGKG 42 (87)
Q Consensus 15 ~~~~c~~c~~~~~~~~~~~~~c~~c~~~ 42 (87)
..|.|..|+..... +.+.|+.|+.+
T Consensus 6 ~~y~C~~Cg~~~~~---~~g~Cp~C~~w 30 (446)
T PRK11823 6 TAYVCQECGAESPK---WLGRCPECGAW 30 (446)
T ss_pred CeEECCcCCCCCcc---cCeeCcCCCCc
Confidence 46999999977544 57889999753
No 137
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=77.14 E-value=2 Score=22.01 Aligned_cols=60 Identities=22% Similarity=0.248 Sum_probs=31.5
Q ss_pred CCCCcccccccchhhhccC-CcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccccchH
Q psy12019 12 REPKHNKCLINWSAVQQNH-AGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAH 77 (87)
Q Consensus 12 ~~~~~~~c~~c~~~~~~~~-~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~~~~ 77 (87)
.+.+.|+|.+|..+...+. -+|-+| ||...-..--.. -.+.-+ -- -.|++|.-+|.+++.
T Consensus 76 ~d~~lYeCnIC~etS~ee~FLKPneC--CgY~iCn~Cya~-LWK~~~-~y--pvCPvCkTSFKss~~ 136 (140)
T PF05290_consen 76 LDPKLYECNICKETSAEERFLKPNEC--CGYSICNACYAN-LWKFCN-LY--PVCPVCKTSFKSSSS 136 (140)
T ss_pred cCCCceeccCcccccchhhcCCcccc--cchHHHHHHHHH-HHHHcc-cC--CCCCccccccccccc
Confidence 4557899999998876541 234333 443332222111 112111 12 378888888876543
No 138
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=77.11 E-value=1.7 Score=21.32 Aligned_cols=29 Identities=17% Similarity=0.416 Sum_probs=21.2
Q ss_pred cccccchhhhccCCcceecCcccccccch
Q psy12019 18 KCLINWSAVQQNHAGMFMCDVCGKGYKYK 46 (87)
Q Consensus 18 ~c~~c~~~~~~~~~~~~~c~~c~~~~~~~ 46 (87)
.|+.|...+.......+.|+.|+.-+...
T Consensus 5 ~cp~c~sEytYed~~~~~cpec~~ew~~~ 33 (112)
T COG2824 5 PCPKCNSEYTYEDGGQLICPECAHEWNEN 33 (112)
T ss_pred CCCccCCceEEecCceEeCchhccccccc
Confidence 57888877777655678899988766533
No 139
>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=76.30 E-value=1.7 Score=26.06 Aligned_cols=23 Identities=17% Similarity=0.186 Sum_probs=16.9
Q ss_pred ccccccchhhhccCCcceecCccccc
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGKG 42 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~~ 42 (87)
|.|..|+..... +.+.|+.|+.+
T Consensus 1 ~~c~~cg~~~~~---~~g~cp~c~~w 23 (372)
T cd01121 1 YVCSECGYVSPK---WLGKCPECGEW 23 (372)
T ss_pred CCCCCCCCCCCC---ccEECcCCCCc
Confidence 678889876543 56789999853
No 140
>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=75.95 E-value=2.5 Score=16.36 Aligned_cols=10 Identities=40% Similarity=1.208 Sum_probs=6.0
Q ss_pred ecCccccccc
Q psy12019 35 MCDVCGKGYK 44 (87)
Q Consensus 35 ~c~~c~~~~~ 44 (87)
.|..||+.|.
T Consensus 3 ~C~~Cg~~Yh 12 (36)
T PF05191_consen 3 ICPKCGRIYH 12 (36)
T ss_dssp EETTTTEEEE
T ss_pred CcCCCCCccc
Confidence 5666666654
No 141
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.90 E-value=1 Score=22.74 Aligned_cols=10 Identities=30% Similarity=1.182 Sum_probs=4.8
Q ss_pred cCcccccccc
Q psy12019 36 CDVCGKGYKY 45 (87)
Q Consensus 36 c~~c~~~~~~ 45 (87)
|..||..|.+
T Consensus 71 chncgs~fpw 80 (160)
T COG4306 71 CHNCGSRFPW 80 (160)
T ss_pred hhcCCCCCCc
Confidence 4444444444
No 142
>KOG4167|consensus
Probab=75.36 E-value=0.42 Score=31.00 Aligned_cols=24 Identities=17% Similarity=0.310 Sum_probs=20.3
Q ss_pred CccCCCCCcccccchHHHhhhhhc
Q psy12019 62 KYQCPQCPYRAKQNAHLTTHMAIK 85 (87)
Q Consensus 62 ~~~c~~c~~~f~~~~~l~~h~~~~ 85 (87)
.|-|.+|+|.|----+++.|++.|
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHH
Confidence 488999999998888888888765
No 143
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.17 E-value=1.7 Score=19.94 Aligned_cols=10 Identities=30% Similarity=1.188 Sum_probs=5.6
Q ss_pred eecCcccccc
Q psy12019 34 FMCDVCGKGY 43 (87)
Q Consensus 34 ~~c~~c~~~~ 43 (87)
|+|.+||..|
T Consensus 13 Y~c~~cg~~~ 22 (82)
T COG2331 13 YECTECGNRF 22 (82)
T ss_pred EeecccchHH
Confidence 5566666543
No 144
>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=74.91 E-value=0.54 Score=23.15 Aligned_cols=12 Identities=25% Similarity=0.706 Sum_probs=6.3
Q ss_pred eecCcccccccc
Q psy12019 34 FMCDVCGKGYKY 45 (87)
Q Consensus 34 ~~c~~c~~~~~~ 45 (87)
..|..||..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 456666665543
No 145
>KOG4167|consensus
Probab=74.30 E-value=0.78 Score=29.89 Aligned_cols=27 Identities=30% Similarity=0.472 Sum_probs=23.4
Q ss_pred cceecCcccccccchhhHHHHhhhhcC
Q psy12019 32 GMFMCDVCGKGYKYKNGIYRHKKFECG 58 (87)
Q Consensus 32 ~~~~c~~c~~~~~~~~~~~~h~~~~~~ 58 (87)
.-|.|.+|++.|..-..+..|++.|.-
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 458999999999998889999998764
No 146
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=74.03 E-value=0.97 Score=21.94 Aligned_cols=25 Identities=16% Similarity=0.387 Sum_probs=13.8
Q ss_pred cccccccchhhhccCCc-ceecCccc
Q psy12019 16 HNKCLINWSAVQQNHAG-MFMCDVCG 40 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~-~~~c~~c~ 40 (87)
|+.|..|+..|...... ..-|+.||
T Consensus 2 pH~CtrCG~vf~~g~~~il~GCp~CG 27 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEILSGCPKCG 27 (112)
T ss_pred CceecccccccccccHHHHccCcccc
Confidence 56677777777653111 22366665
No 147
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=73.68 E-value=0.3 Score=19.37 Aligned_cols=10 Identities=40% Similarity=0.939 Sum_probs=5.8
Q ss_pred ccCCCCCccc
Q psy12019 63 YQCPQCPYRA 72 (87)
Q Consensus 63 ~~c~~c~~~f 72 (87)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 5666666544
No 148
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=73.40 E-value=2.5 Score=17.70 Aligned_cols=16 Identities=19% Similarity=0.708 Sum_probs=9.7
Q ss_pred cceecCcccccccchh
Q psy12019 32 GMFMCDVCGKGYKYKN 47 (87)
Q Consensus 32 ~~~~c~~c~~~~~~~~ 47 (87)
+.+.|..||..|....
T Consensus 3 k~l~C~dCg~~FvfTa 18 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTA 18 (49)
T ss_pred eeEEcccCCCeEEEeh
Confidence 3556777776665544
No 149
>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=72.91 E-value=3 Score=16.40 Aligned_cols=10 Identities=30% Similarity=1.212 Sum_probs=4.3
Q ss_pred cceecCcccc
Q psy12019 32 GMFMCDVCGK 41 (87)
Q Consensus 32 ~~~~c~~c~~ 41 (87)
+.|.|..|+.
T Consensus 23 ~~w~C~~C~~ 32 (40)
T PF04810_consen 23 KTWICNFCGT 32 (40)
T ss_dssp TEEEETTT--
T ss_pred CEEECcCCCC
Confidence 3455555553
No 150
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=72.84 E-value=2.3 Score=15.44 Aligned_cols=8 Identities=25% Similarity=1.111 Sum_probs=2.9
Q ss_pred ceecCccc
Q psy12019 33 MFMCDVCG 40 (87)
Q Consensus 33 ~~~c~~c~ 40 (87)
.|.|..|+
T Consensus 15 ~Y~C~~Cd 22 (30)
T PF07649_consen 15 FYRCSECD 22 (30)
T ss_dssp EEE-TTT-
T ss_pred eEECccCC
Confidence 44455443
No 151
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=72.14 E-value=2.3 Score=16.27 Aligned_cols=7 Identities=43% Similarity=1.550 Sum_probs=3.0
Q ss_pred eecCccc
Q psy12019 34 FMCDVCG 40 (87)
Q Consensus 34 ~~c~~c~ 40 (87)
+.|+.||
T Consensus 23 ~vC~~Cg 29 (34)
T PF14803_consen 23 LVCPACG 29 (34)
T ss_dssp EEETTTT
T ss_pred eECCCCC
Confidence 3444444
No 152
>PRK12496 hypothetical protein; Provisional
Probab=72.02 E-value=2.5 Score=22.34 Aligned_cols=11 Identities=36% Similarity=0.776 Sum_probs=5.9
Q ss_pred ceecCcccccc
Q psy12019 33 MFMCDVCGKGY 43 (87)
Q Consensus 33 ~~~c~~c~~~~ 43 (87)
.+.|..|++.|
T Consensus 127 ~~~C~gC~~~~ 137 (164)
T PRK12496 127 RKVCKGCKKKY 137 (164)
T ss_pred eEECCCCCccc
Confidence 34566665554
No 153
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=71.93 E-value=3.5 Score=15.63 Aligned_cols=8 Identities=25% Similarity=0.526 Sum_probs=3.2
Q ss_pred cCCCCCcc
Q psy12019 64 QCPQCPYR 71 (87)
Q Consensus 64 ~c~~c~~~ 71 (87)
.|..||..
T Consensus 23 ~C~~Cg~~ 30 (33)
T PF08792_consen 23 VCIFCGSS 30 (33)
T ss_pred EcccCCcE
Confidence 34444433
No 154
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=71.51 E-value=1.9 Score=21.30 Aligned_cols=10 Identities=20% Similarity=0.305 Sum_probs=6.0
Q ss_pred eecCcccccc
Q psy12019 34 FMCDVCGKGY 43 (87)
Q Consensus 34 ~~c~~c~~~~ 43 (87)
..|..||..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 4566676544
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=71.07 E-value=3.6 Score=16.67 Aligned_cols=8 Identities=38% Similarity=1.186 Sum_probs=5.7
Q ss_pred ccCCCCCc
Q psy12019 63 YQCPQCPY 70 (87)
Q Consensus 63 ~~c~~c~~ 70 (87)
|.|..|++
T Consensus 38 ~~C~~C~~ 45 (46)
T PF12760_consen 38 YRCKACRK 45 (46)
T ss_pred EECCCCCC
Confidence 77777764
No 156
>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=71.00 E-value=3.8 Score=16.88 Aligned_cols=29 Identities=17% Similarity=0.221 Sum_probs=17.0
Q ss_pred CCcccccccchhhhccCCcceecCccccc
Q psy12019 14 PKHNKCLINWSAVQQNHAGMFMCDVCGKG 42 (87)
Q Consensus 14 ~~~~~c~~c~~~~~~~~~~~~~c~~c~~~ 42 (87)
..|-.|..|++.........+.|..|+..
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCSWCGLV 37 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEETTTT-E
T ss_pred CCCCCCcccCcccCCCCCCeEEECCCCCh
Confidence 34667777777764444456777777643
No 157
>KOG2071|consensus
Probab=70.68 E-value=3 Score=26.56 Aligned_cols=25 Identities=32% Similarity=0.656 Sum_probs=21.6
Q ss_pred CCCccCCCCCcccccchHHHhhhhhc
Q psy12019 60 EPKYQCPQCPYRAKQNAHLTTHMAIK 85 (87)
Q Consensus 60 ~~~~~c~~c~~~f~~~~~l~~h~~~~ 85 (87)
.+ -+|..||.+|........|+.+|
T Consensus 417 ~p-nqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 417 SP-NQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred Cc-chhcccccccccchhhhhHhhhh
Confidence 45 89999999999999988888775
No 158
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=69.53 E-value=5.6 Score=15.81 Aligned_cols=11 Identities=36% Similarity=0.827 Sum_probs=5.7
Q ss_pred ecCcccccccc
Q psy12019 35 MCDVCGKGYKY 45 (87)
Q Consensus 35 ~c~~c~~~~~~ 45 (87)
.|..||..+..
T Consensus 15 ~C~~CgM~Y~~ 25 (41)
T PF13878_consen 15 TCPTCGMLYSP 25 (41)
T ss_pred CCCCCCCEECC
Confidence 45555554433
No 159
>KOG0782|consensus
Probab=69.06 E-value=0.8 Score=29.16 Aligned_cols=44 Identities=23% Similarity=0.401 Sum_probs=27.4
Q ss_pred cceeeccccCCCCcccccccchhhhcc------CCcceecCcccccccch
Q psy12019 3 NVIVKPRTHREPKHNKCLINWSAVQQN------HAGMFMCDVCGKGYKYK 46 (87)
Q Consensus 3 ~l~~h~~~h~~~~~~~c~~c~~~~~~~------~~~~~~c~~c~~~~~~~ 46 (87)
.|..|.=+|.....-+|..|++.|+.. ......|.+|..+|-..
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQKf~FhsKEivAisCSWCKqayH~K 289 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQKFFFHSKEIVAISCSWCKQAYHLK 289 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhhheeeccccEEEEEehHHHHHhhcc
Confidence 344555555555566788888888765 22245677777666444
No 160
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=68.58 E-value=1.9 Score=18.62 Aligned_cols=8 Identities=38% Similarity=1.144 Sum_probs=4.6
Q ss_pred ccCCCCCc
Q psy12019 63 YQCPQCPY 70 (87)
Q Consensus 63 ~~c~~c~~ 70 (87)
|.|.+|..
T Consensus 32 YmC~eC~~ 39 (56)
T PF09963_consen 32 YMCDECKE 39 (56)
T ss_pred eeChhHHH
Confidence 66666643
No 161
>KOG2636|consensus
Probab=68.49 E-value=4.2 Score=25.17 Aligned_cols=28 Identities=25% Similarity=0.462 Sum_probs=21.8
Q ss_pred hhhcCCCCCccCCCCC-cccccchHHHhhh
Q psy12019 54 KFECGQEPKYQCPQCP-YRAKQNAHLTTHM 82 (87)
Q Consensus 54 ~~~~~~~~~~~c~~c~-~~f~~~~~l~~h~ 82 (87)
+.|....- |.|.+|| +++...-.+.+|-
T Consensus 394 KLHGL~~e-y~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 394 KLHGLDIE-YNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred hhcCCCcc-cceeeccCccccCcHHHHHHh
Confidence 55666676 9999998 8888887777773
No 162
>KOG4173|consensus
Probab=68.49 E-value=2.2 Score=23.60 Aligned_cols=51 Identities=27% Similarity=0.486 Sum_probs=34.7
Q ss_pred ecCcccccccchhhHHHHhhh----------hcCCCCCccC--CCCCcccccchHHHhhhhhcC
Q psy12019 35 MCDVCGKGYKYKNGIYRHKKF----------ECGQEPKYQC--PQCPYRAKQNAHLTTHMAIKH 86 (87)
Q Consensus 35 ~c~~c~~~~~~~~~~~~h~~~----------~~~~~~~~~c--~~c~~~f~~~~~l~~h~~~~h 86 (87)
.|..|.+.|...-.|..|+.- -.|..- |+| ..|+.-|........|+-..|
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dM-y~ClvEgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDM-YQCLVEGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccH-HHHHHHhhhhhhhhhhhhhhHHHHhc
Confidence 688888888877766666542 223233 777 568888888888777776655
No 163
>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=68.30 E-value=3.7 Score=17.16 Aligned_cols=28 Identities=18% Similarity=0.345 Sum_probs=17.1
Q ss_pred cccccchhhhccCCcceecCcccccccch
Q psy12019 18 KCLINWSAVQQNHAGMFMCDVCGKGYKYK 46 (87)
Q Consensus 18 ~c~~c~~~~~~~~~~~~~c~~c~~~~~~~ 46 (87)
.|..|++.|.... +.+.|..||+.|-..
T Consensus 4 ~C~~C~~~F~~~~-rk~~Cr~Cg~~~C~~ 31 (57)
T cd00065 4 SCMGCGKPFTLTR-RRHHCRNCGRIFCSK 31 (57)
T ss_pred cCcccCccccCCc-cccccCcCcCCcChH
Confidence 4667777776632 345677777766543
No 164
>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=66.86 E-value=4.3 Score=20.95 Aligned_cols=19 Identities=21% Similarity=0.531 Sum_probs=14.9
Q ss_pred ccCCCCCcccccchHHHhh
Q psy12019 63 YQCPQCPYRAKQNAHLTTH 81 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h 81 (87)
+.|+.||+.|..-++..+-
T Consensus 125 ~~C~~C~kiyW~GsH~~~~ 143 (147)
T PF01927_consen 125 WRCPGCGKIYWEGSHWRRM 143 (147)
T ss_pred EECCCCCCEecccccHHHH
Confidence 8999999999877665543
No 165
>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=66.62 E-value=2.8 Score=20.74 Aligned_cols=12 Identities=17% Similarity=0.465 Sum_probs=7.1
Q ss_pred eecCcccccccc
Q psy12019 34 FMCDVCGKGYKY 45 (87)
Q Consensus 34 ~~c~~c~~~~~~ 45 (87)
..|..||..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (115)
T TIGR00100 71 CECEDCSEEVSP 82 (115)
T ss_pred EEcccCCCEEec
Confidence 567777755533
No 166
>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=66.47 E-value=2 Score=18.10 Aligned_cols=16 Identities=13% Similarity=0.439 Sum_probs=5.9
Q ss_pred ceecCcccccccchhh
Q psy12019 33 MFMCDVCGKGYKYKNG 48 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~ 48 (87)
.|+|+.|.+.|-..-.
T Consensus 21 ~y~C~~C~~~FC~dCD 36 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCD 36 (51)
T ss_dssp EE--TTTT--B-HHHH
T ss_pred eEECCCCCCccccCcC
Confidence 4566666665554443
No 167
>KOG0320|consensus
Probab=66.42 E-value=2 Score=23.09 Aligned_cols=49 Identities=20% Similarity=0.343 Sum_probs=29.2
Q ss_pred CCcccccccchhhhccCCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCccc
Q psy12019 14 PKHNKCLINWSAVQQNHAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRA 72 (87)
Q Consensus 14 ~~~~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f 72 (87)
+..|.|++|...+.... -....||-.|...-. +.... .. ..|+.|+|..
