Query psy10073
Match_columns 144
No_of_seqs 310 out of 2043
Neff 10.6
Searched_HMMs 46136
Date Fri Aug 16 17:15:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10073.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10073hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 4.3E-29 9.3E-34 165.4 6.2 107 15-135 130-264 (279)
2 KOG2462|consensus 100.0 4.9E-29 1.1E-33 165.1 4.9 111 16-144 128-245 (279)
3 KOG1074|consensus 99.8 5.4E-21 1.2E-25 142.5 2.6 58 85-142 604-661 (958)
4 KOG1074|consensus 99.8 3.8E-19 8.3E-24 132.7 4.8 57 87-143 880-936 (958)
5 KOG3576|consensus 99.7 2E-19 4.4E-24 114.9 0.9 112 12-142 114-240 (267)
6 KOG3623|consensus 99.6 1E-17 2.2E-22 123.9 -2.3 113 16-135 211-330 (1007)
7 KOG3576|consensus 99.6 8.6E-17 1.9E-21 102.9 0.8 81 47-139 114-198 (267)
8 KOG3623|consensus 99.6 1.6E-16 3.5E-21 117.6 0.8 77 47-135 891-971 (1007)
9 KOG3608|consensus 99.6 6E-16 1.3E-20 106.4 1.8 116 16-138 178-316 (467)
10 KOG3608|consensus 99.5 2.8E-14 6.1E-19 98.3 3.9 105 16-139 264-377 (467)
11 PHA00733 hypothetical protein 99.3 1E-12 2.2E-17 80.4 3.5 81 47-140 37-125 (128)
12 PHA02768 hypothetical protein; 99.3 1.3E-12 2.8E-17 67.1 1.5 43 87-131 6-48 (55)
13 PLN03086 PRLI-interacting fact 99.3 1.1E-11 2.3E-16 91.8 5.8 99 14-137 452-563 (567)
14 PHA00733 hypothetical protein 99.1 5.8E-11 1.3E-15 72.7 3.6 86 10-111 35-124 (128)
15 PLN03086 PRLI-interacting fact 99.1 2.8E-10 6E-15 84.4 6.7 111 15-143 407-542 (567)
16 PF13465 zf-H2C2_2: Zinc-finge 99.1 1.2E-10 2.7E-15 51.4 2.1 26 101-126 1-26 (26)
17 PHA00616 hypothetical protein 98.9 1.3E-09 2.8E-14 53.4 2.1 34 87-120 2-35 (44)
18 PHA02768 hypothetical protein; 98.8 1.2E-09 2.5E-14 56.3 -0.1 39 15-62 5-44 (55)
19 PHA00616 hypothetical protein 98.8 3E-09 6.4E-14 52.2 1.1 30 114-143 1-30 (44)
20 PHA00732 hypothetical protein 98.7 1.7E-08 3.6E-13 56.6 2.7 46 87-138 2-48 (79)
21 KOG3993|consensus 98.6 1.2E-08 2.6E-13 72.4 0.4 26 114-139 356-381 (500)
22 PF05605 zf-Di19: Drought indu 98.5 4E-07 8.7E-12 47.4 4.4 50 87-139 3-54 (54)
23 PF00096 zf-C2H2: Zinc finger, 98.5 1.4E-07 2.9E-12 40.3 2.0 23 115-137 1-23 (23)
24 KOG3993|consensus 98.4 8.5E-08 1.8E-12 68.2 1.0 86 16-109 268-379 (500)
25 PF13465 zf-H2C2_2: Zinc-finge 98.3 3.3E-07 7.2E-12 40.3 1.5 22 64-97 4-25 (26)
26 PF00096 zf-C2H2: Zinc finger, 98.3 4.9E-07 1.1E-11 38.5 2.0 23 87-109 1-23 (23)
27 PF13894 zf-C2H2_4: C2H2-type 98.3 9.7E-07 2.1E-11 37.8 2.4 24 115-138 1-24 (24)
28 PHA00732 hypothetical protein 98.2 5.7E-07 1.2E-11 50.4 1.4 46 15-71 1-48 (79)
29 PF13912 zf-C2H2_6: C2H2-type 98.2 1E-06 2.2E-11 39.1 1.7 25 114-138 1-25 (27)
30 PF12756 zf-C2H2_2: C2H2 type 98.1 3.4E-06 7.3E-11 49.3 3.0 24 114-137 50-73 (100)
31 PF05605 zf-Di19: Drought indu 98.0 6.5E-06 1.4E-10 42.8 3.3 46 51-109 3-52 (54)
32 PF13894 zf-C2H2_4: C2H2-type 98.0 6.4E-06 1.4E-10 35.1 2.4 23 87-109 1-23 (24)
33 PF09237 GAGA: GAGA factor; I 98.0 9.3E-06 2E-10 40.8 2.9 33 110-142 20-52 (54)
34 PF13912 zf-C2H2_6: C2H2-type 97.9 8.5E-06 1.8E-10 36.0 1.7 25 86-110 1-25 (27)
35 COG5189 SFP1 Putative transcri 97.8 7.2E-06 1.6E-10 56.7 0.7 52 84-135 347-419 (423)
36 smart00355 ZnF_C2H2 zinc finge 97.8 2.9E-05 6.3E-10 33.6 2.4 24 115-138 1-24 (26)
37 PF13909 zf-H2C2_5: C2H2-type 97.6 6.8E-05 1.5E-09 32.1 2.2 23 115-138 1-23 (24)
38 PF12874 zf-met: Zinc-finger o 97.5 6E-05 1.3E-09 32.6 1.6 22 115-136 1-22 (25)
39 smart00355 ZnF_C2H2 zinc finge 97.5 0.00012 2.6E-09 31.5 2.3 24 87-110 1-24 (26)
40 PRK04860 hypothetical protein; 97.5 8E-05 1.7E-09 47.4 2.2 40 85-128 118-157 (160)
41 PF09237 GAGA: GAGA factor; I 97.4 0.00025 5.3E-09 35.8 3.1 28 87-114 25-52 (54)
42 COG5189 SFP1 Putative transcri 97.3 8.5E-05 1.8E-09 51.6 1.3 23 85-107 397-419 (423)
43 PF12874 zf-met: Zinc-finger o 97.2 0.00023 4.9E-09 30.7 1.7 23 87-109 1-23 (25)
44 PF12756 zf-C2H2_2: C2H2 type 97.2 0.00033 7.2E-09 40.8 2.7 69 17-109 1-73 (100)
45 PF13909 zf-H2C2_5: C2H2-type 97.1 0.00055 1.2E-08 29.2 2.2 23 87-110 1-23 (24)
46 PF12171 zf-C2H2_jaz: Zinc-fin 97.0 0.00013 2.7E-09 32.2 -0.3 20 87-106 2-21 (27)
47 PF12171 zf-C2H2_jaz: Zinc-fin 96.9 0.0004 8.7E-09 30.6 0.6 23 114-136 1-23 (27)
48 PRK04860 hypothetical protein; 96.8 0.00047 1E-08 44.0 0.7 37 50-99 119-156 (160)
49 PF13913 zf-C2HC_2: zinc-finge 96.3 0.004 8.7E-08 26.8 1.9 18 88-106 4-21 (25)
50 smart00451 ZnF_U1 U1-like zinc 96.0 0.0054 1.2E-07 28.5 1.7 22 114-135 3-24 (35)
51 smart00451 ZnF_U1 U1-like zinc 95.8 0.0089 1.9E-07 27.7 2.1 23 86-108 3-25 (35)
52 COG5048 FOG: Zn-finger [Genera 95.7 0.0087 1.9E-07 43.6 2.6 119 14-140 288-444 (467)
53 COG5048 FOG: Zn-finger [Genera 95.4 0.0029 6.2E-08 46.1 -0.8 59 85-143 288-352 (467)
54 KOG2893|consensus 95.2 0.0049 1.1E-07 41.5 -0.0 46 88-137 12-58 (341)
55 cd00350 rubredoxin_like Rubred 95.0 0.017 3.7E-07 26.6 1.4 24 87-122 2-25 (33)
56 COG4049 Uncharacterized protei 94.7 0.025 5.3E-07 29.1 1.6 25 83-107 14-38 (65)
57 KOG1146|consensus 94.2 0.032 7E-07 46.0 2.0 55 82-136 461-540 (1406)
58 COG4049 Uncharacterized protei 93.7 0.039 8.5E-07 28.4 1.1 31 109-139 12-42 (65)
59 TIGR02098 MJ0042_CXXC MJ0042 f 93.3 0.051 1.1E-06 25.7 1.2 14 16-29 3-16 (38)
60 TIGR00622 ssl1 transcription f 93.3 0.16 3.5E-06 30.4 3.5 24 114-137 81-104 (112)
61 PF09986 DUF2225: Uncharacteri 93.2 0.081 1.7E-06 35.6 2.5 21 13-33 3-23 (214)
62 PF13717 zinc_ribbon_4: zinc-r 93.2 0.079 1.7E-06 24.9 1.7 32 16-59 3-35 (36)
63 PF13719 zinc_ribbon_5: zinc-r 93.2 0.11 2.4E-06 24.6 2.2 34 87-125 3-36 (37)
64 KOG2186|consensus 93.1 0.052 1.1E-06 36.9 1.4 45 51-109 4-51 (276)
65 PF09723 Zn-ribbon_8: Zinc rib 92.9 0.067 1.5E-06 26.1 1.3 13 15-27 5-17 (42)
66 smart00834 CxxC_CXXC_SSSS Puta 92.5 0.086 1.9E-06 25.3 1.4 13 15-27 5-17 (41)
67 PF06524 NOA36: NOA36 protein; 92.5 0.041 8.8E-07 37.6 0.2 89 43-137 135-232 (314)
68 COG2888 Predicted Zn-ribbon RN 92.4 0.21 4.6E-06 26.1 2.8 8 50-57 27-34 (61)
69 PF09986 DUF2225: Uncharacteri 92.4 0.034 7.3E-07 37.4 -0.2 13 115-127 49-61 (214)
70 TIGR02605 CxxC_CxxC_SSSS putat 91.6 0.12 2.7E-06 26.3 1.4 13 15-27 5-17 (52)
71 cd00729 rubredoxin_SM Rubredox 91.4 0.14 3.1E-06 23.7 1.4 24 87-122 3-26 (34)
72 TIGR00373 conserved hypothetic 91.2 0.15 3.3E-06 32.5 1.8 31 86-125 109-139 (158)
73 KOG1146|consensus 91.1 0.15 3.3E-06 42.4 2.1 104 15-139 1228-1353(1406)
74 PRK14890 putative Zn-ribbon RN 90.7 0.55 1.2E-05 24.6 3.2 9 49-57 24-32 (59)
75 PRK00464 nrdR transcriptional 90.6 0.18 3.9E-06 32.0 1.7 13 50-62 28-41 (154)
76 PRK06266 transcription initiat 90.0 0.2 4.4E-06 32.7 1.6 31 86-125 117-147 (178)
77 PF03604 DNA_RNApol_7kD: DNA d 89.8 0.31 6.6E-06 22.3 1.7 11 16-26 1-11 (32)
78 smart00531 TFIIE Transcription 89.1 0.31 6.8E-06 30.7 1.9 14 15-28 99-112 (147)
79 COG1996 RPC10 DNA-directed RNA 89.1 0.26 5.7E-06 24.8 1.2 13 14-26 5-17 (49)
80 PF09538 FYDLN_acid: Protein o 88.8 0.31 6.6E-06 29.1 1.6 30 87-127 10-39 (108)
81 PF07754 DUF1610: Domain of un 88.8 0.47 1E-05 20.1 1.7 7 87-93 17-23 (24)
82 PHA00626 hypothetical protein 88.8 0.43 9.2E-06 24.7 1.9 14 49-62 22-36 (59)
83 smart00659 RPOLCX RNA polymera 88.6 0.35 7.6E-06 23.8 1.5 13 15-27 2-14 (44)
84 PF00301 Rubredoxin: Rubredoxi 88.4 0.51 1.1E-05 23.6 2.0 15 16-30 2-16 (47)
85 KOG2893|consensus 88.0 0.14 2.9E-06 34.8 -0.2 19 87-105 35-53 (341)
86 PF02892 zf-BED: BED zinc fing 87.9 0.55 1.2E-05 22.9 2.0 22 113-134 15-40 (45)
87 COG3357 Predicted transcriptio 87.8 0.34 7.3E-06 27.7 1.3 26 2-27 41-70 (97)
88 smart00531 TFIIE Transcription 87.5 0.62 1.3E-05 29.4 2.5 36 86-125 99-134 (147)
89 smart00614 ZnF_BED BED zinc fi 87.3 0.56 1.2E-05 23.6 1.9 20 116-135 20-44 (50)
90 smart00734 ZnF_Rad18 Rad18-lik 87.2 0.66 1.4E-05 20.0 1.8 19 116-135 3-21 (26)
91 COG4888 Uncharacterized Zn rib 87.0 0.46 9.9E-06 27.7 1.5 40 12-62 19-59 (104)
92 cd00730 rubredoxin Rubredoxin; 86.8 0.72 1.6E-05 23.4 2.1 13 16-28 2-14 (50)
93 COG1592 Rubrerythrin [Energy p 86.7 0.51 1.1E-05 30.4 1.8 24 50-94 134-157 (166)
94 COG1592 Rubrerythrin [Energy p 86.6 0.55 1.2E-05 30.2 1.9 23 87-122 135-157 (166)
95 PRK14873 primosome assembly pr 86.4 0.69 1.5E-05 36.5 2.7 8 87-94 411-418 (665)
96 PF12013 DUF3505: Protein of u 85.9 0.77 1.7E-05 27.3 2.2 25 115-139 81-109 (109)
97 PRK00398 rpoP DNA-directed RNA 85.7 0.74 1.6E-05 22.8 1.8 30 14-60 2-32 (46)
98 TIGR00373 conserved hypothetic 85.3 0.45 9.7E-06 30.4 1.1 14 15-28 109-122 (158)
99 KOG2785|consensus 85.1 0.99 2.1E-05 32.8 2.7 52 85-136 165-242 (390)
100 PF05443 ROS_MUCR: ROS/MUCR tr 85.0 0.54 1.2E-05 29.1 1.3 22 115-139 73-94 (132)
101 PRK06266 transcription initiat 85.0 0.39 8.4E-06 31.4 0.7 14 15-28 117-130 (178)
102 COG1198 PriA Primosomal protei 84.0 0.9 1.9E-05 36.2 2.4 11 112-122 473-483 (730)
103 PF14353 CpXC: CpXC protein 83.8 0.27 5.8E-06 30.1 -0.4 14 16-29 2-15 (128)
104 KOG2231|consensus 83.4 1.1 2.4E-05 35.1 2.6 48 87-138 183-236 (669)
105 COG1773 Rubredoxin [Energy pro 83.0 2 4.2E-05 22.3 2.6 15 15-29 3-17 (55)
106 PRK09678 DNA-binding transcrip 82.9 0.73 1.6E-05 25.3 1.1 16 47-62 24-42 (72)
107 KOG4173|consensus 81.8 0.6 1.3E-05 31.0 0.6 50 87-136 107-168 (253)
108 PF04959 ARS2: Arsenite-resist 81.3 0.64 1.4E-05 31.3 0.6 28 83-110 74-101 (214)
109 PF01363 FYVE: FYVE zinc finge 81.0 0.58 1.3E-05 25.2 0.3 27 13-41 7-33 (69)
110 COG1198 PriA Primosomal protei 80.2 2.1 4.6E-05 34.2 3.2 12 16-27 436-447 (730)
111 KOG2186|consensus 79.8 1.1 2.4E-05 30.7 1.4 47 87-136 4-50 (276)
112 PF08792 A2L_zn_ribbon: A2L zi 79.6 1.6 3.5E-05 20.0 1.5 10 48-57 19-28 (33)
113 KOG2593|consensus 79.4 0.96 2.1E-05 33.4 1.0 37 13-59 126-163 (436)
114 PF05191 ADK_lid: Adenylate ki 78.7 0.49 1.1E-05 22.2 -0.4 32 87-126 2-33 (36)
115 KOG2785|consensus 77.9 2.2 4.7E-05 31.1 2.4 25 112-136 66-90 (390)
116 PF09845 DUF2072: Zn-ribbon co 77.5 1.3 2.8E-05 27.3 1.0 15 15-29 1-15 (131)
117 PF04959 ARS2: Arsenite-resist 77.4 0.92 2E-05 30.5 0.4 30 111-140 74-103 (214)
118 KOG3408|consensus 77.0 1.7 3.6E-05 26.4 1.4 26 83-108 54-79 (129)
119 COG1997 RPL43A Ribosomal prote 76.8 1.6 3.5E-05 24.8 1.2 11 87-97 54-64 (89)
120 PF06524 NOA36: NOA36 protein; 76.5 1.1 2.4E-05 30.9 0.6 82 9-109 136-232 (314)
121 COG3364 Zn-ribbon containing p 76.3 1.2 2.6E-05 26.1 0.7 19 15-33 2-20 (112)
122 COG4957 Predicted transcriptio 76.2 1.9 4E-05 26.7 1.5 22 116-140 78-99 (148)
123 TIGR00595 priA primosomal prot 76.2 2.2 4.8E-05 32.6 2.2 32 52-95 215-249 (505)
124 PF12013 DUF3505: Protein of u 76.1 2.8 6E-05 24.9 2.2 25 87-111 81-109 (109)
125 KOG2907|consensus 75.6 2.6 5.7E-05 25.2 1.9 38 51-98 75-114 (116)
126 smart00440 ZnF_C2C2 C2C2 Zinc 74.8 1.8 3.9E-05 20.8 1.0 9 51-59 29-38 (40)
127 KOG2593|consensus 74.0 2.6 5.6E-05 31.3 2.0 37 83-122 125-161 (436)
128 COG0068 HypF Hydrogenase matur 73.9 0.92 2E-05 35.7 -0.3 54 52-122 125-181 (750)
129 PF02176 zf-TRAF: TRAF-type zi 73.8 2.9 6.3E-05 21.6 1.7 40 86-126 9-54 (60)
130 PRK03824 hypA hydrogenase nick 73.6 2.8 6E-05 26.1 1.8 14 15-28 70-83 (135)
131 PF01096 TFIIS_C: Transcriptio 73.0 1 2.2E-05 21.5 -0.2 9 51-59 29-38 (39)
132 COG3091 SprT Zn-dependent meta 72.9 2.3 4.9E-05 26.9 1.3 30 87-121 118-147 (156)
133 PF07282 OrfB_Zn_ribbon: Putat 72.8 2.5 5.4E-05 22.7 1.3 10 87-96 47-56 (69)
134 PF10571 UPF0547: Uncharacteri 72.5 2.1 4.7E-05 18.4 0.8 11 16-26 15-25 (26)
135 KOG4167|consensus 72.5 1.2 2.6E-05 35.2 0.1 25 114-138 792-816 (907)
136 COG5236 Uncharacterized conser 72.5 1.7 3.7E-05 31.3 0.8 48 87-135 221-272 (493)
137 KOG4167|consensus 72.2 0.9 1.9E-05 35.9 -0.7 27 84-110 790-816 (907)
138 cd00065 FYVE FYVE domain; Zinc 71.1 3.5 7.6E-05 21.1 1.6 23 17-41 4-26 (57)
139 PF15269 zf-C2H2_7: Zinc-finge 70.8 3.4 7.4E-05 20.3 1.4 21 115-135 21-41 (54)
140 KOG1280|consensus 69.6 5.4 0.00012 28.8 2.7 35 87-121 80-116 (381)
141 PF14446 Prok-RING_1: Prokaryo 69.2 3.1 6.7E-05 21.5 1.1 19 15-33 5-23 (54)
142 smart00661 RPOL9 RNA polymeras 68.8 4.6 0.0001 20.2 1.8 11 50-60 20-31 (52)
143 KOG3507|consensus 67.2 4.3 9.4E-05 21.2 1.4 9 49-57 36-44 (62)
144 COG1655 Uncharacterized protei 66.8 3.2 6.9E-05 28.3 1.1 20 13-32 17-36 (267)
145 TIGR01206 lysW lysine biosynth 66.6 2.8 6E-05 21.7 0.6 30 87-124 3-32 (54)
146 smart00154 ZnF_AN1 AN1-like Zi 66.6 3.5 7.7E-05 19.6 1.0 17 15-31 12-28 (39)
147 PF13453 zf-TFIIB: Transcripti 65.7 4.6 0.0001 19.3 1.3 19 114-132 19-37 (41)
148 PF12760 Zn_Tnp_IS1595: Transp 65.4 7 0.00015 19.2 2.0 8 16-23 19-26 (46)
149 PHA02998 RNA polymerase subuni 64.3 7.4 0.00016 25.4 2.3 11 87-97 172-182 (195)
150 PF01780 Ribosomal_L37ae: Ribo 64.1 2.6 5.5E-05 24.3 0.2 10 87-96 54-63 (90)
151 smart00064 FYVE Protein presen 63.9 7.4 0.00016 20.7 2.1 25 15-41 10-34 (68)
152 KOG1729|consensus 63.9 2.8 6E-05 29.6 0.4 30 10-41 163-193 (288)
153 PF07975 C1_4: TFIIH C1-like d 63.6 4 8.7E-05 20.8 0.9 20 14-33 20-39 (51)
154 KOG3408|consensus 62.9 6.5 0.00014 23.9 1.8 25 112-136 55-79 (129)
155 COG0068 HypF Hydrogenase matur 61.9 3.9 8.4E-05 32.5 0.9 56 17-96 125-183 (750)
156 PF08274 PhnA_Zn_Ribbon: PhnA 61.9 3.9 8.5E-05 18.3 0.6 7 51-57 20-26 (30)
157 PHA02942 putative transposase; 61.6 6.9 0.00015 28.9 2.1 10 87-96 343-352 (383)
158 PRK11032 hypothetical protein; 61.2 5.7 0.00012 25.5 1.4 7 51-57 125-131 (160)
159 PRK12496 hypothetical protein; 60.8 8.1 0.00018 24.9 2.1 12 16-27 128-139 (164)
160 PF05290 Baculo_IE-1: Baculovi 60.1 8.8 0.00019 23.8 2.0 13 116-128 123-135 (140)
161 PF05129 Elf1: Transcription e 59.9 2.5 5.3E-05 23.8 -0.3 10 13-22 20-29 (81)
162 COG4391 Uncharacterized protei 59.8 7.9 0.00017 20.5 1.6 16 42-57 16-31 (62)
163 PTZ00255 60S ribosomal protein 59.7 4.5 9.9E-05 23.3 0.7 30 87-126 37-66 (90)
164 TIGR00100 hypA hydrogenase nic 59.3 4.9 0.00011 24.2 0.9 26 86-123 70-95 (115)
165 PF01286 XPA_N: XPA protein N- 59.2 4.9 0.00011 18.6 0.7 14 16-29 4-17 (34)
166 PTZ00303 phosphatidylinositol 59.2 6.2 0.00013 32.0 1.6 26 16-41 461-489 (1374)
167 KOG2482|consensus 58.8 6.1 0.00013 28.6 1.4 23 86-108 195-217 (423)
168 KOG3214|consensus 58.7 6.5 0.00014 23.0 1.2 12 51-62 48-60 (109)
169 PRK05580 primosome assembly pr 58.7 7.6 0.00016 31.0 2.0 8 87-94 409-416 (679)
170 KOG2482|consensus 57.9 6.1 0.00013 28.6 1.3 50 87-136 145-217 (423)
171 KOG4173|consensus 56.9 5.5 0.00012 26.7 0.9 47 87-136 80-128 (253)
172 PF13878 zf-C2H2_3: zinc-finge 56.9 13 0.00029 17.8 2.0 9 88-96 15-23 (41)
173 PF08790 zf-LYAR: LYAR-type C2 56.7 2.4 5.2E-05 18.7 -0.6 18 87-105 1-18 (28)
174 KOG2906|consensus 56.6 12 0.00026 21.8 2.1 18 15-32 21-38 (105)
175 TIGR00570 cdk7 CDK-activating 56.5 9.6 0.00021 27.3 2.0 43 16-59 4-53 (309)
176 PF13824 zf-Mss51: Zinc-finger 56.3 16 0.00034 19.0 2.3 15 48-62 12-27 (55)
177 PF01428 zf-AN1: AN1-like Zinc 56.0 5.2 0.00011 19.4 0.5 15 113-127 12-26 (43)
178 PRK05452 anaerobic nitric oxid 55.8 12 0.00027 28.5 2.7 13 15-27 425-437 (479)
179 PF07295 DUF1451: Protein of u 55.7 8.2 0.00018 24.4 1.4 7 51-57 113-119 (146)
180 PRK14714 DNA polymerase II lar 55.5 15 0.00033 31.5 3.2 32 16-57 668-699 (1337)
181 PF09082 DUF1922: Domain of un 55.3 3.7 8.1E-05 22.2 -0.1 23 16-40 4-26 (68)
182 COG5151 SSL1 RNA polymerase II 55.2 4.3 9.3E-05 28.9 0.2 25 113-137 387-411 (421)
183 TIGR00280 L37a ribosomal prote 55.1 5.1 0.00011 23.1 0.4 29 87-125 36-64 (91)
184 TIGR02300 FYDLN_acid conserved 55.1 11 0.00025 23.1 1.9 13 14-26 8-20 (129)
185 COG2331 Uncharacterized protei 54.2 2.3 5.1E-05 23.5 -1.0 12 15-26 12-23 (82)
186 PF12907 zf-met2: Zinc-binding 54.2 9.7 0.00021 18.3 1.3 7 87-93 2-8 (40)
187 KOG2272|consensus 54.1 2.8 6E-05 28.9 -0.8 42 16-57 100-144 (332)
188 PF04810 zf-Sec23_Sec24: Sec23 53.5 10 0.00023 18.0 1.3 10 48-57 22-31 (40)
189 COG5236 Uncharacterized conser 53.4 17 0.00036 26.5 2.8 67 52-138 222-305 (493)
190 smart00731 SprT SprT homologue 52.3 12 0.00027 23.4 1.9 10 87-96 134-143 (146)
191 COG1675 TFA1 Transcription ini 51.5 11 0.00024 24.7 1.6 28 87-123 114-141 (176)
192 KOG2636|consensus 51.4 10 0.00022 28.5 1.6 29 107-135 394-423 (497)
193 cd00924 Cyt_c_Oxidase_Vb Cytoc 51.1 7 0.00015 22.9 0.6 15 12-26 76-90 (97)
194 KOG0717|consensus 51.1 9.5 0.00021 28.8 1.4 21 115-135 293-313 (508)
195 COG3677 Transposase and inacti 50.9 12 0.00027 23.1 1.7 11 87-97 54-64 (129)
196 PLN02294 cytochrome c oxidase 50.8 8 0.00017 25.1 0.9 16 11-26 137-152 (174)
197 PF14311 DUF4379: Domain of un 50.8 14 0.0003 18.9 1.6 12 87-98 29-40 (55)
198 COG1594 RPB9 DNA-directed RNA 50.7 7.6 0.00016 23.4 0.7 11 87-97 101-111 (113)
199 PF11672 DUF3268: Protein of u 50.7 16 0.00036 21.6 2.1 14 14-27 1-14 (102)
200 TIGR00595 priA primosomal prot 50.3 14 0.00031 28.4 2.3 19 35-57 242-260 (505)
201 smart00249 PHD PHD zinc finger 50.1 28 0.0006 16.2 2.9 8 50-57 14-21 (47)
202 smart00132 LIM Zinc-binding do 49.6 17 0.00037 16.3 1.8 7 51-57 28-34 (39)
203 PF13451 zf-trcl: Probable zin 49.2 9.8 0.00021 19.2 0.9 14 49-62 3-17 (49)
204 KOG0978|consensus 48.8 5.7 0.00012 31.6 -0.0 11 51-61 644-655 (698)
205 PRK03976 rpl37ae 50S ribosomal 48.7 6.9 0.00015 22.5 0.3 30 87-126 37-66 (90)
206 COG1571 Predicted DNA-binding 48.5 13 0.00029 27.8 1.8 12 87-98 368-379 (421)
207 COG4530 Uncharacterized protei 48.4 12 0.00025 22.4 1.2 28 87-125 10-37 (129)
208 TIGR03831 YgiT_finger YgiT-typ 48.3 10 0.00022 18.2 0.9 7 51-57 33-39 (46)
209 PF10263 SprT-like: SprT-like 47.4 11 0.00023 23.7 1.1 9 87-95 144-152 (157)
210 TIGR00244 transcriptional regu 47.3 15 0.00033 23.2 1.7 13 50-62 28-41 (147)
211 PRK04351 hypothetical protein; 47.2 16 0.00034 23.2 1.8 12 87-98 133-144 (149)
212 PF04423 Rad50_zn_hook: Rad50 46.8 22 0.00049 18.0 2.0 12 116-127 22-33 (54)
213 PF04780 DUF629: Protein of un 46.2 18 0.0004 27.5 2.2 27 113-139 56-83 (466)
214 PRK03681 hypA hydrogenase nick 45.8 14 0.00031 22.2 1.4 10 16-25 71-80 (114)
215 PF15227 zf-C3HC4_4: zinc fing 45.3 24 0.00052 16.9 1.9 11 18-28 1-11 (42)
216 PRK00432 30S ribosomal protein 45.1 20 0.00042 18.1 1.6 7 51-57 38-44 (50)
217 PF10276 zf-CHCC: Zinc-finger 45.0 13 0.00028 17.9 0.9 10 87-96 30-39 (40)
218 PF11781 RRN7: RNA polymerase 45.0 16 0.00035 17.0 1.2 8 17-24 10-17 (36)
219 PF04780 DUF629: Protein of un 44.6 18 0.00039 27.5 2.0 25 87-111 58-83 (466)
220 PRK00762 hypA hydrogenase nick 44.6 17 0.00037 22.2 1.6 11 16-27 71-81 (124)
221 PRK10220 hypothetical protein; 44.2 24 0.00052 21.1 2.1 11 17-27 5-15 (111)
222 COG1779 C4-type Zn-finger prot 44.1 9.4 0.0002 25.4 0.4 10 16-25 15-24 (201)
223 KOG2071|consensus 43.9 15 0.00033 28.6 1.5 28 112-139 416-443 (579)
224 TIGR00686 phnA alkylphosphonat 43.9 21 0.00044 21.3 1.8 11 17-27 4-14 (109)
225 PRK05580 primosome assembly pr 43.9 20 0.00043 28.7 2.3 19 35-57 410-428 (679)
226 PF09416 UPF1_Zn_bind: RNA hel 43.4 36 0.00078 21.7 2.9 36 87-122 15-68 (152)
227 KOG0717|consensus 43.4 16 0.00034 27.7 1.5 22 87-108 293-314 (508)
228 PRK12380 hydrogenase nickel in 43.4 16 0.00035 21.9 1.4 10 16-25 71-80 (113)
229 COG1439 Predicted nucleic acid 43.2 17 0.00037 23.8 1.5 24 15-42 139-162 (177)
230 PF06220 zf-U1: U1 zinc finger 43.1 19 0.00041 17.0 1.3 10 115-124 4-13 (38)
231 PF06397 Desulfoferrod_N: Desu 42.9 11 0.00023 17.7 0.4 12 14-25 5-16 (36)
232 PF07503 zf-HYPF: HypF finger; 42.8 5.9 0.00013 18.4 -0.5 10 50-59 21-31 (35)
233 KOG2231|consensus 42.7 33 0.00072 27.4 3.2 65 51-135 183-260 (669)
234 KOG2636|consensus 42.3 18 0.00039 27.3 1.7 29 79-107 394-423 (497)
235 PF05495 zf-CHY: CHY zinc fing 41.8 6.8 0.00015 21.4 -0.4 29 87-123 42-70 (71)
236 PRK03564 formate dehydrogenase 41.6 28 0.0006 25.1 2.5 36 87-126 227-264 (309)
237 PF14634 zf-RING_5: zinc-RING 41.4 25 0.00054 16.9 1.7 8 18-25 2-9 (44)
238 PRK00420 hypothetical protein; 41.0 29 0.00063 20.9 2.1 9 87-95 41-49 (112)
239 COG1327 Predicted transcriptio 40.8 19 0.00042 22.9 1.4 13 50-62 28-41 (156)
240 COG1998 RPS31 Ribosomal protei 40.6 23 0.00051 17.9 1.4 7 87-93 38-44 (51)
241 PF03811 Zn_Tnp_IS1: InsA N-te 39.4 36 0.00077 15.9 1.9 11 46-56 25-35 (36)