T Consensus 129 ~~~~~CPiCl~~~sek~---~vsTkCGHvFC~~Ci-----k~alk-~~-~~CP~C~kkI 177 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKV---PVSTKCGHVFCSQCI-----KDALK-NT-NKCPTCRKKI 177 (187)
T ss_pred ccccCCCceecchhhcc---ccccccchhHHHHHH-----HHHHH-hC-CCCCCccccc
Confidence 44589999988876641 134567777755432 22111 23 6788888744
No 168
>KOG2785|consensus
Probab=66.34 E-value=6.2 Score=23.91 Aligned_cols=21 Identities=14% Similarity=0.297 Sum_probs=15.4
Q ss_pred ccCCCCCcccccchHHHhhhh
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMA 83 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~ 83 (87)
+.|.+|.+.|........|+.
T Consensus 69 ~~c~~c~k~~~s~~a~~~hl~ 89 (390)
T KOG2785|consen 69 VYCEACNKSFASPKAHENHLK 89 (390)
T ss_pred eehHHhhccccChhhHHHHHH
Confidence 788888888877766666653
No 169
>PHA02942 putative transposase; Provisional
Probab=66.30 E-value=8.9 Score=23.26 Aligned_cols=8 Identities=50% Similarity=1.800 Sum_probs=4.0
Q ss_pred ccCCCCCc
Q psy12019 63 YQCPQCPY 70 (87)
Q Consensus 63 ~~c~~c~~ 70 (87)
|.|+.||.
T Consensus 343 f~C~~CG~ 350 (383)
T PHA02942 343 FHCPSCGY 350 (383)
T ss_pred EECCCCCC
Confidence 55555543
No 170
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=65.47 E-value=9 Score=15.42 Aligned_cols=28 Identities=14% Similarity=0.196 Sum_probs=12.0
Q ss_pred ccccchhhhccCCcceecCcccccccchhh
Q psy12019 19 CLINWSAVQQNHAGMFMCDVCGKGYKYKNG 48 (87)
Q Consensus 19 c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~ 48 (87)
|++|.. |......|..-. ||-.|.....
T Consensus 1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl 28 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLP-CGHVFCKDCL 28 (43)
T ss_dssp -TTT-----TTSS-EEE-S-SS-EEEHHHH
T ss_pred CCcccc-ccCCCCCCEEEe-CccHHHHHHH
Confidence 556666 655444455544 8877766654
No 171
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=65.32 E-value=5.2 Score=16.00 Aligned_cols=26 Identities=12% Similarity=0.185 Sum_probs=13.8
Q ss_pred cccccccchhhhccCCcceecCcccc
Q psy12019 16 HNKCLINWSAVQQNHAGMFMCDVCGK 41 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~~~~c~~c~~ 41 (87)
+..|..|.+.+.......+.|..|+.
T Consensus 11 ~~~C~~C~~~i~~~~~~~~~C~~C~~ 36 (50)
T cd00029 11 PTFCDVCRKSIWGLFKQGLRCSWCKV 36 (50)
T ss_pred CCChhhcchhhhccccceeEcCCCCC
Confidence 44566666665543233455666643
No 172
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=65.31 E-value=3.2 Score=19.25 Aligned_cols=31 Identities=23% Similarity=0.513 Sum_probs=11.1
Q ss_pred Ccccccccchhhhc-------cCCcceecCcccccccc
Q psy12019 15 KHNKCLINWSAVQQ-------NHAGMFMCDVCGKGYKY 45 (87)
Q Consensus 15 ~~~~c~~c~~~~~~-------~~~~~~~c~~c~~~~~~ 45 (87)
+.|.|+.|+..-+- .+.....|..||..|..
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQT 58 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EEEE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEE
Confidence 45778877733211 12234567777765543
No 173
>KOG0317|consensus
Probab=65.01 E-value=6.2 Score=22.98 Aligned_cols=48 Identities=17% Similarity=0.420 Sum_probs=31.0
Q ss_pred CcccccccchhhhccCCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCccccc
Q psy12019 15 KHNKCLINWSAVQQNHAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQ 74 (87)
Q Consensus 15 ~~~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~ 74 (87)
..++|..|...-+. | .|..||-.|.+.--+. +.+++. +|+.|...|..
T Consensus 238 a~~kC~LCLe~~~~----p-SaTpCGHiFCWsCI~~-----w~~ek~--eCPlCR~~~~p 285 (293)
T KOG0317|consen 238 ATRKCSLCLENRSN----P-SATPCGHIFCWSCILE-----WCSEKA--ECPLCREKFQP 285 (293)
T ss_pred CCCceEEEecCCCC----C-CcCcCcchHHHHHHHH-----HHcccc--CCCcccccCCC
Confidence 34677777655332 2 6778999998876543 455555 79999765543
No 174
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=64.11 E-value=3.7 Score=16.16 Aligned_cols=11 Identities=18% Similarity=0.594 Sum_probs=8.4
Q ss_pred ccCCCCCcccc
Q psy12019 63 YQCPQCPYRAK 73 (87)
Q Consensus 63 ~~c~~c~~~f~ 73 (87)
+.|..|++.|-
T Consensus 13 f~C~~C~~~FC 23 (39)
T smart00154 13 FKCRHCGNLFC 23 (39)
T ss_pred eECCccCCccc
Confidence 78888887774
No 175
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=64.03 E-value=8.4 Score=16.17 Aligned_cols=14 Identities=29% Similarity=0.795 Sum_probs=8.9
Q ss_pred ceecCcccccccch
Q psy12019 33 MFMCDVCGKGYKYK 46 (87)
Q Consensus 33 ~~~c~~c~~~~~~~ 46 (87)
-|.|..||..+...
T Consensus 28 ~W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 28 WWKCPKCGHEWKAS 41 (55)
T ss_pred EEECCCCCCeeEcc
Confidence 46777777655443
No 176
>KOG2907|consensus
Probab=63.88 E-value=3 Score=20.68 Aligned_cols=40 Identities=28% Similarity=0.639 Sum_probs=21.1
Q ss_pred eecCcccccccchhhHHHHhh-hhcCCCCCccCCCCCcccccc
Q psy12019 34 FMCDVCGKGYKYKNGIYRHKK-FECGQEPKYQCPQCPYRAKQN 75 (87)
Q Consensus 34 ~~c~~c~~~~~~~~~~~~h~~-~~~~~~~~~~c~~c~~~f~~~ 75 (87)
..|+.||..--.=..+ .+| .-.|.-..|.|+.|++.|...
T Consensus 75 ~kCpkCghe~m~Y~T~--QlRSADEGQTVFYTC~kC~~k~~e~ 115 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTL--QLRSADEGQTVFYTCPKCKYKFTEN 115 (116)
T ss_pred ccCcccCCchhhhhhh--hcccccCCceEEEEcCccceeeecc
Confidence 4688888532111111 122 222333348899998887643
No 177
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=63.38 E-value=4.5 Score=20.68 Aligned_cols=26 Identities=27% Similarity=0.542 Sum_probs=15.3
Q ss_pred ccc--ccchhhhccCCcceecCcccccc
Q psy12019 18 KCL--INWSAVQQNHAGMFMCDVCGKGY 43 (87)
Q Consensus 18 ~c~--~c~~~~~~~~~~~~~c~~c~~~~ 43 (87)
.|+ .|.+.....+...|.|..|++..
T Consensus 20 aC~~~~C~kKv~~~~~~~y~C~~C~~~~ 47 (146)
T PF08646_consen 20 ACPNEKCNKKVTENGDGSYRCEKCNKTV 47 (146)
T ss_dssp E-TSTTTS-B-EEETTTEEEETTTTEEE
T ss_pred CCCCccCCCEeecCCCcEEECCCCCCcC
Confidence 477 77776655544567787777654
No 178
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=63.35 E-value=6.9 Score=15.89 Aligned_cols=12 Identities=42% Similarity=1.054 Sum_probs=7.4
Q ss_pred cceecCcccccc
Q psy12019 32 GMFMCDVCGKGY 43 (87)
Q Consensus 32 ~~~~c~~c~~~~ 43 (87)
....|+.|++.|
T Consensus 13 ~~i~C~~C~~~~ 24 (51)
T PF00628_consen 13 DMIQCDSCNRWY 24 (51)
T ss_dssp SEEEBSTTSCEE
T ss_pred CeEEcCCCChhh
Confidence 345677777654
No 179
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=62.76 E-value=5.4 Score=14.52 Aligned_cols=6 Identities=33% Similarity=1.408 Sum_probs=2.4
Q ss_pred eecCcc
Q psy12019 34 FMCDVC 39 (87)
Q Consensus 34 ~~c~~c 39 (87)
|.|..|
T Consensus 16 Y~C~~c 21 (30)
T PF03107_consen 16 YHCSEC 21 (30)
T ss_pred EEeCCC
Confidence 344333
No 180
>KOG2231|consensus
Probab=61.72 E-value=9.8 Score=24.98 Aligned_cols=51 Identities=20% Similarity=0.440 Sum_probs=31.8
Q ss_pred ecCcccccccchhhHHHHhhhhcCCCCCccC---CCCCcccccchHHHhhhhhcCC
Q psy12019 35 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQC---PQCPYRAKQNAHLTTHMAIKHY 87 (87)
Q Consensus 35 ~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c---~~c~~~f~~~~~l~~h~~~~h~ 87 (87)
.|..|...|.....+..|++...-... -| ..++.-|.....|..|-+..||
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h~~ch--fC~~~~~~neyy~~~~dLe~HfR~~Hf 237 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDHEFCH--FCDYKTGQNEYYNDYDDLEEHFRKGHF 237 (669)
T ss_pred cchhhhhhhccHHHHHHhhccceehee--ecCcccccchhcccchHHHHHhhhcCc
Confidence 577777777777777777775432221 11 1233456677777888777775
No 181
>KOG0402|consensus
Probab=61.69 E-value=4.1 Score=19.07 Aligned_cols=26 Identities=19% Similarity=0.447 Sum_probs=11.5
Q ss_pred ccccccchhhhcc-CCcceecCccccc
Q psy12019 17 NKCLINWSAVQQN-HAGMFMCDVCGKG 42 (87)
Q Consensus 17 ~~c~~c~~~~~~~-~~~~~~c~~c~~~ 42 (87)
|.|+.|++.-... ...-|.|..|.+.
T Consensus 37 y~CsfCGK~~vKR~AvGiW~C~~C~kv 63 (92)
T KOG0402|consen 37 YTCSFCGKKTVKRKAVGIWKCGSCKKV 63 (92)
T ss_pred hhhhhcchhhhhhhceeEEecCCccce
Confidence 4555555543221 2223455555443
No 182
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=61.28 E-value=11 Score=14.94 Aligned_cols=43 Identities=19% Similarity=0.244 Sum_probs=19.7
Q ss_pred ccccchhhhccCCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCc
Q psy12019 19 CLINWSAVQQNHAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 70 (87)
Q Consensus 19 c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~ 70 (87)
|++|...+ ....++.-..||-.|-..-... .. ... ..|+.|++
T Consensus 2 C~~C~~~~--~~~~~~~l~~CgH~~C~~C~~~-----~~-~~~-~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKY--SEERRPRLTSCGHIFCEKCLKK-----LK-GKS-VKCPICRK 44 (44)
T ss_pred CcCcCccc--cCCCCeEEcccCCHHHHHHHHh-----hc-CCC-CCCcCCCC
Confidence 55666665 1122234445555554432211 11 244 67777753
No 183
>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=60.77 E-value=6.1 Score=20.67 Aligned_cols=25 Identities=24% Similarity=0.518 Sum_probs=12.1
Q ss_pred cccccchhhhccCCcceecCccccc
Q psy12019 18 KCLINWSAVQQNHAGMFMCDVCGKG 42 (87)
Q Consensus 18 ~c~~c~~~~~~~~~~~~~c~~c~~~ 42 (87)
.|+.|.+.........|.|..|++.
T Consensus 36 aC~~C~kkv~~~~~~~~~C~~C~~~ 60 (166)
T cd04476 36 ACPGCNKKVVEEGNGTYRCEKCNKS 60 (166)
T ss_pred cccccCcccEeCCCCcEECCCCCCc
Confidence 3555555544333234555555544
No 184
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=59.96 E-value=20 Score=21.26 Aligned_cols=52 Identities=15% Similarity=0.244 Sum_probs=28.9
Q ss_pred ccccccchhh-hccCCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccccc
Q psy12019 17 NKCLINWSAV-QQNHAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQN 75 (87)
Q Consensus 17 ~~c~~c~~~~-~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~~ 75 (87)
+.|+.|...- .+...+.+.. .||-.|..+-.-.. ....+ ..|+.|+..+...
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l-----~~~~~-~~CP~C~~~lrk~ 56 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLL-----FVRGS-GSCPECDTPLRKN 56 (309)
T ss_pred CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHH-----hcCCC-CCCCCCCCccchh
Confidence 5788887642 2222233333 67877766543221 12233 6899998876544
No 185
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=59.72 E-value=4.4 Score=20.37 Aligned_cols=13 Identities=23% Similarity=0.399 Sum_probs=8.2
Q ss_pred ceecCcccccccch
Q psy12019 33 MFMCDVCGKGYKYK 46 (87)
Q Consensus 33 ~~~c~~c~~~~~~~ 46 (87)
.+.| .||..|...
T Consensus 70 ~~~C-~Cg~~~~~~ 82 (124)
T PRK00762 70 EIEC-ECGYEGVVD 82 (124)
T ss_pred eEEe-eCcCccccc
Confidence 3568 888666543
No 186
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=59.55 E-value=6.4 Score=15.91 Aligned_cols=16 Identities=25% Similarity=0.908 Sum_probs=11.0
Q ss_pred ecCcccccccchhhHH
Q psy12019 35 MCDVCGKGYKYKNGIY 50 (87)
Q Consensus 35 ~c~~c~~~~~~~~~~~ 50 (87)
.|..||+.|.......
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 4778888887765544
No 187
>KOG2482|consensus
Probab=59.26 E-value=5.3 Score=23.95 Aligned_cols=22 Identities=23% Similarity=0.434 Sum_probs=19.8
Q ss_pred ccCCCCCcccccchHHHhhhhh
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMAI 84 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~ 84 (87)
.+|-.|.+.|+....|..||+-
T Consensus 196 ~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred heeeeeccccCCcHHHHHHHHh
Confidence 6889999999999999999873
No 188
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=59.16 E-value=9.7 Score=20.57 Aligned_cols=32 Identities=25% Similarity=0.833 Sum_probs=19.1
Q ss_pred CcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCccc
Q psy12019 31 AGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRA 72 (87)
Q Consensus 31 ~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f 72 (87)
..-|.|+.|...++...+. ..+ |.|+.||...
T Consensus 111 ~~~y~C~~~~~r~sfdeA~------~~~----F~Cp~Cg~~L 142 (176)
T COG1675 111 NNYYVCPNCHVKYSFDEAM------ELG----FTCPKCGEDL 142 (176)
T ss_pred CCceeCCCCCCcccHHHHH------HhC----CCCCCCCchh
Confidence 3457887776655544432 222 7888888644
No 189
>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=59.15 E-value=4.1 Score=17.09 Aligned_cols=11 Identities=27% Similarity=0.706 Sum_probs=5.7
Q ss_pred cCCCCCccccc
Q psy12019 64 QCPQCPYRAKQ 74 (87)
Q Consensus 64 ~c~~c~~~f~~ 74 (87)
.|+.|++.|..
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 88999988863
No 190
>KOG0717|consensus
Probab=58.82 E-value=5 Score=25.05 Aligned_cols=21 Identities=24% Similarity=0.412 Sum_probs=16.6
Q ss_pred ccCCCCCcccccchHHHhhhh
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMA 83 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~ 83 (87)
+.|.+|.|.|.+.-.|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 568888888888888887753
No 191
>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=58.46 E-value=7.3 Score=24.49 Aligned_cols=8 Identities=50% Similarity=1.153 Sum_probs=4.4
Q ss_pred ccCCCCCc
Q psy12019 63 YQCPQCPY 70 (87)
Q Consensus 63 ~~c~~c~~ 70 (87)
..|+.|+.
T Consensus 254 ~~Cp~C~s 261 (505)
T TIGR00595 254 KTCPQCGS 261 (505)
T ss_pred CCCCCCCC
Confidence 55555553
No 192
>KOG1729|consensus
Probab=58.33 E-value=0.94 Score=26.18 Aligned_cols=30 Identities=13% Similarity=0.206 Sum_probs=18.6
Q ss_pred cccccccchhhhccCCcceecCcccccccc
Q psy12019 16 HNKCLINWSAVQQNHAGMFMCDVCGKGYKY 45 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~~~~c~~c~~~~~~ 45 (87)
.-.|..|..+.-....+.+.|..||..|..
T Consensus 168 a~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~ 197 (288)
T KOG1729|consen 168 ATECMVCGCTEFTLSERRHHCRNCGDIVCA 197 (288)
T ss_pred ceecccCCCccccHHHHHHHHHhcchHhhh
Confidence 356888888432323334568888877766
No 193
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=57.76 E-value=6.5 Score=14.50 Aligned_cols=8 Identities=38% Similarity=0.929 Sum_probs=3.4
Q ss_pred ceecCccc
Q psy12019 33 MFMCDVCG 40 (87)
Q Consensus 33 ~~~c~~c~ 40 (87)
.-.|+.|+
T Consensus 21 ~r~C~~Cg 28 (32)
T PF09297_consen 21 ARRCPSCG 28 (32)
T ss_dssp -EEESSSS
T ss_pred EeECCCCc
Confidence 33455554
No 194
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=57.67 E-value=7.2 Score=20.61 Aligned_cols=12 Identities=17% Similarity=0.249 Sum_probs=6.4
Q ss_pred ccCCCCCccccc
Q psy12019 63 YQCPQCPYRAKQ 74 (87)
Q Consensus 63 ~~c~~c~~~f~~ 74 (87)
.-|..||+.|++
T Consensus 69 sYC~~CGkpyPW 80 (158)
T PF10083_consen 69 SYCHNCGKPYPW 80 (158)
T ss_pred hhHHhCCCCCch
Confidence 445555555554
No 195
>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=57.61 E-value=4.5 Score=16.13 Aligned_cols=15 Identities=40% Similarity=0.800 Sum_probs=9.1
Q ss_pred cceecCcccccccch
Q psy12019 32 GMFMCDVCGKGYKYK 46 (87)
Q Consensus 32 ~~~~c~~c~~~~~~~ 46 (87)
.++.|..|++.|-..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 478899998888554
No 196
>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=57.59 E-value=4.9 Score=19.61 Aligned_cols=9 Identities=11% Similarity=-0.105 Sum_probs=4.0
Q ss_pred cccccccch
Q psy12019 16 HNKCLINWS 24 (87)
Q Consensus 16 ~~~c~~c~~ 24 (87)
|..|+.|+.
T Consensus 2 p~~CpYCg~ 10 (102)
T PF11672_consen 2 PIICPYCGG 10 (102)
T ss_pred CcccCCCCC
Confidence 344444443
No 197
>PLN02294 cytochrome c oxidase subunit Vb
Probab=57.55 E-value=6.2 Score=21.18 Aligned_cols=20 Identities=25% Similarity=0.581 Sum_probs=14.1
Q ss_pred HhhhhcCCCCCccCCCCCcccc
Q psy12019 52 HKKFECGQEPKYQCPQCPYRAK 73 (87)
Q Consensus 52 h~~~~~~~~~~~~c~~c~~~f~ 73 (87)
....+.| ++ ..|++||..|.