242 PF10013 DUF2256: Uncharacteri 38.9 13 0.00028 18.1 0.4 13 116-128 10-22 (42)
243 COG5112 UFD2 U1-like Zn-finger 37.9 14 0.0003 21.9 0.5 26 83-108 52-77 (126)
244 PF09332 Mcm10: Mcm10 replicat 37.8 9.3 0.0002 27.8 -0.3 39 51-99 253-298 (344)
245 PF15135 UPF0515: Uncharacteri 37.3 30 0.00065 24.0 2.0 14 49-62 154-168 (278)
246 COG2879 Uncharacterized small 36.9 46 0.001 17.8 2.2 19 125-143 23-41 (65)
247 PF14803 Nudix_N_2: Nudix N-te 36.8 11 0.00024 17.4 -0.1 8 50-57 22-29 (34)
248 COG5188 PRP9 Splicing factor 3 35.5 26 0.00057 25.6 1.6 28 107-134 367-395 (470)
249 PF14599 zinc_ribbon_6: Zinc-r 35.3 13 0.00028 19.7 0.1 24 16-39 31-54 (61)
250 PTZ00448 hypothetical protein; 35.3 27 0.00059 25.7 1.7 23 114-136 314-336 (373)
251 PF00097 zf-C3HC4: Zinc finger 35.1 15 0.00032 17.1 0.3 10 18-27 1-10 (41)
252 PRK14892 putative transcriptio 34.7 19 0.00041 21.2 0.7 7 87-93 22-28 (99)
253 PRK00564 hypA hydrogenase nick 33.9 27 0.00058 21.1 1.3 11 16-26 72-82 (117)
254 PRK05978 hypothetical protein; 33.9 30 0.00064 22.0 1.5 18 16-33 34-51 (148)
255 KOG4727|consensus 33.5 30 0.00065 22.5 1.5 25 83-107 72-96 (193)
256 PLN03238 probable histone acet 33.1 58 0.0013 23.2 2.9 21 87-107 49-69 (290)
257 TIGR01384 TFS_arch transcripti 32.7 25 0.00053 20.5 1.0 11 87-97 91-101 (104)
258 PF02748 PyrI_C: Aspartate car 32.5 23 0.00049 18.1 0.7 16 12-27 32-47 (52)
259 KOG1842|consensus 31.9 25 0.00055 26.6 1.1 22 87-108 16-37 (505)
260 COG0675 Transposase and inacti 31.8 28 0.00061 24.7 1.3 13 48-60 320-333 (364)
261 TIGR00319 desulf_FeS4 desulfof 31.8 25 0.00054 15.9 0.7 13 13-25 5-17 (34)
262 cd00974 DSRD Desulforedoxin (D 31.6 26 0.00057 15.8 0.8 12 14-25 3-14 (34)
263 PF02591 DUF164: Putative zinc 31.6 48 0.001 16.9 1.9 8 87-94 47-54 (56)
264 TIGR03830 CxxCG_CxxCG_HTH puta 31.5 23 0.0005 21.3 0.7 15 48-62 29-44 (127)
265 PF01155 HypA: Hydrogenase exp 31.4 13 0.00029 22.2 -0.3 12 16-27 71-82 (113)
266 PF11931 DUF3449: Domain of un 30.7 17 0.00036 24.3 0.0 28 79-106 94-122 (196)
267 PF08209 Sgf11: Sgf11 (transcr 30.6 31 0.00067 15.8 0.9 7 51-57 5-11 (33)
268 PRK01343 zinc-binding protein; 30.2 45 0.00098 17.4 1.6 13 14-26 8-20 (57)
269 PF10122 Mu-like_Com: Mu-like 29.7 15 0.00033 18.7 -0.2 29 87-123 5-33 (51)
270 COG1326 Uncharacterized archae 29.4 73 0.0016 21.3 2.7 12 113-124 29-40 (201)
271 PTZ00043 cytochrome c oxidase 29.3 25 0.00055 24.0 0.7 19 10-28 176-194 (268)
272 KOG0320|consensus 29.2 19 0.00041 23.6 0.1 9 87-95 168-176 (187)
273 PTZ00448 hypothetical protein; 29.1 41 0.00089 24.8 1.7 23 86-108 314-336 (373)
274 PRK12722 transcriptional activ 28.6 46 0.00099 22.1 1.7 9 89-97 137-145 (187)
275 PF07649 C1_3: C1-like domain; 28.2 36 0.00079 14.8 0.9 7 87-93 16-22 (30)
276 COG4896 Uncharacterized protei 28.1 36 0.00079 18.0 1.0 10 114-123 31-40 (68)
277 TIGR01562 FdhE formate dehydro 28.0 56 0.0012 23.5 2.2 35 87-126 225-264 (305)
278 PF14787 zf-CCHC_5: GAG-polypr 27.7 40 0.00087 15.8 1.0 16 16-31 3-18 (36)
279 TIGR01385 TFSII transcription 27.5 44 0.00096 23.9 1.7 8 16-23 259-266 (299)
280 TIGR00143 hypF [NiFe] hydrogen 27.5 15 0.00033 29.6 -0.7 31 87-123 119-149 (711)
281 PF00412 LIM: LIM domain; Int 27.5 35 0.00075 17.1 0.9 8 50-57 26-33 (58)
282 PF08271 TF_Zn_Ribbon: TFIIB z 27.0 36 0.00078 16.3 0.8 8 50-57 19-26 (43)
283 PF09963 DUF2197: Uncharacteri 26.9 29 0.00062 18.1 0.5 38 87-125 3-42 (56)
284 PF04641 Rtf2: Rtf2 RING-finge 26.7 34 0.00073 23.8 1.0 48 13-62 111-163 (260)
285 KOG4118|consensus 26.5 39 0.00085 18.2 0.9 25 115-139 39-63 (74)
286 PF01844 HNH: HNH endonuclease 26.3 25 0.00054 16.8 0.2 16 18-33 1-16 (47)
287 cd01410 SIRT7 SIRT7: Eukaryoti 26.2 93 0.002 20.8 3.0 40 80-122 89-128 (206)
288 PF14447 Prok-RING_4: Prokaryo 26.1 50 0.0011 17.1 1.3 14 47-60 36-50 (55)
289 KOG2817|consensus 26.1 32 0.00069 25.5 0.8 8 87-94 375-382 (394)
290 KOG2071|consensus 26.0 52 0.0011 25.8 1.9 25 86-110 418-442 (579)
291 PRK12860 transcriptional activ 25.9 54 0.0012 21.8 1.7 6 87-92 155-160 (189)
292 PLN03239 histone acetyltransfe 25.9 57 0.0012 23.9 2.0 25 112-136 104-128 (351)
293 PF03833 PolC_DP2: DNA polymer 25.8 23 0.00049 29.1 0.0 9 87-95 681-689 (900)
294 PF02891 zf-MIZ: MIZ/SP-RING z 25.7 30 0.00066 17.3 0.4 9 114-122 41-49 (50)
295 PF14255 Cys_rich_CPXG: Cystei 25.6 30 0.00066 17.7 0.4 11 17-27 2-12 (52)
296 PF04438 zf-HIT: HIT zinc fing 25.3 31 0.00068 15.3 0.4 14 14-27 12-25 (30)
297 KOG1994|consensus 25.0 40 0.00086 23.1 1.0 19 87-105 240-258 (268)
298 PF05876 Terminase_GpA: Phage 25.0 65 0.0014 25.3 2.3 40 16-62 201-242 (557)
299 PRK04023 DNA polymerase II lar 24.7 79 0.0017 26.9 2.7 9 16-24 627-635 (1121)
300 COG2995 PqiA Uncharacterized p 24.6 95 0.0021 23.3 2.9 38 11-49 14-54 (418)
301 PLN03238 probable histone acet 24.5 1.1E+02 0.0024 21.9 3.1 25 112-136 46-70 (290)
302 CHL00174 accD acetyl-CoA carbo 24.4 46 0.001 23.8 1.3 12 51-62 58-70 (296)
303 TIGR00515 accD acetyl-CoA carb 24.2 47 0.001 23.6 1.3 12 51-62 46-58 (285)
304 PF12156 ATPase-cat_bd: Putati 23.8 43 0.00093 19.1 0.9 37 17-62 2-39 (88)
305 PF14319 Zn_Tnp_IS91: Transpos 23.7 58 0.0013 19.5 1.5 11 52-62 62-73 (111)
306 PF10537 WAC_Acf1_DNA_bd: ATP- 23.2 1.5E+02 0.0033 17.5 3.1 36 87-123 4-39 (102)
307 PF03966 Trm112p: Trm112p-like 23.1 36 0.00079 18.2 0.5 11 87-97 54-64 (68)
308 PF02318 FYVE_2: FYVE-type zin 23.1 35 0.00076 20.6 0.4 14 15-28 54-67 (118)
309 PF14369 zf-RING_3: zinc-finge 23.0 60 0.0013 14.9 1.1 10 17-26 23-32 (35)
310 PRK08222 hydrogenase 4 subunit 22.9 54 0.0012 21.4 1.3 20 113-132 113-132 (181)
311 KOG2807|consensus 22.9 39 0.00085 24.5 0.7 29 87-121 346-374 (378)
312 PF11494 Ta0938: Ta0938; Inte 22.9 44 0.00095 19.5 0.8 12 87-98 38-49 (105)
313 PF09297 zf-NADH-PPase: NADH p 22.8 69 0.0015 14.1 1.3 9 49-57 20-28 (32)
314 PF15446 zf-PHD-like: PHD/FYVE 22.8 88 0.0019 20.4 2.2 12 85-96 123-134 (175)
315 PF07800 DUF1644: Protein of u 22.8 1.9E+02 0.0041 18.8 3.6 57 85-143 79-138 (162)
316 PF03145 Sina: Seven in absent 22.7 1.3E+02 0.0028 19.8 3.1 8 101-108 62-69 (198)
317 PF15616 TerY-C: TerY-C metal 22.7 91 0.002 19.4 2.2 9 87-95 106-114 (131)
318 PF05180 zf-DNL: DNL zinc fing 22.3 15 0.00033 19.8 -1.1 8 50-57 29-36 (66)
319 KOG1088|consensus 22.2 47 0.001 20.2 0.9 20 82-101 94-113 (124)
320 COG4338 Uncharacterized protei 22.2 37 0.00079 17.1 0.3 12 116-127 14-25 (54)
321 PLN00104 MYST -like histone ac 22.2 87 0.0019 23.9 2.4 24 112-135 196-219 (450)
322 TIGR00310 ZPR1_znf ZPR1 zinc f 22.0 60 0.0013 21.6 1.4 13 50-62 30-43 (192)
323 PF00628 PHD: PHD-finger; Int 21.7 71 0.0015 15.6 1.4 15 48-62 12-27 (51)
324 PTZ00064 histone acetyltransfe 21.6 1E+02 0.0022 24.0 2.6 25 112-136 278-302 (552)
325 COG1579 Zn-ribbon protein, pos 21.5 62 0.0013 22.4 1.4 8 87-94 222-229 (239)
326 cd01413 SIR2_Af2 SIR2_Af2: Arc 21.2 1.1E+02 0.0023 20.7 2.6 39 79-122 106-144 (222)
327 PF01927 Mut7-C: Mut7-C RNAse 21.1 81 0.0018 19.8 1.8 19 86-104 124-142 (147)
328 PF03107 C1_2: C1 domain; Int 20.6 60 0.0013 14.1 0.9 8 50-57 15-22 (30)
329 PF12647 RNHCP: RNHCP domain; 20.6 1.4E+02 0.003 17.4 2.5 29 13-41 2-32 (92)
330 PF05741 zf-nanos: Nanos RNA b 20.6 40 0.00086 17.5 0.3 11 15-25 33-43 (55)
331 PRK05654 acetyl-CoA carboxylas 20.6 55 0.0012 23.4 1.0 12 51-62 47-59 (292)
332 PF03884 DUF329: Domain of unk 20.5 43 0.00093 17.5 0.4 12 16-27 3-14 (57)
333 PRK09263 anaerobic ribonucleos 20.4 75 0.0016 25.8 1.9 7 51-57 660-666 (711)
334 PLN02748 tRNA dimethylallyltra 20.4 78 0.0017 24.3 1.9 24 85-108 417-441 (468)
335 PF00130 C1_1: Phorbol esters/ 20.3 84 0.0018 15.5 1.5 12 14-25 10-21 (53)
336 PF10080 DUF2318: Predicted me 20.3 41 0.00089 19.9 0.3 11 50-60 52-63 (102)
337 PRK14559 putative protein seri 20.3 1.1E+02 0.0023 24.7 2.6 37 17-62 17-54 (645)
No 1
>KOG2462|consensus
Probab=99.96 E-value=4.3e-29 Score=165.37 Aligned_cols=107 Identities=22% Similarity=0.439 Sum_probs=65.1
Q ss_pred ceecCccCCccCCccccccc-------------cCCCCC-----------CccccCCCCCeeCCCCC-CCcch---hhhh
Q psy10073 15 KKTCLYCNKYVPSDIDVFIG-------------HCQTCP-----------NMSFLNSVIPQSCKHCK-NFTSS---DVNL 66 (144)
Q Consensus 15 ~~~C~~C~~~f~~~~~l~~H-------------~c~~c~-----------h~~~h~~~~~~~C~~C~-~f~~~---~~H~ 66 (144)
.|.|+.||+.+.+.++|.+| .|.+|+ |+++|+ .+++|.+|| .|... +.|+
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHi 207 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHI 207 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhccc
Confidence 47888888888888888774 333333 233333 455555555 55544 5555
Q ss_pred hhcccCCCCcccccCCCCCceeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhccChHHHHHHHH
Q psy10073 67 LMEHSENCPCMVRPDPVKYKFICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAYQKEKLQFHVK 135 (144)
Q Consensus 67 ~~~h~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 135 (144)
++|+|||| |.|+.|+++|.+.++|+.||++|.+.++|+|..|+|+|+..+.|.+|+.
T Consensus 208 -RTHTGEKP-----------F~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 208 -RTHTGEKP-----------FSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred -ccccCCCC-----------ccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 55555555 6666666666666666666666666666666666666666666666654
No 2
>KOG2462|consensus
Probab=99.95 E-value=4.9e-29 Score=165.10 Aligned_cols=111 Identities=20% Similarity=0.290 Sum_probs=90.7
Q ss_pred eecCccCCccCCccccccccCCCCCCccccC---CCCCeeCCCCC-CCcch---hhhhhhcccCCCCcccccCCCCCcee
Q psy10073 16 KTCLYCNKYVPSDIDVFIGHCQTCPNMSFLN---SVIPQSCKHCK-NFTSS---DVNLLMEHSENCPCMVRPDPVKYKFI 88 (144)
Q Consensus 16 ~~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~---~~~~~~C~~C~-~f~~~---~~H~~~~h~~~~~~~~~~~~~~~~~~ 88 (144)
-..-.|++--...+.... .--|..+|- ..+.+.|++|| .+.+. ..|+ ++|. -+ ..
T Consensus 128 ~~r~~c~eCgk~ysT~sn----LsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHi-rTH~--l~-----------c~ 189 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSN----LSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHI-RTHT--LP-----------CE 189 (279)
T ss_pred CCceeccccccccccccc----cchhhcccccccccccccCCCCCceeeehHHHhhHh-hccC--CC-----------cc
Confidence 345556665555554443 111344552 35669999999 88887 8899 9997 45 99
Q ss_pred CCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhccChHHHHHHHHhhcCCCCCC
Q psy10073 89 CVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAYQKEKLQFHVKNKHSTKVKD 144 (144)
Q Consensus 89 C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~ 144 (144)
|.+||+.|.....|+.|+++|+|||||.|..|+++|+++++|+.||.+|.+.|+|+
T Consensus 190 C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~q 245 (279)
T KOG2462|consen 190 CGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQ 245 (279)
T ss_pred cccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCcccc
Confidence 99999999999999999999999999999999999999999999999999999985
No 3
>KOG1074|consensus
Probab=99.81 E-value=5.4e-21 Score=142.45 Aligned_cols=58 Identities=21% Similarity=0.387 Sum_probs=52.5
Q ss_pred CceeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhccChHHHHHHHHhhcCCCC
Q psy10073 85 YKFICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAYQKEKLQFHVKNKHSTKV 142 (144)
Q Consensus 85 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~kp 142 (144)
.+-.|.+|.+...-.+.|+.|.++|+||+||+|.+||+.|+++.+|+.|+.+|-..-|
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~ 661 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPP 661 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCcc
Confidence 3578999999999999999999999999999999999999999999999998875433
No 4
>KOG1074|consensus
Probab=99.77 E-value=3.8e-19 Score=132.73 Aligned_cols=57 Identities=21% Similarity=0.372 Sum_probs=54.1
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhccChHHHHHHHHhhcCCCCC
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAYQKEKLQFHVKNKHSTKVK 143 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~ 143 (144)
..|..|++.|...+.|..|+++|++++||.|..|++.|..+.+|+.||.+|....|.
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~ 936 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPP 936 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCC
Confidence 689999999999999999999999999999999999999999999999999976653
No 5
>KOG3576|consensus
Probab=99.75 E-value=2e-19 Score=114.85 Aligned_cols=112 Identities=20% Similarity=0.319 Sum_probs=100.2
Q ss_pred CCCceecCccCCccCCccccccccCCCCCCccccCCCCCeeCCCCC-CCcch---hhhhhhcccCCCCcccccCCCCCce
Q psy10073 12 LSTKKTCLYCNKYVPSDIDVFIGHCQTCPNMSFLNSVIPQSCKHCK-NFTSS---DVNLLMEHSENCPCMVRPDPVKYKF 87 (144)
Q Consensus 12 ~~~~~~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~~~~~~~C~~C~-~f~~~---~~H~~~~h~~~~~~~~~~~~~~~~~ 87 (144)
....|.|.+|++.|.....|.+ |++-|+..+.|-|..|| .|.+. ++|+ ++|+|.+| |
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnr-------h~kch~~vkr~lct~cgkgfndtfdlkrh~-rthtgvrp-----------y 174 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNR-------HLKCHSDVKRHLCTFCGKGFNDTFDLKRHT-RTHTGVRP-----------Y 174 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHH-------HhhhccHHHHHHHhhccCcccchhhhhhhh-ccccCccc-----------c
Confidence 3456999999999999999999 89999999999999999 99998 9999 99999999 9
Q ss_pred eCCCCCcccCChhHHHHHHHh-hc----------CCcceeCCCcchhccChHHHHHHHHhhcCCCC
Q psy10073 88 ICVACDYFTIISQNMRNHTLI-HL----------GDKQFKCCLCSYGAYQKEKLQFHVKNKHSTKV 142 (144)
Q Consensus 88 ~C~~C~~~f~~~~~l~~H~~~-h~----------~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~kp 142 (144)
+|..|+++|.+.-+|..|++. |. .++.|.|+.||.+-.....+..|++.|+..-|
T Consensus 175 kc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 175 KCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred chhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 999999999999999999754 32 25679999999999999999999999886543
No 6
>KOG3623|consensus
Probab=99.63 E-value=1e-17 Score=123.87 Aligned_cols=113 Identities=19% Similarity=0.321 Sum_probs=93.3
Q ss_pred eecCccCCccCCccccccccCCCCCCcccc-CCCCCeeCCCCC-CCcch---hhhhhhcccCCCCc--ccccCCCCCcee
Q psy10073 16 KTCLYCNKYVPSDIDVFIGHCQTCPNMSFL-NSVIPQSCKHCK-NFTSS---DVNLLMEHSENCPC--MVRPDPVKYKFI 88 (144)
Q Consensus 16 ~~C~~C~~~f~~~~~l~~H~c~~c~h~~~h-~~~~~~~C~~C~-~f~~~---~~H~~~~h~~~~~~--~~~~~~~~~~~~ 88 (144)
..|++|+..+.....|+.|+ +-.| ..+..|.|..|. +|... .+|| .+|....+- ........+.|+
T Consensus 211 ltcpycdrgykrltslkeHi------kyrhekne~nfsC~lCsytFAyRtQLErhm-~~hkpg~dqa~sltqsa~lRKFK 283 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHI------KYRHEKNEPNFSCMLCSYTFAYRTQLERHM-QLHKPGGDQAISLTQSALLRKFK 283 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHH------HHHHhhCCCCCcchhhhhhhhhHHHHHHHH-HhhcCCCcccccccchhhhcccc
Confidence 68999999999999999953 2233 345669999999 99888 8899 888644331 112234566799
Q ss_pred CCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhccChHHHHHHHH
Q psy10073 89 CVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAYQKEKLQFHVK 135 (144)
Q Consensus 89 C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 135 (144)
|.+|+++|..+..|..|+++|.|+|||.|+.|+|.|+...++..|+.
T Consensus 284 CtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 284 CTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred ccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 99999999999999999999999999999999999999999999975
No 7
>KOG3576|consensus
Probab=99.62 E-value=8.6e-17 Score=102.94 Aligned_cols=81 Identities=26% Similarity=0.456 Sum_probs=74.6
Q ss_pred CCCCeeCCCCC-CCcch---hhhhhhcccCCCCcccccCCCCCceeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcch
Q psy10073 47 SVIPQSCKHCK-NFTSS---DVNLLMEHSENCPCMVRPDPVKYKFICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSY 122 (144)
Q Consensus 47 ~~~~~~C~~C~-~f~~~---~~H~~~~h~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 122 (144)
+...|.|.+|+ .|... .+|+ +-|...+. +-|..||+.|.+..+|.+|+++|+|.+||+|..|++
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~-kch~~vkr-----------~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~k 181 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHL-KCHSDVKR-----------HLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEK 181 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHh-hhccHHHH-----------HHHhhccCcccchhhhhhhhccccCccccchhhhhH
Confidence 34569999999 99887 8999 99988888 999999999999999999999999999999999999
Q ss_pred hccChHHHHHHHHhhcC
Q psy10073 123 GAYQKEKLQFHVKNKHS 139 (144)
Q Consensus 123 ~f~~~~~l~~H~~~h~~ 139 (144)
+|+++-+|..|++.-+|
T Consensus 182 aftqrcsleshl~kvhg 198 (267)
T KOG3576|consen 182 AFTQRCSLESHLKKVHG 198 (267)
T ss_pred HHHhhccHHHHHHHHcC
Confidence 99999999999886555
No 8
>KOG3623|consensus
Probab=99.60 E-value=1.6e-16 Score=117.62 Aligned_cols=77 Identities=22% Similarity=0.460 Sum_probs=71.4
Q ss_pred CCCCeeCCCCC-CCcch---hhhhhhcccCCCCcccccCCCCCceeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcch
Q psy10073 47 SVIPQSCKHCK-NFTSS---DVNLLMEHSENCPCMVRPDPVKYKFICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSY 122 (144)
Q Consensus 47 ~~~~~~C~~C~-~f~~~---~~H~~~~h~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 122 (144)
.+.+|.|+.|+ .|... .+|. ..|+|.+| |.|.+|.++|..+..|..|.+.|.|+|||+|+.|+|
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHK-YEHsGqRP-----------yqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClK 958 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHK-YEHSGQRP-----------YQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLK 958 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhh-hhhcCCCC-----------cccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhh
Confidence 45679999999 88776 8898 89999999 999999999999999999999999999999999999
Q ss_pred hccChHHHHHHHH
Q psy10073 123 GAYQKEKLQFHVK 135 (144)
Q Consensus 123 ~f~~~~~l~~H~~ 135 (144)
.|+...++.+||.
T Consensus 959 RFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 959 RFSHSGSYSQHMN 971 (1007)
T ss_pred hcccccchHhhhc
Confidence 9999999999985
No 9
>KOG3608|consensus
Probab=99.57 E-value=6e-16 Score=106.40 Aligned_cols=116 Identities=19% Similarity=0.292 Sum_probs=73.4
Q ss_pred eecC--ccCCccCCccccccccCCCCCCccccCCCCCeeCCCCC-CCcch---hhhhhh-cccCCCCccc----------
Q psy10073 16 KTCL--YCNKYVPSDIDVFIGHCQTCPNMSFLNSVIPQSCKHCK-NFTSS---DVNLLM-EHSENCPCMV---------- 78 (144)
Q Consensus 16 ~~C~--~C~~~f~~~~~l~~H~c~~c~h~~~h~~~~~~~C~~C~-~f~~~---~~H~~~-~h~~~~~~~~---------- 78 (144)
+.|. .|-+.|.++..|++ |.++|++++...|+.|| -|.+. ..|+++ +-....+|.|
T Consensus 178 ~~C~W~~Ct~~~~~k~~Lre-------H~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTe 250 (467)
T KOG3608|consen 178 TMCNWAMCTKHMGNKYRLRE-------HIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATE 250 (467)
T ss_pred eeccchhhhhhhccHHHHHH-------HHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHH
Confidence 5554 47788888888888 77888888888888888 77666 556521 1122334444
Q ss_pred ---c--cCCCCCceeCCCCCcccCChhHHHHHHHh-hcCCcceeCCCcchhccChHHHHHHHHhhc
Q psy10073 79 ---R--PDPVKYKFICVACDYFTIISQNMRNHTLI-HLGDKQFKCCLCSYGAYQKEKLQFHVKNKH 138 (144)
Q Consensus 79 ---~--~~~~~~~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 138 (144)
+ +..-..-|+|+.|+......++|..|++. |..++||+|+.|++.|.+.++|.+|..+|+
T Consensus 251 klL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 251 KLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred HHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 0 00111226677776666666777777654 556667777777777777777777766665
No 10
>KOG3608|consensus
Probab=99.48 E-value=2.8e-14 Score=98.28 Aligned_cols=105 Identities=21% Similarity=0.346 Sum_probs=70.1
Q ss_pred eecCccCCccCCccccccccCCCCCCccccCCCCCeeCCCCC-CCcch---hhhhhhcccCCCCcccccCCCCCceeCCC
Q psy10073 16 KTCLYCNKYVPSDIDVFIGHCQTCPNMSFLNSVIPQSCKHCK-NFTSS---DVNLLMEHSENCPCMVRPDPVKYKFICVA 91 (144)
Q Consensus 16 ~~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~~~~~~~C~~C~-~f~~~---~~H~~~~h~~~~~~~~~~~~~~~~~~C~~ 91 (144)
|+|+.|+.+....++|.+|+ +-.|+..+||+|+.|+ .|... .+|. .+|+ +.. |.|..