T Consensus 133 Wf~L~kG-kp-~RCpeCG~~fk 152 (174)
T PLN02294 133 WFWLEKG-KS-FECPVCTQYFE 152 (174)
T ss_pred EEEecCC-Cc-eeCCCCCCEEE
Confidence 3344555 66 89999998875
No 198
>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 PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=57.34 E-value=9 Score=16.12 Aligned_cols=40 Identities=25% Similarity=0.533 Sum_probs=18.8
Q ss_pred ceecCc-ccccccchhhHHHHhhhhcCCCCCccCCC----CCcccc
Q psy12019 33 MFMCDV-CGKGYKYKNGIYRHKKFECGQEPKYQCPQ----CPYRAK 73 (87)
Q Consensus 33 ~~~c~~-c~~~~~~~~~~~~h~~~~~~~~~~~~c~~----c~~~f~ 73 (87)
+..|+. |+..-.....|..|....-...+ ..|.. |+..+.
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~-v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECPKRP-VPCPYSPYGCKERVP 53 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTSTTSE-EE-SS----S--EEE
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCCCCc-EECCCCCCCCCCccc
Confidence 446766 33332334557788774334344 67776 766654
No 200
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=56.80 E-value=7.7 Score=19.30 Aligned_cols=29 Identities=10% Similarity=0.032 Sum_probs=16.6
Q ss_pred CcccccccchhhhccCCcceecCccccccc
Q psy12019 15 KHNKCLINWSAVQQNHAGMFMCDVCGKGYK 44 (87)
Q Consensus 15 ~~~~c~~c~~~~~~~~~~~~~c~~c~~~~~ 44 (87)
...+|+.|++...-.+.. ..|..|+....
T Consensus 68 v~V~CP~C~K~TKmLGr~-D~CM~C~~pLT 96 (114)
T PF11023_consen 68 VQVECPNCGKQTKMLGRV-DACMHCKEPLT 96 (114)
T ss_pred eeeECCCCCChHhhhchh-hccCcCCCcCc
Confidence 345677777766544333 36666665443
No 201
>PRK04023 DNA polymerase II large subunit; Validated
Probab=56.55 E-value=9.9 Score=26.32 Aligned_cols=22 Identities=23% Similarity=0.353 Sum_probs=13.7
Q ss_pred cccccccchhhhccCCcceecCccccc
Q psy12019 16 HNKCLINWSAVQQNHAGMFMCDVCGKG 42 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~~~~c~~c~~~ 42 (87)
...|+.|+... ..+.|+.||..
T Consensus 626 ~RfCpsCG~~t-----~~frCP~CG~~ 647 (1121)
T PRK04023 626 RRKCPSCGKET-----FYRRCPFCGTH 647 (1121)
T ss_pred CccCCCCCCcC-----CcccCCCCCCC
Confidence 45677777663 23567777754
No 202
>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=55.84 E-value=5.9 Score=15.21 Aligned_cols=12 Identities=17% Similarity=0.528 Sum_probs=4.9
Q ss_pred cCCCCCcccccc
Q psy12019 64 QCPQCPYRAKQN 75 (87)
Q Consensus 64 ~c~~c~~~f~~~ 75 (87)
.|.+|++.|..+
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 566777766543
No 203
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=55.76 E-value=4.5 Score=23.66 Aligned_cols=11 Identities=36% Similarity=0.906 Sum_probs=5.3
Q ss_pred eecCccccccc
Q psy12019 34 FMCDVCGKGYK 44 (87)
Q Consensus 34 ~~c~~c~~~~~ 44 (87)
+.|+.|+..|.
T Consensus 58 ~vcp~c~~h~r 68 (296)
T CHL00174 58 NICEQCGYHLK 68 (296)
T ss_pred CCCCCCCCCcC
Confidence 45555554443
No 204
>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=55.45 E-value=6 Score=20.67 Aligned_cols=14 Identities=21% Similarity=0.427 Sum_probs=11.1
Q ss_pred ccCCCCCcccccch
Q psy12019 63 YQCPQCPYRAKQNA 76 (87)
Q Consensus 63 ~~c~~c~~~f~~~~ 76 (87)
-+|..|++.|.+..
T Consensus 29 ReC~~C~~RFTTyE 42 (147)
T TIGR00244 29 RECLECHERFTTFE 42 (147)
T ss_pred ccCCccCCccceee
Confidence 68899999987654
No 205
>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=55.43 E-value=21 Score=17.41 Aligned_cols=36 Identities=8% Similarity=0.147 Sum_probs=17.9
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 70 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~ 70 (87)
.|.|+..|..|.+=......+..... +. |.|...|+
T Consensus 3 Vf~i~~T~EiF~dYe~Y~~R~~~y~~-~v-wtC~~TGk 38 (102)
T PF10537_consen 3 VFYIPFTGEIFRDYEEYLKRMILYNQ-RV-WTCEITGK 38 (102)
T ss_pred eEEeCCCCcccCCHHHHHHHHHHHhC-Ce-eEEecCCC
Confidence 35555555555555444444433332 33 66665554
No 206
>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=55.19 E-value=4.6 Score=23.46 Aligned_cols=28 Identities=14% Similarity=0.342 Sum_probs=15.6
Q ss_pred cccccchhhhcc--CCcceecCcccccccc
Q psy12019 18 KCLINWSAVQQN--HAGMFMCDVCGKGYKY 45 (87)
Q Consensus 18 ~c~~c~~~~~~~--~~~~~~c~~c~~~~~~ 45 (87)
+|+.|+...-.. ....+.|+.||..|.-
T Consensus 28 ~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 28 KCPKCGQVLYTKELERNLEVCPKCDHHMRM 57 (285)
T ss_pred ECCCCcchhhHHHHHhhCCCCCCCCCcCcC
Confidence 566666665432 2234567777766543
No 207
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=54.57 E-value=26 Score=19.31 Aligned_cols=53 Identities=19% Similarity=0.350 Sum_probs=29.8
Q ss_pred CcccccccchhhhccCCcceecCcccccccchhhHHHHhhh----------hcCCCCCccCCCCCcccc
Q psy12019 15 KHNKCLINWSAVQQNHAGMFMCDVCGKGYKYKNGIYRHKKF----------ECGQEPKYQCPQCPYRAK 73 (87)
Q Consensus 15 ~~~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~----------~~~~~~~~~c~~c~~~f~ 73 (87)
..+.|++|...+... ....||-.|.+.-........ ...... ..|+.|...+.
T Consensus 17 ~~~~CpICld~~~dP-----VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~-~~CPvCR~~Is 79 (193)
T PLN03208 17 GDFDCNICLDQVRDP-----VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREP-PKCPVCKSDVS 79 (193)
T ss_pred CccCCccCCCcCCCc-----EEcCCCchhHHHHHHHHHHhccccccccccccccCCC-CcCCCCCCcCC
Confidence 468999998876543 223577766665543221100 011233 68999987654
No 208
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=54.50 E-value=14 Score=15.89 Aligned_cols=9 Identities=44% Similarity=0.988 Sum_probs=4.4
Q ss_pred ceecCcccc
Q psy12019 33 MFMCDVCGK 41 (87)
Q Consensus 33 ~~~c~~c~~ 41 (87)
.|+|+.||-
T Consensus 14 ~~~Cp~cGi 22 (55)
T PF13824_consen 14 NFECPDCGI 22 (55)
T ss_pred CCcCCCCCC
Confidence 345555553
No 209
>PHA02998 RNA polymerase subunit; Provisional
Probab=54.28 E-value=1.9 Score=23.21 Aligned_cols=11 Identities=27% Similarity=0.588 Sum_probs=8.3
Q ss_pred ccCCCCCcccc
Q psy12019 63 YQCPQCPYRAK 73 (87)
Q Consensus 63 ~~c~~c~~~f~ 73 (87)
|.|..||+.|.
T Consensus 172 YkC~~CG~~wk 182 (195)
T PHA02998 172 HACRDCKKHFK 182 (195)
T ss_pred EEcCCCCCccC
Confidence 68888887765
No 210
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=54.00 E-value=2.4 Score=21.01 Aligned_cols=11 Identities=45% Similarity=1.328 Sum_probs=8.1
Q ss_pred ccCCCCCcccc
Q psy12019 63 YQCPQCPYRAK 73 (87)
Q Consensus 63 ~~c~~c~~~f~ 73 (87)
|.|..||..++
T Consensus 101 y~C~~Cg~~wr 111 (113)
T COG1594 101 YKCTRCGYRWR 111 (113)
T ss_pred EEecccCCEee
Confidence 77888887664
No 211
>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=53.44 E-value=8.8 Score=18.56 Aligned_cols=15 Identities=27% Similarity=0.561 Sum_probs=10.5
Q ss_pred CCcceecCccccccc
Q psy12019 30 HAGMFMCDVCGKGYK 44 (87)
Q Consensus 30 ~~~~~~c~~c~~~~~ 44 (87)
...+..|.+||..|.
T Consensus 76 ~g~~~rC~eCG~~fk 90 (97)
T cd00924 76 KGKPKRCPECGHVFK 90 (97)
T ss_pred CCCceeCCCCCcEEE
Confidence 335778888887764
No 212
>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=53.02 E-value=9.6 Score=23.88 Aligned_cols=22 Identities=23% Similarity=0.616 Sum_probs=14.5
Q ss_pred ccCCCCCcccccchHHHhhhhh
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMAI 84 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~ 84 (87)
|.|+.|.+.|.....+..|+..
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHH
Confidence 6666676667766666666543
No 213
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=52.57 E-value=18 Score=17.79 Aligned_cols=17 Identities=18% Similarity=0.434 Sum_probs=11.0
Q ss_pred ceecCcccccccchhhH
Q psy12019 33 MFMCDVCGKGYKYKNGI 49 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~ 49 (87)
.+.|+.||..+......
T Consensus 31 ~~~C~~CGe~~~~~e~~ 47 (127)
T TIGR03830 31 GWYCPACGEELLDPEES 47 (127)
T ss_pred eeECCCCCCEEEcHHHH
Confidence 46788888766655443
No 214
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=52.49 E-value=8.2 Score=22.41 Aligned_cols=25 Identities=24% Similarity=0.392 Sum_probs=15.8
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCccc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRA 72 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f 72 (87)
.|.|+.|.-.|.. -| -+|+.||-.|
T Consensus 255 GyvCs~Clsi~C~--------------~p-~~C~~Cgt~f 279 (279)
T TIGR00627 255 GFVCSVCLSVLCQ--------------YT-PICKTCKTAF 279 (279)
T ss_pred eEECCCccCCcCC--------------CC-CCCCCCCCCC
Confidence 4888888655432 23 4778887554
No 215
>PF12773 DZR: Double zinc ribbon
Probab=52.16 E-value=8.3 Score=15.66 Aligned_cols=10 Identities=30% Similarity=0.786 Sum_probs=5.8
Q ss_pred ccCCCCCccc
Q psy12019 63 YQCPQCPYRA 72 (87)
Q Consensus 63 ~~c~~c~~~f 72 (87)
..|+.|+...
T Consensus 30 ~~C~~Cg~~~ 39 (50)
T PF12773_consen 30 KICPNCGAEN 39 (50)
T ss_pred CCCcCCcCCC
Confidence 5566666543
No 216
>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=51.87 E-value=10 Score=15.78 Aligned_cols=23 Identities=13% Similarity=0.519 Sum_probs=9.1
Q ss_pred ccchhhHHHHhhhhcCCCCCccCCCCCc
Q psy12019 43 YKYKNGIYRHKKFECGQEPKYQCPQCPY 70 (87)
Q Consensus 43 ~~~~~~~~~h~~~~~~~~~~~~c~~c~~ 70 (87)
|...+.+....+. .. |.|++|++
T Consensus 27 FDl~~fl~~~~~~----~~-W~CPiC~~ 49 (50)
T PF02891_consen 27 FDLESFLESNQRT----PK-WKCPICNK 49 (50)
T ss_dssp EEHHHHHHHHHHS--------B-TTT--
T ss_pred ECHHHHHHHhhcc----CC-eECcCCcC
Confidence 5444444433332 33 89999875
No 217
>PF15616 TerY-C: TerY-C metal binding domain
Probab=51.83 E-value=12 Score=19.21 Aligned_cols=9 Identities=33% Similarity=0.896 Sum_probs=5.4
Q ss_pred ccCCCCCcc
Q psy12019 63 YQCPQCPYR 71 (87)
Q Consensus 63 ~~c~~c~~~ 71 (87)
..|+.|++.
T Consensus 106 ~~CPwCg~~ 114 (131)
T PF15616_consen 106 VTCPWCGNE 114 (131)
T ss_pred EECCCCCCe
Confidence 566666654
No 218
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=51.64 E-value=5.4 Score=23.26 Aligned_cols=28 Identities=21% Similarity=0.479 Sum_probs=15.9
Q ss_pred cccccchhhhcc--CCcceecCcccccccc
Q psy12019 18 KCLINWSAVQQN--HAGMFMCDVCGKGYKY 45 (87)
Q Consensus 18 ~c~~c~~~~~~~--~~~~~~c~~c~~~~~~ 45 (87)
+|+.|+...-.. ....+.|+.|+..|.-
T Consensus 29 ~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl 58 (292)
T PRK05654 29 KCPSCGQVLYRKELEANLNVCPKCGHHMRI 58 (292)
T ss_pred ECCCccchhhHHHHHhcCCCCCCCCCCeeC
Confidence 567776665433 2234567777766543
No 219
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=51.34 E-value=8 Score=17.54 Aligned_cols=24 Identities=25% Similarity=0.665 Sum_probs=8.7
Q ss_pred ccccchhhhccCCcceecCcccccc
Q psy12019 19 CLINWSAVQQNHAGMFMCDVCGKGY 43 (87)
Q Consensus 19 c~~c~~~~~~~~~~~~~c~~c~~~~ 43 (87)
|+.|.......+ ..|.|..|++.|
T Consensus 4 CP~C~~~L~~~~-~~~~C~~C~~~~ 27 (70)
T PF07191_consen 4 CPKCQQELEWQG-GHYHCEACQKDY 27 (70)
T ss_dssp -SSS-SBEEEET-TEEEETTT--EE
T ss_pred CCCCCCccEEeC-CEEECccccccc
Confidence 445554433322 334555555443
No 220
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=51.06 E-value=5.8 Score=15.29 Aligned_cols=10 Identities=30% Similarity=0.703 Sum_probs=3.8
Q ss_pred ccCCCCCccc
Q psy12019 63 YQCPQCPYRA 72 (87)
Q Consensus 63 ~~c~~c~~~f 72 (87)
..|..||-.+
T Consensus 22 isC~~CGPr~ 31 (35)
T PF07503_consen 22 ISCTNCGPRY 31 (35)
T ss_dssp --BTTCC-SC
T ss_pred ccCCCCCCCE
Confidence 4555565443
No 221
>PRK07591 threonine synthase; Validated
Probab=51.06 E-value=8.4 Score=23.60 Aligned_cols=27 Identities=15% Similarity=0.165 Sum_probs=19.8
Q ss_pred cccccccchhhhccCCcceecCccccccc
Q psy12019 16 HNKCLINWSAVQQNHAGMFMCDVCGKGYK 44 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~~~~c~~c~~~~~ 44 (87)
-+.|..|++.+... .. +.|+.||..+.
T Consensus 18 ~l~C~~Cg~~~~~~-~~-~~C~~cg~~l~ 44 (421)
T PRK07591 18 ALKCRECGAEYPLG-PI-HVCEECFGPLE 44 (421)
T ss_pred EEEeCCCCCcCCCC-CC-ccCCCCCCeEE
Confidence 47899999998764 33 88998975443
No 222
>KOG1813|consensus
Probab=50.86 E-value=5.8 Score=23.24 Aligned_cols=16 Identities=19% Similarity=0.119 Sum_probs=12.2
Q ss_pred CCcccccccchhhhcc
Q psy12019 14 PKHNKCLINWSAVQQN 29 (87)
Q Consensus 14 ~~~~~c~~c~~~~~~~ 29 (87)
.-||.|.+|.+.|...
T Consensus 239 ~~Pf~c~icr~~f~~p 254 (313)
T KOG1813|consen 239 LLPFKCFICRKYFYRP 254 (313)
T ss_pred cCCccccccccccccc
Confidence 3578888888888765
No 223
>PF15269 zf-C2H2_7: Zinc-finger
Probab=50.45 E-value=11 Score=15.44 Aligned_cols=21 Identities=43% Similarity=1.059 Sum_probs=10.6
Q ss_pred ccCCCCCcccccchHHHhhhh
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMA 83 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~ 83 (87)
|+|-.|.-+..-.+.|-.|++
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 344445544455555555554
No 224
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=50.24 E-value=13 Score=15.64 Aligned_cols=9 Identities=33% Similarity=1.213 Sum_probs=6.2
Q ss_pred ccCCCCCcc
Q psy12019 63 YQCPQCPYR 71 (87)
Q Consensus 63 ~~c~~c~~~ 71 (87)
+.|..||++
T Consensus 38 ~~CGkCgyT 46 (51)
T COG1998 38 WACGKCGYT 46 (51)
T ss_pred eEeccccce
Confidence 677777764
No 225
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=50.09 E-value=11 Score=19.21 Aligned_cols=14 Identities=21% Similarity=0.667 Sum_probs=11.1
Q ss_pred CCCCccCCCCCcccc
Q psy12019 59 QEPKYQCPQCPYRAK 73 (87)
Q Consensus 59 ~~~~~~c~~c~~~f~ 73 (87)
... |.|..|++.|.
T Consensus 51 ~qR-yrC~~C~~tf~ 64 (129)
T COG3677 51 HQR-YKCKSCGSTFT 64 (129)
T ss_pred ccc-cccCCcCccee
Confidence 344 99999999885
No 226
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=49.44 E-value=19 Score=15.16 Aligned_cols=32 Identities=22% Similarity=0.393 Sum_probs=18.0
Q ss_pred ecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcc
Q psy12019 35 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYR 71 (87)
Q Consensus 35 ~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~ 71 (87)
.|..|+...+..... ....++.. ..|+.||+.
T Consensus 24 ~C~gC~~~l~~~~~~----~i~~~~~i-~~Cp~CgRi 55 (56)
T PF02591_consen 24 TCSGCHMELPPQELN----EIRKGDEI-VFCPNCGRI 55 (56)
T ss_pred ccCCCCEEcCHHHHH----HHHcCCCe-EECcCCCcc
Confidence 567776555443321 22334455 788888864
No 227
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=49.43 E-value=10 Score=23.75 Aligned_cols=14 Identities=29% Similarity=0.487 Sum_probs=8.0
Q ss_pred cceecCcccccccc
Q psy12019 32 GMFMCDVCGKGYKY 45 (87)
Q Consensus 32 ~~~~c~~c~~~~~~ 45 (87)
..|+|..||..+..
T Consensus 424 ~~~~c~~c~~~yd~ 437 (479)
T PRK05452 424 PRMQCSVCQWIYDP 437 (479)
T ss_pred CeEEECCCCeEECC
Confidence 35666666655543
No 228
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=48.86 E-value=10 Score=14.80 Aligned_cols=15 Identities=20% Similarity=0.414 Sum_probs=8.5
Q ss_pred ccCCCCCcccccchH
Q psy12019 63 YQCPQCPYRAKQNAH 77 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~ 77 (87)
-.|+.|++.|-..+.
T Consensus 3 ~~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 3 GLCPRCGKGFHWASE 17 (36)
T ss_dssp -C-TTTSSSCS-TTT
T ss_pred ccCcccCCCcchhhh
Confidence 468888888755443
No 229
>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=48.58 E-value=5.1 Score=20.85 Aligned_cols=31 Identities=23% Similarity=0.606 Sum_probs=17.6
Q ss_pred CCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcc
Q psy12019 30 HAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYR 71 (87)
Q Consensus 30 ~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~ 71 (87)
+.+.+.|..||..... .+++.- -.|+.|+..