T Consensus 264 ykCplCdmtc~~~ssL~~H~------r~rHs~dkpfKCd~Cd~~c~~esdL~kH~-~~HS-~~~-----------y~C~h 324 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHI------RYRHSKDKPFKCDECDTRCVRESDLAKHV-QVHS-KTV-----------YQCEH 324 (467)
T ss_pred ccccccccCCCChHHHHHHH------HhhhccCCCccccchhhhhccHHHHHHHH-Hhcc-ccc-----------eecCC
Confidence 55666666665555665522 2346667777777777 66555 6676 6665 334 77866
Q ss_pred --CCcccCChhHHHHHHHhhc-CC--cceeCCCcchhccChHHHHHHHHhhcC
Q psy10073 92 --CDYFTIISQNMRNHTLIHL-GD--KQFKCCLCSYGAYQKEKLQFHVKNKHS 139 (144)
Q Consensus 92 --C~~~f~~~~~l~~H~~~h~-~~--~~~~C~~C~~~f~~~~~l~~H~~~h~~ 139 (144)
|..+|.+...+++|++.+. |. .+|.|-.|++.|++..+|..|+...++
T Consensus 325 ~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~ 377 (467)
T KOG3608|consen 325 PDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHG 377 (467)
T ss_pred CCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhc
Confidence 8888888888888865533 43 348888888888888888888765554
No 11
>PHA00733 hypothetical protein
Probab=99.33 E-value=1e-12 Score=80.43 Aligned_cols=81 Identities=19% Similarity=0.245 Sum_probs=63.8
Q ss_pred CCCCeeCCCCC-CCcch---hhh--h--hhcccCCCCcccccCCCCCceeCCCCCcccCChhHHHHHHHhhcCCcceeCC
Q psy10073 47 SVIPQSCKHCK-NFTSS---DVN--L--LMEHSENCPCMVRPDPVKYKFICVACDYFTIISQNMRNHTLIHLGDKQFKCC 118 (144)
Q Consensus 47 ~~~~~~C~~C~-~f~~~---~~H--~--~~~h~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~ 118 (144)
..+++.|.+|+ .|... ..+ + ...+.+++| |.|+.|++.|.+...|..|++.+ +.+|.|.
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kP-----------y~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~ 103 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSP-----------YVCPLCLMPFSSSVSLKQHIRYT--EHSKVCP 103 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCC-----------ccCCCCCCcCCCHHHHHHHHhcC--CcCccCC
Confidence 45678899998 77666 222 1 012233566 99999999999999999999876 3579999
Q ss_pred CcchhccChHHHHHHHHhhcCC
Q psy10073 119 LCSYGAYQKEKLQFHVKNKHST 140 (144)
Q Consensus 119 ~C~~~f~~~~~l~~H~~~h~~~ 140 (144)
.|++.|.....|..|+...++.
T Consensus 104 ~CgK~F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 104 VCGKEFRNTDSTLDHVCKKHNI 125 (128)
T ss_pred CCCCccCCHHHHHHHHHHhcCc
Confidence 9999999999999999887763
No 12
>PHA02768 hypothetical protein; Provisional
Probab=99.28 E-value=1.3e-12 Score=67.12 Aligned_cols=43 Identities=19% Similarity=0.291 Sum_probs=40.3
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhccChHHHH
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAYQKEKLQ 131 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~ 131 (144)
|.|++||+.|...++|..|+++|+ ++|+|..|++.|...+.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 899999999999999999999998 7999999999999887764
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.25 E-value=1.1e-11 Score=91.76 Aligned_cols=99 Identities=16% Similarity=0.303 Sum_probs=76.2
Q ss_pred CceecCccCCccCCccccccccCCCCCCccccCCCCCeeCCCCC-CCcch--hhhhhhcccCCCCcccccCCCCCceeCC
Q psy10073 14 TKKTCLYCNKYVPSDIDVFIGHCQTCPNMSFLNSVIPQSCKHCK-NFTSS--DVNLLMEHSENCPCMVRPDPVKYKFICV 90 (144)
Q Consensus 14 ~~~~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~~~~~~~C~~C~-~f~~~--~~H~~~~h~~~~~~~~~~~~~~~~~~C~ 90 (144)
+.+.|+.|++.|. ..+|.. |+.++. .++.|+ || .+... ..|+ .+|.+.++ +.|.
T Consensus 452 ~H~~C~~Cgk~f~-~s~Lek-------H~~~~H--kpv~Cp-Cg~~~~R~~L~~H~-~thCp~Kp-----------i~C~ 508 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEK-------HMKVFH--EPLQCP-CGVVLEKEQMVQHQ-ASTCPLRL-----------ITCR 508 (567)
T ss_pred cCccCCCCCCccc-hHHHHH-------HHHhcC--CCccCC-CCCCcchhHHHhhh-hccCCCCc-----------eeCC
Confidence 3467888888775 466777 666663 789999 99 76555 7888 88888888 9999
Q ss_pred CCCcccCC----------hhHHHHHHHhhcCCcceeCCCcchhccChHHHHHHHHhh
Q psy10073 91 ACDYFTII----------SQNMRNHTLIHLGDKQFKCCLCSYGAYQKEKLQFHVKNK 137 (144)
Q Consensus 91 ~C~~~f~~----------~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 137 (144)
.|++.|.. ...|..|.... |.+++.|..||+.+..+ .+..|+..-
T Consensus 509 fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~~ 563 (567)
T PLN03086 509 FCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIAV 563 (567)
T ss_pred CCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHHh
Confidence 99998852 35788998885 78999999999887655 667786543
No 14
>PHA00733 hypothetical protein
Probab=99.12 E-value=5.8e-11 Score=72.75 Aligned_cols=86 Identities=13% Similarity=0.134 Sum_probs=65.7
Q ss_pred CCCCCceecCccCCccCCccccccccCCCCCCccccCCCCCeeCCCCC-CCcch---hhhhhhcccCCCCcccccCCCCC
Q psy10073 10 VPLSTKKTCLYCNKYVPSDIDVFIGHCQTCPNMSFLNSVIPQSCKHCK-NFTSS---DVNLLMEHSENCPCMVRPDPVKY 85 (144)
Q Consensus 10 ~~~~~~~~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~~~~~~~C~~C~-~f~~~---~~H~~~~h~~~~~~~~~~~~~~~ 85 (144)
.+..+.+.|.+|+..|.....|..+. ....++.. .+.+||.|+.|| .|... ..|+ +.+ +.+
T Consensus 35 ~~~~~~~~~~~~~~~~~~~~~l~~~~-~l~~~~~~-~~~kPy~C~~Cgk~Fss~s~L~~H~-r~h--~~~---------- 99 (128)
T PHA00733 35 TPEQKRLIRAVVKTLIYNPQLLDESS-YLYKLLTS-KAVSPYVCPLCLMPFSSSVSLKQHI-RYT--EHS---------- 99 (128)
T ss_pred ChhhhhHHHHHHhhhccChhhhcchH-HHHhhccc-CCCCCccCCCCCCcCCCHHHHHHHH-hcC--CcC----------
Confidence 55577899999999999887777630 00002333 458899999999 99988 7788 655 346
Q ss_pred ceeCCCCCcccCChhHHHHHHHhhcC
Q psy10073 86 KFICVACDYFTIISQNMRNHTLIHLG 111 (144)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 111 (144)
|.|+.|++.|.....|..|+...++
T Consensus 100 -~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 100 -KVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred -ccCCCCCCccCCHHHHHHHHHHhcC
Confidence 9999999999999999999876543
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.09 E-value=2.8e-10 Score=84.41 Aligned_cols=111 Identities=16% Similarity=0.372 Sum_probs=83.7
Q ss_pred ceecCccCCccCCccccccc---------cCCC--CCC-ccccCCCCCeeCCCCC-CCcch--hhhhhhcccCCCCcccc
Q psy10073 15 KKTCLYCNKYVPSDIDVFIG---------HCQT--CPN-MSFLNSVIPQSCKHCK-NFTSS--DVNLLMEHSENCPCMVR 79 (144)
Q Consensus 15 ~~~C~~C~~~f~~~~~l~~H---------~c~~--c~h-~~~h~~~~~~~C~~C~-~f~~~--~~H~~~~h~~~~~~~~~ 79 (144)
.-.|+.|...... .+|..| .|.. ||. .+....+..+.|+.|+ .|... ..|+ .+++ ++
T Consensus 407 ~V~C~NC~~~i~l-~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~~s~LekH~-~~~H--kp---- 478 (567)
T PLN03086 407 TVECRNCKHYIPS-RSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQQGEMEKHM-KVFH--EP---- 478 (567)
T ss_pred eEECCCCCCccch-hHHHHHHhhCCCcceeCCcccccceeeccccccCccCCCCCCccchHHHHHHH-HhcC--CC----
Confidence 3578888877665 456676 2331 553 2334456678999999 88755 8899 7764 67
Q ss_pred cCCCCCceeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhcc----------ChHHHHHHHHhhcCCCCC
Q psy10073 80 PDPVKYKFICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAY----------QKEKLQFHVKNKHSTKVK 143 (144)
Q Consensus 80 ~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~----------~~~~l~~H~~~h~~~kp~ 143 (144)
+.|+ |++.+ ....|..|+.+|...+++.|..|++.|. ..+.|..|..+. |.+++
T Consensus 479 -------v~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~ 542 (567)
T PLN03086 479 -------LQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTA 542 (567)
T ss_pred -------ccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcce
Confidence 9999 99765 6689999999999999999999999985 245899998885 66665
No 16
>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=99.05 E-value=1.2e-10 Score=51.42 Aligned_cols=26 Identities=35% Similarity=0.700 Sum_probs=23.2
Q ss_pred HHHHHHHhhcCCcceeCCCcchhccC
Q psy10073 101 NMRNHTLIHLGDKQFKCCLCSYGAYQ 126 (144)
Q Consensus 101 ~l~~H~~~h~~~~~~~C~~C~~~f~~ 126 (144)
+|..|+++|++++||.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47899999999999999999999864
No 17
>PHA00616 hypothetical protein
Probab=98.88 E-value=1.3e-09 Score=53.45 Aligned_cols=34 Identities=12% Similarity=0.220 Sum_probs=24.6
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCc
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLC 120 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C 120 (144)
|+|+.||+.|...+.|..|++.|++++++.|+.-
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~ 35 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEYF 35 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCccceeEE
Confidence 6777777777777777777777777777776643
No 18
>PHA02768 hypothetical protein; Provisional
Probab=98.77 E-value=1.2e-09 Score=56.25 Aligned_cols=39 Identities=13% Similarity=0.193 Sum_probs=29.8
Q ss_pred ceecCccCCccCCccccccccCCCCCCccccCCCCCeeCCCCC-CCcch
Q psy10073 15 KKTCLYCNKYVPSDIDVFIGHCQTCPNMSFLNSVIPQSCKHCK-NFTSS 62 (144)
Q Consensus 15 ~~~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~~~~~~~C~~C~-~f~~~ 62 (144)
.|.|+.||+.|...++|.. |+++|. ++|+|..|+ .|...
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~-------H~r~H~--k~~kc~~C~k~f~~~ 44 (55)
T PHA02768 5 GYECPICGEIYIKRKSMIT-------HLRKHN--TNLKLSNCKRISLRT 44 (55)
T ss_pred ccCcchhCCeeccHHHHHH-------HHHhcC--CcccCCcccceeccc
Confidence 4788888888888888888 777777 577888888 66543
No 19
>PHA00616 hypothetical protein
Probab=98.75 E-value=3e-09 Score=52.19 Aligned_cols=30 Identities=17% Similarity=0.266 Sum_probs=28.5
Q ss_pred ceeCCCcchhccChHHHHHHHHhhcCCCCC
Q psy10073 114 QFKCCLCSYGAYQKEKLQFHVKNKHSTKVK 143 (144)
Q Consensus 114 ~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~ 143 (144)
||+|+.||+.|.+.++|.+|++.|+|++|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~ 30 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKL 30 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcc
Confidence 689999999999999999999999999886
No 20
>PHA00732 hypothetical protein
Probab=98.67 E-value=1.7e-08 Score=56.57 Aligned_cols=46 Identities=24% Similarity=0.483 Sum_probs=37.0
Q ss_pred eeCCCCCcccCChhHHHHHHHh-hcCCcceeCCCcchhccChHHHHHHHHhhc
Q psy10073 87 FICVACDYFTIISQNMRNHTLI-HLGDKQFKCCLCSYGAYQKEKLQFHVKNKH 138 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 138 (144)
|.|+.|++.|.+...|..|++. |. ++.|+.|++.|. .|..|..++.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccC
Confidence 8899999999999999999874 55 357999999997 4777776544
No 21
>KOG3993|consensus
Probab=98.58 E-value=1.2e-08 Score=72.41 Aligned_cols=26 Identities=19% Similarity=0.339 Sum_probs=23.3
Q ss_pred ceeCCCcchhccChHHHHHHHHhhcC
Q psy10073 114 QFKCCLCSYGAYQKEKLQFHVKNKHS 139 (144)
Q Consensus 114 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 139 (144)
-|.|..|++.|.....|+.|+.+|+.
T Consensus 356 i~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 356 IFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred eeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 48999999999999999999888764
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=98.47 E-value=4e-07 Score=47.42 Aligned_cols=50 Identities=24% Similarity=0.481 Sum_probs=39.6
Q ss_pred eeCCCCCcccCChhHHHHHHHh-hcCC-cceeCCCcchhccChHHHHHHHHhhcC
Q psy10073 87 FICVACDYFTIISQNMRNHTLI-HLGD-KQFKCCLCSYGAYQKEKLQFHVKNKHS 139 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~-h~~~-~~~~C~~C~~~f~~~~~l~~H~~~h~~ 139 (144)
|.||+|++ ..+...|..|... |..+ +.+.|++|...+. .+|..|+..+++
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 89999999 5567889999765 5443 4699999998655 489999988764
No 23
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.46 E-value=1.4e-07 Score=40.33 Aligned_cols=23 Identities=26% Similarity=0.629 Sum_probs=14.5
Q ss_pred eeCCCcchhccChHHHHHHHHhh
Q psy10073 115 FKCCLCSYGAYQKEKLQFHVKNK 137 (144)
Q Consensus 115 ~~C~~C~~~f~~~~~l~~H~~~h 137 (144)
|.|+.|++.|.+.+.|.+|+++|
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 45666666666666666666553
No 24
>KOG3993|consensus
Probab=98.40 E-value=8.5e-08 Score=68.19 Aligned_cols=86 Identities=19% Similarity=0.314 Sum_probs=54.5
Q ss_pred eecCccCCccCCccccccccCCCCCCccccCCCCCeeCCCCC-CCcch---hhhhhhcccC--------CCCccc-----
Q psy10073 16 KTCLYCNKYVPSDIDVFIGHCQTCPNMSFLNSVIPQSCKHCK-NFTSS---DVNLLMEHSE--------NCPCMV----- 78 (144)
Q Consensus 16 ~~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~~~~~~~C~~C~-~f~~~---~~H~~~~h~~--------~~~~~~----- 78 (144)
|.|..|...|...-.|.+|.|.. .....|+|++|+ .|.-. ..|. +.|.. ..|-+-
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~R-------IV~vEYrCPEC~KVFsCPANLASHR-RWHKPR~eaa~a~~~P~k~~~~~r 339 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPR-------IVHVEYRCPECDKVFSCPANLASHR-RWHKPRPEAAKAGSPPPKQAVETR 339 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCe-------eEEeeecCCcccccccCchhhhhhh-cccCCchhhhhcCCCChhhhhhhh
Confidence 77888888888888888865431 112347788888 77766 5666 55532 111110
Q ss_pred ---------ccCCCCCceeCCCCCcccCChhHHHHHHHhh
Q psy10073 79 ---------RPDPVKYKFICVACDYFTIISQNMRNHTLIH 109 (144)
Q Consensus 79 ---------~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 109 (144)
-..+.+..|.|.+|++.|.+..-|+.|+.+|
T Consensus 340 ae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlth 379 (500)
T KOG3993|consen 340 AEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTH 379 (500)
T ss_pred hhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhh
Confidence 0113445688888888888888888886654
No 25
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.31 E-value=3.3e-07 Score=40.31 Aligned_cols=22 Identities=18% Similarity=0.392 Sum_probs=13.1
Q ss_pred hhhhhcccCCCCcccccCCCCCceeCCCCCcccC
Q psy10073 64 VNLLMEHSENCPCMVRPDPVKYKFICVACDYFTI 97 (144)
Q Consensus 64 ~H~~~~h~~~~~~~~~~~~~~~~~~C~~C~~~f~ 97 (144)
.|+ ++|++++| |.|++|++.|.
T Consensus 4 ~H~-~~H~~~k~-----------~~C~~C~k~F~ 25 (26)
T PF13465_consen 4 RHM-RTHTGEKP-----------YKCPYCGKSFS 25 (26)
T ss_dssp HHH-HHHSSSSS-----------EEESSSSEEES
T ss_pred HHh-hhcCCCCC-----------CCCCCCcCeeC
Confidence 455 55666666 66666666554
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=98.31 E-value=4.9e-07 Score=38.53 Aligned_cols=23 Identities=22% Similarity=0.428 Sum_probs=21.3
Q ss_pred eeCCCCCcccCChhHHHHHHHhh
Q psy10073 87 FICVACDYFTIISQNMRNHTLIH 109 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h 109 (144)
|.|+.|++.|.+...|..|++.|
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 68999999999999999999874
No 27
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.26 E-value=9.7e-07 Score=37.81 Aligned_cols=24 Identities=29% Similarity=0.707 Sum_probs=14.2
Q ss_pred eeCCCcchhccChHHHHHHHHhhc
Q psy10073 115 FKCCLCSYGAYQKEKLQFHVKNKH 138 (144)
Q Consensus 115 ~~C~~C~~~f~~~~~l~~H~~~h~ 138 (144)
|.|++|++.|.+...|..|+.+|+
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 456666666666666666666553
No 28
>PHA00732 hypothetical protein
Probab=98.22 E-value=5.7e-07 Score=50.40 Aligned_cols=46 Identities=9% Similarity=0.183 Sum_probs=34.8
Q ss_pred ceecCccCCccCCccccccccCCCCCCccc-cCCCCCeeCCCCC-CCcchhhhhhhccc
Q psy10073 15 KKTCLYCNKYVPSDIDVFIGHCQTCPNMSF-LNSVIPQSCKHCK-NFTSSDVNLLMEHS 71 (144)
Q Consensus 15 ~~~C~~C~~~f~~~~~l~~H~c~~c~h~~~-h~~~~~~~C~~C~-~f~~~~~H~~~~h~ 71 (144)
+|.|+.||+.|.+..+|.. |++. |. ++.|+.|| .|.....|+ .+..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~-------H~r~~H~---~~~C~~CgKsF~~l~~H~-~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQ-------HARRNHT---LTKCPVCNKSYRRLNQHF-YSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHH-------HhhcccC---CCccCCCCCEeCChhhhh-cccC
Confidence 4789999999999999998 6663 54 35799999 887667777 5543
No 29
>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=98.19 E-value=1e-06 Score=39.09 Aligned_cols=25 Identities=20% Similarity=0.331 Sum_probs=15.4
Q ss_pred ceeCCCcchhccChHHHHHHHHhhc
Q psy10073 114 QFKCCLCSYGAYQKEKLQFHVKNKH 138 (144)
Q Consensus 114 ~~~C~~C~~~f~~~~~l~~H~~~h~ 138 (144)
||.|..|++.|.+...|..|++.|.
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 4566666666666666666665554
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.09 E-value=3.4e-06 Score=49.34 Aligned_cols=24 Identities=33% Similarity=0.649 Sum_probs=19.6
Q ss_pred ceeCCCcchhccChHHHHHHHHhh
Q psy10073 114 QFKCCLCSYGAYQKEKLQFHVKNK 137 (144)
Q Consensus 114 ~~~C~~C~~~f~~~~~l~~H~~~h 137 (144)
.+.|..|++.|.+...|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 688999999999999999998864
No 31
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.05 E-value=6.5e-06 Score=42.82 Aligned_cols=46 Identities=22% Similarity=0.364 Sum_probs=24.1
Q ss_pred eeCCCCC-CCcch--hhhhhhcccCC-CCcccccCCCCCceeCCCCCcccCChhHHHHHHHhh
Q psy10073 51 QSCKHCK-NFTSS--DVNLLMEHSEN-CPCMVRPDPVKYKFICVACDYFTIISQNMRNHTLIH 109 (144)
Q Consensus 51 ~~C~~C~-~f~~~--~~H~~~~h~~~-~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 109 (144)
|.|+.|+ .|... ..|....|..+ +. +.|++|...+. .+|..|+..+
T Consensus 3 f~CP~C~~~~~~~~L~~H~~~~H~~~~~~-----------v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 3 FTCPYCGKGFSESSLVEHCEDEHRSESKN-----------VVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred cCCCCCCCccCHHHHHHHHHhHCcCCCCC-----------ccCCCchhhhh--hHHHHHHHHh
Confidence 5566666 55444 55553334332 22 66666665433 3666666544
No 32
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.01 E-value=6.4e-06 Score=35.14 Aligned_cols=23 Identities=26% Similarity=0.469 Sum_probs=19.4
Q ss_pred eeCCCCCcccCChhHHHHHHHhh
Q psy10073 87 FICVACDYFTIISQNMRNHTLIH 109 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h 109 (144)
|.|++|++.|.+...|..|+..+
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 68999999999999999999876
No 33
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.99 E-value=9.3e-06 Score=40.81 Aligned_cols=33 Identities=21% Similarity=0.360 Sum_probs=21.9
Q ss_pred cCCcceeCCCcchhccChHHHHHHHHhhcCCCC
Q psy10073 110 LGDKQFKCCLCSYGAYQKEKLQFHVKNKHSTKV 142 (144)
Q Consensus 110 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~kp 142 (144)
..+.|-.|++|+..+.+..+|.+|+.+.++.||
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 346678888888888888888888888888776
No 34
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.89 E-value=8.5e-06 Score=36.02 Aligned_cols=25 Identities=24% Similarity=0.356 Sum_probs=22.8
Q ss_pred ceeCCCCCcccCChhHHHHHHHhhc
Q psy10073 86 KFICVACDYFTIISQNMRNHTLIHL 110 (144)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~H~~~h~ 110 (144)
+|.|..|++.|.+...|..|++.|.
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 3899999999999999999998775
No 35
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.78 E-value=7.2e-06 Score=56.72 Aligned_cols=52 Identities=23% Similarity=0.471 Sum_probs=43.5
Q ss_pred CCceeCCC--CCcccCChhHHHHHHHh-h------------------cCCcceeCCCcchhccChHHHHHHHH
Q psy10073 84 KYKFICVA--CDYFTIISQNMRNHTLI-H------------------LGDKQFKCCLCSYGAYQKEKLQFHVK 135 (144)
Q Consensus 84 ~~~~~C~~--C~~~f~~~~~l~~H~~~-h------------------~~~~~~~C~~C~~~f~~~~~l~~H~~ 135 (144)
+++|+|++ |++.|.+...|.-|+.- | ...|||.|++|+|.+++...|+-|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 36799987 99999999999999753 2 12589999999999999999988864
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.76 E-value=2.9e-05 Score=33.55 Aligned_cols=24 Identities=21% Similarity=0.430 Sum_probs=14.7
Q ss_pred eeCCCcchhccChHHHHHHHHhhc
Q psy10073 115 FKCCLCSYGAYQKEKLQFHVKNKH 138 (144)
Q Consensus 115 ~~C~~C~~~f~~~~~l~~H~~~h~ 138 (144)
|.|..|++.|.+.+.|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 356666666666666666666543
No 37
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.59 E-value=6.8e-05 Score=32.09 Aligned_cols=23 Identities=43% Similarity=0.866 Sum_probs=13.6
Q ss_pred eeCCCcchhccChHHHHHHHHhhc
Q psy10073 115 FKCCLCSYGAYQKEKLQFHVKNKH 138 (144)
Q Consensus 115 ~~C~~C~~~f~~~~~l~~H~~~h~ 138 (144)
|+|+.|+.... ...|.+|+++++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 56666766665 666777766654
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.54 E-value=6e-05 Score=32.56 Aligned_cols=22 Identities=23% Similarity=0.594 Sum_probs=15.4
Q ss_pred eeCCCcchhccChHHHHHHHHh
Q psy10073 115 FKCCLCSYGAYQKEKLQFHVKN 136 (144)
Q Consensus 115 ~~C~~C~~~f~~~~~l~~H~~~ 136 (144)
|.|.+|++.|.+...|..|++.
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 5677777777777777777654
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.48 E-value=0.00012 Score=31.47 Aligned_cols=24 Identities=17% Similarity=0.425 Sum_probs=21.5
Q ss_pred eeCCCCCcccCChhHHHHHHHhhc
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHL 110 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~ 110 (144)
|.|+.|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998765
No 40
>PRK04860 hypothetical protein; Provisional
Probab=97.47 E-value=8e-05 Score=47.44 Aligned_cols=40 Identities=20% Similarity=0.512 Sum_probs=34.8
Q ss_pred CceeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhccChH
Q psy10073 85 YKFICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAYQKE 128 (144)
Q Consensus 85 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~ 128 (144)
.+|.|. |+. ....+++|.++|+++++|.|..|+..|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 469998 987 6778899999999999999999999887543
No 41
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.42 E-value=0.00025 Score=35.76 Aligned_cols=28 Identities=29% Similarity=0.344 Sum_probs=22.0
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcc
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQ 114 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 114 (144)
-.|++|+..+.+..+|++|+.+.++.+|
T Consensus 25 atCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 25 ATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCcchhhccchhhHHHHHHHHhcccC
Confidence 8999999999999999999988877765
No 42
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.35 E-value=8.5e-05 Score=51.58 Aligned_cols=23 Identities=17% Similarity=0.300 Sum_probs=19.2
Q ss_pred CceeCCCCCcccCChhHHHHHHH
Q psy10073 85 YKFICVACDYFTIISQNMRNHTL 107 (144)
Q Consensus 85 ~~~~C~~C~~~f~~~~~l~~H~~ 107 (144)
+||+|++|++.|.....|.-|+.
T Consensus 397 KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 397 KPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceeccccchhhccCccceeccc
Confidence 33999999999999988887753
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.24 E-value=0.00023 Score=30.67 Aligned_cols=23 Identities=22% Similarity=0.413 Sum_probs=20.7
Q ss_pred eeCCCCCcccCChhHHHHHHHhh
Q psy10073 87 FICVACDYFTIISQNMRNHTLIH 109 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h 109 (144)
|.|.+|++.|.+...|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 68999999999999999998754
No 44
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.22 E-value=0.00033 Score=40.76 Aligned_cols=69 Identities=20% Similarity=0.307 Sum_probs=21.4
Q ss_pred ecCccCCccCCccccccccCCCCCCccc-cCCCCCeeCCCCCCCcch---hhhhhhcccCCCCcccccCCCCCceeCCCC
Q psy10073 17 TCLYCNKYVPSDIDVFIGHCQTCPNMSF-LNSVIPQSCKHCKNFTSS---DVNLLMEHSENCPCMVRPDPVKYKFICVAC 92 (144)
Q Consensus 17 ~C~~C~~~f~~~~~l~~H~c~~c~h~~~-h~~~~~~~C~~C~~f~~~---~~H~~~~h~~~~~~~~~~~~~~~~~~C~~C 92 (144)
.|..|+..|.+...|.. |+.. |.-..+ ....+... ...+ ..-.. .. +.|..|
T Consensus 1 ~C~~C~~~f~~~~~l~~-------H~~~~H~~~~~----~~~~l~~~~~~~~~~-~~~~~-~~-----------~~C~~C 56 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQ-------HMKKKHGFDIP----DQKYLVDPNRLLNYL-RKKVK-ES-----------FRCPYC 56 (100)
T ss_dssp -------------------------------------------------------------SS-----------EEBSSS
T ss_pred Ccccccccccccccccc-------ccccccccccc----ccccccccccccccc-ccccC-CC-----------CCCCcc
Confidence 48899999999999999 5543 332221 11111111 2222 11111 13 999999
Q ss_pred CcccCChhHHHHHHHhh
Q psy10073 93 DYFTIISQNMRNHTLIH 109 (144)
Q Consensus 93 ~~~f~~~~~l~~H~~~h 109 (144)
++.|.+...|..|++.+
T Consensus 57 ~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 57 NKTFRSREALQEHMRSK 73 (100)
T ss_dssp S-EESSHHHHHHHHHHT
T ss_pred CCCCcCHHHHHHHHcCc
Confidence 99999999999999874
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.11 E-value=0.00055 Score=29.17 Aligned_cols=23 Identities=30% Similarity=0.635 Sum_probs=18.3
Q ss_pred eeCCCCCcccCChhHHHHHHHhhc
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHL 110 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~ 110 (144)
|.|+.|+.... ...|.+|++.+.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 68999999888 889999998764
No 46
>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=97.03 E-value=0.00013 Score=32.22 Aligned_cols=20 Identities=30% Similarity=0.732 Sum_probs=10.1
Q ss_pred eeCCCCCcccCChhHHHHHH
Q psy10073 87 FICVACDYFTIISQNMRNHT 106 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~ 106 (144)
|.|..|++.|.+...|..|+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHM 21 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCT
T ss_pred CCcccCCCCcCCHHHHHHHH
Confidence 44555555555555555444
No 47
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.86 E-value=0.0004 Score=30.55 Aligned_cols=23 Identities=30% Similarity=0.505 Sum_probs=19.5
Q ss_pred ceeCCCcchhccChHHHHHHHHh
Q psy10073 114 QFKCCLCSYGAYQKEKLQFHVKN 136 (144)
Q Consensus 114 ~~~C~~C~~~f~~~~~l~~H~~~ 136 (144)
.|.|..|++.|.+...|..|++.
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCCcccCCCCcCCHHHHHHHHcc
Confidence 05799999999999999998875
No 48
>PRK04860 hypothetical protein; Provisional
Probab=96.77 E-value=0.00047 Score=43.97 Aligned_cols=37 Identities=16% Similarity=0.373 Sum_probs=26.8
Q ss_pred CeeCCCCC-CCcchhhhhhhcccCCCCcccccCCCCCceeCCCCCcccCCh
Q psy10073 50 PQSCKHCK-NFTSSDVNLLMEHSENCPCMVRPDPVKYKFICVACDYFTIIS 99 (144)
Q Consensus 50 ~~~C~~C~-~f~~~~~H~~~~h~~~~~~~~~~~~~~~~~~C~~C~~~f~~~ 99 (144)
+|.|. |+ ...+..+|. ++|.++++ |.|..|+..|...
T Consensus 119 ~Y~C~-C~~~~~~~rrH~-ri~~g~~~-----------YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQEHQLTVRRHN-RVVRGEAV-----------YRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCCeeCHHHHHH-HHhcCCcc-----------EECCCCCceeEEe
Confidence 58887 87 433337787 88888887 8888888777654
No 49
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.29 E-value=0.004 Score=26.83 Aligned_cols=18 Identities=17% Similarity=0.359 Sum_probs=8.8
Q ss_pred eCCCCCcccCChhHHHHHH
Q psy10073 88 ICVACDYFTIISQNMRNHT 106 (144)
Q Consensus 88 ~C~~C~~~f~~~~~l~~H~ 106 (144)
.|+.||+.| ..+.|..|+
T Consensus 4 ~C~~CgR~F-~~~~l~~H~ 21 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHE 21 (25)
T ss_pred cCCCCCCEE-CHHHHHHHH
Confidence 455555555 344444443
No 50
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=96.01 E-value=0.0054 Score=28.50 Aligned_cols=22 Identities=27% Similarity=0.520 Sum_probs=15.3
Q ss_pred ceeCCCcchhccChHHHHHHHH
Q psy10073 114 QFKCCLCSYGAYQKEKLQFHVK 135 (144)
Q Consensus 114 ~~~C~~C~~~f~~~~~l~~H~~ 135 (144)
+|.|++|++.|.+...+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4667777777777777777764
No 51
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.84 E-value=0.0089 Score=27.72 Aligned_cols=23 Identities=17% Similarity=0.242 Sum_probs=20.4
Q ss_pred ceeCCCCCcccCChhHHHHHHHh
Q psy10073 86 KFICVACDYFTIISQNMRNHTLI 108 (144)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~H~~~ 108 (144)
+|.|+.|+..|.+...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 38999999999999999999754
No 52
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.71 E-value=0.0087 Score=43.60 Aligned_cols=119 Identities=18% Similarity=0.155 Sum_probs=75.4
Q ss_pred CceecCccCCccCCccccccccCCCCCCcc--ccCCC--CCeeCC--CCC-CCcch---hhhhhhcccCCCCccc-----
Q psy10073 14 TKKTCLYCNKYVPSDIDVFIGHCQTCPNMS--FLNSV--IPQSCK--HCK-NFTSS---DVNLLMEHSENCPCMV----- 78 (144)
Q Consensus 14 ~~~~C~~C~~~f~~~~~l~~H~c~~c~h~~--~h~~~--~~~~C~--~C~-~f~~~---~~H~~~~h~~~~~~~~----- 78 (144)
.++.|..|...|.....|.. |.+ .|.++ +++.|+ .|+ .|... ..|. ..|.+..++.+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~-------~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ 359 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTR-------HLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHI-LLHTSISPAKEKLLNS 359 (467)
T ss_pred cCCCCccccCCccccccccc-------cccccccccccCCceeeeccCCCccccccccccCCc-ccccCCCccccccccC
Confidence 46899999999999999999 777 79999 999999 799 88877 7777 77776655432
Q ss_pred -------------------ccCCCCCceeC--CCCCcccCChhHHHHHHHhhcCCc--ceeCCCcchhccChHHHHHHHH
Q psy10073 79 -------------------RPDPVKYKFIC--VACDYFTIISQNMRNHTLIHLGDK--QFKCCLCSYGAYQKEKLQFHVK 135 (144)
Q Consensus 79 -------------------~~~~~~~~~~C--~~C~~~f~~~~~l~~H~~~h~~~~--~~~C~~C~~~f~~~~~l~~H~~ 135 (144)
........+.+ ..|...+.....+..|...+.... .+.+..|.+.|.....+..|++
T Consensus 360 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 (467)
T COG5048 360 SSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKK 439 (467)
T ss_pred ccccccccCCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCccccccccc
Confidence 00011111222 113344444444445544444433 3455667777777666666666
Q ss_pred hhcCC
Q psy10073 136 NKHST 140 (144)
Q Consensus 136 ~h~~~ 140 (144)
.+...
T Consensus 440 ~~~~~ 444 (467)
T COG5048 440 IHTNH 444 (467)
T ss_pred ccccC
Confidence 65543
No 53
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.42 E-value=0.0029 Score=46.11 Aligned_cols=59 Identities=22% Similarity=0.295 Sum_probs=53.4
Q ss_pred CceeCCCCCcccCChhHHHHHHH--hhcCC--cceeCC--CcchhccChHHHHHHHHhhcCCCCC
Q psy10073 85 YKFICVACDYFTIISQNMRNHTL--IHLGD--KQFKCC--LCSYGAYQKEKLQFHVKNKHSTKVK 143 (144)
Q Consensus 85 ~~~~C~~C~~~f~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~~~kp~ 143 (144)
..+.|..|...|.....|..|.+ .|.++ +++.|+ .|++.|.....+..|..+|.+.++.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPA 352 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcc
Confidence 35899999999999999999999 89999 999999 7999999999999999999887653
No 54
>KOG2893|consensus
Probab=95.25 E-value=0.0049 Score=41.45 Aligned_cols=46 Identities=22% Similarity=0.410 Sum_probs=35.8
Q ss_pred eCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhccChHHHHHH-HHhh
Q psy10073 88 ICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAYQKEKLQFH-VKNK 137 (144)
Q Consensus 88 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H-~~~h 137 (144)
.|=+|++.|.+..-|.+|++ .+-|+|.+|.+..-+-..|..| +.+|
T Consensus 12 wcwycnrefddekiliqhqk----akhfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeeecccccchhhhhhhhhh----hccceeeeehhhhccCCCceeehhhhh
Confidence 57789999999988988876 4568999998887777777777 3343
No 55
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=94.98 E-value=0.017 Score=26.62 Aligned_cols=24 Identities=21% Similarity=0.713 Sum_probs=17.0
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcch
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSY 122 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 122 (144)
|.|..||..+.... .++.|++||.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 78888887765432 5778888874
No 56
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.69 E-value=0.025 Score=29.11 Aligned_cols=25 Identities=12% Similarity=0.126 Sum_probs=14.3
Q ss_pred CCCceeCCCCCcccCChhHHHHHHH
Q psy10073 83 VKYKFICVACDYFTIISQNMRNHTL 107 (144)
Q Consensus 83 ~~~~~~C~~C~~~f~~~~~l~~H~~ 107 (144)
++..+.|+.|+..|....++.+|..
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhh
Confidence 3444566666666666666666653
No 57
>KOG1146|consensus
Probab=94.15 E-value=0.032 Score=46.05 Aligned_cols=55 Identities=18% Similarity=0.455 Sum_probs=45.8
Q ss_pred CCCCceeCCCCCcccCChhHHHHHHHhh-------------------------cCCcceeCCCcchhccChHHHHHHHHh
Q psy10073 82 PVKYKFICVACDYFTIISQNMRNHTLIH-------------------------LGDKQFKCCLCSYGAYQKEKLQFHVKN 136 (144)
Q Consensus 82 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h-------------------------~~~~~~~C~~C~~~f~~~~~l~~H~~~ 136 (144)
.-.+.+.|+.|+..|.....|..|++.- .+.++|.|..|..+++.+.+|.+|+..
T Consensus 461 S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 461 SFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred cccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 3346699999999999999999999871 124579999999999999999999863
No 58
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.66 E-value=0.039 Score=28.37 Aligned_cols=31 Identities=19% Similarity=0.404 Sum_probs=24.9
Q ss_pred hcCCcceeCCCcchhccChHHHHHHHHhhcC
Q psy10073 109 HLGDKQFKCCLCSYGAYQKEKLQFHVKNKHS 139 (144)
Q Consensus 109 h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 139 (144)
-.||.-+.|+.|+..|....++.+|...-++
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 3567788999999999999999999765443
No 59
>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=93.32 E-value=0.051 Score=25.74 Aligned_cols=14 Identities=14% Similarity=0.185 Sum_probs=8.3
Q ss_pred eecCccCCccCCcc
Q psy10073 16 KTCLYCNKYVPSDI 29 (144)
Q Consensus 16 ~~C~~C~~~f~~~~ 29 (144)
+.|+.|+..|.-..
T Consensus 3 ~~CP~C~~~~~v~~ 16 (38)
T TIGR02098 3 IQCPNCKTSFRVVD 16 (38)
T ss_pred EECCCCCCEEEeCH
Confidence 45667776665443
No 60
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.29 E-value=0.16 Score=30.37 Aligned_cols=24 Identities=13% Similarity=0.285 Sum_probs=13.3
Q ss_pred ceeCCCcchhccChHHHHHHHHhh
Q psy10073 114 QFKCCLCSYGAYQKEKLQFHVKNK 137 (144)
Q Consensus 114 ~~~C~~C~~~f~~~~~l~~H~~~h 137 (144)
.|.|+.|...|-..-+.-.|...|
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred ceeCCCCCCccccccchhhhhhcc
Confidence 456666666665555555555444
No 61
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=93.24 E-value=0.081 Score=35.56 Aligned_cols=21 Identities=24% Similarity=0.191 Sum_probs=15.1
Q ss_pred CCceecCccCCccCCcccccc
Q psy10073 13 STKKTCLYCNKYVPSDIDVFI 33 (144)
Q Consensus 13 ~~~~~C~~C~~~f~~~~~l~~ 33 (144)
.+.+.|++|++.|.+..-...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~ 23 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSG 23 (214)
T ss_pred CCceECCCCCCeeeeeEEEcC
Confidence 356789999999988654443
No 62
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=93.22 E-value=0.079 Score=24.91 Aligned_cols=32 Identities=22% Similarity=0.349 Sum_probs=17.5
Q ss_pred eecCccCCccCCccccccccCCCCCCccccCCCCCeeCCCCC-CC
Q psy10073 16 KTCLYCNKYVPSDIDVFIGHCQTCPNMSFLNSVIPQSCKHCK-NF 59 (144)
Q Consensus 16 ~~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~~~~~~~C~~C~-~f 59 (144)
..|+.|+..|.-..+... ......+|+.|+ .|
T Consensus 3 i~Cp~C~~~y~i~d~~ip------------~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIP------------PKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCC------------CCCcEEECCCCCCEe
Confidence 356777766655443222 233456677776 55
No 63
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.19 E-value=0.11 Score=24.56 Aligned_cols=34 Identities=15% Similarity=0.398 Sum_probs=24.1
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhcc
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAY 125 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 125 (144)
..|+.|+..|.-...- +-.+....+|+.|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~-----l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-----LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH-----cccCCcEEECCCCCcEee
Confidence 6789999888776542 223455788999987774
No 64
>KOG2186|consensus
Probab=93.11 E-value=0.052 Score=36.92 Aligned_cols=45 Identities=18% Similarity=0.368 Sum_probs=31.3
Q ss_pred eeCCCCC-CCcch--hhhhhhcccCCCCcccccCCCCCceeCCCCCcccCChhHHHHHHHhh
Q psy10073 51 QSCKHCK-NFTSS--DVNLLMEHSENCPCMVRPDPVKYKFICVACDYFTIISQNMRNHTLIH 109 (144)
Q Consensus 51 ~~C~~C~-~f~~~--~~H~~~~h~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 109 (144)
|.|..|| ...-+ .+|+ ..-++. - |.|..|++.|.. .++..|...-
T Consensus 4 FtCnvCgEsvKKp~vekH~-srCrn~-~-----------fSCIDC~k~F~~-~sYknH~kCI 51 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQVEKHM-SRCRNA-Y-----------FSCIDCGKTFER-VSYKNHTKCI 51 (276)
T ss_pred EehhhhhhhccccchHHHH-HhccCC-e-----------eEEeeccccccc-chhhhhhhhc
Confidence 6788888 76666 6677 555552 2 888888888877 6677776543
No 65
>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=92.91 E-value=0.067 Score=26.07 Aligned_cols=13 Identities=15% Similarity=0.342 Sum_probs=8.9
Q ss_pred ceecCccCCccCC
Q psy10073 15 KKTCLYCNKYVPS 27 (144)
Q Consensus 15 ~~~C~~C~~~f~~ 27 (144)
.|.|..||..|..
T Consensus 5 ey~C~~Cg~~fe~ 17 (42)
T PF09723_consen 5 EYRCEECGHEFEV 17 (42)
T ss_pred EEEeCCCCCEEEE
Confidence 3777777777754
No 66
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=92.49 E-value=0.086 Score=25.28 Aligned_cols=13 Identities=15% Similarity=0.360 Sum_probs=9.0
Q ss_pred ceecCccCCccCC
Q psy10073 15 KKTCLYCNKYVPS 27 (144)
Q Consensus 15 ~~~C~~C~~~f~~ 27 (144)
.|+|..||..|..
T Consensus 5 ~y~C~~Cg~~fe~ 17 (41)
T smart00834 5 EYRCEDCGHTFEV 17 (41)
T ss_pred EEEcCCCCCEEEE
Confidence 4677778777753
No 67
>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=92.47 E-value=0.041 Score=37.61 Aligned_cols=89 Identities=15% Similarity=0.228 Sum_probs=49.8
Q ss_pred cccCCCCCeeCCCCCCCcch---hhhhhhcc--cCCCCcccccCCCCCceeCCCCCcccCChhHHHHHHHh----hcCCc
Q psy10073 43 SFLNSVIPQSCKHCKNFTSS---DVNLLMEH--SENCPCMVRPDPVKYKFICVACDYFTIISQNMRNHTLI----HLGDK 113 (144)
Q Consensus 43 ~~h~~~~~~~C~~C~~f~~~---~~H~~~~h--~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~----h~~~~ 113 (144)
....|.+.|+|..|..|.-. -.|+ ..- .....|+|..-+....|.|..|.-.|-. .|++. -...+
T Consensus 135 vw~hGGrif~CsfC~~flCEDDQFEHQ-AsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCd-----dHvrrKg~ky~k~k 208 (314)
T PF06524_consen 135 VWDHGGRIFKCSFCDNFLCEDDQFEHQ-ASCQVLESETFKCQSCNRLGQYSCLRCKICFCD-----DHVRRKGFKYEKGK 208 (314)
T ss_pred cccCCCeEEEeecCCCeeeccchhhhh-hhhhhhhcccccccccccccchhhhheeeeehh-----hhhhhcccccccCC
Confidence 34467788999999844443 5565 321 1223444444344444555555555533 34433 12347
Q ss_pred ceeCCCcchhccChHHHHHHHHhh
Q psy10073 114 QFKCCLCSYGAYQKEKLQFHVKNK 137 (144)
Q Consensus 114 ~~~C~~C~~~f~~~~~l~~H~~~h 137 (144)
++.|+.||........|..-.++|
T Consensus 209 ~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 209 PIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCcccccccceeeeecc
Confidence 889999998777666665444433
No 68
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=92.43 E-value=0.21 Score=26.13 Aligned_cols=8 Identities=25% Similarity=0.821 Sum_probs=5.2
Q ss_pred CeeCCCCC
Q psy10073 50 PQSCKHCK 57 (144)
Q Consensus 50 ~~~C~~C~ 57 (144)
.|.|+.||
T Consensus 27 ~F~CPnCG 34 (61)
T COG2888 27 KFPCPNCG 34 (61)
T ss_pred EeeCCCCC
Confidence 46666666
No 69
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=92.43 E-value=0.034 Score=37.35 Aligned_cols=13 Identities=31% Similarity=0.999 Sum_probs=9.3
Q ss_pred eeCCCcchhccCh
Q psy10073 115 FKCCLCSYGAYQK 127 (144)
Q Consensus 115 ~~C~~C~~~f~~~ 127 (144)
..|+.||.+|...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 5788888776643
No 70
>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=91.61 E-value=0.12 Score=26.26 Aligned_cols=13 Identities=15% Similarity=0.416 Sum_probs=9.6
Q ss_pred ceecCccCCccCC
Q psy10073 15 KKTCLYCNKYVPS 27 (144)
Q Consensus 15 ~~~C~~C~~~f~~ 27 (144)
.|+|..||..|..
T Consensus 5 ey~C~~Cg~~fe~ 17 (52)
T TIGR02605 5 EYRCTACGHRFEV 17 (52)
T ss_pred EEEeCCCCCEeEE
Confidence 4788888887764
No 71
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=91.43 E-value=0.14 Score=23.70 Aligned_cols=24 Identities=25% Similarity=0.721 Sum_probs=16.2
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcch
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSY 122 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 122 (144)
|.|..||..+... +.|..|++||.
T Consensus 3 ~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred EECCCCCCEeECC------------cCCCcCcCCCC
Confidence 7888888765432 24568888875
No 72
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=91.19 E-value=0.15 Score=32.54 Aligned_cols=31 Identities=23% Similarity=0.302 Sum_probs=25.2
Q ss_pred ceeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhcc
Q psy10073 86 KFICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAY 125 (144)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 125 (144)
-|.|+.|+..|+....+. .-|.|+.||....
T Consensus 109 ~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred eEECCCCCcEeeHHHHHH---------cCCcCCCCCCEee
Confidence 399999999998888874 3699999997543
No 73
>KOG1146|consensus
Probab=91.12 E-value=0.15 Score=42.37 Aligned_cols=104 Identities=13% Similarity=0.101 Sum_probs=72.4
Q ss_pred ceecCccCCccCCccccccccCCCCCCcccc--CCCCCeeCCCCC-CCcch--hhhhhhcccCCCCcccccCCCCCceeC
Q psy10073 15 KKTCLYCNKYVPSDIDVFIGHCQTCPNMSFL--NSVIPQSCKHCK-NFTSS--DVNLLMEHSENCPCMVRPDPVKYKFIC 89 (144)
Q Consensus 15 ~~~C~~C~~~f~~~~~l~~H~c~~c~h~~~h--~~~~~~~C~~C~-~f~~~--~~H~~~~h~~~~~~~~~~~~~~~~~~C 89 (144)
...|..|...|.....+..+- -...+ .....+.|..|+ .|... ..++ ....+ |.|
T Consensus 1228 gl~~~~~e~~f~~~~~~~~~a-----~~~~~~~~~sGe~~c~~~~~~~~~~~~~~~l----~~~~~-----------~~~ 1287 (1406)
T KOG1146|consen 1228 GLLPNALEQPFPQEPEPTATA-----PPKPPELPASGEGECGAVDELLTPSFGISTL----DVTHR-----------YLC 1287 (1406)
T ss_pred cccHHhhhcCccCcccccccC-----CCCCCcCcCCCcchhhhccccccCccceeec----ccchh-----------HHH
Confidence 367888888888887776621 11111 122347899998 77666 3354 22334 899
Q ss_pred CCCCcccCChhHHHHHHHhh-----------------cCCcceeCCCcchhccChHHHHHHHHhhcC
Q psy10073 90 VACDYFTIISQNMRNHTLIH-----------------LGDKQFKCCLCSYGAYQKEKLQFHVKNKHS 139 (144)
Q Consensus 90 ~~C~~~f~~~~~l~~H~~~h-----------------~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 139 (144)
..|...|.....|..|.+.- ..-..| |..|...|.....|..|+++-++
T Consensus 1288 ~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~~~ 1353 (1406)
T KOG1146|consen 1288 RQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSSAH 1353 (1406)
T ss_pred HHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHhhh
Confidence 99999999999999887431 112345 99999999999999999996443
No 74
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=90.69 E-value=0.55 Score=24.61 Aligned_cols=9 Identities=22% Similarity=0.752 Sum_probs=5.7
Q ss_pred CCeeCCCCC
Q psy10073 49 IPQSCKHCK 57 (144)
Q Consensus 49 ~~~~C~~C~ 57 (144)
..|.|+.||
T Consensus 24 ~~F~CPnCG 32 (59)
T PRK14890 24 VKFLCPNCG 32 (59)
T ss_pred CEeeCCCCC
Confidence 346677776
No 75
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=90.57 E-value=0.18 Score=32.04 Aligned_cols=13 Identities=31% Similarity=0.726 Sum_probs=11.0
Q ss_pred CeeCCCCC-CCcch
Q psy10073 50 PQSCKHCK-NFTSS 62 (144)
Q Consensus 50 ~~~C~~C~-~f~~~ 62 (144)
.++|+.|| +|.+.
T Consensus 28 ~~~c~~c~~~f~~~ 41 (154)
T PRK00464 28 RRECLACGKRFTTF 41 (154)
T ss_pred eeeccccCCcceEe
Confidence 38899999 99887
No 76
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=89.99 E-value=0.2 Score=32.67 Aligned_cols=31 Identities=23% Similarity=0.453 Sum_probs=24.8
Q ss_pred ceeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhcc
Q psy10073 86 KFICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAY 125 (144)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 125 (144)
.|.|+.|+..|+....+. .-|.|+.||....
T Consensus 117 ~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred EEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 399999999998887753 3699999996543
No 77
>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=89.84 E-value=0.31 Score=22.29 Aligned_cols=11 Identities=27% Similarity=0.407 Sum_probs=7.4
Q ss_pred eecCccCCccC
Q psy10073 16 KTCLYCNKYVP 26 (144)
Q Consensus 16 ~~C~~C~~~f~ 26 (144)
|.|..||..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 56778887766
No 78
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=89.09 E-value=0.31 Score=30.69 Aligned_cols=14 Identities=14% Similarity=0.147 Sum_probs=8.9
Q ss_pred ceecCccCCccCCc
Q psy10073 15 KKTCLYCNKYVPSD 28 (144)
Q Consensus 15 ~~~C~~C~~~f~~~ 28 (144)
.|.|+.|+..|...
T Consensus 99 ~Y~Cp~C~~~y~~~ 112 (147)
T smart00531 99 YYKCPNCQSKYTFL 112 (147)
T ss_pred EEECcCCCCEeeHH
Confidence 46677776666643
No 79
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=89.08 E-value=0.26 Score=24.84 Aligned_cols=13 Identities=23% Similarity=0.562 Sum_probs=11.0
Q ss_pred CceecCccCCccC
Q psy10073 14 TKKTCLYCNKYVP 26 (144)
Q Consensus 14 ~~~~C~~C~~~f~ 26 (144)
..|.|..||+.|.
T Consensus 5 ~~Y~C~~Cg~~~~ 17 (49)
T COG1996 5 MEYKCARCGREVE 17 (49)
T ss_pred EEEEhhhcCCeee
Confidence 4699999999993
No 80
>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=88.84 E-value=0.31 Score=29.09 Aligned_cols=30 Identities=13% Similarity=0.178 Sum_probs=20.4
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhccCh
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAYQK 127 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 127 (144)
..|+.||..|-.. +..|..|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 5788888777542 23577788888777654
No 81
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=88.80 E-value=0.47 Score=20.14 Aligned_cols=7 Identities=43% Similarity=1.208 Sum_probs=2.9
Q ss_pred eeCCCCC
Q psy10073 87 FICVACD 93 (144)
Q Consensus 87 ~~C~~C~ 93 (144)
|.|+.||
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 4444443
No 82
>PHA00626 hypothetical protein
Probab=88.77 E-value=0.43 Score=24.68 Aligned_cols=14 Identities=21% Similarity=0.328 Sum_probs=8.5
Q ss_pred CCeeCCCCC-CCcch
Q psy10073 49 IPQSCKHCK-NFTSS 62 (144)
Q Consensus 49 ~~~~C~~C~-~f~~~ 62 (144)
..|.|+.|| .|...
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 357777777 66443
No 83
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=88.60 E-value=0.35 Score=23.85 Aligned_cols=13 Identities=15% Similarity=0.181 Sum_probs=9.5
Q ss_pred ceecCccCCccCC
Q psy10073 15 KKTCLYCNKYVPS 27 (144)
Q Consensus 15 ~~~C~~C~~~f~~ 27 (144)
.|.|..||..|..
T Consensus 2 ~Y~C~~Cg~~~~~ 14 (44)
T smart00659 2 IYICGECGRENEI 14 (44)
T ss_pred EEECCCCCCEeec
Confidence 3788888887654
No 84
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=88.36 E-value=0.51 Score=23.63 Aligned_cols=15 Identities=13% Similarity=0.313 Sum_probs=9.6
Q ss_pred eecCccCCccCCccc
Q psy10073 16 KTCLYCNKYVPSDID 30 (144)
Q Consensus 16 ~~C~~C~~~f~~~~~ 30 (144)
|.|..||..+.....
T Consensus 2 y~C~~CgyvYd~~~G 16 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKG 16 (47)
T ss_dssp EEETTTSBEEETTTB
T ss_pred cCCCCCCEEEcCCcC
Confidence 667777766665443
No 85
>KOG2893|consensus
Probab=88.03 E-value=0.14 Score=34.75 Aligned_cols=19 Identities=21% Similarity=0.429 Sum_probs=10.7
Q ss_pred eeCCCCCcccCChhHHHHH
Q psy10073 87 FICVACDYFTIISQNMRNH 105 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H 105 (144)
|+|.+|.+.+-+--.|..|
T Consensus 35 fkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 35 FKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred ceeeeehhhhccCCCceee
Confidence 6676666554444444444
No 86
>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=87.88 E-value=0.55 Score=22.92 Aligned_cols=22 Identities=27% Similarity=0.416 Sum_probs=10.2
Q ss_pred cceeCCCcchhccC----hHHHHHHH
Q psy10073 113 KQFKCCLCSYGAYQ----KEKLQFHV 134 (144)
Q Consensus 113 ~~~~C~~C~~~f~~----~~~l~~H~ 134 (144)
....|..|++.+.. .+.|.+|+
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHH
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 34556666655544 25666666
No 87
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=87.79 E-value=0.34 Score=27.69 Aligned_cols=26 Identities=19% Similarity=0.206 Sum_probs=16.4
Q ss_pred hhhhhhhcCCCC----CceecCccCCccCC
Q psy10073 2 EHWEQCLLVPLS----TKKTCLYCNKYVPS 27 (144)
Q Consensus 2 ~~~~~~~~~~~~----~~~~C~~C~~~f~~ 27 (144)
+|.+.-+..-+. .|-.|..||..|..