T Consensus 109 g~G~l~C~~Cg~~~~~---------~~~~~l--~~Cp~C~~~ 139 (146)
T PF07295_consen 109 GPGTLVCENCGHEVEL---------THPERL--PPCPKCGHT 139 (146)
T ss_pred cCceEecccCCCEEEe---------cCCCcC--CCCCCCCCC
Confidence 4456888888864311 123323 477888753
No 230
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=48.23 E-value=9.7 Score=18.77 Aligned_cols=26 Identities=23% Similarity=0.424 Sum_probs=21.5
Q ss_pred CCcceecCcccccccchhhHHHHhhh
Q psy12019 30 HAGMFMCDVCGKGYKYKNGIYRHKKF 55 (87)
Q Consensus 30 ~~~~~~c~~c~~~~~~~~~~~~h~~~ 55 (87)
+...+-|.+|.+-|....+|..|.+.
T Consensus 52 GlGqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 52 GLGQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred CCceeeeehhHHHHHHHHHHHHHhcc
Confidence 44567899999999999999888764
No 231
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the 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=47.10 E-value=6.3 Score=21.63 Aligned_cols=26 Identities=19% Similarity=0.336 Sum_probs=0.0
Q ss_pred hhcCCCCCccCCCCC-cccccchHHHhh
Q psy12019 55 FECGQEPKYQCPQCP-YRAKQNAHLTTH 81 (87)
Q Consensus 55 ~~~~~~~~~~c~~c~-~~f~~~~~l~~h 81 (87)
.|-.... |.|.+|| ..|.....+.+|
T Consensus 95 LhGL~~e-y~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 95 LHGLGVE-YKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp ----------------------------
T ss_pred HhCCCCe-eeeEeCCCcceecHHHHHHh
Confidence 3444455 8888886 344344444444
No 233
>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=46.79 E-value=4.1 Score=16.65 Aligned_cols=13 Identities=31% Similarity=0.580 Sum_probs=7.5
Q ss_pred ccCC--CCCcccccc
Q psy12019 63 YQCP--QCPYRAKQN 75 (87)
Q Consensus 63 ~~c~--~c~~~f~~~ 75 (87)
++|. +||..|...
T Consensus 26 ~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 26 CQCTNPECGHTFVAN 40 (47)
T ss_pred EEECCCcCCCEEEEE
Confidence 5564 377776543
No 234
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.77 E-value=7.6 Score=16.18 Aligned_cols=16 Identities=19% Similarity=0.750 Sum_probs=10.7
Q ss_pred ecCcccccccchhhHH
Q psy12019 35 MCDVCGKGYKYKNGIY 50 (87)
Q Consensus 35 ~c~~c~~~~~~~~~~~ 50 (87)
.|+.|++.|.+.....
T Consensus 14 ICpvCqRPFsWRkKW~ 29 (54)
T COG4338 14 ICPVCQRPFSWRKKWA 29 (54)
T ss_pred hhhhhcCchHHHHHHH
Confidence 4777887777665544
No 235
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=46.61 E-value=18 Score=14.13 Aligned_cols=24 Identities=17% Similarity=0.408 Sum_probs=10.9
Q ss_pred cccccccchhhhccCCcceecCccc
Q psy12019 16 HNKCLINWSAVQQNHAGMFMCDVCG 40 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~~~~c~~c~ 40 (87)
+..|..|.+.+.... ..+.|..|+
T Consensus 11 ~~~C~~C~~~i~~~~-~~~~C~~C~ 34 (49)
T smart00109 11 PTKCCVCRKSIWGSF-QGLRCSWCK 34 (49)
T ss_pred CCCccccccccCcCC-CCcCCCCCC
Confidence 444555555544322 234455553
No 236
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=46.53 E-value=3.8 Score=15.22 Aligned_cols=10 Identities=20% Similarity=0.856 Sum_probs=5.5
Q ss_pred ccCCCCCccc
Q psy12019 63 YQCPQCPYRA 72 (87)
Q Consensus 63 ~~c~~c~~~f 72 (87)
|.|..|+..+
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 5566665544
No 237
>KOG3362|consensus
Probab=46.00 E-value=6.8 Score=20.41 Aligned_cols=19 Identities=32% Similarity=0.576 Sum_probs=8.1
Q ss_pred ccCCCCCcccccchHHHhh
Q psy12019 63 YQCPQCPYRAKQNAHLTTH 81 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h 81 (87)
|.|..||-.+-...-+..|
T Consensus 130 ysC~~CG~kyCsv~C~~~H 148 (156)
T KOG3362|consen 130 YSCVNCGTKYCSVRCLKTH 148 (156)
T ss_pred hHHHhcCCceeechhhhhc
Confidence 4444444444433334333
No 238
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=45.94 E-value=9.7 Score=20.06 Aligned_cols=13 Identities=23% Similarity=0.447 Sum_probs=10.4
Q ss_pred ccCCCCCcccccc
Q psy12019 63 YQCPQCPYRAKQN 75 (87)
Q Consensus 63 ~~c~~c~~~f~~~ 75 (87)
-+|..|+..|.+.
T Consensus 29 ReC~~C~~RFTTf 41 (156)
T COG1327 29 RECLECGERFTTF 41 (156)
T ss_pred hcccccccccchh
Confidence 6888899888754
No 239
>PRK06450 threonine synthase; Validated
Probab=45.68 E-value=11 Score=22.44 Aligned_cols=25 Identities=16% Similarity=0.387 Sum_probs=17.0
Q ss_pred ccccccchhhhccCCcceecCcccccc
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGKGY 43 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~~~ 43 (87)
+.|..|++.+.. ...+.|+.||..+
T Consensus 4 ~~C~~Cg~~~~~--~~~~~C~~cg~~l 28 (338)
T PRK06450 4 EVCMKCGKERES--IYEIRCKKCGGPF 28 (338)
T ss_pred eEECCcCCcCCC--cccccCCcCCCEe
Confidence 678888888754 2346788887543
No 240
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.55 E-value=25 Score=20.35 Aligned_cols=24 Identities=21% Similarity=0.330 Sum_probs=15.2
Q ss_pred cccccchhhhccCCcceecCcccccccc
Q psy12019 18 KCLINWSAVQQNHAGMFMCDVCGKGYKY 45 (87)
Q Consensus 18 ~c~~c~~~~~~~~~~~~~c~~c~~~~~~ 45 (87)
.|+.|+. ...+.|.|+.||..+..
T Consensus 311 ~C~~cg~----~~~r~~~C~~cg~~~~r 334 (364)
T COG0675 311 TCPCCGH----LSGRLFKCPRCGFVHDR 334 (364)
T ss_pred cccccCC----ccceeEECCCCCCeehh
Confidence 4777776 23456778888865443
No 241
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=45.09 E-value=39 Score=18.10 Aligned_cols=52 Identities=15% Similarity=0.181 Sum_probs=32.3
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccc-cchHHHhhhhhcC
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK-QNAHLTTHMAIKH 86 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~-~~~~l~~h~~~~h 86 (87)
...|+.|.-....+..... .|.+...++ -.|..=+-.|. ....|..|.+.-|
T Consensus 80 ~L~CPLCRG~V~GWtvve~-AR~~LN~K~-RsC~~e~C~F~GtY~eLrKHar~~H 132 (162)
T PF07800_consen 80 ELACPLCRGEVKGWTVVEP-ARRFLNAKK-RSCSQESCSFSGTYSELRKHARSEH 132 (162)
T ss_pred cccCccccCceeceEEchH-HHHHhccCC-ccCcccccccccCHHHHHHHHHhhC
Confidence 3578888866666655444 444455566 66754333443 5678999988665
No 242
>KOG1842|consensus
Probab=45.04 E-value=11 Score=23.60 Aligned_cols=21 Identities=19% Similarity=0.502 Sum_probs=10.4
Q ss_pred eecCcccccccchhhHHHHhh
Q psy12019 34 FMCDVCGKGYKYKNGIYRHKK 54 (87)
Q Consensus 34 ~~c~~c~~~~~~~~~~~~h~~ 54 (87)
|.|+.|...|..-..|..|..
T Consensus 16 flCPiC~~dl~~~~~L~~H~d 36 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLD 36 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHh
Confidence 445555555555555544433
No 243
>PRK04351 hypothetical protein; Provisional
Probab=44.96 E-value=14 Score=19.35 Aligned_cols=34 Identities=26% Similarity=0.750 Sum_probs=21.8
Q ss_pred cceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCccccc
Q psy12019 32 GMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQ 74 (87)
Q Consensus 32 ~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~ 74 (87)
-.|.|..||..+... .+. .... |.|..|+-.+..
T Consensus 111 y~Y~C~~Cg~~~~r~------Rr~--n~~~-yrCg~C~g~L~~ 144 (149)
T PRK04351 111 YLYECQSCGQQYLRK------RRI--NTKR-YRCGKCRGKLKL 144 (149)
T ss_pred EEEECCCCCCEeeee------eec--CCCc-EEeCCCCcEeee
Confidence 368899999765332 122 2255 999999876643
No 244
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=44.65 E-value=9.4 Score=21.05 Aligned_cols=28 Identities=14% Similarity=0.355 Sum_probs=15.4
Q ss_pred ccccccchhhhcc---------CC---cceecCccccccc
Q psy12019 17 NKCLINWSAVQQN---------HA---GMFMCDVCGKGYK 44 (87)
Q Consensus 17 ~~c~~c~~~~~~~---------~~---~~~~c~~c~~~~~ 44 (87)
..|+.|+..+.-. +. ..+.|..||..+.
T Consensus 15 ~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 15 IDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred ecCCcccceeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 4677777755432 11 1346777775543
No 245
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=44.32 E-value=15 Score=18.86 Aligned_cols=23 Identities=26% Similarity=0.598 Sum_probs=10.8
Q ss_pred cccccchhhhccCCcceecCcccc
Q psy12019 18 KCLINWSAVQQNHAGMFMCDVCGK 41 (87)
Q Consensus 18 ~c~~c~~~~~~~~~~~~~c~~c~~ 41 (87)
.|+.|+-..-. ..+...|+.|+.
T Consensus 30 hCp~Cg~PLF~-KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPLFR-KDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCccee-eCCeEECCCCCc
Confidence 45555554333 222335666663
No 246
>PRK06260 threonine synthase; Validated
Probab=44.25 E-value=12 Score=22.63 Aligned_cols=26 Identities=19% Similarity=0.410 Sum_probs=17.2
Q ss_pred ccccccchhhhccCCcceecCcccccc
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGKGY 43 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~~~ 43 (87)
+.|..|+..+... ...+.|+.||..+
T Consensus 4 ~~C~~cg~~~~~~-~~~~~Cp~cg~~l 29 (397)
T PRK06260 4 LKCIECGKEYDPD-EIIYTCPECGGLL 29 (397)
T ss_pred EEECCCCCCCCCC-CccccCCCCCCeE
Confidence 5788888887643 2356788887543
No 247
>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=44.15 E-value=10 Score=14.86 Aligned_cols=12 Identities=33% Similarity=1.010 Sum_probs=7.9
Q ss_pred ceecCccccccc
Q psy12019 33 MFMCDVCGKGYK 44 (87)
Q Consensus 33 ~~~c~~c~~~~~ 44 (87)
.+.|+.||..+.
T Consensus 32 ~~~C~~CGE~~~ 43 (46)
T TIGR03831 32 ALVCPQCGEEYL 43 (46)
T ss_pred ccccccCCCEee
Confidence 356888886653
No 248
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=44.11 E-value=28 Score=14.60 Aligned_cols=45 Identities=11% Similarity=0.011 Sum_probs=25.1
Q ss_pred ccccccchhhhccCCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccc
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 73 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~ 73 (87)
+.|++|...+.. | ....||..|..... ..+... . ..|+.|+..+.
T Consensus 2 ~~Cpi~~~~~~~----P-v~~~~G~v~~~~~i-~~~~~~-----~-~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKD----P-VILPSGQTYERRAI-EKWLLS-----H-GTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCC----C-EECCCCCEEeHHHH-HHHHHH-----C-CCCCCCcCCCC
Confidence 457777777655 3 23356766655543 333332 2 36777776663
No 249
>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=43.94 E-value=23 Score=13.47 Aligned_cols=21 Identities=19% Similarity=0.425 Sum_probs=11.7
Q ss_pred ceecCcccccccchhhHHHHhh
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKK 54 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~ 54 (87)
.+.|+.|++.+. .+.+..|+.
T Consensus 4 ~~~C~nC~R~v~-a~RfA~HLe 24 (33)
T PF08209_consen 4 YVECPNCGRPVA-ASRFAPHLE 24 (33)
T ss_dssp EEE-TTTSSEEE-GGGHHHHHH
T ss_pred eEECCCCcCCcc-hhhhHHHHH
Confidence 467888887653 334555554
No 250
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=43.88 E-value=27 Score=19.34 Aligned_cols=10 Identities=30% Similarity=0.780 Sum_probs=5.0
Q ss_pred eecCcccccc
Q psy12019 34 FMCDVCGKGY 43 (87)
Q Consensus 34 ~~c~~c~~~~ 43 (87)
..|..||..+
T Consensus 31 vrC~eCG~V~ 40 (201)
T COG1326 31 VRCEECGTVH 40 (201)
T ss_pred EEccCCCcEe
Confidence 4455555443
No 251
>COG4640 Predicted membrane protein [Function unknown]
Probab=43.87 E-value=18 Score=22.33 Aligned_cols=15 Identities=20% Similarity=0.751 Sum_probs=9.4
Q ss_pred eecCcccccccchhh
Q psy12019 34 FMCDVCGKGYKYKNG 48 (87)
Q Consensus 34 ~~c~~c~~~~~~~~~ 48 (87)
..|..||..|.....
T Consensus 16 ~qC~qCG~~~t~~~s 30 (465)
T COG4640 16 VQCTQCGHKFTSRQS 30 (465)
T ss_pred ccccccCCcCCchhh
Confidence 347777776665544
No 252
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=43.41 E-value=12 Score=23.23 Aligned_cols=24 Identities=17% Similarity=0.213 Sum_probs=16.8
Q ss_pred CcccccccchhhhccCCcceecCcccc
Q psy12019 15 KHNKCLINWSAVQQNHAGMFMCDVCGK 41 (87)
Q Consensus 15 ~~~~c~~c~~~~~~~~~~~~~c~~c~~ 41 (87)
..|.|+.|+..+.. |.=+|+.|+.
T Consensus 6 t~f~C~~CG~~s~K---W~GkCp~Cg~ 29 (456)
T COG1066 6 TAFVCQECGYVSPK---WLGKCPACGA 29 (456)
T ss_pred cEEEcccCCCCCcc---ccccCCCCCC
Confidence 46899999977654 3336788874
No 253
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=43.15 E-value=8.6 Score=15.33 Aligned_cols=10 Identities=40% Similarity=0.843 Sum_probs=5.9
Q ss_pred ccCCCCCccc
Q psy12019 63 YQCPQCPYRA 72 (87)
Q Consensus 63 ~~c~~c~~~f 72 (87)
-.|+.|+..|
T Consensus 30 ~~CpYCg~~y 39 (40)
T PF10276_consen 30 VVCPYCGTRY 39 (40)
T ss_dssp EEETTTTEEE
T ss_pred EECCCCCCEE
Confidence 4566666554
No 254
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=42.61 E-value=16 Score=24.90 Aligned_cols=31 Identities=16% Similarity=0.150 Sum_probs=22.9
Q ss_pred ccccccchhhhcc----CCcceecCcccccccchh
Q psy12019 17 NKCLINWSAVQQN----HAGMFMCDVCGKGYKYKN 47 (87)
Q Consensus 17 ~~c~~c~~~~~~~----~~~~~~c~~c~~~~~~~~ 47 (87)
-.|..|++.|... ..+.+.|..||..|...-
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~C 495 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFC 495 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccc
Confidence 4699999999653 345678999998776653
No 255
>PRK05978 hypothetical protein; Provisional
Probab=42.09 E-value=16 Score=19.22 Aligned_cols=11 Identities=18% Similarity=0.446 Sum_probs=7.1
Q ss_pred ccCCCCCcccc
Q psy12019 63 YQCPQCPYRAK 73 (87)
Q Consensus 63 ~~c~~c~~~f~ 73 (87)
-.|+.||-.|.
T Consensus 53 ~~C~~CG~~~~ 63 (148)
T PRK05978 53 DHCAACGEDFT 63 (148)
T ss_pred CCccccCCccc
Confidence 46777776554
No 256
>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=41.17 E-value=13 Score=19.12 Aligned_cols=32 Identities=25% Similarity=0.736 Sum_probs=19.6
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 73 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~ 73 (87)
.|.|..|+..+... .+. .... |.|..|+..|.
T Consensus 123 ~~~C~~C~~~~~r~------~~~--~~~~-~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKRH------RRS--KRKR-YRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeeee------ccc--chhh-EECCCCCCEEE
Confidence 57888888765222 222 2233 78888886654
No 257
>PRK12366 replication factor A; Reviewed
Probab=41.11 E-value=14 Score=24.09 Aligned_cols=22 Identities=27% Similarity=0.800 Sum_probs=9.3
Q ss_pred ccccchhhhccCCcceecCcccc
Q psy12019 19 CLINWSAVQQNHAGMFMCDVCGK 41 (87)
Q Consensus 19 c~~c~~~~~~~~~~~~~c~~c~~ 41 (87)
|+.|.+.... ....|.|+.|++
T Consensus 535 Cp~CnkKv~~-~~g~~~C~~c~~ 556 (637)
T PRK12366 535 CPNCRKRVEE-VDGEYICEFCGE 556 (637)
T ss_pred ccccCeEeEc-CCCcEECCCCCC
Confidence 4444444332 223344544443
No 258
>KOG1280|consensus
Probab=41.02 E-value=27 Score=21.20 Aligned_cols=24 Identities=25% Similarity=0.614 Sum_probs=16.8
Q ss_pred ccCCCCCcccccchHHHhhhhhcC
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMAIKH 86 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~~h 86 (87)
|.|+.|++.--....+..|....|
T Consensus 80 ftCPyC~~~Gfte~~f~~Hv~s~H 103 (381)
T KOG1280|consen 80 FTCPYCGIMGFTERQFGTHVLSQH 103 (381)
T ss_pred ccCCcccccccchhHHHHHhhhcC
Confidence 778888877666777777765444
No 259
>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=40.86 E-value=47 Score=17.62 Aligned_cols=35 Identities=29% Similarity=0.646 Sum_probs=20.6
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCccc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRA 72 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f 72 (87)
...|..|++.+....... ..... .. -.|+.|+...