T Consensus 41 ~hiak~lkr~g~~Llv~Pa~CkkCGfef~~ 70 (97)
T COG3357 41 EHIAKSLKRKGKRLLVRPARCKKCGFEFRD 70 (97)
T ss_pred HHHHHHHHhCCceEEecChhhcccCccccc
Confidence 445555544443 25678888888876
No 88
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=87.52 E-value=0.62 Score=29.37 Aligned_cols=36 Identities=17% Similarity=0.362 Sum_probs=24.6
Q ss_pred ceeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhcc
Q psy10073 86 KFICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAY 125 (144)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 125 (144)
.|.|+.|+..|.....+.. ... ...|.|+.||....
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEELE 134 (147)
T ss_pred EEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEEE
Confidence 3999999999986554432 011 33499999997653
No 89
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=87.30 E-value=0.56 Score=23.65 Aligned_cols=20 Identities=25% Similarity=0.549 Sum_probs=10.1
Q ss_pred eCCCcchhccCh-----HHHHHHHH
Q psy10073 116 KCCLCSYGAYQK-----EKLQFHVK 135 (144)
Q Consensus 116 ~C~~C~~~f~~~-----~~l~~H~~ 135 (144)
.|..|++.++.. +.|.+|++
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHH
Confidence 455555544332 45666655
No 90
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=87.17 E-value=0.66 Score=20.03 Aligned_cols=19 Identities=16% Similarity=0.469 Sum_probs=11.3
Q ss_pred eCCCcchhccChHHHHHHHH
Q psy10073 116 KCCLCSYGAYQKEKLQFHVK 135 (144)
Q Consensus 116 ~C~~C~~~f~~~~~l~~H~~ 135 (144)
.|++|++.+ ....++.|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 466666665 4455666654
No 91
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=86.97 E-value=0.46 Score=27.71 Aligned_cols=40 Identities=23% Similarity=0.352 Sum_probs=24.4
Q ss_pred CCCceecCccCCccCCccccccccCCCCCCccccCCCCCeeCCCCC-CCcch
Q psy10073 12 LSTKKTCLYCNKYVPSDIDVFIGHCQTCPNMSFLNSVIPQSCKHCK-NFTSS 62 (144)
Q Consensus 12 ~~~~~~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~~~~~~~C~~C~-~f~~~ 62 (144)
..+.|.|+.||..-...-.++. -.......|..|| .|...
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk-----------~~~~g~~~Cg~CGls~e~e 59 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKK-----------TVNIGTAVCGNCGLSFECE 59 (104)
T ss_pred CCceEecCccCCeeeeEEEEEe-----------cCceeEEEcccCcceEEEe
Confidence 5567888888876665544444 1222345688888 66543
No 92
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=86.76 E-value=0.72 Score=23.41 Aligned_cols=13 Identities=15% Similarity=0.355 Sum_probs=8.5
Q ss_pred eecCccCCccCCc
Q psy10073 16 KTCLYCNKYVPSD 28 (144)
Q Consensus 16 ~~C~~C~~~f~~~ 28 (144)
|.|..||..+.-.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 5677777666643
No 93
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=86.65 E-value=0.51 Score=30.37 Aligned_cols=24 Identities=25% Similarity=0.631 Sum_probs=15.8
Q ss_pred CeeCCCCCCCcchhhhhhhcccCCCCcccccCCCCCceeCCCCCc
Q psy10073 50 PQSCKHCKNFTSSDVNLLMEHSENCPCMVRPDPVKYKFICVACDY 94 (144)
Q Consensus 50 ~~~C~~C~~f~~~~~H~~~~h~~~~~~~~~~~~~~~~~~C~~C~~ 94 (144)
-|.|++|| -++.++.| -.||+||-
T Consensus 134 ~~vC~vCG----------y~~~ge~P-----------~~CPiCga 157 (166)
T COG1592 134 VWVCPVCG----------YTHEGEAP-----------EVCPICGA 157 (166)
T ss_pred EEEcCCCC----------CcccCCCC-----------CcCCCCCC
Confidence 57777777 33445666 77777773
No 94
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=86.58 E-value=0.55 Score=30.25 Aligned_cols=23 Identities=26% Similarity=0.791 Sum_probs=18.8
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcch
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSY 122 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 122 (144)
|.|++||..+ .|+.|-+|++||-
T Consensus 135 ~vC~vCGy~~-------------~ge~P~~CPiCga 157 (166)
T COG1592 135 WVCPVCGYTH-------------EGEAPEVCPICGA 157 (166)
T ss_pred EEcCCCCCcc-------------cCCCCCcCCCCCC
Confidence 9999999753 4578899999983
No 95
>PRK14873 primosome assembly protein PriA; Provisional
Probab=86.45 E-value=0.69 Score=36.51 Aligned_cols=8 Identities=25% Similarity=0.397 Sum_probs=4.2
Q ss_pred eeCCCCCc
Q psy10073 87 FICVACDY 94 (144)
Q Consensus 87 ~~C~~C~~ 94 (144)
..|..||.
T Consensus 411 l~Ch~CG~ 418 (665)
T PRK14873 411 PRCRWCGR 418 (665)
T ss_pred eECCCCcC
Confidence 55555553
No 96
>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=85.87 E-value=0.77 Score=27.29 Aligned_cols=25 Identities=24% Similarity=0.647 Sum_probs=18.6
Q ss_pred eeC----CCcchhccChHHHHHHHHhhcC
Q psy10073 115 FKC----CLCSYGAYQKEKLQFHVKNKHS 139 (144)
Q Consensus 115 ~~C----~~C~~~f~~~~~l~~H~~~h~~ 139 (144)
|.| ..|+..+.+...+.+|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 677 7777777777777777776654
No 97
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=85.69 E-value=0.74 Score=22.75 Aligned_cols=30 Identities=20% Similarity=0.358 Sum_probs=19.6
Q ss_pred CceecCccCCccCCccccccccCCCCCCccccCCCCCeeCCCCC-CCc
Q psy10073 14 TKKTCLYCNKYVPSDIDVFIGHCQTCPNMSFLNSVIPQSCKHCK-NFT 60 (144)
Q Consensus 14 ~~~~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~~~~~~~C~~C~-~f~ 60 (144)
..|.|+.||..|..... .....|+.|| .+.
T Consensus 2 ~~y~C~~CG~~~~~~~~-----------------~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 2 AEYKCARCGREVELDEY-----------------GTGVRCPYCGYRIL 32 (46)
T ss_pred CEEECCCCCCEEEECCC-----------------CCceECCCCCCeEE
Confidence 35889999987754321 1157888888 554
No 98
>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=85.29 E-value=0.45 Score=30.43 Aligned_cols=14 Identities=7% Similarity=-0.140 Sum_probs=6.9
Q ss_pred ceecCccCCccCCc
Q psy10073 15 KKTCLYCNKYVPSD 28 (144)
Q Consensus 15 ~~~C~~C~~~f~~~ 28 (144)
-|.|+.|+..|+..
T Consensus 109 ~Y~Cp~c~~r~tf~ 122 (158)
T TIGR00373 109 FFICPNMCVRFTFN 122 (158)
T ss_pred eEECCCCCcEeeHH
Confidence 35555555544443
No 99
>KOG2785|consensus
Probab=85.09 E-value=0.99 Score=32.80 Aligned_cols=52 Identities=19% Similarity=0.340 Sum_probs=44.2
Q ss_pred CceeCCCCCcccCChhHHHHHHHhhcC-----------------------CcceeCCCcc---hhccChHHHHHHHHh
Q psy10073 85 YKFICVACDYFTIISQNMRNHTLIHLG-----------------------DKQFKCCLCS---YGAYQKEKLQFHVKN 136 (144)
Q Consensus 85 ~~~~C~~C~~~f~~~~~l~~H~~~h~~-----------------------~~~~~C~~C~---~~f~~~~~l~~H~~~ 136 (144)
.|-.|..|++.+.+...-..||..++| ..-|.|-.|+ +.|.+....+.||..
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 457899999999999999999988765 2347899998 999999999999874
No 100
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=85.04 E-value=0.54 Score=29.11 Aligned_cols=22 Identities=18% Similarity=0.374 Sum_probs=9.4
Q ss_pred eeCCCcchhccChHHHHHHHHhhcC
Q psy10073 115 FKCCLCSYGAYQKEKLQFHVKNKHS 139 (144)
Q Consensus 115 ~~C~~C~~~f~~~~~l~~H~~~h~~ 139 (144)
..|-+||+.|... .+|++.|+|
T Consensus 73 i~clecGk~~k~L---krHL~~~~g 94 (132)
T PF05443_consen 73 IICLECGKKFKTL---KRHLRTHHG 94 (132)
T ss_dssp EE-TBT--EESBH---HHHHHHTT-
T ss_pred eEEccCCcccchH---HHHHHHccC
Confidence 4555555555432 555555544
No 101
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=84.97 E-value=0.39 Score=31.36 Aligned_cols=14 Identities=21% Similarity=0.237 Sum_probs=7.3
Q ss_pred ceecCccCCccCCc
Q psy10073 15 KKTCLYCNKYVPSD 28 (144)
Q Consensus 15 ~~~C~~C~~~f~~~ 28 (144)
-|.|+.|+..|+..
T Consensus 117 ~Y~Cp~C~~rytf~ 130 (178)
T PRK06266 117 FFFCPNCHIRFTFD 130 (178)
T ss_pred EEECCCCCcEEeHH
Confidence 35555555555443
No 102
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=83.98 E-value=0.9 Score=36.19 Aligned_cols=11 Identities=18% Similarity=0.307 Sum_probs=6.1
Q ss_pred CcceeCCCcch
Q psy10073 112 DKQFKCCLCSY 122 (144)
Q Consensus 112 ~~~~~C~~C~~ 122 (144)
..|..|+.||.
T Consensus 473 ~~p~~Cp~Cgs 483 (730)
T COG1198 473 PIPQSCPECGS 483 (730)
T ss_pred CCCCCCCCCCC
Confidence 34556666653
No 103
>PF14353 CpXC: CpXC protein
Probab=83.85 E-value=0.27 Score=30.13 Aligned_cols=14 Identities=21% Similarity=0.472 Sum_probs=9.7
Q ss_pred eecCccCCccCCcc
Q psy10073 16 KTCLYCNKYVPSDI 29 (144)
Q Consensus 16 ~~C~~C~~~f~~~~ 29 (144)
..|+.|+..|....
T Consensus 2 itCP~C~~~~~~~v 15 (128)
T PF14353_consen 2 ITCPHCGHEFEFEV 15 (128)
T ss_pred cCCCCCCCeeEEEE
Confidence 36888888776543
No 104
>KOG2231|consensus
Probab=83.43 E-value=1.1 Score=35.11 Aligned_cols=48 Identities=17% Similarity=0.281 Sum_probs=32.1
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCc------chhccChHHHHHHHHhhc
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLC------SYGAYQKEKLQFHVKNKH 138 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C------~~~f~~~~~l~~H~~~h~ 138 (144)
-.|..|...|.....|.+|++.++ |.|..| +..|.....|..|-+..|
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 578888888888888888877544 233333 455666777777766554
No 105
>COG1773 Rubredoxin [Energy production and conversion]
Probab=83.02 E-value=2 Score=22.29 Aligned_cols=15 Identities=13% Similarity=0.339 Sum_probs=8.8
Q ss_pred ceecCccCCccCCcc
Q psy10073 15 KKTCLYCNKYVPSDI 29 (144)
Q Consensus 15 ~~~C~~C~~~f~~~~ 29 (144)
.|+|..||..|.-..
T Consensus 3 ~~~C~~CG~vYd~e~ 17 (55)
T COG1773 3 RWRCSVCGYVYDPEK 17 (55)
T ss_pred ceEecCCceEecccc
Confidence 466666666665433
No 106
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=82.89 E-value=0.73 Score=25.33 Aligned_cols=16 Identities=19% Similarity=0.550 Sum_probs=10.5
Q ss_pred CCCCeeCC--CCC-CCcch
Q psy10073 47 SVIPQSCK--HCK-NFTSS 62 (144)
Q Consensus 47 ~~~~~~C~--~C~-~f~~~ 62 (144)
.+.-+.|. .|| +|...
T Consensus 24 ~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 24 KERYHQCQNVNCSATFITY 42 (72)
T ss_pred heeeeecCCCCCCCEEEEE
Confidence 34556776 777 77666
No 107
>KOG4173|consensus
Probab=81.80 E-value=0.6 Score=31.00 Aligned_cols=50 Identities=16% Similarity=0.231 Sum_probs=40.6
Q ss_pred eeCCCCCcccCChhHHHHHHHhh----------cCCcceeC--CCcchhccChHHHHHHHHh
Q psy10073 87 FICVACDYFTIISQNMRNHTLIH----------LGDKQFKC--CLCSYGAYQKEKLQFHVKN 136 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h----------~~~~~~~C--~~C~~~f~~~~~l~~H~~~ 136 (144)
-.|..|.+.|.+...|..|+.-. -|...|+| +.|+..|.+......|+-.
T Consensus 107 ~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 107 NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIR 168 (253)
T ss_pred chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHH
Confidence 48999999999999999998532 34456899 5699999999999999654
No 108
>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=81.33 E-value=0.64 Score=31.28 Aligned_cols=28 Identities=18% Similarity=0.246 Sum_probs=20.6
Q ss_pred CCCceeCCCCCcccCChhHHHHHHHhhc
Q psy10073 83 VKYKFICVACDYFTIISQNMRNHTLIHL 110 (144)
Q Consensus 83 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 110 (144)
++..|.|+.|+|.|....-.+.|+..-+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcC
Confidence 4445999999999999999999987643
No 109
>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=81.00 E-value=0.58 Score=25.22 Aligned_cols=27 Identities=26% Similarity=0.538 Sum_probs=12.0
Q ss_pred CCceecCccCCccCCccccccccCCCCCC
Q psy10073 13 STKKTCLYCNKYVPSDIDVFIGHCQTCPN 41 (144)
Q Consensus 13 ~~~~~C~~C~~~f~~~~~l~~H~c~~c~h 41 (144)
...-.|..|++.|.. -..+|+|..||.
T Consensus 7 ~~~~~C~~C~~~F~~--~~rrhhCr~CG~ 33 (69)
T PF01363_consen 7 SEASNCMICGKKFSL--FRRRHHCRNCGR 33 (69)
T ss_dssp GG-SB-TTT--B-BS--SS-EEE-TTT--
T ss_pred CCCCcCcCcCCcCCC--ceeeEccCCCCC
Confidence 345679999999953 355677777765
No 110
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=80.24 E-value=2.1 Score=34.21 Aligned_cols=12 Identities=17% Similarity=0.332 Sum_probs=6.6
Q ss_pred eecCccCCccCC
Q psy10073 16 KTCLYCNKYVPS 27 (144)
Q Consensus 16 ~~C~~C~~~f~~ 27 (144)
..|..||..+..
T Consensus 436 l~C~~Cg~v~~C 447 (730)
T COG1198 436 LLCRDCGYIAEC 447 (730)
T ss_pred eecccCCCcccC
Confidence 346666665543
No 111
>KOG2186|consensus
Probab=79.79 E-value=1.1 Score=30.74 Aligned_cols=47 Identities=19% Similarity=0.281 Sum_probs=38.0
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhccChHHHHHHHHh
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAYQKEKLQFHVKN 136 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 136 (144)
|.|..||....- ..+.+|+....+ .-|.|-.|++.|.. .++..|..-
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 899999988764 456779888776 67999999999998 677778653
No 112
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=79.61 E-value=1.6 Score=20.04 Aligned_cols=10 Identities=20% Similarity=0.355 Sum_probs=5.0
Q ss_pred CCCeeCCCCC
Q psy10073 48 VIPQSCKHCK 57 (144)
Q Consensus 48 ~~~~~C~~C~ 57 (144)
..-+.|..||
T Consensus 19 ~~~~~C~~Cg 28 (33)
T PF08792_consen 19 DDYEVCIFCG 28 (33)
T ss_pred CCeEEcccCC
Confidence 3334555555
No 113
>KOG2593|consensus
Probab=79.44 E-value=0.96 Score=33.43 Aligned_cols=37 Identities=19% Similarity=0.325 Sum_probs=26.0
Q ss_pred CCceecCccCCccCCccccccccCCCCCCccccCCCCCeeCCCCC-CC
Q psy10073 13 STKKTCLYCNKYVPSDIDVFIGHCQTCPNMSFLNSVIPQSCKHCK-NF 59 (144)
Q Consensus 13 ~~~~~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~~~~~~~C~~C~-~f 59 (144)
...|.|+.|++.|.....++. + -.....|.|..|+ ..
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L--------~--~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQL--------L--DNETGEFHCENCGGEL 163 (436)
T ss_pred cccccCCccccchhhhHHHHh--------h--cccCceEEEecCCCch
Confidence 346999999999987665544 2 2334568999998 54
No 114
>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=78.70 E-value=0.49 Score=22.21 Aligned_cols=32 Identities=22% Similarity=0.232 Sum_probs=19.1
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhccC
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAYQ 126 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 126 (144)
+.|+.||..|.... .....+-.|+.||-.+.+
T Consensus 2 r~C~~Cg~~Yh~~~--------~pP~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 2 RICPKCGRIYHIEF--------NPPKVEGVCDNCGGELVQ 33 (36)
T ss_dssp EEETTTTEEEETTT--------B--SSTTBCTTTTEBEBE
T ss_pred cCcCCCCCcccccc--------CCCCCCCccCCCCCeeEe
Confidence 57888888874332 223344578888865543
No 115
>KOG2785|consensus
Probab=77.94 E-value=2.2 Score=31.14 Aligned_cols=25 Identities=16% Similarity=0.292 Sum_probs=21.2
Q ss_pred CcceeCCCcchhccChHHHHHHHHh
Q psy10073 112 DKQFKCCLCSYGAYQKEKLQFHVKN 136 (144)
Q Consensus 112 ~~~~~C~~C~~~f~~~~~l~~H~~~ 136 (144)
+.++.|.+|.+.|.+......|+..
T Consensus 66 ~~~~~c~~c~k~~~s~~a~~~hl~S 90 (390)
T KOG2785|consen 66 ESVVYCEACNKSFASPKAHENHLKS 90 (390)
T ss_pred ccceehHHhhccccChhhHHHHHHH
Confidence 4568899999999999988888764
No 116
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=77.51 E-value=1.3 Score=27.29 Aligned_cols=15 Identities=13% Similarity=0.445 Sum_probs=12.5
Q ss_pred ceecCccCCccCCcc
Q psy10073 15 KKTCLYCNKYVPSDI 29 (144)
Q Consensus 15 ~~~C~~C~~~f~~~~ 29 (144)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 568999999998765
No 117
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=77.37 E-value=0.92 Score=30.53 Aligned_cols=30 Identities=27% Similarity=0.471 Sum_probs=22.7
Q ss_pred CCcceeCCCcchhccChHHHHHHHHhhcCC
Q psy10073 111 GDKQFKCCLCSYGAYQKEKLQFHVKNKHST 140 (144)
Q Consensus 111 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~ 140 (144)
++..|.|.+|+|.|.-..-...|+...|.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 345699999999999999999999876654
No 118
>KOG3408|consensus
Probab=76.95 E-value=1.7 Score=26.37 Aligned_cols=26 Identities=19% Similarity=0.461 Sum_probs=22.8
Q ss_pred CCCceeCCCCCcccCChhHHHHHHHh
Q psy10073 83 VKYKFICVACDYFTIISQNMRNHTLI 108 (144)
Q Consensus 83 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 108 (144)
|.+.|.|..|.+-|.+...|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 55669999999999999999999865
No 119
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=76.79 E-value=1.6 Score=24.83 Aligned_cols=11 Identities=18% Similarity=0.416 Sum_probs=7.3
Q ss_pred eeCCCCCcccC
Q psy10073 87 FICVACDYFTI 97 (144)
Q Consensus 87 ~~C~~C~~~f~ 97 (144)
|.|..|+..|.
T Consensus 54 W~C~kCg~~fA 64 (89)
T COG1997 54 WKCRKCGAKFA 64 (89)
T ss_pred EEcCCCCCeec
Confidence 67777776664
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=76.47 E-value=1.1 Score=30.92 Aligned_cols=82 Identities=17% Similarity=0.310 Sum_probs=45.0
Q ss_pred cCCCCCceecCccCCccCCccccccccCCCCCCccc--cCCCCCeeCCCCCCCcch----------hhhhhh---cccCC
Q psy10073 9 LVPLSTKKTCLYCNKYVPSDIDVFIGHCQTCPNMSF--LNSVIPQSCKHCKNFTSS----------DVNLLM---EHSEN 73 (144)
Q Consensus 9 ~~~~~~~~~C~~C~~~f~~~~~l~~H~c~~c~h~~~--h~~~~~~~C~~C~~f~~~----------~~H~~~---~h~~~ 73 (144)
..++.+.|+|..|+...-. ..--. |+.. -.....|+|.-|+++... ..|+++ .....
T Consensus 136 w~hGGrif~CsfC~~flCE-DDQFE-------HQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~ 207 (314)
T PF06524_consen 136 WDHGGRIFKCSFCDNFLCE-DDQFE-------HQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKG 207 (314)
T ss_pred ccCCCeEEEeecCCCeeec-cchhh-------hhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccccC
Confidence 3566777888888764333 22222 2221 122345677666622111 444411 11223
Q ss_pred CCcccccCCCCCceeCCCCCcccCChhHHHHHHHhh
Q psy10073 74 CPCMVRPDPVKYKFICVACDYFTIISQNMRNHTLIH 109 (144)
Q Consensus 74 ~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 109 (144)
++ +.||.|+........|..-.++|
T Consensus 208 k~-----------~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 208 KP-----------IPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CC-----------CCCCCCCCcccccccceeeeecc
Confidence 44 99999999887777776665555
No 121
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=76.31 E-value=1.2 Score=26.07 Aligned_cols=19 Identities=11% Similarity=0.408 Sum_probs=13.9
Q ss_pred ceecCccCCccCCcccccc
Q psy10073 15 KKTCLYCNKYVPSDIDVFI 33 (144)
Q Consensus 15 ~~~C~~C~~~f~~~~~l~~ 33 (144)
++.|..||..|.+-+.+..
T Consensus 2 pH~CtrCG~vf~~g~~~il 20 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEIL 20 (112)
T ss_pred CceecccccccccccHHHH
Confidence 4679999999988654443
No 122
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=76.25 E-value=1.9 Score=26.70 Aligned_cols=22 Identities=14% Similarity=0.048 Sum_probs=11.2
Q ss_pred eCCCcchhccChHHHHHHHHhhcCC
Q psy10073 116 KCCLCSYGAYQKEKLQFHVKNKHST 140 (144)
Q Consensus 116 ~C~~C~~~f~~~~~l~~H~~~h~~~ 140 (144)
.|-.+|+.|. +|.+|+.+|.|-
T Consensus 78 icLEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 78 ICLEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred EEeccCcchH---HHHHHHhcccCC
Confidence 4555555553 345555555543
No 123
>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=76.15 E-value=2.2 Score=32.63 Aligned_cols=32 Identities=28% Similarity=0.631 Sum_probs=17.1
Q ss_pred eCCCCC-CCcch--hhhhhhcccCCCCcccccCCCCCceeCCCCCcc
Q psy10073 52 SCKHCK-NFTSS--DVNLLMEHSENCPCMVRPDPVKYKFICVACDYF 95 (144)
Q Consensus 52 ~C~~C~-~f~~~--~~H~~~~h~~~~~~~~~~~~~~~~~~C~~C~~~ 95 (144)
.|..|| ...-. ...+ ..|..... ..|..||..
T Consensus 215 ~C~~Cg~~~~C~~C~~~l-~~h~~~~~-----------l~Ch~Cg~~ 249 (505)
T TIGR00595 215 LCRSCGYILCCPNCDVSL-TYHKKEGK-----------LRCHYCGYQ 249 (505)
T ss_pred EhhhCcCccCCCCCCCce-EEecCCCe-----------EEcCCCcCc
Confidence 466666 44444 3344 55555444 666666643
No 124
>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=76.05 E-value=2.8 Score=24.87 Aligned_cols=25 Identities=32% Similarity=0.607 Sum_probs=22.5
Q ss_pred eeC----CCCCcccCChhHHHHHHHhhcC
Q psy10073 87 FIC----VACDYFTIISQNMRNHTLIHLG 111 (144)
Q Consensus 87 ~~C----~~C~~~f~~~~~l~~H~~~h~~ 111 (144)
|.| ..|+..+.+...+.+|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 9999999999999999887653
No 125
>KOG2907|consensus
Probab=75.59 E-value=2.6 Score=25.19 Aligned_cols=38 Identities=16% Similarity=0.441 Sum_probs=22.2
Q ss_pred eeCCCCC-C-CcchhhhhhhcccCCCCcccccCCCCCceeCCCCCcccCC
Q psy10073 51 QSCKHCK-N-FTSSDVNLLMEHSENCPCMVRPDPVKYKFICVACDYFTII 98 (144)
Q Consensus 51 ~~C~~C~-~-f~~~~~H~~~~h~~~~~~~~~~~~~~~~~~C~~C~~~f~~ 98 (144)
.+|+.|| . .......++..-.|...| |.|+.|++.|..
T Consensus 75 ~kCpkCghe~m~Y~T~QlRSADEGQTVF----------YTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQLRSADEGQTVF----------YTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCchhhhhhhhcccccCCceEE----------EEcCccceeeec
Confidence 6899999 3 222222231223344444 899999988764
No 126
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=74.79 E-value=1.8 Score=20.76 Aligned_cols=9 Identities=22% Similarity=0.881 Sum_probs=5.3
Q ss_pred eeCCCCC-CC
Q psy10073 51 QSCKHCK-NF 59 (144)
Q Consensus 51 ~~C~~C~-~f 59 (144)
|.|..|+ .|
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 5666666 44
No 127
>KOG2593|consensus
Probab=73.96 E-value=2.6 Score=31.30 Aligned_cols=37 Identities=16% Similarity=0.377 Sum_probs=25.8
Q ss_pred CCCceeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcch
Q psy10073 83 VKYKFICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSY 122 (144)
Q Consensus 83 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 122 (144)
....|.|+.|.+.|.....++ ..-...-.|.|..|+-
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGG 161 (436)
T ss_pred ccccccCCccccchhhhHHHH---hhcccCceEEEecCCC
Confidence 334499999999998776654 2223344699999973
No 128
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=73.85 E-value=0.92 Score=35.74 Aligned_cols=54 Identities=24% Similarity=0.339 Sum_probs=32.4
Q ss_pred eCCCCC-CCcch--hhhhhhcccCCCCcccccCCCCCceeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcch
Q psy10073 52 SCKHCK-NFTSS--DVNLLMEHSENCPCMVRPDPVKYKFICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSY 122 (144)
Q Consensus 52 ~C~~C~-~f~~~--~~H~~~~h~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 122 (144)
.|..|| +|+.. .--- +..+.-+.| -.|+.|.+.|.++.+-+-| ..|..|+.||-
T Consensus 125 ~CT~CGPRfTIi~alPYD-R~nTsM~~F----------~lC~~C~~EY~dP~nRRfH------AQp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYD-RENTSMADF----------PLCPFCDKEYKDPLNRRFH------AQPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCC-cccCccccC----------cCCHHHHHHhcCccccccc------cccccCcccCC
Confidence 488888 88765 1111 222222222 3688888888887764433 24678888885
No 129
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=73.76 E-value=2.9 Score=21.61 Aligned_cols=40 Identities=13% Similarity=0.304 Sum_probs=24.2
Q ss_pred ceeCCC--CCcccCChhHHHHHHHhhcCCcceeCCC----cchhccC
Q psy10073 86 KFICVA--CDYFTIISQNMRNHTLIHLGDKQFKCCL----CSYGAYQ 126 (144)
Q Consensus 86 ~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~----C~~~f~~ 126 (144)
+..|+. |...+. ...|..|+...-..++..|+. |+..+..
T Consensus 9 ~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 9 PVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp EEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEEH
T ss_pred EeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccch
Confidence 378877 544444 557888988666677888988 8876653
No 130
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=73.56 E-value=2.8 Score=26.09 Aligned_cols=14 Identities=14% Similarity=0.249 Sum_probs=10.4
Q ss_pred ceecCccCCccCCc
Q psy10073 15 KKTCLYCNKYVPSD 28 (144)
Q Consensus 15 ~~~C~~C~~~f~~~ 28 (144)
.+.|..||..|...