T Consensus 105 ~~~C~~C~~~~~~~~~~~---~~~~~-~~-~~C~~C~~~l 139 (178)
T PF02146_consen 105 RLRCSKCGKEYDREDIVD---SIDEE-EP-PRCPKCGGLL 139 (178)
T ss_dssp EEEETTTSBEEEGHHHHH---HHHTT-SS-CBCTTTSCBE
T ss_pred eeeecCCCccccchhhcc---ccccc-cc-ccccccCccC
Confidence 357889998876554322 12222 33 4888888644
No 260
>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=40.67 E-value=22 Score=17.02 Aligned_cols=10 Identities=30% Similarity=1.052 Sum_probs=7.1
Q ss_pred ccCCCCCccc
Q psy12019 63 YQCPQCPYRA 72 (87)
Q Consensus 63 ~~c~~c~~~f 72 (87)
..|+.||..-
T Consensus 63 ~~Cp~Cg~~~ 72 (104)
T TIGR01384 63 VECPKCGHKE 72 (104)
T ss_pred CCCCCCCCCe
Confidence 6888888543
No 261
>PRK05580 primosome assembly protein PriA; Validated
Probab=40.57 E-value=21 Score=23.56 Aligned_cols=24 Identities=17% Similarity=0.415 Sum_probs=9.6
Q ss_pred ccccccchhhhcc-CCcceecCccc
Q psy12019 17 NKCLINWSAVQQN-HAGMFMCDVCG 40 (87)
Q Consensus 17 ~~c~~c~~~~~~~-~~~~~~c~~c~ 40 (87)
..|+.|+..+... ......|..||
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg 415 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCG 415 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCc
Confidence 3444444443321 22233455554
No 262
>PRK08402 replication factor A; Reviewed
Probab=40.53 E-value=17 Score=21.93 Aligned_cols=23 Identities=17% Similarity=0.378 Sum_probs=13.2
Q ss_pred cccccchhhh-ccCCcceecCccc
Q psy12019 18 KCLINWSAVQ-QNHAGMFMCDVCG 40 (87)
Q Consensus 18 ~c~~c~~~~~-~~~~~~~~c~~c~ 40 (87)
.|+.|.+.+. ..+...|.|..|+
T Consensus 214 aCp~CnKkv~~~~~~~~~~Ce~~~ 237 (355)
T PRK08402 214 ACPECRRKVDYDPATDTWICPEHG 237 (355)
T ss_pred cCCCCCeEEEEecCCCCEeCCCCC
Confidence 4666666665 3334456666665
No 263
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=40.51 E-value=17 Score=15.84 Aligned_cols=6 Identities=50% Similarity=1.669 Sum_probs=2.5
Q ss_pred ccCCCC
Q psy12019 63 YQCPQC 68 (87)
Q Consensus 63 ~~c~~c 68 (87)
-.|+.|
T Consensus 45 ArCPSC 50 (67)
T COG5216 45 ARCPSC 50 (67)
T ss_pred EEcCCc
Confidence 444444
No 264
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=40.43 E-value=19 Score=21.93 Aligned_cols=28 Identities=18% Similarity=0.344 Sum_probs=18.9
Q ss_pred hhhhcCCCCCccCCCCC-cccccchHHHhh
Q psy12019 53 KKFECGQEPKYQCPQCP-YRAKQNAHLTTH 81 (87)
Q Consensus 53 ~~~~~~~~~~~~c~~c~-~~f~~~~~l~~h 81 (87)
-+.|..++- |.|.+|| +.+.....+.+|
T Consensus 366 ~klhgLd~e-f~CEICgNyvy~GR~~FdrH 394 (470)
T COG5188 366 CKLHGLDIE-FECEICGNYVYYGRDRFDRH 394 (470)
T ss_pred HHhcCCCcc-eeeeecccccccchHHHHhh
Confidence 345666676 9999998 666655555555
No 265
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=40.31 E-value=9.5 Score=14.91 Aligned_cols=9 Identities=44% Similarity=1.028 Sum_probs=4.0
Q ss_pred ccCCCCCcc
Q psy12019 63 YQCPQCPYR 71 (87)
Q Consensus 63 ~~c~~c~~~ 71 (87)
|.|..|++.
T Consensus 29 y~C~~C~~~ 37 (39)
T PF01096_consen 29 YVCCNCGHR 37 (39)
T ss_dssp EEESSSTEE
T ss_pred EEeCCCCCe
Confidence 444444443
No 266
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=40.01 E-value=23 Score=14.16 Aligned_cols=6 Identities=50% Similarity=1.370 Sum_probs=2.7
Q ss_pred ecCccc
Q psy12019 35 MCDVCG 40 (87)
Q Consensus 35 ~c~~c~ 40 (87)
.|+.|+
T Consensus 19 ~Cp~C~ 24 (41)
T PF06677_consen 19 HCPDCG 24 (41)
T ss_pred ccCCCC
Confidence 344454
No 267
>PF04641 Rtf2: Rtf2 RING-finger
Probab=39.78 E-value=19 Score=20.57 Aligned_cols=51 Identities=18% Similarity=0.280 Sum_probs=29.9
Q ss_pred CCCcccccccchhhhccCCcceec-CcccccccchhhHHHHhhhhcCCCCCccCCCCCcccc
Q psy12019 13 EPKHNKCLINWSAVQQNHAGMFMC-DVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 73 (87)
Q Consensus 13 ~~~~~~c~~c~~~~~~~~~~~~~c-~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~ 73 (87)
....|.|++.+..|... ..|.. ..||-.|..... ..- . .. ..|+.|+..|.
T Consensus 110 ~~~~~~CPvt~~~~~~~--~~fv~l~~cG~V~s~~al-ke~-k-----~~-~~Cp~c~~~f~ 161 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGK--HKFVYLRPCGCVFSEKAL-KEL-K-----KS-KKCPVCGKPFT 161 (260)
T ss_pred CCceeECCCCCcccCCc--eeEEEEcCCCCEeeHHHH-Hhh-c-----cc-ccccccCCccc
Confidence 34578999988888332 23333 347766655542 211 1 22 56888888876
No 268
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=39.68 E-value=42 Score=19.07 Aligned_cols=33 Identities=30% Similarity=0.640 Sum_probs=18.7
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 70 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~ 70 (87)
...|..|++.+....... ..... .. -.|+.|+.
T Consensus 119 ~~~C~~C~~~~~~~~~~~---~~~~~-~~-p~Cp~Cgg 151 (244)
T PRK14138 119 EYYCVRCGKRYTVEDVIE---KLEKS-DV-PRCDDCSG 151 (244)
T ss_pred eeEECCCCCcccHHHHHH---HHhcC-CC-CCCCCCCC
Confidence 356888988776544332 11112 22 36888874
No 269
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=39.60 E-value=26 Score=20.10 Aligned_cols=33 Identities=30% Similarity=0.547 Sum_probs=17.6
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 70 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~ 70 (87)
.+.|..|+..+........ ...+ .+ -.|+.||.
T Consensus 122 ~~~C~~C~~~~~~~~~~~~---~~~~-~~-p~C~~Cg~ 154 (250)
T COG0846 122 RVRCSKCGNQYYDEDVIKF---IEDG-LI-PRCPKCGG 154 (250)
T ss_pred eeEeCCCcCccchhhhhhh---cccC-CC-CcCccCCC
Confidence 4568888877654442111 1112 22 46777876
No 270
>PRK11827 hypothetical protein; Provisional
Probab=39.39 E-value=28 Score=15.27 Aligned_cols=30 Identities=10% Similarity=0.257 Sum_probs=16.3
Q ss_pred ccccccchhhhcc-CCcceecCcccccccch
Q psy12019 17 NKCLINWSAVQQN-HAGMFMCDVCGKGYKYK 46 (87)
Q Consensus 17 ~~c~~c~~~~~~~-~~~~~~c~~c~~~~~~~ 46 (87)
..|+.|...+... ......|..|+..|.-.
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~~~~laYPI~ 39 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICKLDNLAFPLR 39 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECCccCeecccc
Confidence 3566666555443 22345677777666544
No 271
>PF12907 zf-met2: Zinc-binding
Probab=39.36 E-value=8.2 Score=15.42 Aligned_cols=6 Identities=33% Similarity=0.982 Sum_probs=2.6
Q ss_pred cCCCCC
Q psy12019 64 QCPQCP 69 (87)
Q Consensus 64 ~c~~c~ 69 (87)
.|.+|-
T Consensus 3 ~C~iC~ 8 (40)
T PF12907_consen 3 ICKICR 8 (40)
T ss_pred CcHHhh
Confidence 344444
No 272
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=39.21 E-value=3.4 Score=27.08 Aligned_cols=29 Identities=34% Similarity=0.914 Sum_probs=15.7
Q ss_pred cCcccccccchhhHHHHhhhhcCCCCCccCCCCCcc
Q psy12019 36 CDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYR 71 (87)
Q Consensus 36 c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~ 71 (87)
|+.|.+.+....+ +|.|. .+ ..|+.||-.
T Consensus 154 C~~C~~EY~dP~n----RRfHA--Qp-~aCp~CGP~ 182 (750)
T COG0068 154 CPFCDKEYKDPLN----RRFHA--QP-IACPKCGPH 182 (750)
T ss_pred CHHHHHHhcCccc----ccccc--cc-ccCcccCCC
Confidence 5555554444432 34443 33 778888753
No 273
>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=38.75 E-value=10 Score=21.11 Aligned_cols=22 Identities=23% Similarity=0.366 Sum_probs=0.0
Q ss_pred ccCCCCCcccccchHHHhhhhhc
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMAIK 85 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~~ 85 (87)
..|++||...+ .+.+..|+|+.
T Consensus 169 ~~cPitGe~IP-~~e~~eHmRi~ 190 (229)
T PF12230_consen 169 IICPITGEMIP-ADEMDEHMRIE 190 (229)
T ss_dssp -----------------------
T ss_pred ccccccccccc-ccccccccccc
Confidence 78999998876 44677888763
No 274
>PRK07218 replication factor A; Provisional
Probab=38.42 E-value=17 Score=22.59 Aligned_cols=9 Identities=11% Similarity=0.239 Sum_probs=4.3
Q ss_pred cccccchhh
Q psy12019 18 KCLINWSAV 26 (87)
Q Consensus 18 ~c~~c~~~~ 26 (87)
.|+.|.+..
T Consensus 299 rCP~C~r~v 307 (423)
T PRK07218 299 RCPECGRVI 307 (423)
T ss_pred cCcCccccc
Confidence 355555443
No 275
>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=38.28 E-value=17 Score=18.82 Aligned_cols=17 Identities=29% Similarity=0.589 Sum_probs=12.2
Q ss_pred CCcceecCcccccccch
Q psy12019 30 HAGMFMCDVCGKGYKYK 46 (87)
Q Consensus 30 ~~~~~~c~~c~~~~~~~ 46 (87)
..++..|.+||..|.-.
T Consensus 109 ~g~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 109 KGKPQRCPECGQVFKLK 125 (136)
T ss_dssp TTSEEEETTTEEEEEEE
T ss_pred CCCccCCCCCCeEEEEE
Confidence 34578899999877543
No 276
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=37.88 E-value=17 Score=13.05 Aligned_cols=7 Identities=29% Similarity=0.852 Sum_probs=1.7
Q ss_pred ccccchh
Q psy12019 19 CLINWSA 25 (87)
Q Consensus 19 c~~c~~~ 25 (87)
|+-|+..
T Consensus 4 C~rC~~~ 10 (30)
T PF06827_consen 4 CPRCWNY 10 (30)
T ss_dssp -TTT--B
T ss_pred CccCCCc
Confidence 4444444
No 277
>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=37.65 E-value=17 Score=14.15 Aligned_cols=11 Identities=27% Similarity=0.933 Sum_probs=5.5
Q ss_pred ceecCcccccc
Q psy12019 33 MFMCDVCGKGY 43 (87)
Q Consensus 33 ~~~c~~c~~~~ 43 (87)
-|.|..||+..
T Consensus 6 ~YkC~~CGniV 16 (36)
T PF06397_consen 6 FYKCEHCGNIV 16 (36)
T ss_dssp EEE-TTT--EE
T ss_pred EEEccCCCCEE
Confidence 57788888654
No 278
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=37.65 E-value=19 Score=18.55 Aligned_cols=34 Identities=21% Similarity=0.524 Sum_probs=19.5
Q ss_pred cceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccc
Q psy12019 32 GMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 73 (87)
Q Consensus 32 ~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~ 73 (87)
-.|.|..|+..+.. +.+.. .... |.|..|+-.+.
T Consensus 111 ~~y~C~~C~~~~~~------~rr~~-~~~~-y~C~~C~g~l~ 144 (146)
T smart00731 111 YPYRCTGCGQRYLR------VRRSN-NVSR-YRCGKCGGKLI 144 (146)
T ss_pred EEEECCCCCCCCce------Ecccc-Ccce-EEcCCCCCEEE
Confidence 36788888876532 22221 1144 88888876553
No 279
>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=37.04 E-value=24 Score=17.52 Aligned_cols=49 Identities=16% Similarity=0.243 Sum_probs=27.2
Q ss_pred cccccccchhhhccCCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCc
Q psy12019 16 HNKCLINWSAVQQNHAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 70 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~ 70 (87)
...|..|...|.........|..|...+-..-... ..++.. |.|..|.+
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~-----~~~~~~-WlC~vC~k 102 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY-----SKKEPI-WLCKVCQK 102 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE-----TSSSCC-EEEHHHHH
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCc-----CCCCCC-EEChhhHH
Confidence 45788898888766544456666665554443211 223344 78877743
No 280
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=35.95 E-value=26 Score=17.04 Aligned_cols=8 Identities=13% Similarity=-0.126 Sum_probs=4.4
Q ss_pred cccccccc
Q psy12019 16 HNKCLINW 23 (87)
Q Consensus 16 ~~~c~~c~ 23 (87)
.|.|+.|+
T Consensus 21 ~f~CP~Cg 28 (99)
T PRK14892 21 IFECPRCG 28 (99)
T ss_pred EeECCCCC
Confidence 35566655
No 281
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=35.92 E-value=24 Score=20.79 Aligned_cols=21 Identities=14% Similarity=0.308 Sum_probs=9.4
Q ss_pred ccccccchhhhccCCcceecCccc
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCG 40 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~ 40 (87)
+.|..|+.+... +.+.|+.|+
T Consensus 355 ~~c~~cg~~~~~---~~~~c~~c~ 375 (389)
T PRK11788 355 YRCRNCGFTART---LYWHCPSCK 375 (389)
T ss_pred EECCCCCCCCcc---ceeECcCCC
Confidence 445555543222 344555554
No 282
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=35.88 E-value=3.7 Score=17.29 Aligned_cols=12 Identities=17% Similarity=0.080 Sum_probs=5.9
Q ss_pred ccccccchhhhc
Q psy12019 17 NKCLINWSAVQQ 28 (87)
Q Consensus 17 ~~c~~c~~~~~~ 28 (87)
|.|..|..++..
T Consensus 8 y~CDLCn~~~p~ 19 (57)
T PF14445_consen 8 YSCDLCNSSHPI 19 (57)
T ss_pred HhHHhhcccCcH
Confidence 445555555443
No 283
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=35.87 E-value=28 Score=18.73 Aligned_cols=17 Identities=12% Similarity=0.413 Sum_probs=13.4
Q ss_pred ccCCCCCcccccchHHH
Q psy12019 63 YQCPQCPYRAKQNAHLT 79 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~ 79 (87)
..|..||+.|.....+.
T Consensus 115 ~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 115 QRCSRCERPFAPQKTVA 131 (181)
T ss_pred CcCcccCCccCcHhHHH
Confidence 88999999998665543
No 284
>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=35.85 E-value=42 Score=18.68 Aligned_cols=32 Identities=28% Similarity=0.521 Sum_probs=17.4
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 70 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~ 70 (87)
...|..|++.+..... ...... .. -.|+.|+.
T Consensus 113 ~~~C~~C~~~~~~~~~----~~~~~~-~~-p~C~~Cgg 144 (222)
T cd01413 113 TAYCVNCGSKYDLEEV----KYAKKH-EV-PRCPKCGG 144 (222)
T ss_pred cceECCCCCCcchhHH----HHhccC-CC-CcCCCCCC
Confidence 3568888877655432 111112 22 36888874
No 285
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=35.70 E-value=28 Score=18.71 Aligned_cols=18 Identities=28% Similarity=0.695 Sum_probs=14.1
Q ss_pred ccCCCCCcccccchHHHh
Q psy12019 63 YQCPQCPYRAKQNAHLTT 80 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~ 80 (87)
+.|+.||+.|---++...
T Consensus 131 ~~C~~CgkiYW~GsHw~~ 148 (165)
T COG1656 131 YRCPKCGKIYWKGSHWRR 148 (165)
T ss_pred eECCCCcccccCchHHHH
Confidence 779999999887766544
No 286
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=35.66 E-value=14 Score=19.10 Aligned_cols=23 Identities=17% Similarity=0.313 Sum_probs=16.4
Q ss_pred ccccccchhhhccCCcceecCcccc
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGK 41 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~ 41 (87)
-.|+.|++.|... ....|+.|.+
T Consensus 4 ~nC~~CgklF~~~--~~~iCp~C~~ 26 (137)
T TIGR03826 4 ANCPKCGRLFVKT--GRDVCPSCYE 26 (137)
T ss_pred ccccccchhhhhc--CCccCHHHhH
Confidence 3688999999874 2345888774
No 287
>KOG3214|consensus
Probab=35.27 E-value=21 Score=17.44 Aligned_cols=12 Identities=17% Similarity=0.767 Sum_probs=6.4
Q ss_pred eecCcccccccc
Q psy12019 34 FMCDVCGKGYKY 45 (87)
Q Consensus 34 ~~c~~c~~~~~~ 45 (87)
..|..|+.+|..
T Consensus 48 ~sC~iC~esFqt 59 (109)
T KOG3214|consen 48 ASCRICEESFQT 59 (109)
T ss_pred eeeeehhhhhcc
Confidence 345556555544
No 288
>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=35.00 E-value=9.7 Score=15.10 Aligned_cols=10 Identities=10% Similarity=0.192 Sum_probs=3.4
Q ss_pred cccccchhhh
Q psy12019 18 KCLINWSAVQ 27 (87)
Q Consensus 18 ~c~~c~~~~~ 27 (87)
.|+.|++.-.
T Consensus 3 ~CSFCgr~~~ 12 (41)
T PF06689_consen 3 RCSFCGRPES 12 (41)
T ss_dssp B-TTT--BTT
T ss_pred CccCCCCCHH
Confidence 3555555543
No 289
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=34.99 E-value=46 Score=20.37 Aligned_cols=51 Identities=20% Similarity=0.319 Sum_probs=29.4
Q ss_pred ecCcccccccchhhHHHHhhhhcCCCCCccCCCCC----cccccchHHHhhhhhcCC
Q psy12019 35 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCP----YRAKQNAHLTTHMAIKHY 87 (87)
Q Consensus 35 ~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~----~~f~~~~~l~~h~~~~h~ 87 (87)
.|..|...|.....|..|.+.... +- +-|..-+ .-|....+|-.|-+--||
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE-~C-hICD~v~p~~~QYFK~Y~~Le~HF~~~hy 276 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHE-AC-HICDMVGPIRYQYFKSYEDLEAHFRNAHY 276 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhh-hh-hhhhccCccchhhhhCHHHHHHHhhcCce
Confidence 477777777777777777775332 33 3333222 235555666666655554
No 290
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=34.42 E-value=20 Score=18.98 Aligned_cols=34 Identities=26% Similarity=0.672 Sum_probs=21.6
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCccc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRA 72 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f 72 (87)
+|.|. |+..+... ..|-..-.|+ . |.|..|+-.+
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~-~-YrC~~C~gkL 150 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGE-V-YRCGKCGGKL 150 (156)
T ss_pred eEEee-cCCccchh---hhcccccccc-e-EEeccCCceE
Confidence 68898 98775443 2333444554 5 8998887543
No 291
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=34.40 E-value=20 Score=20.37 Aligned_cols=16 Identities=6% Similarity=-0.276 Sum_probs=12.7
Q ss_pred CCcccccccchhhhcc
Q psy12019 14 PKHNKCLINWSAVQQN 29 (87)
Q Consensus 14 ~~~~~c~~c~~~~~~~ 29 (87)
.++.+|.+|+..|.-.
T Consensus 179 GkpqRCpECGqVFKLV 194 (268)
T PTZ00043 179 GFLYRCGECDQIFMLV 194 (268)
T ss_pred CCCccCCCCCcEEEEE
Confidence 3488999999998753
No 292
>KOG2923|consensus
Probab=34.21 E-value=28 Score=15.51 Aligned_cols=7 Identities=43% Similarity=1.450 Sum_probs=3.2
Q ss_pred ccCCCCC
Q psy12019 63 YQCPQCP 69 (87)
Q Consensus 63 ~~c~~c~ 69 (87)
-.|+.|.
T Consensus 45 a~CpsCS 51 (67)
T KOG2923|consen 45 ARCPSCS 51 (67)
T ss_pred ecCCCce
Confidence 4444443
No 293
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=34.09 E-value=24 Score=13.90 Aligned_cols=10 Identities=20% Similarity=0.537 Sum_probs=5.0
Q ss_pred cccccccchh
Q psy12019 38 VCGKGYKYKN 47 (87)
Q Consensus 38 ~c~~~~~~~~ 47 (87)
.||-.|-..-
T Consensus 15 ~CGH~FC~~C 24 (42)
T PF15227_consen 15 PCGHSFCRSC 24 (42)
T ss_dssp SSSSEEEHHH
T ss_pred CCcCHHHHHH
Confidence 4555554443
No 294
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=33.98 E-value=25 Score=21.37 Aligned_cols=9 Identities=11% Similarity=0.017 Sum_probs=4.3
Q ss_pred cccccccch
Q psy12019 16 HNKCLINWS 24 (87)
Q Consensus 16 ~~~c~~c~~ 24 (87)
.|.|..|+-
T Consensus 354 ~YRC~~CGF 362 (389)
T COG2956 354 RYRCQNCGF 362 (389)
T ss_pred CceecccCC
Confidence 355555543
No 295
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=33.93 E-value=12 Score=22.56 Aligned_cols=28 Identities=18% Similarity=0.369 Sum_probs=17.0
Q ss_pred cccccchhhhccC--CcceecCcccccccc
Q psy12019 18 KCLINWSAVQQNH--AGMFMCDVCGKGYKY 45 (87)
Q Consensus 18 ~c~~c~~~~~~~~--~~~~~c~~c~~~~~~ 45 (87)
.|..|...|+-.. ...|.|+.||..+..
T Consensus 248 AC~rC~t~y~le~A~~~~wrCpkCGg~ikK 277 (403)
T COG1379 248 ACSRCYTRYSLEEAKSLRWRCPKCGGKIKK 277 (403)
T ss_pred HHHHhhhccCcchhhhhcccCcccccchhh
Confidence 4666666665542 224788888875544
No 296
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=33.63 E-value=4.8 Score=16.72 Aligned_cols=10 Identities=20% Similarity=0.856 Sum_probs=4.4
Q ss_pred ccCCCCCccc
Q psy12019 63 YQCPQCPYRA 72 (87)
Q Consensus 63 ~~c~~c~~~f 72 (87)
+.|..|++.+
T Consensus 27 f~C~~C~~~l 36 (58)
T PF00412_consen 27 FKCSKCGKPL 36 (58)
T ss_dssp SBETTTTCBT
T ss_pred cccCCCCCcc
Confidence 4444444443
No 297
>KOG4215|consensus
Probab=33.62 E-value=17 Score=22.24 Aligned_cols=37 Identities=27% Similarity=0.461 Sum_probs=21.2
Q ss_pred ccccccchhhhccCCcceecCcccccccchhhHHHHhh
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGKGYKYKNGIYRHKK 54 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~ 54 (87)
-.|-+|+..-....-+...|+-| |.|...+..+.|+-
T Consensus 20 ~~CaICGDkaTGKHYGA~SCdGC-KGFFRRSVrk~~~Y 56 (432)
T KOG4215|consen 20 EFCAICGDKATGKHYGAISCDGC-KGFFRRSVRKNHQY 56 (432)
T ss_pred chhheeCCcccccccceeecCcc-hHHHHHHHHhccee
Confidence 45777776543333334567777 46666666665543
No 298
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=33.07 E-value=28 Score=18.64 Aligned_cols=18 Identities=11% Similarity=0.255 Sum_probs=13.7
Q ss_pred CccCCCCCcccccchHHH
Q psy12019 62 KYQCPQCPYRAKQNAHLT 79 (87)
Q Consensus 62 ~~~c~~c~~~f~~~~~l~ 79 (87)
++.|..||+.|.....+.
T Consensus 114 ~~~C~~CG~~f~~~~~i~ 131 (180)
T PRK12387 114 LCNCRVCGRPFAVQKEID 131 (180)
T ss_pred cccchhhCCccccHHHHH
Confidence 389999999997665443
No 299
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=32.68 E-value=37 Score=19.38 Aligned_cols=21 Identities=10% Similarity=0.398 Sum_probs=13.2
Q ss_pred ccccccchhhhccCCcceecCc
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDV 38 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~ 38 (87)
+.|+.|...+.. ....+.|..
T Consensus 3 ~~CP~C~~~l~~-~~~~~~C~~ 23 (272)
T PRK11088 3 YQCPLCHQPLTL-EENSWICPQ 23 (272)
T ss_pred ccCCCCCcchhc-CCCEEEcCC
Confidence 678888887743 233456654
No 300
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=32.67 E-value=36 Score=14.68 Aligned_cols=7 Identities=43% Similarity=1.251 Sum_probs=3.5
Q ss_pred eecCccc
Q psy12019 34 FMCDVCG 40 (87)
Q Consensus 34 ~~c~~c~ 40 (87)
..|..||
T Consensus 41 ~vC~~CG 47 (57)
T PRK12286 41 RVCPSCG 47 (57)
T ss_pred EECCCCC
Confidence 3455555
No 301
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=32.55 E-value=17 Score=16.07 Aligned_cols=11 Identities=27% Similarity=0.745 Sum_probs=7.6
Q ss_pred ccCCCCCcccc
Q psy12019 63 YQCPQCPYRAK 73 (87)
Q Consensus 63 ~~c~~c~~~f~ 73 (87)
-.|+.|++.|+
T Consensus 54 L~Cp~c~r~YP 64 (68)
T PF03966_consen 54 LICPECGREYP 64 (68)
T ss_dssp EEETTTTEEEE
T ss_pred EEcCCCCCEEe
Confidence 66777777664
No 302
>PF03563 Bunya_G2: Bunyavirus glycoprotein G2; InterPro: IPR005168 Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This entry represents the polyprotein region forming the G2 glycoprotein, which interacts with the IPR005167 from INTERPRO G1 glycoprotein [].
Probab=32.04 E-value=46 Score=19.48 Aligned_cols=17 Identities=24% Similarity=0.653 Sum_probs=11.3
Q ss_pred cccccccchhhHHHHhh
Q psy12019 38 VCGKGYKYKNGIYRHKK 54 (87)
Q Consensus 38 ~c~~~~~~~~~~~~h~~ 54 (87)
.||..|....++..|+.
T Consensus 255 vCG~~f~~sd~mk~HR~ 271 (285)
T PF03563_consen 255 VCGMKFETSDRMKMHRE 271 (285)
T ss_pred eccccccchHHHHHHHh
Confidence 37777777777666654
No 303
>KOG0823|consensus
Probab=32.03 E-value=43 Score=19.07 Aligned_cols=46 Identities=15% Similarity=0.313 Sum_probs=27.3
Q ss_pred CcccccccchhhhccCCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCC
Q psy12019 15 KHNKCLINWSAVQQNHAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCP 69 (87)
Q Consensus 15 ~~~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~ 69 (87)
.-|.|.+|...-+. | .-..||-.|.+.-..+.- .++. .. -.|++|.
T Consensus 46 ~~FdCNICLd~akd----P-VvTlCGHLFCWpClyqWl-~~~~--~~-~~cPVCK 91 (230)
T KOG0823|consen 46 GFFDCNICLDLAKD----P-VVTLCGHLFCWPCLYQWL-QTRP--NS-KECPVCK 91 (230)
T ss_pred CceeeeeeccccCC----C-EEeecccceehHHHHHHH-hhcC--CC-eeCCccc
Confidence 45788888776433 3 345688888888754433 3222 22 4667774
No 304
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=31.40 E-value=35 Score=16.60 Aligned_cols=35 Identities=23% Similarity=0.405 Sum_probs=14.0
Q ss_pred CCCCcccccccchhhhcc-----CCc-ceecCcccccccch
Q psy12019 12 REPKHNKCLINWSAVQQN-----HAG-MFMCDVCGKGYKYK 46 (87)
Q Consensus 12 ~~~~~~~c~~c~~~~~~~-----~~~-~~~c~~c~~~~~~~ 46 (87)
++.+.-.|..|+.+...- +.+ -|-|+.|.+-|...
T Consensus 10 ag~ke~~CalCG~tWg~~y~Ev~G~rLfFCCd~ca~EF~nm 50 (105)
T PF11494_consen 10 AGTKEMGCALCGATWGDYYEEVDGERLFFCCDDCAKEFKNM 50 (105)
T ss_dssp --SGGGS-SS---S---SS-B-TT--BSSS--SSSS-TTS-
T ss_pred cccccccccccCCcHHHHHHhhcCCEEEEEcHHHHHHHHHH
Confidence 455667888888887643 333 46688888877664
No 305
>KOG2164|consensus
Probab=31.16 E-value=67 Score=20.71 Aligned_cols=50 Identities=16% Similarity=0.212 Sum_probs=29.8
Q ss_pred cccccccchhhhccCCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCccc
Q psy12019 16 HNKCLINWSAVQQNHAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRA 72 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f 72 (87)
++.|++|.....-. - -..||-.|.....|+-.... .-..+ ..|+.|...+
T Consensus 186 ~~~CPICL~~~~~p----~-~t~CGHiFC~~CiLqy~~~s-~~~~~-~~CPiC~s~I 235 (513)
T KOG2164|consen 186 DMQCPICLEPPSVP----V-RTNCGHIFCGPCILQYWNYS-AIKGP-CSCPICRSTI 235 (513)
T ss_pred CCcCCcccCCCCcc----c-ccccCceeeHHHHHHHHhhh-cccCC-ccCCchhhhc
Confidence 67788887553322 1 12388888887766543332 23344 7888887654
No 306
>PRK01343 zinc-binding protein; Provisional
Probab=31.13 E-value=28 Score=15.14 Aligned_cols=12 Identities=25% Similarity=0.750 Sum_probs=9.2
Q ss_pred CccCCCCCcccc
Q psy12019 62 KYQCPQCPYRAK 73 (87)
Q Consensus 62 ~~~c~~c~~~f~ 73 (87)
...|+.|++.+.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 367999998764
No 307
>PLN02748 tRNA dimethylallyltransferase
Probab=31.03 E-value=44 Score=21.19 Aligned_cols=23 Identities=17% Similarity=0.388 Sum_probs=17.9
Q ss_pred CCCccCCCCCc-ccccchHHHhhhh
Q psy12019 60 EPKYQCPQCPY-RAKQNAHLTTHMA 83 (87)
Q Consensus 60 ~~~~~c~~c~~-~f~~~~~l~~h~~ 83 (87)
+. |.|..|++ .+........|++
T Consensus 417 ~~-~~Ce~C~~~~~~G~~eW~~Hlk 440 (468)
T PLN02748 417 TQ-YVCEACGNKVLRGAHEWEQHKQ 440 (468)
T ss_pred cc-ccccCCCCcccCCHHHHHHHhc
Confidence 45 78999997 7888877777764
No 308
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=30.55 E-value=28 Score=21.38 Aligned_cols=22 Identities=9% Similarity=0.082 Sum_probs=14.7
Q ss_pred ccccccchhhhccCCcceecCccc
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCG 40 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~ 40 (87)
+.|..|++.+. . ...+.|+.|+
T Consensus 3 l~C~~Cg~~~~-~-~~~~~C~~c~ 24 (398)
T TIGR03844 3 LRCPGCGEVLP-D-HYTLSCPLDC 24 (398)
T ss_pred EEeCCCCCccC-C-ccccCCCCCC
Confidence 56888888875 2 2356777665
No 309
>PF14369 zf-RING_3: zinc-finger
Probab=30.37 E-value=29 Score=13.23 Aligned_cols=10 Identities=30% Similarity=0.727 Sum_probs=6.8
Q ss_pred cCCCCCcccc
Q psy12019 64 QCPQCPYRAK 73 (87)
Q Consensus 64 ~c~~c~~~f~ 73 (87)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4777776664
No 310
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=30.08 E-value=30 Score=15.37 Aligned_cols=7 Identities=57% Similarity=1.891 Sum_probs=3.6
Q ss_pred ccCCCCC
Q psy12019 63 YQCPQCP 69 (87)
Q Consensus 63 ~~c~~c~ 69 (87)
|.|+.||
T Consensus 1 y~C~KCg 7 (64)
T PF09855_consen 1 YKCPKCG 7 (64)
T ss_pred CCCCCCC
Confidence 3455555
No 311
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=30.00 E-value=32 Score=15.05 Aligned_cols=6 Identities=17% Similarity=0.368 Sum_probs=2.6
Q ss_pred ccccch
Q psy12019 19 CLINWS 24 (87)
Q Consensus 19 c~~c~~ 24 (87)
|..|+.
T Consensus 6 C~~CG~ 11 (59)
T PF09889_consen 6 CPVCGK 11 (59)
T ss_pred CCcCCC
Confidence 444443
No 312
>PTZ00448 hypothetical protein; Provisional
Probab=30.00 E-value=42 Score=20.61 Aligned_cols=21 Identities=14% Similarity=0.439 Sum_probs=16.7
Q ss_pred ccCCCCCcccccchHHHhhhh
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMA 83 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~ 83 (87)
+.|..|+-.|........|.+
T Consensus 315 ~tC~~C~v~F~~~~~qR~H~K 335 (373)
T PTZ00448 315 LLCRKCNIQLMDHNAFKQHYR 335 (373)
T ss_pred ccccccccccCCHHHHHHHhh
Confidence 789999999977776677765
No 313
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=29.98 E-value=30 Score=17.30 Aligned_cols=8 Identities=38% Similarity=1.190 Sum_probs=4.0
Q ss_pred eecCcccc
Q psy12019 34 FMCDVCGK 41 (87)
Q Consensus 34 ~~c~~c~~ 41 (87)
+.|+.|+-
T Consensus 13 l~C~~C~t 20 (113)
T PF09862_consen 13 LKCPSCGT 20 (113)
T ss_pred EEcCCCCC
Confidence 44555553
No 314
>KOG1409|consensus
Probab=29.77 E-value=14 Score=22.41 Aligned_cols=41 Identities=12% Similarity=0.280 Sum_probs=26.4
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcccccc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQN 75 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~~ 75 (87)
.+.|+.|...|.++.. ..+.+.-.|-+. .-|..||+++...
T Consensus 282 s~~cQ~c~qpffwn~~-~m~~~k~~glr~-h~crkcg~avc~~ 322 (404)
T KOG1409|consen 282 SDSCQKCNQPFFWNFR-QMWDRKQLGLRQ-HHCRKCGKAVCGK 322 (404)
T ss_pred cchhhhhCchHHHHHH-HHHhhhhhhhhh-hhhhhhhhhcCcc
Confidence 3568888888766653 445555556565 7777777776543
No 315
>KOG1088|consensus
Probab=29.27 E-value=26 Score=17.69 Aligned_cols=18 Identities=11% Similarity=0.135 Sum_probs=12.6
Q ss_pred hcCCCCCccCCCCCccccc
Q psy12019 56 ECGQEPKYQCPQCPYRAKQ 74 (87)
Q Consensus 56 ~~~~~~~~~c~~c~~~f~~ 74 (87)
+..+.. -.|++||+.|+=
T Consensus 93 ~v~EG~-l~CpetG~vfpI 110 (124)
T KOG1088|consen 93 DVIEGE-LVCPETGRVFPI 110 (124)
T ss_pred hhccce-EecCCCCcEeec
Confidence 334444 789999998863
No 316
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=29.15 E-value=26 Score=19.07 Aligned_cols=13 Identities=15% Similarity=0.419 Sum_probs=7.8
Q ss_pred cceecCccccccc
Q psy12019 32 GMFMCDVCGKGYK 44 (87)
Q Consensus 32 ~~~~c~~c~~~~~ 44 (87)
+.+.|.-|++.|.
T Consensus 138 w~~rC~GC~~~f~ 150 (177)
T COG1439 138 WRLRCHGCKRIFP 150 (177)
T ss_pred eeEEEecCceecC
Confidence 3456666766664
No 317
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=28.92 E-value=31 Score=12.81 Aligned_cols=11 Identities=36% Similarity=1.096 Sum_probs=7.4
Q ss_pred ceecCcccccc
Q psy12019 33 MFMCDVCGKGY 43 (87)
Q Consensus 33 ~~~c~~c~~~~ 43 (87)
-|.|..||..+
T Consensus 7 ~ykC~~Cgniv 17 (34)
T TIGR00319 7 VYKCEVCGNIV 17 (34)
T ss_pred EEEcCCCCcEE
Confidence 46777777654
No 318
>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=28.76 E-value=31 Score=12.83 Aligned_cols=11 Identities=27% Similarity=1.087 Sum_probs=7.3
Q ss_pred ceecCcccccc
Q psy12019 33 MFMCDVCGKGY 43 (87)
Q Consensus 33 ~~~c~~c~~~~ 43 (87)
-|.|..||...
T Consensus 4 ~ykC~~CGniv 14 (34)
T cd00974 4 VYKCEICGNIV 14 (34)
T ss_pred EEEcCCCCcEE
Confidence 46777777654
No 319
>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=28.65 E-value=40 Score=16.12 Aligned_cols=21 Identities=19% Similarity=0.521 Sum_probs=15.3
Q ss_pred eecCcccccccchhhHHHHhh
Q psy12019 34 FMCDVCGKGYKYKNGIYRHKK 54 (87)
Q Consensus 34 ~~c~~c~~~~~~~~~~~~h~~ 54 (87)
..|+.||..+........-.+
T Consensus 36 ~~C~~CGe~y~~dev~~eIE~ 56 (89)
T TIGR03829 36 ISCSHCGMEYQDDTTVKEIED 56 (89)
T ss_pred ccccCCCcEeecHHHHHHHHh
Confidence 579999999888776554333
No 320
>KOG3352|consensus
Probab=28.60 E-value=36 Score=18.04 Aligned_cols=19 Identities=37% Similarity=0.625 Sum_probs=12.7
Q ss_pred hhhhcCCCCCccCCCCCcccc
Q psy12019 53 KKFECGQEPKYQCPQCPYRAK 73 (87)
Q Consensus 53 ~~~~~~~~~~~~c~~c~~~f~ 73 (87)
+-.+.+ +. ..|++||.-|.
T Consensus 126 mwl~Kg-e~-~rc~eCG~~fk 144 (153)
T KOG3352|consen 126 MWLEKG-ET-QRCPECGHYFK 144 (153)
T ss_pred EEEEcC-Cc-ccCCcccceEE
Confidence 344555 44 68999998775
No 321
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=28.04 E-value=82 Score=17.44 Aligned_cols=34 Identities=26% Similarity=0.518 Sum_probs=17.7
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYR 71 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~ 71 (87)
...|..|++.+...... ...... .. -.|+.|+..