T Consensus 70 ~~~C~~CG~~~~~~ 83 (135)
T PRK03824 70 VLKCRNCGNEWSLK 83 (135)
T ss_pred EEECCCCCCEEecc
Confidence 47888888777654
No 131
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=72.96 E-value=1 Score=21.50 Aligned_cols=9 Identities=22% Similarity=0.796 Sum_probs=5.5
Q ss_pred eeCCCCC-CC
Q psy10073 51 QSCKHCK-NF 59 (144)
Q Consensus 51 ~~C~~C~-~f 59 (144)
|.|..|+ .|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 6666666 44
No 132
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=72.94 E-value=2.3 Score=26.95 Aligned_cols=30 Identities=23% Similarity=0.788 Sum_probs=13.7
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcc
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCS 121 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~ 121 (144)
|.|. |+..|.+ .++|-.+-.|+ .|.|..|+
T Consensus 118 Y~C~-C~q~~l~---~RRhn~~~~g~-~YrC~~C~ 147 (156)
T COG3091 118 YRCQ-CQQHYLR---IRRHNTVRRGE-VYRCGKCG 147 (156)
T ss_pred EEee-cCCccch---hhhcccccccc-eEEeccCC
Confidence 5555 5544333 23344444444 55555554
No 133
>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=72.80 E-value=2.5 Score=22.71 Aligned_cols=10 Identities=30% Similarity=0.932 Sum_probs=5.1
Q ss_pred eeCCCCCccc
Q psy10073 87 FICVACDYFT 96 (144)
Q Consensus 87 ~~C~~C~~~f 96 (144)
|.|+.||..+
T Consensus 47 ~~C~~Cg~~~ 56 (69)
T PF07282_consen 47 FTCPNCGFEM 56 (69)
T ss_pred EEcCCCCCEE
Confidence 5555555443
No 134
>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=72.50 E-value=2.1 Score=18.44 Aligned_cols=11 Identities=27% Similarity=0.443 Sum_probs=8.1
Q ss_pred eecCccCCccC
Q psy10073 16 KTCLYCNKYVP 26 (144)
Q Consensus 16 ~~C~~C~~~f~ 26 (144)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 46888888774
No 135
>KOG4167|consensus
Probab=72.47 E-value=1.2 Score=35.21 Aligned_cols=25 Identities=20% Similarity=0.397 Sum_probs=21.8
Q ss_pred ceeCCCcchhccChHHHHHHHHhhc
Q psy10073 114 QFKCCLCSYGAYQKEKLQFHVKNKH 138 (144)
Q Consensus 114 ~~~C~~C~~~f~~~~~l~~H~~~h~ 138 (144)
-|.|..|++.|.--.+++.||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 3889999999998889999998885
No 136
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=72.45 E-value=1.7 Score=31.31 Aligned_cols=48 Identities=17% Similarity=0.344 Sum_probs=29.7
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcc----hhccChHHHHHHHH
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCS----YGAYQKEKLQFHVK 135 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~----~~f~~~~~l~~H~~ 135 (144)
-.|..|...|-+...|..|++..+ ++-+.|+.-+ ..|.+..+|-.|.+
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~ 272 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFR 272 (493)
T ss_pred chhhhccceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhh
Confidence 467778877777777887776544 3333333222 34666777777755
No 137
>KOG4167|consensus
Probab=72.22 E-value=0.9 Score=35.89 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=24.2
Q ss_pred CCceeCCCCCcccCChhHHHHHHHhhc
Q psy10073 84 KYKFICVACDYFTIISQNMRNHTLIHL 110 (144)
Q Consensus 84 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 110 (144)
...|.|.+|++.|....++..||++|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 456999999999999999999999885
No 138
>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=71.13 E-value=3.5 Score=21.07 Aligned_cols=23 Identities=26% Similarity=0.618 Sum_probs=13.5
Q ss_pred ecCccCCccCCccccccccCCCCCC
Q psy10073 17 TCLYCNKYVPSDIDVFIGHCQTCPN 41 (144)
Q Consensus 17 ~C~~C~~~f~~~~~l~~H~c~~c~h 41 (144)
.|..|++.|.. ...+|+|..||.
T Consensus 4 ~C~~C~~~F~~--~~rk~~Cr~Cg~ 26 (57)
T cd00065 4 SCMGCGKPFTL--TRRRHHCRNCGR 26 (57)
T ss_pred cCcccCccccC--CccccccCcCcC
Confidence 57788888875 334444444443
No 139
>PF15269 zf-C2H2_7: Zinc-finger
Probab=70.84 E-value=3.4 Score=20.33 Aligned_cols=21 Identities=33% Similarity=0.749 Sum_probs=11.1
Q ss_pred eeCCCcchhccChHHHHHHHH
Q psy10073 115 FKCCLCSYGAYQKEKLQFHVK 135 (144)
Q Consensus 115 ~~C~~C~~~f~~~~~l~~H~~ 135 (144)
|+|-.|..+..-++.|-.||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 445555555555555555554
No 140
>KOG1280|consensus
Probab=69.64 E-value=5.4 Score=28.84 Aligned_cols=35 Identities=23% Similarity=0.578 Sum_probs=24.2
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcc--eeCCCcc
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQ--FKCCLCS 121 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~--~~C~~C~ 121 (144)
|.|++|+..-.+...|..|....+-+-+ ..|++|+
T Consensus 80 ftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 80 FTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 8999999888888888888755332322 3466665
No 141
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=69.24 E-value=3.1 Score=21.48 Aligned_cols=19 Identities=21% Similarity=0.433 Sum_probs=13.1
Q ss_pred ceecCccCCccCCcccccc
Q psy10073 15 KKTCLYCNKYVPSDIDVFI 33 (144)
Q Consensus 15 ~~~C~~C~~~f~~~~~l~~ 33 (144)
.-+|+.||+.|....++..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVv 23 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVV 23 (54)
T ss_pred CccChhhCCcccCCCCEEE
Confidence 3578889988876555443
No 142
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=68.79 E-value=4.6 Score=20.20 Aligned_cols=11 Identities=18% Similarity=0.540 Sum_probs=6.9
Q ss_pred CeeCCCCC-CCc
Q psy10073 50 PQSCKHCK-NFT 60 (144)
Q Consensus 50 ~~~C~~C~-~f~ 60 (144)
.+.|+.|| .+.
T Consensus 20 ~~vC~~Cg~~~~ 31 (52)
T smart00661 20 RFVCRKCGYEEP 31 (52)
T ss_pred EEECCcCCCeEE
Confidence 46677777 543
No 143
>KOG3507|consensus
Probab=67.20 E-value=4.3 Score=21.23 Aligned_cols=9 Identities=22% Similarity=0.641 Sum_probs=4.9
Q ss_pred CCeeCCCCC
Q psy10073 49 IPQSCKHCK 57 (144)
Q Consensus 49 ~~~~C~~C~ 57 (144)
..+.|.+||
T Consensus 36 D~irCReCG 44 (62)
T KOG3507|consen 36 DVIRCRECG 44 (62)
T ss_pred CcEehhhcc
Confidence 345555555
No 144
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.76 E-value=3.2 Score=28.26 Aligned_cols=20 Identities=15% Similarity=0.207 Sum_probs=13.6
Q ss_pred CCceecCccCCccCCccccc
Q psy10073 13 STKKTCLYCNKYVPSDIDVF 32 (144)
Q Consensus 13 ~~~~~C~~C~~~f~~~~~l~ 32 (144)
.+.+.|++|+..|....-+.
T Consensus 17 kk~ieCPvC~tkFkkeev~t 36 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKT 36 (267)
T ss_pred hceeccCcccchhhhhheec
Confidence 34578888888887654433
No 145
>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=66.56 E-value=2.8 Score=21.66 Aligned_cols=30 Identities=23% Similarity=0.441 Sum_probs=15.0
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhc
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGA 124 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 124 (144)
|.|+.|+..+.-.... .|+ ...|+.||..+
T Consensus 3 ~~CP~CG~~iev~~~~-------~Ge-iV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPE-------LGE-LVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCc-------cCC-EEeCCCCCCEE
Confidence 5667776655333221 122 34666666543
No 146
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=66.56 E-value=3.5 Score=19.63 Aligned_cols=17 Identities=12% Similarity=0.294 Sum_probs=13.9
Q ss_pred ceecCccCCccCCcccc
Q psy10073 15 KKTCLYCNKYVPSDIDV 31 (144)
Q Consensus 15 ~~~C~~C~~~f~~~~~l 31 (144)
+|.|+.|+..|-....+
T Consensus 12 ~f~C~~C~~~FC~~HR~ 28 (39)
T smart00154 12 GFKCRHCGNLFCGEHRL 28 (39)
T ss_pred CeECCccCCccccccCC
Confidence 79999999999876543
No 147
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=65.66 E-value=4.6 Score=19.29 Aligned_cols=19 Identities=16% Similarity=0.114 Sum_probs=11.5
Q ss_pred ceeCCCcchhccChHHHHH
Q psy10073 114 QFKCCLCSYGAYQKEKLQF 132 (144)
Q Consensus 114 ~~~C~~C~~~f~~~~~l~~ 132 (144)
...|+.|+-.+-....|.+
T Consensus 19 id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEECCCCCeEEccHHHHHH
Confidence 3567777666666665543
No 148
>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=65.42 E-value=7 Score=19.20 Aligned_cols=8 Identities=25% Similarity=0.654 Sum_probs=4.1
Q ss_pred eecCccCC
Q psy10073 16 KTCLYCNK 23 (144)
Q Consensus 16 ~~C~~C~~ 23 (144)
+.|+.||.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 44555554
No 149
>PHA02998 RNA polymerase subunit; Provisional
Probab=64.34 E-value=7.4 Score=25.41 Aligned_cols=11 Identities=18% Similarity=0.419 Sum_probs=5.8
Q ss_pred eeCCCCCcccC
Q psy10073 87 FICVACDYFTI 97 (144)
Q Consensus 87 ~~C~~C~~~f~ 97 (144)
|.|..||..|.
T Consensus 172 YkC~~CG~~wk 182 (195)
T PHA02998 172 HACRDCKKHFK 182 (195)
T ss_pred EEcCCCCCccC
Confidence 55555555443
No 150
>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=64.12 E-value=2.6 Score=24.27 Aligned_cols=10 Identities=20% Similarity=0.497 Sum_probs=6.0
Q ss_pred eeCCCCCccc
Q psy10073 87 FICVACDYFT 96 (144)
Q Consensus 87 ~~C~~C~~~f 96 (144)
|.|..|++.|
T Consensus 54 W~C~~C~~~~ 63 (90)
T PF01780_consen 54 WKCKKCGKKF 63 (90)
T ss_dssp EEETTTTEEE
T ss_pred eecCCCCCEE
Confidence 6666666554
No 151
>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 KOG1729|consensus
Probab=63.90 E-value=2.8 Score=29.64 Aligned_cols=30 Identities=23% Similarity=0.597 Sum_probs=21.5
Q ss_pred CCCCCceecCccCCc-cCCccccccccCCCCCC
Q psy10073 10 VPLSTKKTCLYCNKY-VPSDIDVFIGHCQTCPN 41 (144)
Q Consensus 10 ~~~~~~~~C~~C~~~-f~~~~~l~~H~c~~c~h 41 (144)
.|....-.|..|+++ |. -..++|+|..||.
T Consensus 163 ~PD~ea~~C~~C~~~~Ft--l~~RRHHCR~CG~ 193 (288)
T KOG1729|consen 163 LPDSEATECMVCGCTEFT--LSERRHHCRNCGD 193 (288)
T ss_pred cCcccceecccCCCcccc--HHHHHHHHHhcch
Confidence 455566899999995 43 3457788888886
No 153
>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=63.61 E-value=4 Score=20.80 Aligned_cols=20 Identities=35% Similarity=0.630 Sum_probs=10.1
Q ss_pred CceecCccCCccCCcccccc
Q psy10073 14 TKKTCLYCNKYVPSDIDVFI 33 (144)
Q Consensus 14 ~~~~C~~C~~~f~~~~~l~~ 33 (144)
..|.|+.|+..|--.-++-.
T Consensus 20 ~~y~C~~C~~~FC~dCD~fi 39 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFI 39 (51)
T ss_dssp EEE--TTTT--B-HHHHHTT
T ss_pred CeEECCCCCCccccCcChhh
Confidence 35777777777776666666
No 154
>KOG3408|consensus
Probab=62.92 E-value=6.5 Score=23.90 Aligned_cols=25 Identities=28% Similarity=0.433 Sum_probs=22.0
Q ss_pred CcceeCCCcchhccChHHHHHHHHh
Q psy10073 112 DKQFKCCLCSYGAYQKEKLQFHVKN 136 (144)
Q Consensus 112 ~~~~~C~~C~~~f~~~~~l~~H~~~ 136 (144)
.-.|.|-.|.+-|.+...|..|.++
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHhc
Confidence 3359999999999999999999875
No 155
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=61.94 E-value=3.9 Score=32.50 Aligned_cols=56 Identities=16% Similarity=0.308 Sum_probs=36.3
Q ss_pred ecCccCCccCCccccccccCCCCCCccccCCCCCee-CCCCC-CCcch-hhhhhhcccCCCCcccccCCCCCceeCCCCC
Q psy10073 17 TCLYCNKYVPSDIDVFIGHCQTCPNMSFLNSVIPQS-CKHCK-NFTSS-DVNLLMEHSENCPCMVRPDPVKYKFICVACD 93 (144)
Q Consensus 17 ~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~~~~~~~-C~~C~-~f~~~-~~H~~~~h~~~~~~~~~~~~~~~~~~C~~C~ 93 (144)
.|..||-.|+-...|=. -+-.+....|. |+.|. .+.+. .+ +.|. .| ..|+.||
T Consensus 125 ~CT~CGPRfTIi~alPY--------DR~nTsM~~F~lC~~C~~EY~dP~nR---RfHA--Qp-----------~aCp~CG 180 (750)
T COG0068 125 NCTNCGPRFTIIEALPY--------DRENTSMADFPLCPFCDKEYKDPLNR---RFHA--QP-----------IACPKCG 180 (750)
T ss_pred ccCCCCcceeeeccCCC--------CcccCccccCcCCHHHHHHhcCcccc---cccc--cc-----------ccCcccC
Confidence 58888888877666654 33344444554 99999 88777 22 3343 34 7899999
Q ss_pred ccc
Q psy10073 94 YFT 96 (144)
Q Consensus 94 ~~f 96 (144)
-..
T Consensus 181 P~~ 183 (750)
T COG0068 181 PHL 183 (750)
T ss_pred CCe
Confidence 743
No 156
>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=61.86 E-value=3.9 Score=18.33 Aligned_cols=7 Identities=29% Similarity=0.909 Sum_probs=2.9
Q ss_pred eeCCCCC
Q psy10073 51 QSCKHCK 57 (144)
Q Consensus 51 ~~C~~C~ 57 (144)
+.|+.|+
T Consensus 20 ~vCp~C~ 26 (30)
T PF08274_consen 20 LVCPECG 26 (30)
T ss_dssp EEETTTT
T ss_pred EeCCccc
Confidence 3444443
No 157
>PHA02942 putative transposase; Provisional
Probab=61.62 E-value=6.9 Score=28.91 Aligned_cols=10 Identities=40% Similarity=1.052 Sum_probs=5.3
Q ss_pred eeCCCCCccc
Q psy10073 87 FICVACDYFT 96 (144)
Q Consensus 87 ~~C~~C~~~f 96 (144)
|.|+.||...
T Consensus 343 f~C~~CG~~~ 352 (383)
T PHA02942 343 FHCPSCGYEN 352 (383)
T ss_pred EECCCCCCEe
Confidence 5555555443
No 158
>PRK11032 hypothetical protein; Provisional
Probab=61.25 E-value=5.7 Score=25.53 Aligned_cols=7 Identities=29% Similarity=1.085 Sum_probs=3.3
Q ss_pred eeCCCCC
Q psy10073 51 QSCKHCK 57 (144)
Q Consensus 51 ~~C~~C~ 57 (144)
+.|..||
T Consensus 125 LvC~~Cg 131 (160)
T PRK11032 125 LVCEKCH 131 (160)
T ss_pred EEecCCC
Confidence 4444444
No 159
>PRK12496 hypothetical protein; Provisional
Probab=60.78 E-value=8.1 Score=24.90 Aligned_cols=12 Identities=42% Similarity=0.797 Sum_probs=10.3
Q ss_pred eecCccCCccCC
Q psy10073 16 KTCLYCNKYVPS 27 (144)
Q Consensus 16 ~~C~~C~~~f~~ 27 (144)
|.|.-|++.|..
T Consensus 128 ~~C~gC~~~~~~ 139 (164)
T PRK12496 128 KVCKGCKKKYPE 139 (164)
T ss_pred EECCCCCccccC
Confidence 789999998864
No 160
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=60.10 E-value=8.8 Score=23.81 Aligned_cols=13 Identities=15% Similarity=0.378 Sum_probs=9.6
Q ss_pred eCCCcchhccChH
Q psy10073 116 KCCLCSYGAYQKE 128 (144)
Q Consensus 116 ~C~~C~~~f~~~~ 128 (144)
+|++|.-+|.+.+
T Consensus 123 vCPvCkTSFKss~ 135 (140)
T PF05290_consen 123 VCPVCKTSFKSSS 135 (140)
T ss_pred CCCcccccccccc
Confidence 6888888877654
No 161
>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=59.87 E-value=2.5 Score=23.85 Aligned_cols=10 Identities=30% Similarity=0.836 Sum_probs=2.8
Q ss_pred CCceecCccC
Q psy10073 13 STKKTCLYCN 22 (144)
Q Consensus 13 ~~~~~C~~C~ 22 (144)
.+.|.|+.|+
T Consensus 20 ~~~F~CPfC~ 29 (81)
T PF05129_consen 20 PKVFDCPFCN 29 (81)
T ss_dssp SS----TTT-
T ss_pred CceEcCCcCC
Confidence 3446666666
No 162
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.79 E-value=7.9 Score=20.49 Aligned_cols=16 Identities=13% Similarity=0.156 Sum_probs=10.1
Q ss_pred ccccCCCCCeeCCCCC
Q psy10073 42 MSFLNSVIPQSCKHCK 57 (144)
Q Consensus 42 ~~~h~~~~~~~C~~C~ 57 (144)
..++.+..++.|+.-+
T Consensus 16 ~~I~~~~~~l~C~g~~ 31 (62)
T COG4391 16 ETIEIGDLPLMCPGPE 31 (62)
T ss_pred eEEEeCCeeEEcCCCC
Confidence 4556666777776555
No 163
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=59.67 E-value=4.5 Score=23.26 Aligned_cols=30 Identities=13% Similarity=0.370 Sum_probs=17.6
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhccC
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAYQ 126 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 126 (144)
|.|+.|++.-... .+.-.+.|..|++.|+-
T Consensus 37 y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 37 YFCPFCGKHAVKR----------QAVGIWRCKGCKKTVAG 66 (90)
T ss_pred ccCCCCCCCceee----------eeeEEEEcCCCCCEEeC
Confidence 7888887531110 11235788888877763
No 164
>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=59.31 E-value=4.9 Score=24.23 Aligned_cols=26 Identities=15% Similarity=0.285 Sum_probs=17.1
Q ss_pred ceeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchh
Q psy10073 86 KFICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYG 123 (144)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 123 (144)
...|..|+..|.... ..+.|+.||..
T Consensus 70 ~~~C~~Cg~~~~~~~------------~~~~CP~Cgs~ 95 (115)
T TIGR00100 70 ECECEDCSEEVSPEI------------DLYRCPKCHGI 95 (115)
T ss_pred EEEcccCCCEEecCC------------cCccCcCCcCC
Confidence 378888887765432 13678888743
No 165
>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=59.17 E-value=4.9 Score=18.61 Aligned_cols=14 Identities=21% Similarity=0.342 Sum_probs=7.1
Q ss_pred eecCccCCccCCcc
Q psy10073 16 KTCLYCNKYVPSDI 29 (144)
Q Consensus 16 ~~C~~C~~~f~~~~ 29 (144)
-.|..|++.|....
T Consensus 4 ~~C~eC~~~f~dSy 17 (34)
T PF01286_consen 4 PKCDECGKPFMDSY 17 (34)
T ss_dssp EE-TTT--EES-SS
T ss_pred chHhHhCCHHHHHH
Confidence 46888888887643
No 166
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=59.17 E-value=6.2 Score=31.98 Aligned_cols=26 Identities=23% Similarity=0.487 Sum_probs=20.2
Q ss_pred eecCccCCccCCcc---ccccccCCCCCC
Q psy10073 16 KTCLYCNKYVPSDI---DVFIGHCQTCPN 41 (144)
Q Consensus 16 ~~C~~C~~~f~~~~---~l~~H~c~~c~h 41 (144)
-.|..|++.|.+.. ..++|+|..||.
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 56999999997642 357888888886
No 167
>KOG2482|consensus
Probab=58.82 E-value=6.1 Score=28.60 Aligned_cols=23 Identities=13% Similarity=0.391 Sum_probs=21.0
Q ss_pred ceeCCCCCcccCChhHHHHHHHh
Q psy10073 86 KFICVACDYFTIISQNMRNHTLI 108 (144)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~H~~~ 108 (144)
.+.|..|.+.|..+..|+.||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 38999999999999999999974
No 168
>KOG3214|consensus
Probab=58.68 E-value=6.5 Score=23.00 Aligned_cols=12 Identities=33% Similarity=1.043 Sum_probs=6.8
Q ss_pred eeCCCCC-CCcch
Q psy10073 51 QSCKHCK-NFTSS 62 (144)
Q Consensus 51 ~~C~~C~-~f~~~ 62 (144)
..|.+|+ .|.+.
T Consensus 48 ~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 48 ASCRICEESFQTT 60 (109)
T ss_pred eeeeehhhhhccc
Confidence 4566666 55544
No 169
>PRK05580 primosome assembly protein PriA; Validated
Probab=58.66 E-value=7.6 Score=30.98 Aligned_cols=8 Identities=38% Similarity=1.153 Sum_probs=4.2
Q ss_pred eeCCCCCc
Q psy10073 87 FICVACDY 94 (144)
Q Consensus 87 ~~C~~C~~ 94 (144)
..|..||.
T Consensus 409 l~Ch~Cg~ 416 (679)
T PRK05580 409 LRCHHCGY 416 (679)
T ss_pred EECCCCcC
Confidence 45555554
No 170
>KOG2482|consensus
Probab=57.89 E-value=6.1 Score=28.59 Aligned_cols=50 Identities=20% Similarity=0.481 Sum_probs=35.2
Q ss_pred eeCCCCCcccC-ChhHHHHHHHh-hc---C----------------C--cceeCCCcchhccChHHHHHHHHh
Q psy10073 87 FICVACDYFTI-ISQNMRNHTLI-HL---G----------------D--KQFKCCLCSYGAYQKEKLQFHVKN 136 (144)
Q Consensus 87 ~~C~~C~~~f~-~~~~l~~H~~~-h~---~----------------~--~~~~C~~C~~~f~~~~~l~~H~~~ 136 (144)
..|..|...+. ..+.+..|+-. |. | + ..+.|-.|.+.|..+..|..||+.
T Consensus 145 lqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 145 LQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred eEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHh
Confidence 67888876553 34555566432 21 1 1 147999999999999999999985
No 171
>KOG4173|consensus
Probab=56.88 E-value=5.5 Score=26.65 Aligned_cols=47 Identities=19% Similarity=0.366 Sum_probs=36.8
Q ss_pred eeCCC--CCcccCChhHHHHHHHhhcCCcceeCCCcchhccChHHHHHHHHh
Q psy10073 87 FICVA--CDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAYQKEKLQFHVKN 136 (144)
Q Consensus 87 ~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 136 (144)
|.|++ |...|.....+..|..+-++. .|..|.+.|.+..-|..|+..
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E 128 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILE 128 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHH
Confidence 78876 667888888888776543332 699999999999999999753
No 172
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=56.87 E-value=13 Score=17.83 Aligned_cols=9 Identities=22% Similarity=0.785 Sum_probs=4.3
Q ss_pred eCCCCCccc
Q psy10073 88 ICVACDYFT 96 (144)
Q Consensus 88 ~C~~C~~~f 96 (144)
.|+.||..|
T Consensus 15 ~C~~CgM~Y 23 (41)
T PF13878_consen 15 TCPTCGMLY 23 (41)
T ss_pred CCCCCCCEE
Confidence 455555444
No 173
>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=56.68 E-value=2.4 Score=18.68 Aligned_cols=18 Identities=22% Similarity=0.565 Sum_probs=8.4
Q ss_pred eeCCCCCcccCChhHHHHH
Q psy10073 87 FICVACDYFTIISQNMRNH 105 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H 105 (144)
|.|..|++.| .......|
T Consensus 1 ~sCiDC~~~F-~~~~y~~H 18 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSH 18 (28)
T ss_dssp EEETTTTEEE-EGGGTTT-
T ss_pred CeeecCCCCc-CcCCcCCC
Confidence 3455666666 33334444
No 174
>KOG2906|consensus
Probab=56.64 E-value=12 Score=21.85 Aligned_cols=18 Identities=17% Similarity=0.421 Sum_probs=12.6
Q ss_pred ceecCccCCccCCccccc
Q psy10073 15 KKTCLYCNKYVPSDIDVF 32 (144)
Q Consensus 15 ~~~C~~C~~~f~~~~~l~ 32 (144)
.|.|..|+..|.-...+.
T Consensus 21 rf~C~tCpY~~~I~~ei~ 38 (105)
T KOG2906|consen 21 RFSCRTCPYVFPISREIS 38 (105)
T ss_pred eEEcCCCCceeeEeeeee
Confidence 588899988876554443
No 175
>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=56.47 E-value=9.6 Score=27.26 Aligned_cols=43 Identities=16% Similarity=0.290 Sum_probs=21.6
Q ss_pred eecCccCCccCCccccccccCCCCCCcc------ccCCCCCeeCCCCC-CC
Q psy10073 16 KTCLYCNKYVPSDIDVFIGHCQTCPNMS------FLNSVIPQSCKHCK-NF 59 (144)
Q Consensus 16 ~~C~~C~~~f~~~~~l~~H~c~~c~h~~------~h~~~~~~~C~~C~-~f 59 (144)
+.|+.|...-....+++.=+. .|||.- ......+..|+.|+ .+
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~~~~~~CP~C~~~l 53 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFVRGSGSCPECDTPL 53 (309)
T ss_pred CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhcCCCCCCCCCCCcc
Confidence 679999875333334322122 567621 11122344677776 44
No 176
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=56.35 E-value=16 Score=19.00 Aligned_cols=15 Identities=20% Similarity=0.410 Sum_probs=8.8
Q ss_pred CCCeeCCCCC-CCcch
Q psy10073 48 VIPQSCKHCK-NFTSS 62 (144)
Q Consensus 48 ~~~~~C~~C~-~f~~~ 62 (144)
...|.|+.|| .+.-+
T Consensus 12 ~v~~~Cp~cGipthcS 27 (55)
T PF13824_consen 12 HVNFECPDCGIPTHCS 27 (55)
T ss_pred ccCCcCCCCCCcCccC
Confidence 4457777777 44333
No 177
>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=56.00 E-value=5.2 Score=19.38 Aligned_cols=15 Identities=33% Similarity=0.527 Sum_probs=8.8
Q ss_pred cceeCCCcchhccCh
Q psy10073 113 KQFKCCLCSYGAYQK 127 (144)
Q Consensus 113 ~~~~C~~C~~~f~~~ 127 (144)
.|+.|+.|++.|-..
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 478888888887643
No 178
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=55.79 E-value=12 Score=28.46 Aligned_cols=13 Identities=15% Similarity=0.416 Sum_probs=6.1
Q ss_pred ceecCccCCccCC
Q psy10073 15 KKTCLYCNKYVPS 27 (144)
Q Consensus 15 ~~~C~~C~~~f~~ 27 (144)
.|.|..||..+..