T Consensus 109 ~~~C~~C~~~~~~~~~~---~~~~~~-~~-p~C~~Cg~~ 142 (218)
T cd01407 109 RVRCTKCGKEYPRDELQ---ADIDRE-EV-PRCPKCGGL 142 (218)
T ss_pred cceeCCCcCCCcHHHHh---HhhccC-CC-CcCCCCCCc
Confidence 35688888776544321 111112 22 368888754
No 322
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=27.94 E-value=27 Score=17.08 Aligned_cols=30 Identities=17% Similarity=0.391 Sum_probs=16.8
Q ss_pred cccccchhhhccCCcceecCcccccccchh
Q psy12019 18 KCLINWSAVQQNHAGMFMCDVCGKGYKYKN 47 (87)
Q Consensus 18 ~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~ 47 (87)
.|..|+..--........|..|+..|...+
T Consensus 37 aCeiC~~~GY~q~g~~lvC~~C~~~~~~~~ 66 (102)
T PF10080_consen 37 ACEICGPKGYYQEGDQLVCKNCGVRFNLPT 66 (102)
T ss_pred eccccCCCceEEECCEEEEecCCCEEehhh
Confidence 466674332122333467888888775544
No 323
>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=27.23 E-value=33 Score=14.80 Aligned_cols=16 Identities=19% Similarity=0.476 Sum_probs=10.2
Q ss_pred CcceecCcccccccch
Q psy12019 31 AGMFMCDVCGKGYKYK 46 (87)
Q Consensus 31 ~~~~~c~~c~~~~~~~ 46 (87)
...|.|..||..+-..
T Consensus 9 ~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 9 SNLWLCLTCGYVGCGR 24 (63)
T ss_dssp SSEEEETTTS-EEETT
T ss_pred CceEEeCCCCcccccC
Confidence 3467888888766554
No 324
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=27.19 E-value=43 Score=21.64 Aligned_cols=9 Identities=33% Similarity=1.316 Sum_probs=6.4
Q ss_pred ccCCCCCcc
Q psy12019 63 YQCPQCPYR 71 (87)
Q Consensus 63 ~~c~~c~~~ 71 (87)
+.|+.||..
T Consensus 533 ~~CP~CGs~ 541 (555)
T cd01675 533 FKCPKCGSE 541 (555)
T ss_pred CCCcCCCCc
Confidence 778888743
No 325
>KOG0801|consensus
Probab=26.99 E-value=18 Score=19.42 Aligned_cols=11 Identities=27% Similarity=0.748 Sum_probs=8.2
Q ss_pred ccCCCCCcccc
Q psy12019 63 YQCPQCPYRAK 73 (87)
Q Consensus 63 ~~c~~c~~~f~ 73 (87)
++|++|.|...
T Consensus 139 ~KCPvC~K~V~ 149 (205)
T KOG0801|consen 139 MKCPVCHKVVP 149 (205)
T ss_pred ccCCccccccC
Confidence 78888887654
No 326
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=26.92 E-value=22 Score=20.82 Aligned_cols=31 Identities=16% Similarity=0.412 Sum_probs=17.8
Q ss_pred ccccccchhhhcc--CCcceecCcccccccchh
Q psy12019 17 NKCLINWSAVQQN--HAGMFMCDVCGKGYKYKN 47 (87)
Q Consensus 17 ~~c~~c~~~~~~~--~~~~~~c~~c~~~~~~~~ 47 (87)
.+|+.|+...-.. ....+.|+.|+..+.-..
T Consensus 29 ~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~A 61 (294)
T COG0777 29 TKCPSCGEMLYRKELESNLKVCPKCGHHMRISA 61 (294)
T ss_pred eECCCccceeeHHHHHhhhhcccccCcccccCH
Confidence 3677777664332 334567777776555443
No 327
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=26.76 E-value=27 Score=21.02 Aligned_cols=10 Identities=10% Similarity=-0.041 Sum_probs=5.9
Q ss_pred ccccccchhh
Q psy12019 17 NKCLINWSAV 26 (87)
Q Consensus 17 ~~c~~c~~~~ 26 (87)
..|..|+.+.
T Consensus 236 lqC~~C~~TS 245 (415)
T COG5533 236 LQCEACNYTS 245 (415)
T ss_pred hhhhhcCCce
Confidence 3566666654
No 328
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=26.65 E-value=97 Score=18.44 Aligned_cols=27 Identities=22% Similarity=0.440 Sum_probs=22.1
Q ss_pred CcceecCcccccccchhhHHHHhhhhc
Q psy12019 31 AGMFMCDVCGKGYKYKNGIYRHKKFEC 57 (87)
Q Consensus 31 ~~~~~c~~c~~~~~~~~~~~~h~~~~~ 57 (87)
...|.|..|-+-|.....+..|+..-.
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~C~ 72 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAKCD 72 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHhCC
Confidence 346899999999999999999987433
No 329
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=26.56 E-value=43 Score=18.42 Aligned_cols=23 Identities=22% Similarity=0.629 Sum_probs=10.9
Q ss_pred cccccchhhhccCCcceecCcccc
Q psy12019 18 KCLINWSAVQQNHAGMFMCDVCGK 41 (87)
Q Consensus 18 ~c~~c~~~~~~~~~~~~~c~~c~~ 41 (87)
.|+.|+..+.. ......|+.||.
T Consensus 151 ~CsrC~~~L~~-~~~~l~Cp~Cg~ 173 (188)
T COG1096 151 RCSRCRAPLVK-KGNMLKCPNCGN 173 (188)
T ss_pred EccCCCcceEE-cCcEEECCCCCC
Confidence 34455544444 233345566654
No 330
>KOG1818|consensus
Probab=26.30 E-value=19 Score=23.58 Aligned_cols=50 Identities=18% Similarity=0.321 Sum_probs=27.8
Q ss_pred cccccchhhhccCCcceecCcccccccchhhHHHHhhhhcCC-CCCccCCCC
Q psy12019 18 KCLINWSAVQQNHAGMFMCDVCGKGYKYKNGIYRHKKFECGQ-EPKYQCPQC 68 (87)
Q Consensus 18 ~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~-~~~~~c~~c 68 (87)
.|-.|...|...+. .+.|..||..|...-....-.....|- ++.-.|..|
T Consensus 167 ~C~rCr~~F~~~~r-kHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C 217 (634)
T KOG1818|consen 167 ECLRCRVKFGLTNR-KHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSC 217 (634)
T ss_pred ccceeeeeeeeccc-cccccccchhhccCccccccCcccccccccceehhhh
Confidence 45556666766553 357888888887665444333334442 332345555
No 331
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=26.23 E-value=10 Score=14.91 Aligned_cols=9 Identities=22% Similarity=0.634 Sum_probs=1.9
Q ss_pred CCCCCcccc
Q psy12019 65 CPQCPYRAK 73 (87)
Q Consensus 65 c~~c~~~f~ 73 (87)
|..|++.+.
T Consensus 1 C~~C~~~~~ 9 (47)
T PF01844_consen 1 CQYCGKPGS 9 (47)
T ss_dssp -TTT--B--
T ss_pred CCCCCCcCc
Confidence 344554443
No 332
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=26.23 E-value=60 Score=12.98 Aligned_cols=7 Identities=14% Similarity=0.036 Sum_probs=3.3
Q ss_pred cccccch
Q psy12019 18 KCLINWS 24 (87)
Q Consensus 18 ~c~~c~~ 24 (87)
.|..|+.
T Consensus 2 ~C~~C~~ 8 (46)
T cd02249 2 SCDGCLK 8 (46)
T ss_pred CCcCCCC
Confidence 3444544
No 333
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=25.25 E-value=34 Score=16.16 Aligned_cols=11 Identities=36% Similarity=0.875 Sum_probs=7.8
Q ss_pred ecCcccccccc
Q psy12019 35 MCDVCGKGYKY 45 (87)
Q Consensus 35 ~c~~c~~~~~~ 45 (87)
+|+.||..+..
T Consensus 10 ~C~~CG~d~~~ 20 (86)
T PF06170_consen 10 RCPHCGLDYSH 20 (86)
T ss_pred cccccCCcccc
Confidence 68888876644
No 334
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.23 E-value=42 Score=22.25 Aligned_cols=9 Identities=33% Similarity=0.848 Sum_probs=6.8
Q ss_pred ccCCCCCcc
Q psy12019 63 YQCPQCPYR 71 (87)
Q Consensus 63 ~~c~~c~~~ 71 (87)
+.|+.||..
T Consensus 640 ~~CP~CG~~ 648 (656)
T PRK08270 640 EFCPKCGEE 648 (656)
T ss_pred CCCcCCcCc
Confidence 788888753
No 335
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=25.20 E-value=52 Score=12.77 Aligned_cols=28 Identities=14% Similarity=0.335 Sum_probs=14.8
Q ss_pred cccccchhhhccCCcceecCcccccccchh
Q psy12019 18 KCLINWSAVQQNHAGMFMCDVCGKGYKYKN 47 (87)
Q Consensus 18 ~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~ 47 (87)
.|.+|...+.. +....... ||..|-..-
T Consensus 2 ~C~IC~~~~~~-~~~~~~l~-C~H~fh~~C 29 (44)
T PF13639_consen 2 ECPICLEEFED-GEKVVKLP-CGHVFHRSC 29 (44)
T ss_dssp CETTTTCBHHT-TSCEEEET-TSEEEEHHH
T ss_pred CCcCCChhhcC-CCeEEEcc-CCCeeCHHH
Confidence 46667766654 22233333 776664443
No 336
>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=25.07 E-value=30 Score=15.65 Aligned_cols=24 Identities=29% Similarity=0.412 Sum_probs=9.1
Q ss_pred ccccccchhhhc-cCCcceecCccccc
Q psy12019 17 NKCLINWSAVQQ-NHAGMFMCDVCGKG 42 (87)
Q Consensus 17 ~~c~~c~~~~~~-~~~~~~~c~~c~~~ 42 (87)
|.| .|++..-. .+.+.-.| .||+.
T Consensus 4 frC-~Cgr~lya~e~~kTkkC-~CG~~ 28 (68)
T PF09082_consen 4 FRC-DCGRYLYAKEGAKTKKC-VCGKT 28 (68)
T ss_dssp EEE-TTS--EEEETT-SEEEE-TTTEE
T ss_pred EEe-cCCCEEEecCCcceeEe-cCCCe
Confidence 344 35544322 23334455 56653
No 337
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=25.06 E-value=44 Score=14.13 Aligned_cols=11 Identities=27% Similarity=0.135 Sum_probs=7.0
Q ss_pred cccccccchhh
Q psy12019 16 HNKCLINWSAV 26 (87)
Q Consensus 16 ~~~c~~c~~~~ 26 (87)
...|+.|+...
T Consensus 3 LkPCPFCG~~~ 13 (61)
T PF14354_consen 3 LKPCPFCGSAD 13 (61)
T ss_pred CcCCCCCCCcc
Confidence 45678876554
No 338
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=24.96 E-value=55 Score=13.96 Aligned_cols=19 Identities=21% Similarity=0.298 Sum_probs=9.0
Q ss_pred cccccchhhhccCCcceecCccc
Q psy12019 18 KCLINWSAVQQNHAGMFMCDVCG 40 (87)
Q Consensus 18 ~c~~c~~~~~~~~~~~~~c~~c~ 40 (87)
.|+.|+.... ....|..||
T Consensus 28 ~C~~cG~~~~----~H~vc~~cG 46 (55)
T TIGR01031 28 VCPNCGEFKL----PHRVCPSCG 46 (55)
T ss_pred ECCCCCCccc----CeeECCccC
Confidence 4555554321 134555555
No 339
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=24.93 E-value=1.4e+02 Score=18.02 Aligned_cols=46 Identities=15% Similarity=0.366 Sum_probs=25.0
Q ss_pred CcccccccchhhhccCCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCc
Q psy12019 15 KHNKCLINWSAVQQNHAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 70 (87)
Q Consensus 15 ~~~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~ 70 (87)
-+..|+.|.....+. ..-.-|+..|.... +..-..+.- |+|+.|.+
T Consensus 273 i~LkCplc~~Llrnp----~kT~cC~~~fc~ec-----i~~al~dsD-f~CpnC~r 318 (427)
T COG5222 273 ISLKCPLCHCLLRNP----MKTPCCGHTFCDEC-----IGTALLDSD-FKCPNCSR 318 (427)
T ss_pred ccccCcchhhhhhCc----ccCccccchHHHHH-----Hhhhhhhcc-ccCCCccc
Confidence 356787777765553 22233555554332 222333455 78888875
No 340
>PRK08329 threonine synthase; Validated
Probab=24.93 E-value=49 Score=19.83 Aligned_cols=24 Identities=17% Similarity=0.330 Sum_probs=15.5
Q ss_pred ccccccchhhhccCCcceecCcccccc
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGKGY 43 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~~~ 43 (87)
++|..|+..+... ..+.| .|+-.+
T Consensus 2 l~C~~Cg~~~~~~--~~~~C-~c~~~l 25 (347)
T PRK08329 2 LRCTKCGRTYEEK--FKLRC-DCGGTL 25 (347)
T ss_pred cCcCCCCCCcCCC--Cceec-CCCCcE
Confidence 5788888888632 23678 676543
No 341
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=24.85 E-value=59 Score=19.23 Aligned_cols=31 Identities=23% Similarity=0.284 Sum_probs=18.6
Q ss_pred CCCcccccccchhhh--ccCCcceecCcccccc
Q psy12019 13 EPKHNKCLINWSAVQ--QNHAGMFMCDVCGKGY 43 (87)
Q Consensus 13 ~~~~~~c~~c~~~~~--~~~~~~~~c~~c~~~~ 43 (87)
.++...|+.|+..-- ........|..||-..
T Consensus 8 ~~~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 8 EEEKLVCPECGSDKLIYDYERGEIVCADCGLVI 40 (310)
T ss_pred cccCCcCcCCCCCCeeEECCCCeEeecccCCcc
Confidence 345678999985211 1134456788888643
No 342
>PRK05638 threonine synthase; Validated
Probab=24.68 E-value=43 Score=20.78 Aligned_cols=24 Identities=21% Similarity=0.292 Sum_probs=15.3
Q ss_pred ccccccchhhhccCCcceecCcccccc
Q psy12019 17 NKCLINWSAVQQNHAGMFMCDVCGKGY 43 (87)
Q Consensus 17 ~~c~~c~~~~~~~~~~~~~c~~c~~~~ 43 (87)
+.|..|+..+... ..+.| .||..+
T Consensus 2 l~C~~Cg~~~~~~--~~~~C-~c~~~l 25 (442)
T PRK05638 2 MKCPKCGREYNSY--IPPFC-ICGELL 25 (442)
T ss_pred eEeCCCCCCCCCC--Cceec-CCCCcE
Confidence 4688888887632 23678 687443
No 343
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=24.68 E-value=40 Score=14.55 Aligned_cols=13 Identities=23% Similarity=0.841 Sum_probs=9.1
Q ss_pred eecCcccccccch
Q psy12019 34 FMCDVCGKGYKYK 46 (87)
Q Consensus 34 ~~c~~c~~~~~~~ 46 (87)
.-|+.|++.|...
T Consensus 40 ngCPfC~~~~~~~ 52 (55)
T PF14447_consen 40 NGCPFCGTPFEFD 52 (55)
T ss_pred cCCCCCCCcccCC
Confidence 3588888877544
No 344
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=24.62 E-value=32 Score=14.94 Aligned_cols=12 Identities=25% Similarity=0.642 Sum_probs=4.9
Q ss_pred ccCCCCCccccc
Q psy12019 63 YQCPQCPYRAKQ 74 (87)
Q Consensus 63 ~~c~~c~~~f~~ 74 (87)
..|++|++.+..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 357777776544
No 345
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=24.60 E-value=45 Score=15.74 Aligned_cols=12 Identities=17% Similarity=0.426 Sum_probs=9.0
Q ss_pred ccCCCCCccccc
Q psy12019 63 YQCPQCPYRAKQ 74 (87)
Q Consensus 63 ~~c~~c~~~f~~ 74 (87)
-.|..|++.+..
T Consensus 79 ~~C~vC~k~l~~ 90 (109)
T PF10367_consen 79 TKCSVCGKPLGN 90 (109)
T ss_pred CCccCcCCcCCC
Confidence 468889887754
No 346
>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=24.46 E-value=14 Score=21.69 Aligned_cols=10 Identities=30% Similarity=0.707 Sum_probs=7.2
Q ss_pred ccCCCCCccc
Q psy12019 63 YQCPQCPYRA 72 (87)
Q Consensus 63 ~~c~~c~~~f 72 (87)
|.|..||..+
T Consensus 287 ~~C~~Cg~~w 296 (299)
T TIGR01385 287 VTCEECGNRW 296 (299)
T ss_pred EEcCCCCCee
Confidence 6788887654
No 347
>PF14122 YokU: YokU-like protein
Probab=24.32 E-value=82 Score=15.02 Aligned_cols=16 Identities=31% Similarity=0.735 Sum_probs=9.7
Q ss_pred eecCcccccccchhhH
Q psy12019 34 FMCDVCGKGYKYKNGI 49 (87)
Q Consensus 34 ~~c~~c~~~~~~~~~~ 49 (87)
..|..||..+.....+
T Consensus 36 i~C~~CgmvYq~d~vi 51 (87)
T PF14122_consen 36 IICSNCGMVYQDDEVI 51 (87)
T ss_pred eeecCCCcEEehhHHH
Confidence 4577777666555443
No 348
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=24.30 E-value=41 Score=21.69 Aligned_cols=9 Identities=33% Similarity=0.663 Sum_probs=3.1
Q ss_pred ceecCcccc
Q psy12019 33 MFMCDVCGK 41 (87)
Q Consensus 33 ~~~c~~c~~ 41 (87)
.+.|+.||.
T Consensus 504 ~~~CP~CGs 512 (546)
T PF13597_consen 504 GDKCPKCGS 512 (546)
T ss_dssp EEE-CCC--
T ss_pred CCCCCCCCC
Confidence 445555554
No 349
>PRK08359 transcription factor; Validated
Probab=24.29 E-value=24 Score=19.12 Aligned_cols=30 Identities=27% Similarity=0.513 Sum_probs=20.3
Q ss_pred Ccccccccchhhhcc-------CCcceecCccccccc
Q psy12019 15 KHNKCLINWSAVQQN-------HAGMFMCDVCGKGYK 44 (87)
Q Consensus 15 ~~~~c~~c~~~~~~~-------~~~~~~c~~c~~~~~ 44 (87)
++-.|..|+...... +.....|+.|...|-
T Consensus 5 ~~~~CEiCG~~i~g~~~~v~ieGael~VC~~Ca~k~G 41 (176)
T PRK08359 5 KPRYCEICGAEIRGPGHRIRIEGAELLVCDRCYEKYG 41 (176)
T ss_pred CcceeecCCCccCCCCeEEEEcCeEEehHHHHHHHhC
Confidence 455699999887654 334567888874443
No 350
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=24.23 E-value=49 Score=14.78 Aligned_cols=25 Identities=12% Similarity=0.091 Sum_probs=13.4
Q ss_pred cccccchhhhcc----CCcceecCccccc
Q psy12019 18 KCLINWSAVQQN----HAGMFMCDVCGKG 42 (87)
Q Consensus 18 ~c~~c~~~~~~~----~~~~~~c~~c~~~ 42 (87)
.|+.|+..-... +...+.|..|+..