T Consensus 425 ~~~c~~c~~~yd~ 437 (479)
T PRK05452 425 RMQCSVCQWIYDP 437 (479)
T ss_pred eEEECCCCeEECC
Confidence 3555555544443
No 179
>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=55.65 E-value=8.2 Score=24.42 Aligned_cols=7 Identities=29% Similarity=1.032 Sum_probs=4.3
Q ss_pred eeCCCCC
Q psy10073 51 QSCKHCK 57 (144)
Q Consensus 51 ~~C~~C~ 57 (144)
|.|..||
T Consensus 113 l~C~~Cg 119 (146)
T PF07295_consen 113 LVCENCG 119 (146)
T ss_pred EecccCC
Confidence 5666665
No 180
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=55.49 E-value=15 Score=31.46 Aligned_cols=32 Identities=19% Similarity=0.540 Sum_probs=22.1
Q ss_pred eecCccCCccCCccccccccCCCCCCccccCCCCCeeCCCCC
Q psy10073 16 KTCLYCNKYVPSDIDVFIGHCQTCPNMSFLNSVIPQSCKHCK 57 (144)
Q Consensus 16 ~~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~~~~~~~C~~C~ 57 (144)
++|+.||..-.. -.|..||... ..+|.|+.||
T Consensus 668 rkCPkCG~~t~~------~fCP~CGs~t----e~vy~CPsCG 699 (1337)
T PRK14714 668 RRCPSCGTETYE------NRCPDCGTHT----EPVYVCPDCG 699 (1337)
T ss_pred EECCCCCCcccc------ccCcccCCcC----CCceeCccCC
Confidence 789999975321 1688888753 2357788887
No 181
>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=55.30 E-value=3.7 Score=22.23 Aligned_cols=23 Identities=22% Similarity=0.615 Sum_probs=11.5
Q ss_pred eecCccCCccCCccccccccCCCCC
Q psy10073 16 KTCLYCNKYVPSDIDVFIGHCQTCP 40 (144)
Q Consensus 16 ~~C~~C~~~f~~~~~l~~H~c~~c~ 40 (144)
|.| .||...-...+.+.+.| .||
T Consensus 4 frC-~Cgr~lya~e~~kTkkC-~CG 26 (68)
T PF09082_consen 4 FRC-DCGRYLYAKEGAKTKKC-VCG 26 (68)
T ss_dssp EEE-TTS--EEEETT-SEEEE-TTT
T ss_pred EEe-cCCCEEEecCCcceeEe-cCC
Confidence 677 57776555555555444 444
No 182
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=55.24 E-value=4.3 Score=28.94 Aligned_cols=25 Identities=16% Similarity=0.341 Sum_probs=13.1
Q ss_pred cceeCCCcchhccChHHHHHHHHhh
Q psy10073 113 KQFKCCLCSYGAYQKEKLQFHVKNK 137 (144)
Q Consensus 113 ~~~~C~~C~~~f~~~~~l~~H~~~h 137 (144)
..|.|+.|...|-..-+.-.|...|
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHHh
Confidence 3455666655555555555554433
No 183
>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=55.11 E-value=5.1 Score=23.10 Aligned_cols=29 Identities=17% Similarity=0.359 Sum_probs=16.9
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhcc
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAY 125 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 125 (144)
|.|+.|++.-.. + .+.-.+.|..|++.|+
T Consensus 36 y~CpfCgk~~vk--------R--~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 36 YVCPFCGKKTVK--------R--GSTGIWTCRKCGAKFA 64 (91)
T ss_pred ccCCCCCCCceE--------E--EeeEEEEcCCCCCEEe
Confidence 788888753111 0 1123478888887776
No 184
>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=55.08 E-value=11 Score=23.12 Aligned_cols=13 Identities=23% Similarity=0.271 Sum_probs=8.2
Q ss_pred CceecCccCCccC
Q psy10073 14 TKKTCLYCNKYVP 26 (144)
Q Consensus 14 ~~~~C~~C~~~f~ 26 (144)
.+..|+.||+.|-
T Consensus 8 tKr~Cp~cg~kFY 20 (129)
T TIGR02300 8 TKRICPNTGSKFY 20 (129)
T ss_pred ccccCCCcCcccc
Confidence 3456777776664
No 185
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.18 E-value=2.3 Score=23.48 Aligned_cols=12 Identities=17% Similarity=0.437 Sum_probs=8.3
Q ss_pred ceecCccCCccC
Q psy10073 15 KKTCLYCNKYVP 26 (144)
Q Consensus 15 ~~~C~~C~~~f~ 26 (144)
.|+|..||..|.
T Consensus 12 ~Y~c~~cg~~~d 23 (82)
T COG2331 12 SYECTECGNRFD 23 (82)
T ss_pred EEeecccchHHH
Confidence 377888877664
No 186
>PF12907 zf-met2: Zinc-binding
Probab=54.17 E-value=9.7 Score=18.32 Aligned_cols=7 Identities=43% Similarity=1.198 Sum_probs=3.3
Q ss_pred eeCCCCC
Q psy10073 87 FICVACD 93 (144)
Q Consensus 87 ~~C~~C~ 93 (144)
+.|.+|.
T Consensus 2 i~C~iC~ 8 (40)
T PF12907_consen 2 IICKICR 8 (40)
T ss_pred cCcHHhh
Confidence 3445554
No 187
>KOG2272|consensus
Probab=54.13 E-value=2.8 Score=28.92 Aligned_cols=42 Identities=19% Similarity=0.331 Sum_probs=24.1
Q ss_pred eecCccCCccCCcccccc---ccCCCCCCccccCCCCCeeCCCCC
Q psy10073 16 KTCLYCNKYVPSDIDVFI---GHCQTCPNMSFLNSVIPQSCKHCK 57 (144)
Q Consensus 16 ~~C~~C~~~f~~~~~l~~---H~c~~c~h~~~h~~~~~~~C~~C~ 57 (144)
|.|+.|.+...+..-++. +.|..|+....-.+...|.|..|.
T Consensus 100 F~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh 144 (332)
T KOG2272|consen 100 FRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCH 144 (332)
T ss_pred chhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhh
Confidence 778888877766555443 355555544333344445555554
No 188
>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=53.51 E-value=10 Score=18.02 Aligned_cols=10 Identities=20% Similarity=0.428 Sum_probs=4.3
Q ss_pred CCCeeCCCCC
Q psy10073 48 VIPQSCKHCK 57 (144)
Q Consensus 48 ~~~~~C~~C~ 57 (144)
.+.+.|..|+
T Consensus 22 ~~~w~C~~C~ 31 (40)
T PF04810_consen 22 GKTWICNFCG 31 (40)
T ss_dssp TTEEEETTT-
T ss_pred CCEEECcCCC
Confidence 3345555554
No 189
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=53.43 E-value=17 Score=26.54 Aligned_cols=67 Identities=21% Similarity=0.392 Sum_probs=39.6
Q ss_pred eCCCCC-CCcch---hhhhhhcccCCCCcccccCCCCCceeCCCCCc-------ccCChhHHHHHHHhhcCCcceeCCC-
Q psy10073 52 SCKHCK-NFTSS---DVNLLMEHSENCPCMVRPDPVKYKFICVACDY-------FTIISQNMRNHTLIHLGDKQFKCCL- 119 (144)
Q Consensus 52 ~C~~C~-~f~~~---~~H~~~~h~~~~~~~~~~~~~~~~~~C~~C~~-------~f~~~~~l~~H~~~h~~~~~~~C~~- 119 (144)
.|..|. .|.+- ..|+ +..+ =.|-+|++ -|.+..+|..|.+. .-|.|.+
T Consensus 222 ~C~FC~~~FYdDDEL~~Hc-R~~H---------------E~ChICD~v~p~~~QYFK~Y~~Le~HF~~----~hy~ct~q 281 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHC-RLRH---------------EACHICDMVGPIRYQYFKSYEDLEAHFRN----AHYCCTFQ 281 (493)
T ss_pred hhhhccceecChHHHHHHH-Hhhh---------------hhhhhhhccCccchhhhhCHHHHHHHhhc----CceEEEEE
Confidence 577788 77665 6666 4322 24444443 36667777777643 2344432
Q ss_pred -cc----hhccChHHHHHHHHhhc
Q psy10073 120 -CS----YGAYQKEKLQFHVKNKH 138 (144)
Q Consensus 120 -C~----~~f~~~~~l~~H~~~h~ 138 (144)
|- ..|.....|..|+..-+
T Consensus 282 tc~~~k~~vf~~~~el~~h~~~~h 305 (493)
T COG5236 282 TCRVGKCYVFPYHTELLEHLTRFH 305 (493)
T ss_pred EEecCcEEEeccHHHHHHHHHHHh
Confidence 21 46888888888876544
No 190
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=52.29 E-value=12 Score=23.38 Aligned_cols=10 Identities=20% Similarity=0.451 Sum_probs=6.4
Q ss_pred eeCCCCCccc
Q psy10073 87 FICVACDYFT 96 (144)
Q Consensus 87 ~~C~~C~~~f 96 (144)
|.|..|+..+
T Consensus 134 y~C~~C~g~l 143 (146)
T smart00731 134 YRCGKCGGKL 143 (146)
T ss_pred EEcCCCCCEE
Confidence 6777776544
No 191
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=51.51 E-value=11 Score=24.65 Aligned_cols=28 Identities=21% Similarity=0.579 Sum_probs=20.8
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchh
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYG 123 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 123 (144)
|.|+.|...|+...++. .-|.|+.||..
T Consensus 114 y~C~~~~~r~sfdeA~~---------~~F~Cp~Cg~~ 141 (176)
T COG1675 114 YVCPNCHVKYSFDEAME---------LGFTCPKCGED 141 (176)
T ss_pred eeCCCCCCcccHHHHHH---------hCCCCCCCCch
Confidence 99999988776655542 23999999954
No 192
>KOG2636|consensus
Probab=51.40 E-value=10 Score=28.49 Aligned_cols=29 Identities=21% Similarity=0.468 Sum_probs=22.4
Q ss_pred HhhcCCcceeCCCcc-hhccChHHHHHHHH
Q psy10073 107 LIHLGDKQFKCCLCS-YGAYQKEKLQFHVK 135 (144)
Q Consensus 107 ~~h~~~~~~~C~~C~-~~f~~~~~l~~H~~ 135 (144)
+.|.-...|.|.+|| +++.-+..+.+|-.
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 456667788999998 78888888888843
No 193
>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=51.09 E-value=7 Score=22.86 Aligned_cols=15 Identities=20% Similarity=0.406 Sum_probs=9.6
Q ss_pred CCCceecCccCCccC
Q psy10073 12 LSTKKTCLYCNKYVP 26 (144)
Q Consensus 12 ~~~~~~C~~C~~~f~ 26 (144)
..++.+|..||..|.
T Consensus 76 ~g~~~rC~eCG~~fk 90 (97)
T cd00924 76 KGKPKRCPECGHVFK 90 (97)
T ss_pred CCCceeCCCCCcEEE
Confidence 345667777777664
No 194
>KOG0717|consensus
Probab=51.06 E-value=9.5 Score=28.83 Aligned_cols=21 Identities=19% Similarity=0.491 Sum_probs=17.7
Q ss_pred eeCCCcchhccChHHHHHHHH
Q psy10073 115 FKCCLCSYGAYQKEKLQFHVK 135 (144)
Q Consensus 115 ~~C~~C~~~f~~~~~l~~H~~ 135 (144)
+.|.+|+++|.+...|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 778889999998888888865
No 195
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=50.89 E-value=12 Score=23.07 Aligned_cols=11 Identities=18% Similarity=0.564 Sum_probs=5.3
Q ss_pred eeCCCCCcccC
Q psy10073 87 FICVACDYFTI 97 (144)
Q Consensus 87 ~~C~~C~~~f~ 97 (144)
|.|..|++.|.
T Consensus 54 yrC~~C~~tf~ 64 (129)
T COG3677 54 YKCKSCGSTFT 64 (129)
T ss_pred cccCCcCccee
Confidence 45555554443
No 196
>PLN02294 cytochrome c oxidase subunit Vb
Probab=50.84 E-value=8 Score=25.06 Aligned_cols=16 Identities=19% Similarity=0.492 Sum_probs=9.0
Q ss_pred CCCCceecCccCCccC
Q psy10073 11 PLSTKKTCLYCNKYVP 26 (144)
Q Consensus 11 ~~~~~~~C~~C~~~f~ 26 (144)
...++.+|+.||..|.
T Consensus 137 ~kGkp~RCpeCG~~fk 152 (174)
T PLN02294 137 EKGKSFECPVCTQYFE 152 (174)
T ss_pred cCCCceeCCCCCCEEE
Confidence 3344566666666554
No 197
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=50.76 E-value=14 Score=18.87 Aligned_cols=12 Identities=17% Similarity=0.277 Sum_probs=6.6
Q ss_pred eeCCCCCcccCC
Q psy10073 87 FICVACDYFTII 98 (144)
Q Consensus 87 ~~C~~C~~~f~~ 98 (144)
+.|+.|+..|..
T Consensus 29 W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 29 WKCPKCGHEWKA 40 (55)
T ss_pred EECCCCCCeeEc
Confidence 556666555544
No 198
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=50.73 E-value=7.6 Score=23.38 Aligned_cols=11 Identities=27% Similarity=0.733 Sum_probs=6.6
Q ss_pred eeCCCCCcccC
Q psy10073 87 FICVACDYFTI 97 (144)
Q Consensus 87 ~~C~~C~~~f~ 97 (144)
|.|..||..|.
T Consensus 101 y~C~~Cg~~wr 111 (113)
T COG1594 101 YKCTRCGYRWR 111 (113)
T ss_pred EEecccCCEee
Confidence 66666666553
No 199
>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=50.67 E-value=16 Score=21.56 Aligned_cols=14 Identities=21% Similarity=0.453 Sum_probs=9.0
Q ss_pred CceecCccCCccCC
Q psy10073 14 TKKTCLYCNKYVPS 27 (144)
Q Consensus 14 ~~~~C~~C~~~f~~ 27 (144)
+|-.|+.||.....
T Consensus 1 ~p~~CpYCg~~~~l 14 (102)
T PF11672_consen 1 KPIICPYCGGPAEL 14 (102)
T ss_pred CCcccCCCCCeeEE
Confidence 35678888865433
No 200
>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=50.34 E-value=14 Score=28.36 Aligned_cols=19 Identities=32% Similarity=0.954 Sum_probs=12.1
Q ss_pred cCCCCCCccccCCCCCeeCCCCC
Q psy10073 35 HCQTCPNMSFLNSVIPQSCKHCK 57 (144)
Q Consensus 35 ~c~~c~h~~~h~~~~~~~C~~C~ 57 (144)
.|..||+. ...|..|+.||
T Consensus 242 ~Ch~Cg~~----~~~~~~Cp~C~ 260 (505)
T TIGR00595 242 RCHYCGYQ----EPIPKTCPQCG 260 (505)
T ss_pred EcCCCcCc----CCCCCCCCCCC
Confidence 46666653 34467788888
No 201
>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 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=49.61 E-value=17 Score=16.31 Aligned_cols=7 Identities=29% Similarity=0.957 Sum_probs=4.3
Q ss_pred eeCCCCC
Q psy10073 51 QSCKHCK 57 (144)
Q Consensus 51 ~~C~~C~ 57 (144)
|.|..|+
T Consensus 28 f~C~~C~ 34 (39)
T smart00132 28 FKCSKCG 34 (39)
T ss_pred CCCcccC
Confidence 5666666
No 203
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=49.23 E-value=9.8 Score=19.22 Aligned_cols=14 Identities=29% Similarity=0.714 Sum_probs=7.5
Q ss_pred CCeeCCCCC-CCcch
Q psy10073 49 IPQSCKHCK-NFTSS 62 (144)
Q Consensus 49 ~~~~C~~C~-~f~~~ 62 (144)
+.+.|..|| .|...
T Consensus 3 k~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFT 17 (49)
T ss_pred eeEEcccCCCeEEEe
Confidence 345566666 55444
No 204
>KOG0978|consensus
Probab=48.79 E-value=5.7 Score=31.60 Aligned_cols=11 Identities=18% Similarity=0.755 Sum_probs=5.8
Q ss_pred eeCCCCC-CCcc
Q psy10073 51 QSCKHCK-NFTS 61 (144)
Q Consensus 51 ~~C~~C~-~f~~ 61 (144)
..|+.|. .+..
T Consensus 644 LkCs~Cn~R~Kd 655 (698)
T KOG0978|consen 644 LKCSVCNTRWKD 655 (698)
T ss_pred eeCCCccCchhh
Confidence 4566665 4433
No 205
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=48.71 E-value=6.9 Score=22.52 Aligned_cols=30 Identities=17% Similarity=0.425 Sum_probs=17.2
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhccC
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAYQ 126 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 126 (144)
|.|+.|++.-.. + .+.-.+.|..|++.|+-
T Consensus 37 y~CpfCgk~~vk--------R--~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 37 HVCPVCGRPKVK--------R--VGTGIWECRKCGAKFAG 66 (90)
T ss_pred ccCCCCCCCceE--------E--EEEEEEEcCCCCCEEeC
Confidence 788888653111 0 11234788888877763
No 206
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=48.50 E-value=13 Score=27.75 Aligned_cols=12 Identities=25% Similarity=0.445 Sum_probs=6.2
Q ss_pred eeCCCCCcccCC
Q psy10073 87 FICVACDYFTII 98 (144)
Q Consensus 87 ~~C~~C~~~f~~ 98 (144)
|+|+.|+..+..
T Consensus 368 ~rC~kCg~~~~~ 379 (421)
T COG1571 368 FRCKKCGTRARE 379 (421)
T ss_pred cccccccccCCc
Confidence 555555554443
No 207
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.44 E-value=12 Score=22.42 Aligned_cols=28 Identities=4% Similarity=-0.344 Sum_probs=18.4
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchhcc
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYGAY 125 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 125 (144)
-.|+.|++.|-.. ...|..|++||++|.
T Consensus 10 ridPetg~KFYDL-----------NrdPiVsPytG~s~P 37 (129)
T COG4530 10 RIDPETGKKFYDL-----------NRDPIVSPYTGKSYP 37 (129)
T ss_pred ccCccccchhhcc-----------CCCccccCcccccch
Confidence 3677777776432 245777888888773
No 208
>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=48.30 E-value=10 Score=18.20 Aligned_cols=7 Identities=29% Similarity=0.947 Sum_probs=4.1
Q ss_pred eeCCCCC
Q psy10073 51 QSCKHCK 57 (144)
Q Consensus 51 ~~C~~C~ 57 (144)
+.|+.||
T Consensus 33 ~~C~~CG 39 (46)
T TIGR03831 33 LVCPQCG 39 (46)
T ss_pred cccccCC
Confidence 4566666
No 209
>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=47.45 E-value=11 Score=23.72 Aligned_cols=9 Identities=22% Similarity=0.523 Sum_probs=4.6
Q ss_pred eeCCCCCcc
Q psy10073 87 FICVACDYF 95 (144)
Q Consensus 87 ~~C~~C~~~ 95 (144)
|.|+.|+..
T Consensus 144 ~~C~~C~~~ 152 (157)
T PF10263_consen 144 YRCGRCGGP 152 (157)
T ss_pred EECCCCCCE
Confidence 555555543
No 210
>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=47.26 E-value=15 Score=23.20 Aligned_cols=13 Identities=31% Similarity=0.800 Sum_probs=10.0
Q ss_pred CeeCCCCC-CCcch
Q psy10073 50 PQSCKHCK-NFTSS 62 (144)
Q Consensus 50 ~~~C~~C~-~f~~~ 62 (144)
.=.|..|| .|.+.
T Consensus 28 RReC~~C~~RFTTy 41 (147)
T TIGR00244 28 RRECLECHERFTTF 41 (147)
T ss_pred cccCCccCCcccee
Confidence 35788888 88887
No 211
>PRK04351 hypothetical protein; Provisional
Probab=47.20 E-value=16 Score=23.20 Aligned_cols=12 Identities=17% Similarity=0.384 Sum_probs=7.7
Q ss_pred eeCCCCCcccCC
Q psy10073 87 FICVACDYFTII 98 (144)
Q Consensus 87 ~~C~~C~~~f~~ 98 (144)
|.|..|+-.+..
T Consensus 133 yrCg~C~g~L~~ 144 (149)
T PRK04351 133 YRCGKCRGKLKL 144 (149)
T ss_pred EEeCCCCcEeee
Confidence 777777765543
No 212
>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=46.76 E-value=22 Score=18.00 Aligned_cols=12 Identities=25% Similarity=0.473 Sum_probs=6.4
Q ss_pred eCCCcchhccCh
Q psy10073 116 KCCLCSYGAYQK 127 (144)
Q Consensus 116 ~C~~C~~~f~~~ 127 (144)
.|++|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 899999988753
No 213
>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=46.20 E-value=18 Score=27.50 Aligned_cols=27 Identities=19% Similarity=0.279 Sum_probs=21.2
Q ss_pred cceeCCCcchhccChHHHHHHHHh-hcC
Q psy10073 113 KQFKCCLCSYGAYQKEKLQFHVKN-KHS 139 (144)
Q Consensus 113 ~~~~C~~C~~~f~~~~~l~~H~~~-h~~ 139 (144)
+-+.|+.|.+.|.....+..|+.. |.+
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 347899999999999999999874 443
No 214
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=45.78 E-value=14 Score=22.17 Aligned_cols=10 Identities=40% Similarity=0.846 Sum_probs=5.3
Q ss_pred eecCccCCcc
Q psy10073 16 KTCLYCNKYV 25 (144)
Q Consensus 16 ~~C~~C~~~f 25 (144)
+.|..||..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 5555555444
No 215
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=45.33 E-value=24 Score=16.90 Aligned_cols=11 Identities=18% Similarity=0.510 Sum_probs=4.6
Q ss_pred cCccCCccCCc
Q psy10073 18 CLYCNKYVPSD 28 (144)
Q Consensus 18 C~~C~~~f~~~ 28 (144)
|++|...|...
T Consensus 1 CpiC~~~~~~P 11 (42)
T PF15227_consen 1 CPICLDLFKDP 11 (42)
T ss_dssp ETTTTSB-SSE
T ss_pred CCccchhhCCc
Confidence 34454444443
No 216
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=45.14 E-value=20 Score=18.14 Aligned_cols=7 Identities=29% Similarity=0.881 Sum_probs=3.2
Q ss_pred eeCCCCC
Q psy10073 51 QSCKHCK 57 (144)
Q Consensus 51 ~~C~~C~ 57 (144)
+.|..||
T Consensus 38 ~~C~~Cg 44 (50)
T PRK00432 38 WHCGKCG 44 (50)
T ss_pred EECCCcC
Confidence 4444444
No 217
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=45.04 E-value=13 Score=17.89 Aligned_cols=10 Identities=20% Similarity=0.511 Sum_probs=5.1
Q ss_pred eeCCCCCccc
Q psy10073 87 FICVACDYFT 96 (144)
Q Consensus 87 ~~C~~C~~~f 96 (144)
-.|++|+..|
T Consensus 30 ~~CpYCg~~y 39 (40)
T PF10276_consen 30 VVCPYCGTRY 39 (40)
T ss_dssp EEETTTTEEE
T ss_pred EECCCCCCEE
Confidence 4555555443
No 218
>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=44.98 E-value=16 Score=17.03 Aligned_cols=8 Identities=25% Similarity=0.766 Sum_probs=4.0
Q ss_pred ecCccCCc
Q psy10073 17 TCLYCNKY 24 (144)
Q Consensus 17 ~C~~C~~~ 24 (144)
.|++|+..
T Consensus 10 ~C~~C~~~ 17 (36)
T PF11781_consen 10 PCPVCGSR 17 (36)
T ss_pred cCCCCCCe
Confidence 35555543
No 219
>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=44.63 E-value=18 Score=27.53 Aligned_cols=25 Identities=20% Similarity=0.293 Sum_probs=21.8
Q ss_pred eeCCCCCcccCChhHHHHHHHh-hcC
Q psy10073 87 FICVACDYFTIISQNMRNHTLI-HLG 111 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~-h~~ 111 (144)
+.|+.|.+.|.....+..|+.. |.+
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhh
Confidence 8999999999999999999864 544
No 220
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.58 E-value=17 Score=22.20 Aligned_cols=11 Identities=18% Similarity=0.232 Sum_probs=7.1
Q ss_pred eecCccCCccCC
Q psy10073 16 KTCLYCNKYVPS 27 (144)
Q Consensus 16 ~~C~~C~~~f~~ 27 (144)
+.| .||..|..
T Consensus 71 ~~C-~Cg~~~~~ 81 (124)
T PRK00762 71 IEC-ECGYEGVV 81 (124)
T ss_pred EEe-eCcCcccc
Confidence 667 77766554
No 221
>PRK10220 hypothetical protein; Provisional
Probab=44.18 E-value=24 Score=21.11 Aligned_cols=11 Identities=27% Similarity=0.504 Sum_probs=6.9
Q ss_pred ecCccCCccCC
Q psy10073 17 TCLYCNKYVPS 27 (144)
Q Consensus 17 ~C~~C~~~f~~ 27 (144)
.|+.|+..|.+
T Consensus 5 ~CP~C~seytY 15 (111)
T PRK10220 5 HCPKCNSEYTY 15 (111)
T ss_pred cCCCCCCcceE
Confidence 47777765554
No 222
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=44.12 E-value=9.4 Score=25.39 Aligned_cols=10 Identities=20% Similarity=0.557 Sum_probs=5.6
Q ss_pred eecCccCCcc
Q psy10073 16 KTCLYCNKYV 25 (144)
Q Consensus 16 ~~C~~C~~~f 25 (144)
..|+.||..+
T Consensus 15 ~~CPvCg~~l 24 (201)
T COG1779 15 IDCPVCGGTL 24 (201)
T ss_pred ecCCccccee
Confidence 4566666533
No 223
>KOG2071|consensus
Probab=43.86 E-value=15 Score=28.63 Aligned_cols=28 Identities=18% Similarity=0.272 Sum_probs=24.2
Q ss_pred CcceeCCCcchhccChHHHHHHHHhhcC
Q psy10073 112 DKQFKCCLCSYGAYQKEKLQFHVKNKHS 139 (144)
Q Consensus 112 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 139 (144)
..|-+|..||..|........||..|..
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhhh
Confidence 5678999999999999999999888764
No 224
>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=43.85 E-value=21 Score=21.35 Aligned_cols=11 Identities=27% Similarity=0.516 Sum_probs=6.7
Q ss_pred ecCccCCccCC
Q psy10073 17 TCLYCNKYVPS 27 (144)
Q Consensus 17 ~C~~C~~~f~~ 27 (144)
.|+.|+..|.+
T Consensus 4 ~CP~C~seytY 14 (109)
T TIGR00686 4 PCPKCNSEYTY 14 (109)
T ss_pred cCCcCCCcceE
Confidence 46777665554
No 225
>PRK05580 primosome assembly protein PriA; Validated
Probab=43.85 E-value=20 Score=28.70 Aligned_cols=19 Identities=32% Similarity=0.961 Sum_probs=12.7
Q ss_pred cCCCCCCccccCCCCCeeCCCCC
Q psy10073 35 HCQTCPNMSFLNSVIPQSCKHCK 57 (144)
Q Consensus 35 ~c~~c~h~~~h~~~~~~~C~~C~ 57 (144)
.|..||+. ...+..|+.||
T Consensus 410 ~Ch~Cg~~----~~~~~~Cp~Cg 428 (679)
T PRK05580 410 RCHHCGYQ----EPIPKACPECG 428 (679)
T ss_pred ECCCCcCC----CCCCCCCCCCc
Confidence 46666653 34567899998
No 226
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=43.43 E-value=36 Score=21.74 Aligned_cols=36 Identities=28% Similarity=0.647 Sum_probs=15.0
Q ss_pred eeCCCCCccc------CChhHHHHHHHh--------h----cCCcceeCCCcch
Q psy10073 87 FICVACDYFT------IISQNMRNHTLI--------H----LGDKQFKCCLCSY 122 (144)
Q Consensus 87 ~~C~~C~~~f------~~~~~l~~H~~~--------h----~~~~~~~C~~C~~ 122 (144)
.+|..|++.| ...+.+..|+.. | .|+..++|..||-
T Consensus 15 v~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~ 68 (152)
T PF09416_consen 15 VKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGS 68 (152)
T ss_dssp EEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT--
T ss_pred eEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCC
Confidence 5666666655 234555666432 1 1344577887774
No 227
>KOG0717|consensus
Probab=43.41 E-value=16 Score=27.74 Aligned_cols=22 Identities=23% Similarity=0.483 Sum_probs=20.1
Q ss_pred eeCCCCCcccCChhHHHHHHHh
Q psy10073 87 FICVACDYFTIISQNMRNHTLI 108 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~ 108 (144)
+.|..|++.|.+...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 8899999999999999999754
No 228
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=43.37 E-value=16 Score=21.91 Aligned_cols=10 Identities=30% Similarity=0.677 Sum_probs=4.9
Q ss_pred eecCccCCcc
Q psy10073 16 KTCLYCNKYV 25 (144)
Q Consensus 16 ~~C~~C~~~f 25 (144)
..|..||..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 4555555444
No 229
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=43.17 E-value=17 Score=23.78 Aligned_cols=24 Identities=21% Similarity=0.546 Sum_probs=17.7
Q ss_pred ceecCccCCccCCccccccccCCCCCCc
Q psy10073 15 KKTCLYCNKYVPSDIDVFIGHCQTCPNM 42 (144)
Q Consensus 15 ~~~C~~C~~~f~~~~~l~~H~c~~c~h~ 42 (144)
.+.|.-|++.|. ...+.|..||+.