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 577777654332 1123567777654
No 351
>PRK11032 hypothetical protein; Provisional
Probab=23.95 E-value=68 Score=17.19 Aligned_cols=31 Identities=19% Similarity=0.560 Sum_probs=17.5
Q ss_pred CCcceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcc
Q psy12019 30 HAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYR 71 (87)
Q Consensus 30 ~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~ 71 (87)
+.+...|..||..... .+++.. -.|+.||..
T Consensus 121 g~G~LvC~~Cg~~~~~---------~~p~~i--~pCp~C~~~ 151 (160)
T PRK11032 121 GLGNLVCEKCHHHLAF---------YTPEVL--PLCPKCGHD 151 (160)
T ss_pred ecceEEecCCCCEEEe---------cCCCcC--CCCCCCCCC
Confidence 3345788888854211 233433 378888753
No 352
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=23.71 E-value=58 Score=11.96 Aligned_cols=8 Identities=38% Similarity=1.032 Sum_probs=5.1
Q ss_pred ccCCCCCc
Q psy12019 63 YQCPQCPY 70 (87)
Q Consensus 63 ~~c~~c~~ 70 (87)
..|+.|..
T Consensus 36 ~~Cp~C~~ 43 (45)
T cd00162 36 NTCPLCRT 43 (45)
T ss_pred CCCCCCCC
Confidence 56777754
No 353
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=23.62 E-value=80 Score=19.61 Aligned_cols=29 Identities=24% Similarity=0.278 Sum_probs=14.2
Q ss_pred CCcccccccchhhhcc---CCcceecCccccc
Q psy12019 14 PKHNKCLINWSAVQQN---HAGMFMCDVCGKG 42 (87)
Q Consensus 14 ~~~~~c~~c~~~~~~~---~~~~~~c~~c~~~ 42 (87)
...-.|++|+...... ....-.|+.||..
T Consensus 11 ~~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~ 42 (403)
T TIGR00155 11 AKHILCSQCDMLVALPRIESGQKAACPRCGTT 42 (403)
T ss_pred CCeeeCCCCCCcccccCCCCCCeeECCCCCCC
Confidence 3334477776665433 1122356666643
No 354
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=23.46 E-value=51 Score=13.98 Aligned_cols=9 Identities=44% Similarity=0.947 Sum_probs=4.8
Q ss_pred cCCCCCccc
Q psy12019 64 QCPQCPYRA 72 (87)
Q Consensus 64 ~c~~c~~~f 72 (87)
.|+.||..+
T Consensus 2 ~CPyCge~~ 10 (52)
T PF14255_consen 2 QCPYCGEPI 10 (52)
T ss_pred CCCCCCCee
Confidence 456666543
No 355
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=23.26 E-value=46 Score=13.72 Aligned_cols=7 Identities=29% Similarity=0.648 Sum_probs=2.9
Q ss_pred CCCCccc
Q psy12019 66 PQCPYRA 72 (87)
Q Consensus 66 ~~c~~~f 72 (87)
+.||..|
T Consensus 2 P~Cg~~f 8 (50)
T PF14375_consen 2 PRCGAPF 8 (50)
T ss_pred CCCCCcC
Confidence 3444443
No 356
>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=23.13 E-value=36 Score=12.49 Aligned_cols=8 Identities=50% Similarity=1.564 Sum_probs=2.4
Q ss_pred ccCCCCCc
Q psy12019 63 YQCPQCPY 70 (87)
Q Consensus 63 ~~c~~c~~ 70 (87)
|.|+.|+.
T Consensus 14 Y~Cp~C~~ 21 (30)
T PF04438_consen 14 YRCPRCGA 21 (30)
T ss_dssp EE-TTT--
T ss_pred EECCCcCC
Confidence 44444443
No 357
>PRK02935 hypothetical protein; Provisional
Probab=23.09 E-value=50 Score=16.38 Aligned_cols=27 Identities=11% Similarity=0.111 Sum_probs=14.3
Q ss_pred cccccccchhhhccCCcceecCcccccc
Q psy12019 16 HNKCLINWSAVQQNHAGMFMCDVCGKGY 43 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~~~~c~~c~~~~ 43 (87)
+..|+.|++...-.+. ...|-.|+...
T Consensus 70 qV~CP~C~K~TKmLGr-vD~CM~C~~PL 96 (110)
T PRK02935 70 QVICPSCEKPTKMLGR-VDACMHCNQPL 96 (110)
T ss_pred eeECCCCCchhhhccc-eeecCcCCCcC
Confidence 4466666666544332 33566666543
No 358
>KOG4727|consensus
Probab=23.02 E-value=65 Score=17.57 Aligned_cols=24 Identities=29% Similarity=0.488 Sum_probs=18.1
Q ss_pred CcceecCcccccccchhhHHHHhh
Q psy12019 31 AGMFMCDVCGKGYKYKNGIYRHKK 54 (87)
Q Consensus 31 ~~~~~c~~c~~~~~~~~~~~~h~~ 54 (87)
...|-|+.|+=.+..+.++.+|+.
T Consensus 73 ~~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 73 KGGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred cCceeeeecceeehhhHHHHHHhc
Confidence 345788888888888877777765
No 359
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=22.55 E-value=26 Score=16.84 Aligned_cols=10 Identities=20% Similarity=0.707 Sum_probs=7.7
Q ss_pred ccCCCCCccc
Q psy12019 63 YQCPQCPYRA 72 (87)
Q Consensus 63 ~~c~~c~~~f 72 (87)
+.|.+|+++-
T Consensus 69 ~~Ct~Cgkah 78 (94)
T COG1631 69 LRCTECGKAH 78 (94)
T ss_pred EEehhhcccc
Confidence 7888998753
No 360
>KOG0562|consensus
Probab=22.51 E-value=42 Score=18.18 Aligned_cols=23 Identities=17% Similarity=0.378 Sum_probs=18.0
Q ss_pred ccCCCCCcccccchHHHhhhhhc
Q psy12019 63 YQCPQCPYRAKQNAHLTTHMAIK 85 (87)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~~ 85 (87)
-.|..|+-..+..+.|..|.+..
T Consensus 154 LrC~~Cq~~~~~~~kLK~Hl~~~ 176 (184)
T KOG0562|consen 154 LRCWRCQTFGPHFPKLKAHLREE 176 (184)
T ss_pred eeehhhhhcccccHHHHHHHHHH
Confidence 68888985556888889998754
No 361
>PRK08197 threonine synthase; Validated
Probab=22.35 E-value=48 Score=20.22 Aligned_cols=26 Identities=23% Similarity=0.438 Sum_probs=17.2
Q ss_pred cccccccchhhhccCCcceecCcccccc
Q psy12019 16 HNKCLINWSAVQQNHAGMFMCDVCGKGY 43 (87)
Q Consensus 16 ~~~c~~c~~~~~~~~~~~~~c~~c~~~~ 43 (87)
-+.|..|++.+.... ..+.| .||..+
T Consensus 7 ~~~C~~Cg~~~~~~~-~~~~C-~cg~~l 32 (394)
T PRK08197 7 HLECSKCGETYDADQ-VHNLC-KCGKPL 32 (394)
T ss_pred EEEECCCCCCCCCCC-cceec-CCCCee
Confidence 368888998876532 24678 686543
No 362
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=22.29 E-value=66 Score=14.75 Aligned_cols=16 Identities=13% Similarity=0.391 Sum_probs=11.8
Q ss_pred CCcccccchHHHhhhh
Q psy12019 68 CPYRAKQNAHLTTHMA 83 (87)
Q Consensus 68 c~~~f~~~~~l~~h~~ 83 (87)
||+.|++..++..++.
T Consensus 36 ~GkklRs~~ev~~YL~ 51 (77)
T smart00391 36 CGKKLRSKSELARYLH 51 (77)
T ss_pred CCCeeeCHHHHHHHHH
Confidence 7888887777776654
No 363
>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=22.26 E-value=1.5e+02 Score=16.38 Aligned_cols=35 Identities=17% Similarity=0.356 Sum_probs=17.6
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCcc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYR 71 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~ 71 (87)
...|..|+..+....... .....+.. -.|+.||..
T Consensus 95 ~~~C~~C~~~~~~~~~~~---~~~~~~~~-p~C~~Cgg~ 129 (206)
T cd01410 95 IEVCKSCGPEYVRDDVVE---TRGDKETG-RRCHACGGI 129 (206)
T ss_pred cccCCCCCCccchHHHHH---HhhcCCCC-CcCCCCcCc
Confidence 356888886654433221 11112223 468888743
No 364
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=22.17 E-value=43 Score=18.51 Aligned_cols=8 Identities=50% Similarity=1.094 Sum_probs=4.4
Q ss_pred eecCcccc
Q psy12019 34 FMCDVCGK 41 (87)
Q Consensus 34 ~~c~~c~~ 41 (87)
-.|+.|++
T Consensus 25 t~C~~C~~ 32 (208)
T PF04161_consen 25 TKCPNCGK 32 (208)
T ss_pred eeccccCC
Confidence 34666654
No 365
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=22.08 E-value=74 Score=12.58 Aligned_cols=7 Identities=43% Similarity=1.284 Sum_probs=3.2
Q ss_pred ceecCcc
Q psy12019 33 MFMCDVC 39 (87)
Q Consensus 33 ~~~c~~c 39 (87)
.|.|..|
T Consensus 13 r~~C~~C 19 (41)
T cd02337 13 RWHCTVC 19 (41)
T ss_pred ceECCCC
Confidence 3444444
No 366
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.01 E-value=49 Score=14.79 Aligned_cols=12 Identities=25% Similarity=0.567 Sum_probs=8.8
Q ss_pred ccCCCCCccccc
Q psy12019 63 YQCPQCPYRAKQ 74 (87)
Q Consensus 63 ~~c~~c~~~f~~ 74 (87)
-.|+.||+....
T Consensus 8 v~CP~Cgkpv~w 19 (65)
T COG3024 8 VPCPTCGKPVVW 19 (65)
T ss_pred ccCCCCCCcccc
Confidence 578899986543
No 367
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.95 E-value=61 Score=18.97 Aligned_cols=45 Identities=20% Similarity=0.454 Sum_probs=29.2
Q ss_pred CCcccccccchhhhccCCcceecCcccccccchhhHHHHhhhhcCCCCCcc-CCCCC
Q psy12019 14 PKHNKCLINWSAVQQNHAGMFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQ-CPQCP 69 (87)
Q Consensus 14 ~~~~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~-c~~c~ 69 (87)
+..|+|..|...... ..|..||-.|.+.-.+.. .+. +. ++ |+.|.
T Consensus 213 ~~d~kC~lC~e~~~~-----ps~t~CgHlFC~~Cl~~~----~t~-~k-~~~CplCR 258 (271)
T COG5574 213 LADYKCFLCLEEPEV-----PSCTPCGHLFCLSCLLIS----WTK-KK-YEFCPLCR 258 (271)
T ss_pred ccccceeeeecccCC-----cccccccchhhHHHHHHH----HHh-hc-cccCchhh
Confidence 456788887765322 367889999988877664 233 33 45 88774
No 368
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.85 E-value=18 Score=20.62 Aligned_cols=8 Identities=50% Similarity=1.281 Sum_probs=5.5
Q ss_pred ccCCCCCc
Q psy12019 63 YQCPQCPY 70 (87)
Q Consensus 63 ~~c~~c~~ 70 (87)
+.|+.|+.
T Consensus 63 vvCP~C~y 70 (267)
T COG1655 63 VVCPICYY 70 (267)
T ss_pred EEcchhhH
Confidence 46777774
No 369
>KOG3268|consensus
Probab=21.78 E-value=1.6e+02 Score=16.30 Aligned_cols=13 Identities=15% Similarity=0.161 Sum_probs=8.0
Q ss_pred cccccccchhhhc
Q psy12019 16 HNKCLINWSAVQQ 28 (87)
Q Consensus 16 ~~~c~~c~~~~~~ 28 (87)
..+|.+|-..|-.
T Consensus 148 ~lE~df~a~a~Le 160 (234)
T KOG3268|consen 148 QLECDFCAAAFLE 160 (234)
T ss_pred eeeeCccHHHhcC
Confidence 4567777666643
No 370
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=21.70 E-value=91 Score=17.62 Aligned_cols=29 Identities=28% Similarity=0.730 Sum_probs=15.9
Q ss_pred ceecCcccccccchhhHHHHhhhhcCCCCCccCCCCCc
Q psy12019 33 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 70 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~ 70 (87)
...|..|++.+.....+ ..+.| .|+.||.
T Consensus 122 ~~~C~~C~~~~~~~~~~-------~~~~p--~C~~Cgg 150 (242)
T PRK00481 122 RARCTKCGQTYDLDEYL-------KPEPP--RCPKCGG 150 (242)
T ss_pred ceeeCCCCCCcChhhhc-------cCCCC--CCCCCCC
Confidence 35688887766544322 12223 4788864
No 371
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=21.58 E-value=1.4e+02 Score=17.44 Aligned_cols=15 Identities=20% Similarity=0.386 Sum_probs=9.7
Q ss_pred ceecCcccccccchh
Q psy12019 33 MFMCDVCGKGYKYKN 47 (87)
Q Consensus 33 ~~~c~~c~~~~~~~~ 47 (87)
...|..|+..+....
T Consensus 137 ~~~C~~C~~~~~~~~ 151 (271)
T PTZ00409 137 EARCCTCRKTIQLNK 151 (271)
T ss_pred cceeCCCCCCcccCH
Confidence 356888887765443
No 372
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=21.57 E-value=56 Score=22.07 Aligned_cols=7 Identities=43% Similarity=1.013 Sum_probs=3.8
Q ss_pred eecCccc
Q psy12019 34 FMCDVCG 40 (87)
Q Consensus 34 ~~c~~c~ 40 (87)
+.|+.||
T Consensus 694 ~~CP~CG 700 (735)
T PRK07111 694 DKCPKCG 700 (735)
T ss_pred ccCcCCC
Confidence 4555555
No 373
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
Probab=21.52 E-value=75 Score=13.69 Aligned_cols=16 Identities=6% Similarity=0.345 Sum_probs=10.8
Q ss_pred CCcccccchHHHhhhh
Q psy12019 68 CPYRAKQNAHLTTHMA 83 (87)
Q Consensus 68 c~~~f~~~~~l~~h~~ 83 (87)
||+.|.+..++...+.
T Consensus 33 ~Gk~~Rs~~ev~~yL~ 48 (62)
T cd00122 33 CGKKLRSKPEVARYLE 48 (62)
T ss_pred CCceecCHHHHHHHHH
Confidence 6777777777666654
No 374
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=21.41 E-value=77 Score=18.23 Aligned_cols=35 Identities=17% Similarity=0.290 Sum_probs=19.6
Q ss_pred ecCcccccccchhhHHHHhhhhcCCCCCccCCCCCccccc
Q psy12019 35 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQ 74 (87)
Q Consensus 35 ~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~c~~c~~~f~~ 74 (87)
.|..|....+... ..-.+. ++.. -.|+.||+..-+
T Consensus 199 ~C~GC~m~l~~~~--~~~V~~--~d~i-v~CP~CgRILy~ 233 (239)
T COG1579 199 VCGGCHMKLPSQT--LSKVRK--KDEI-VFCPYCGRILYY 233 (239)
T ss_pred cccCCeeeecHHH--HHHHhc--CCCC-ccCCccchHHHh
Confidence 5666765543332 222232 4454 789999986543
No 375
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.69 E-value=62 Score=16.03 Aligned_cols=10 Identities=30% Similarity=0.763 Sum_probs=7.0
Q ss_pred ccCCCCCccc
Q psy12019 63 YQCPQCPYRA 72 (87)
Q Consensus 63 ~~c~~c~~~f 72 (87)
..|+.||-.|
T Consensus 50 t~CP~Cg~~~ 59 (115)
T COG1885 50 TSCPKCGEPF 59 (115)
T ss_pred ccCCCCCCcc
Confidence 6778887654
No 376
>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.
Probab=20.53 E-value=50 Score=20.70 Aligned_cols=25 Identities=20% Similarity=0.305 Sum_probs=12.1
Q ss_pred cccchhhhcc--CCcceecCccccccc
Q psy12019 20 LINWSAVQQN--HAGMFMCDVCGKGYK 44 (87)
Q Consensus 20 ~~c~~~~~~~--~~~~~~c~~c~~~~~ 44 (87)
.+|..+|... +.....|+.||-.|.
T Consensus 365 ~ICa~s~tPIY~G~~~v~CP~cgA~y~ 391 (422)
T PF06957_consen 365 DICAASYTPIYRGSPSVKCPYCGAKYH 391 (422)
T ss_dssp EEBTTT--EEETTS-EEE-TTT--EEE
T ss_pred eeeecccccccCCCCCeeCCCCCCccC
Confidence 3577777765 334456999987664
No 377
>KOG4602|consensus
Probab=20.42 E-value=47 Score=19.36 Aligned_cols=11 Identities=27% Similarity=1.053 Sum_probs=7.8
Q ss_pred cceecCccccc
Q psy12019 32 GMFMCDVCGKG 42 (87)
Q Consensus 32 ~~~~c~~c~~~ 42 (87)
+.|.|+.||-+
T Consensus 267 R~YVCPiCGAT 277 (318)
T KOG4602|consen 267 RSYVCPICGAT 277 (318)
T ss_pred hhhcCcccccc
Confidence 35788888854
No 378
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=20.42 E-value=76 Score=13.21 Aligned_cols=10 Identities=30% Similarity=1.065 Sum_probs=4.7
Q ss_pred ccCCCCCccc
Q psy12019 63 YQCPQCPYRA 72 (87)
Q Consensus 63 ~~c~~c~~~f 72 (87)
..|+.|+..|
T Consensus 41 v~C~~C~~~f 50 (64)
T smart00647 41 VTCPKCGFSF 50 (64)
T ss_pred eECCCCCCeE
Confidence 4444455444
No 379
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=20.40 E-value=34 Score=23.50 Aligned_cols=9 Identities=11% Similarity=0.165 Sum_probs=0.0
Q ss_pred ccccccchh
Q psy12019 17 NKCLINWSA 25 (87)
Q Consensus 17 ~~c~~c~~~ 25 (87)
..|+.|+..
T Consensus 656 r~Cp~Cg~~ 664 (900)
T PF03833_consen 656 RRCPKCGKE 664 (900)
T ss_dssp ---------
T ss_pred ccCcccCCc
Confidence 456666654
No 380
>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
Probab=20.12 E-value=62 Score=20.18 Aligned_cols=26 Identities=19% Similarity=0.448 Sum_probs=17.4
Q ss_pred cccccchhhhcc-----CCcceecCcccccc
Q psy12019 18 KCLINWSAVQQN-----HAGMFMCDVCGKGY 43 (87)
Q Consensus 18 ~c~~c~~~~~~~-----~~~~~~c~~c~~~~ 43 (87)
.|+.|++.-... +...|.|+.|-..+
T Consensus 9 ~c~fc~~~~~~~~~~~~~~~~~ic~~c~~~~ 39 (413)
T TIGR00382 9 YCSFCGKSQDEVRKLIAGPGVYICDECIELC 39 (413)
T ss_pred ecCCCCCChhhcccccCCCCCcCCCchHHHH
Confidence 699999876543 33357888886443
Done!