T Consensus 139 ~~rC~GC~~~f~----~~~~~Cp~CG~~ 162 (177)
T COG1439 139 RLRCHGCKRIFP----EPKDFCPICGSP 162 (177)
T ss_pred eEEEecCceecC----CCCCcCCCCCCc
Confidence 388999999998 333567777764
No 230
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=43.11 E-value=19 Score=17.00 Aligned_cols=10 Identities=20% Similarity=0.520 Sum_probs=2.6
Q ss_pred eeCCCcchhc
Q psy10073 115 FKCCLCSYGA 124 (144)
Q Consensus 115 ~~C~~C~~~f 124 (144)
|-|+.|...|
T Consensus 4 yyCdyC~~~~ 13 (38)
T PF06220_consen 4 YYCDYCKKYL 13 (38)
T ss_dssp -B-TTT--B-
T ss_pred eeccccccee
Confidence 4455555555
No 231
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=42.87 E-value=11 Score=17.74 Aligned_cols=12 Identities=25% Similarity=0.459 Sum_probs=6.4
Q ss_pred CceecCccCCcc
Q psy10073 14 TKKTCLYCNKYV 25 (144)
Q Consensus 14 ~~~~C~~C~~~f 25 (144)
+.|+|..||...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 458888888754
No 232
>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=42.83 E-value=5.9 Score=18.43 Aligned_cols=10 Identities=30% Similarity=0.836 Sum_probs=4.9
Q ss_pred CeeCCCCC-CC
Q psy10073 50 PQSCKHCK-NF 59 (144)
Q Consensus 50 ~~~C~~C~-~f 59 (144)
+..|..|| .+
T Consensus 21 ~isC~~CGPr~ 31 (35)
T PF07503_consen 21 FISCTNCGPRY 31 (35)
T ss_dssp T--BTTCC-SC
T ss_pred CccCCCCCCCE
Confidence 34566776 54
No 233
>KOG2231|consensus
Probab=42.72 E-value=33 Score=27.44 Aligned_cols=65 Identities=23% Similarity=0.405 Sum_probs=37.8
Q ss_pred eeCCCCC-CCcch---hhhhhhcccCCCCcccccCCCCCceeCCCCC------cccCChhHHHHHHHhhcCCcceeCC--
Q psy10073 51 QSCKHCK-NFTSS---DVNLLMEHSENCPCMVRPDPVKYKFICVACD------YFTIISQNMRNHTLIHLGDKQFKCC-- 118 (144)
Q Consensus 51 ~~C~~C~-~f~~~---~~H~~~~h~~~~~~~~~~~~~~~~~~C~~C~------~~f~~~~~l~~H~~~h~~~~~~~C~-- 118 (144)
-.|..|. .|... ..|+ +.+. |.|..|. .-|.....|..|-+..+ |.|+
T Consensus 183 p~C~~C~~~fld~~el~rH~-~~~h---------------~~chfC~~~~~~neyy~~~~dLe~HfR~~H----flCE~~ 242 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHL-RFDH---------------EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH----FLCEEE 242 (669)
T ss_pred ccchhhhhhhccHHHHHHhh-ccce---------------eheeecCcccccchhcccchHHHHHhhhcC----cccccc
Confidence 3577788 77666 6666 3322 6666663 45677788888876544 5665
Q ss_pred Ccc-hhccChHHHHHHHH
Q psy10073 119 LCS-YGAYQKEKLQFHVK 135 (144)
Q Consensus 119 ~C~-~~f~~~~~l~~H~~ 135 (144)
.|. +.|.....+..+++
T Consensus 243 ~C~~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 243 FCRTKKFYVAFELEIELK 260 (669)
T ss_pred ccccceeeehhHHHHHHH
Confidence 453 23333334444444
No 234
>KOG2636|consensus
Probab=42.30 E-value=18 Score=27.27 Aligned_cols=29 Identities=14% Similarity=0.317 Sum_probs=25.0
Q ss_pred ccCCCCCceeCCCCC-cccCChhHHHHHHH
Q psy10073 79 RPDPVKYKFICVACD-YFTIISQNMRNHTL 107 (144)
Q Consensus 79 ~~~~~~~~~~C~~C~-~~f~~~~~l~~H~~ 107 (144)
+.|.-...|.|.+|| +++.-...+.+|..
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 667777889999999 88999999999964
No 235
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=41.80 E-value=6.8 Score=21.36 Aligned_cols=29 Identities=24% Similarity=0.527 Sum_probs=12.7
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchh
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYG 123 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 123 (144)
..|..|+..++.... ..+ ..+.|+.|+..
T Consensus 42 v~Cg~C~~~~~~~~~-------~c~-~~~~C~~C~~~ 70 (71)
T PF05495_consen 42 VICGKCRTEQPIDEY-------SCG-ADYFCPICGLY 70 (71)
T ss_dssp EEETTT--EEES-SB-------TT---SEEETTTTEE
T ss_pred eECCCCCCccChhhh-------hcC-CCccCcCcCCC
Confidence 667777665544332 111 34666666543
No 236
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=41.57 E-value=28 Score=25.06 Aligned_cols=36 Identities=14% Similarity=0.133 Sum_probs=19.1
Q ss_pred eeCCCCCcccCChhHHHHH-HHhh-cCCcceeCCCcchhccC
Q psy10073 87 FICVACDYFTIISQNMRNH-TLIH-LGDKQFKCCLCSYGAYQ 126 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H-~~~h-~~~~~~~C~~C~~~f~~ 126 (144)
..|+.||.. ..|.-. +..- .+.+...|..|+...+.
T Consensus 227 ~~C~~Cg~~----~~l~y~~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 227 VKCSNCEQS----GKLHYWSLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred ccCCCCCCC----CceeeeeecCCCcceEeeeccccccccee
Confidence 689999852 122111 1110 12355789999865544
No 237
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=41.42 E-value=25 Score=16.87 Aligned_cols=8 Identities=25% Similarity=0.592 Sum_probs=4.7
Q ss_pred cCccCCcc
Q psy10073 18 CLYCNKYV 25 (144)
Q Consensus 18 C~~C~~~f 25 (144)
|++|...|
T Consensus 2 C~~C~~~~ 9 (44)
T PF14634_consen 2 CNICFEKY 9 (44)
T ss_pred CcCcCccc
Confidence 55565555
No 238
>PRK00420 hypothetical protein; Validated
Probab=41.02 E-value=29 Score=20.92 Aligned_cols=9 Identities=11% Similarity=0.364 Sum_probs=4.2
Q ss_pred eeCCCCCcc
Q psy10073 87 FICVACDYF 95 (144)
Q Consensus 87 ~~C~~C~~~ 95 (144)
..|+.||..
T Consensus 41 ~~Cp~Cg~~ 49 (112)
T PRK00420 41 VVCPVHGKV 49 (112)
T ss_pred eECCCCCCe
Confidence 445555443
No 239
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=40.84 E-value=19 Score=22.88 Aligned_cols=13 Identities=31% Similarity=0.756 Sum_probs=10.2
Q ss_pred CeeCCCCC-CCcch
Q psy10073 50 PQSCKHCK-NFTSS 62 (144)
Q Consensus 50 ~~~C~~C~-~f~~~ 62 (144)
.=.|+.|| .|.+.
T Consensus 28 RReC~~C~~RFTTf 41 (156)
T COG1327 28 RRECLECGERFTTF 41 (156)
T ss_pred hhcccccccccchh
Confidence 35788899 88887
No 240
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=40.58 E-value=23 Score=17.89 Aligned_cols=7 Identities=29% Similarity=1.056 Sum_probs=3.5
Q ss_pred eeCCCCC
Q psy10073 87 FICVACD 93 (144)
Q Consensus 87 ~~C~~C~ 93 (144)
+.|..||
T Consensus 38 ~~CGkCg 44 (51)
T COG1998 38 WACGKCG 44 (51)
T ss_pred eEecccc
Confidence 4555554
No 241
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=39.37 E-value=36 Score=15.89 Aligned_cols=11 Identities=27% Similarity=0.643 Sum_probs=5.3
Q ss_pred CCCCCeeCCCC
Q psy10073 46 NSVIPQSCKHC 56 (144)
Q Consensus 46 ~~~~~~~C~~C 56 (144)
.|...|.|..|
T Consensus 25 ~G~qryrC~~C 35 (36)
T PF03811_consen 25 SGHQRYRCKDC 35 (36)
T ss_pred CCCEeEecCcC
Confidence 33344555554
No 242
>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=38.92 E-value=13 Score=18.08 Aligned_cols=13 Identities=15% Similarity=0.350 Sum_probs=9.4
Q ss_pred eCCCcchhccChH
Q psy10073 116 KCCLCSYGAYQKE 128 (144)
Q Consensus 116 ~C~~C~~~f~~~~ 128 (144)
.|.+|++.|+...
T Consensus 10 ~C~~C~rpf~WRK 22 (42)
T PF10013_consen 10 ICPVCGRPFTWRK 22 (42)
T ss_pred cCcccCCcchHHH
Confidence 5888888887654
No 243
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=37.85 E-value=14 Score=21.92 Aligned_cols=26 Identities=15% Similarity=0.315 Sum_probs=21.9
Q ss_pred CCCceeCCCCCcccCChhHHHHHHHh
Q psy10073 83 VKYKFICVACDYFTIISQNMRNHTLI 108 (144)
Q Consensus 83 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 108 (144)
+.+.+-|.+|.+-|.+...|..|.+.
T Consensus 52 GlGqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 52 GLGQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred CCceeeeehhHHHHHHHHHHHHHhcc
Confidence 55568999999999999999999753
No 244
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=37.78 E-value=9.3 Score=27.81 Aligned_cols=39 Identities=33% Similarity=0.524 Sum_probs=19.4
Q ss_pred eeCCCCC-C-Ccch-----hhhhhhcccCCCCcccccCCCCCceeCCCCCcccCCh
Q psy10073 51 QSCKHCK-N-FTSS-----DVNLLMEHSENCPCMVRPDPVKYKFICVACDYFTIIS 99 (144)
Q Consensus 51 ~~C~~C~-~-f~~~-----~~H~~~~h~~~~~~~~~~~~~~~~~~C~~C~~~f~~~ 99 (144)
+.|..|. + |... ..|....+...+.| |.|..|+......
T Consensus 253 v~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRF----------FkC~~C~~Rt~sl 298 (344)
T PF09332_consen 253 VTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRF----------FKCKDCGNRTISL 298 (344)
T ss_dssp EEETTT--EESS--HHHHHTT--EEEEEEE-EE----------EE-T-TS-EEEES
T ss_pred EEcCCCCCcccCcchhHHhcCCceEEeeeeeee----------EECCCCCCeeeec
Confidence 7888888 3 3333 55654555555655 8999998875543
No 245
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=37.29 E-value=30 Score=24.04 Aligned_cols=14 Identities=29% Similarity=0.710 Sum_probs=9.1
Q ss_pred CCeeCCCCC-CCcch
Q psy10073 49 IPQSCKHCK-NFTSS 62 (144)
Q Consensus 49 ~~~~C~~C~-~f~~~ 62 (144)
..|.|+.|+ .|...
T Consensus 154 aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 154 AEFHCPKCRHNFRGF 168 (278)
T ss_pred eeeecccccccchhh
Confidence 347777777 77554
No 246
>COG2879 Uncharacterized small protein [Function unknown]
Probab=36.88 E-value=46 Score=17.77 Aligned_cols=19 Identities=21% Similarity=0.270 Sum_probs=12.5
Q ss_pred cChHHHHHHHHhhcCCCCC
Q psy10073 125 YQKEKLQFHVKNKHSTKVK 143 (144)
Q Consensus 125 ~~~~~l~~H~~~h~~~kp~ 143 (144)
.+-.+...|++.++.++|.
T Consensus 23 pdYdnYVehmr~~hPd~p~ 41 (65)
T COG2879 23 PDYDNYVEHMRKKHPDKPP 41 (65)
T ss_pred CcHHHHHHHHHHhCcCCCc
Confidence 3445667777777777664
No 247
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=36.79 E-value=11 Score=17.38 Aligned_cols=8 Identities=25% Similarity=0.708 Sum_probs=5.5
Q ss_pred CeeCCCCC
Q psy10073 50 PQSCKHCK 57 (144)
Q Consensus 50 ~~~C~~C~ 57 (144)
.+.|+.||
T Consensus 22 R~vC~~Cg 29 (34)
T PF14803_consen 22 RLVCPACG 29 (34)
T ss_dssp EEEETTTT
T ss_pred ceECCCCC
Confidence 36777776
No 248
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=35.52 E-value=26 Score=25.62 Aligned_cols=28 Identities=29% Similarity=0.674 Sum_probs=19.6
Q ss_pred HhhcCCcceeCCCcc-hhccChHHHHHHH
Q psy10073 107 LIHLGDKQFKCCLCS-YGAYQKEKLQFHV 134 (144)
Q Consensus 107 ~~h~~~~~~~C~~C~-~~f~~~~~l~~H~ 134 (144)
+.|.-++.|.|.+|| +.+.-...+.+|.
T Consensus 367 klhgLd~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 367 KLHGLDIEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred HhcCCCcceeeeecccccccchHHHHhhh
Confidence 446667788888888 6666666666663
No 249
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=35.29 E-value=13 Score=19.74 Aligned_cols=24 Identities=21% Similarity=0.459 Sum_probs=9.6
Q ss_pred eecCccCCccCCccccccccCCCC
Q psy10073 16 KTCLYCNKYVPSDIDVFIGHCQTC 39 (144)
Q Consensus 16 ~~C~~C~~~f~~~~~l~~H~c~~c 39 (144)
..|..|+..........-|.|..|
T Consensus 31 IlCNDC~~~s~v~fH~lg~KC~~C 54 (61)
T PF14599_consen 31 ILCNDCNAKSEVPFHFLGHKCSHC 54 (61)
T ss_dssp EEESSS--EEEEE--TT----TTT
T ss_pred EECCCCCCccceeeeHhhhcCCCC
Confidence 569999986644444444344333
No 250
>PTZ00448 hypothetical protein; Provisional
Probab=35.28 E-value=27 Score=25.68 Aligned_cols=23 Identities=13% Similarity=0.389 Sum_probs=19.3
Q ss_pred ceeCCCcchhccChHHHHHHHHh
Q psy10073 114 QFKCCLCSYGAYQKEKLQFHVKN 136 (144)
Q Consensus 114 ~~~C~~C~~~f~~~~~l~~H~~~ 136 (144)
.|.|..|+..|.+....+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999888888888774
No 251
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=35.13 E-value=15 Score=17.12 Aligned_cols=10 Identities=20% Similarity=0.507 Sum_probs=4.3
Q ss_pred cCccCCccCC
Q psy10073 18 CLYCNKYVPS 27 (144)
Q Consensus 18 C~~C~~~f~~ 27 (144)
|++|...+..
T Consensus 1 C~iC~~~~~~ 10 (41)
T PF00097_consen 1 CPICLEPFED 10 (41)
T ss_dssp ETTTSSBCSS
T ss_pred CCcCCccccC
Confidence 3444444443
No 252
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=34.73 E-value=19 Score=21.19 Aligned_cols=7 Identities=43% Similarity=1.189 Sum_probs=3.5
Q ss_pred eeCCCCC
Q psy10073 87 FICVACD 93 (144)
Q Consensus 87 ~~C~~C~ 93 (144)
|.|+.|+
T Consensus 22 f~CP~Cg 28 (99)
T PRK14892 22 FECPRCG 28 (99)
T ss_pred eECCCCC
Confidence 4555554
No 253
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.94 E-value=27 Score=21.12 Aligned_cols=11 Identities=18% Similarity=0.480 Sum_probs=6.1
Q ss_pred eecCccCCccC
Q psy10073 16 KTCLYCNKYVP 26 (144)
Q Consensus 16 ~~C~~C~~~f~ 26 (144)
+.|..||..|.
T Consensus 72 ~~C~~Cg~~~~ 82 (117)
T PRK00564 72 LECKDCSHVFK 82 (117)
T ss_pred EEhhhCCCccc
Confidence 55666665443
No 254
>PRK05978 hypothetical protein; Provisional
Probab=33.92 E-value=30 Score=22.02 Aligned_cols=18 Identities=11% Similarity=-0.029 Sum_probs=10.3
Q ss_pred eecCccCCccCCcccccc
Q psy10073 16 KTCLYCNKYVPSDIDVFI 33 (144)
Q Consensus 16 ~~C~~C~~~f~~~~~l~~ 33 (144)
-+|+.||+.=--..-|+.
T Consensus 34 grCP~CG~G~LF~g~Lkv 51 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKP 51 (148)
T ss_pred CcCCCCCCCccccccccc
Confidence 579999865333333433
No 255
>KOG4727|consensus
Probab=33.50 E-value=30 Score=22.54 Aligned_cols=25 Identities=28% Similarity=0.371 Sum_probs=21.1
Q ss_pred CCCceeCCCCCcccCChhHHHHHHH
Q psy10073 83 VKYKFICVACDYFTIISQNMRNHTL 107 (144)
Q Consensus 83 ~~~~~~C~~C~~~f~~~~~l~~H~~ 107 (144)
...-|-|.+|+-.|...-++..|+.
T Consensus 72 q~~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 72 QKGGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ccCceeeeecceeehhhHHHHHHhc
Confidence 3445999999999999999999974
No 256
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=33.09 E-value=58 Score=23.21 Aligned_cols=21 Identities=19% Similarity=0.458 Sum_probs=10.9
Q ss_pred eeCCCCCcccCChhHHHHHHH
Q psy10073 87 FICVACDYFTIISQNMRNHTL 107 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~ 107 (144)
|.|+.|-+-|.+...|.+|+.
T Consensus 49 yiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 49 YICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred EEcCCCcchhCCHHHHHHHHH
Confidence 555555555555555555543
No 257
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=32.69 E-value=25 Score=20.55 Aligned_cols=11 Identities=27% Similarity=0.839 Sum_probs=8.3
Q ss_pred eeCCCCCcccC
Q psy10073 87 FICVACDYFTI 97 (144)
Q Consensus 87 ~~C~~C~~~f~ 97 (144)
|.|..|+..+.
T Consensus 91 y~C~~C~~~w~ 101 (104)
T TIGR01384 91 YKCTKCGYVWR 101 (104)
T ss_pred EEeCCCCCeeE
Confidence 88888887664
No 258
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=32.48 E-value=23 Score=18.10 Aligned_cols=16 Identities=25% Similarity=0.690 Sum_probs=10.1
Q ss_pred CCCceecCccCCccCC
Q psy10073 12 LSTKKTCLYCNKYVPS 27 (144)
Q Consensus 12 ~~~~~~C~~C~~~f~~ 27 (144)
....|+|.+|++.+..
T Consensus 32 ~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 32 EPIKLRCHYCERIITE 47 (52)
T ss_dssp TTCEEEETTT--EEEH
T ss_pred CCCEEEeeCCCCEecc
Confidence 4456899999987753
No 259
>KOG1842|consensus
Probab=31.93 E-value=25 Score=26.55 Aligned_cols=22 Identities=18% Similarity=0.333 Sum_probs=19.8
Q ss_pred eeCCCCCcccCChhHHHHHHHh
Q psy10073 87 FICVACDYFTIISQNMRNHTLI 108 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~ 108 (144)
|.||+|..-|.+.+.|..|...
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~ 37 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDV 37 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhh
Confidence 8999999999999999999765
No 260
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.84 E-value=28 Score=24.66 Aligned_cols=13 Identities=15% Similarity=0.235 Sum_probs=7.9
Q ss_pred CCCeeCCCCC-CCc
Q psy10073 48 VIPQSCKHCK-NFT 60 (144)
Q Consensus 48 ~~~~~C~~C~-~f~ 60 (144)
.+.+.|+.|| .+.
T Consensus 320 ~r~~~C~~cg~~~~ 333 (364)
T COG0675 320 GRLFKCPRCGFVHD 333 (364)
T ss_pred ceeEECCCCCCeeh
Confidence 3457777777 443
No 261
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=31.83 E-value=25 Score=15.87 Aligned_cols=13 Identities=23% Similarity=0.506 Sum_probs=9.7
Q ss_pred CCceecCccCCcc
Q psy10073 13 STKKTCLYCNKYV 25 (144)
Q Consensus 13 ~~~~~C~~C~~~f 25 (144)
.+.|+|..||...
T Consensus 5 ~~~ykC~~Cgniv 17 (34)
T TIGR00319 5 GQVYKCEVCGNIV 17 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 3468888888765
No 262
>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=31.62 E-value=26 Score=15.83 Aligned_cols=12 Identities=25% Similarity=0.545 Sum_probs=8.1
Q ss_pred CceecCccCCcc
Q psy10073 14 TKKTCLYCNKYV 25 (144)
Q Consensus 14 ~~~~C~~C~~~f 25 (144)
+.|+|..||...
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 457777777655
No 263
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=31.57 E-value=48 Score=16.89 Aligned_cols=8 Identities=25% Similarity=0.845 Sum_probs=4.1
Q ss_pred eeCCCCCc
Q psy10073 87 FICVACDY 94 (144)
Q Consensus 87 ~~C~~C~~ 94 (144)
..|+.||+
T Consensus 47 ~~Cp~CgR 54 (56)
T PF02591_consen 47 VFCPNCGR 54 (56)
T ss_pred EECcCCCc
Confidence 45555554
No 264
>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=31.54 E-value=23 Score=21.26 Aligned_cols=15 Identities=20% Similarity=0.392 Sum_probs=10.1
Q ss_pred CCCeeCCCCC-CCcch
Q psy10073 48 VIPQSCKHCK-NFTSS 62 (144)
Q Consensus 48 ~~~~~C~~C~-~f~~~ 62 (144)
..-+.|+.|| .+.+.
T Consensus 29 ~~~~~C~~CGe~~~~~ 44 (127)
T TIGR03830 29 VPGWYCPACGEELLDP 44 (127)
T ss_pred eeeeECCCCCCEEEcH
Confidence 3447788888 66655
No 265
>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=31.45 E-value=13 Score=22.25 Aligned_cols=12 Identities=17% Similarity=0.437 Sum_probs=6.9
Q ss_pred eecCccCCccCC
Q psy10073 16 KTCLYCNKYVPS 27 (144)
Q Consensus 16 ~~C~~C~~~f~~ 27 (144)
+.|..||..|.-
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 566667666654
No 266
>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=30.74 E-value=17 Score=24.30 Aligned_cols=28 Identities=11% Similarity=0.216 Sum_probs=0.0
Q ss_pred ccCCCCCceeCCCCC-cccCChhHHHHHH
Q psy10073 79 RPDPVKYKFICVACD-YFTIISQNMRNHT 106 (144)
Q Consensus 79 ~~~~~~~~~~C~~C~-~~f~~~~~l~~H~ 106 (144)
..|.-...|.|.+|| .+|.-...+.+|.
T Consensus 94 KLhGL~~ey~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 94 KLHGLGVEYKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp -----------------------------
T ss_pred HHhCCCCeeeeEeCCCcceecHHHHHHhc
Confidence 344445559999997 4566677777774
No 267
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=30.59 E-value=31 Score=15.79 Aligned_cols=7 Identities=29% Similarity=1.009 Sum_probs=2.9
Q ss_pred eeCCCCC
Q psy10073 51 QSCKHCK 57 (144)
Q Consensus 51 ~~C~~C~ 57 (144)
+.|+.|+
T Consensus 5 ~~C~nC~ 11 (33)
T PF08209_consen 5 VECPNCG 11 (33)
T ss_dssp EE-TTTS
T ss_pred EECCCCc
Confidence 3455555
No 268
>PRK01343 zinc-binding protein; Provisional
Probab=30.22 E-value=45 Score=17.44 Aligned_cols=13 Identities=23% Similarity=0.529 Sum_probs=9.4
Q ss_pred CceecCccCCccC
Q psy10073 14 TKKTCLYCNKYVP 26 (144)
Q Consensus 14 ~~~~C~~C~~~f~ 26 (144)
....|++|++.+.
T Consensus 8 p~~~CP~C~k~~~ 20 (57)
T PRK01343 8 PTRPCPECGKPST 20 (57)
T ss_pred CCCcCCCCCCcCc
Confidence 3467888888764
No 269
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=29.74 E-value=15 Score=18.68 Aligned_cols=29 Identities=17% Similarity=0.362 Sum_probs=15.9
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchh
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYG 123 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 123 (144)
+.|..|++.......+ .....+|+.|+..
T Consensus 5 iRC~~CnklLa~~g~~--------~~leIKCpRC~ti 33 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEV--------IELEIKCPRCKTI 33 (51)
T ss_pred eeccchhHHHhhhcCc--------cEEEEECCCCCcc
Confidence 6777777654332111 1234678877754
No 270
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=29.44 E-value=73 Score=21.29 Aligned_cols=12 Identities=17% Similarity=0.340 Sum_probs=7.8
Q ss_pred cceeCCCcchhc
Q psy10073 113 KQFKCCLCSYGA 124 (144)
Q Consensus 113 ~~~~C~~C~~~f 124 (144)
....|..||..+
T Consensus 29 ~lvrC~eCG~V~ 40 (201)
T COG1326 29 PLVRCEECGTVH 40 (201)
T ss_pred eEEEccCCCcEe
Confidence 346777777655
No 271
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=29.28 E-value=25 Score=24.02 Aligned_cols=19 Identities=11% Similarity=0.032 Sum_probs=13.6
Q ss_pred CCCCCceecCccCCccCCc
Q psy10073 10 VPLSTKKTCLYCNKYVPSD 28 (144)
Q Consensus 10 ~~~~~~~~C~~C~~~f~~~ 28 (144)
....++.+|..||..|...
T Consensus 176 LrEGkpqRCpECGqVFKLV 194 (268)
T PTZ00043 176 CREGFLYRCGECDQIFMLV 194 (268)
T ss_pred ecCCCCccCCCCCcEEEEE
Confidence 3455678888888888654
No 272
>KOG0320|consensus
Probab=29.19 E-value=19 Score=23.61 Aligned_cols=9 Identities=22% Similarity=0.405 Sum_probs=5.3
Q ss_pred eeCCCCCcc
Q psy10073 87 FICVACDYF 95 (144)
Q Consensus 87 ~~C~~C~~~ 95 (144)
-.|+.|++.
T Consensus 168 ~~CP~C~kk 176 (187)
T KOG0320|consen 168 NKCPTCRKK 176 (187)
T ss_pred CCCCCcccc
Confidence 456666653
No 273
>PTZ00448 hypothetical protein; Provisional
Probab=29.12 E-value=41 Score=24.81 Aligned_cols=23 Identities=13% Similarity=0.372 Sum_probs=20.5
Q ss_pred ceeCCCCCcccCChhHHHHHHHh
Q psy10073 86 KFICVACDYFTIISQNMRNHTLI 108 (144)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~H~~~ 108 (144)
.|.|..|+-.|.+....+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 48899999999999999999876
No 274
>PRK12722 transcriptional activator FlhC; Provisional
Probab=28.57 E-value=46 Score=22.09 Aligned_cols=9 Identities=22% Similarity=0.674 Sum_probs=3.7
Q ss_pred CCCCCcccC
Q psy10073 89 CVACDYFTI 97 (144)
Q Consensus 89 C~~C~~~f~ 97 (144)
|..|+-.|.
T Consensus 137 C~~Cgg~fv 145 (187)
T PRK12722 137 CNCCGGHFV 145 (187)
T ss_pred CCCCCCCee
Confidence 444444443
No 275
>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=28.20 E-value=36 Score=14.77 Aligned_cols=7 Identities=43% Similarity=1.398 Sum_probs=2.1
Q ss_pred eeCCCCC
Q psy10073 87 FICVACD 93 (144)
Q Consensus 87 ~~C~~C~ 93 (144)
|.|.+|+
T Consensus 16 Y~C~~Cd 22 (30)
T PF07649_consen 16 YRCSECD 22 (30)
T ss_dssp EE-TTT-
T ss_pred EECccCC
Confidence 4444443
No 276
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.08 E-value=36 Score=18.04 Aligned_cols=10 Identities=20% Similarity=0.594 Sum_probs=5.0
Q ss_pred ceeCCCcchh
Q psy10073 114 QFKCCLCSYG 123 (144)
Q Consensus 114 ~~~C~~C~~~ 123 (144)
.|.|+.|.-.
T Consensus 31 tymC~eC~~R 40 (68)
T COG4896 31 TYMCPECEHR 40 (68)
T ss_pred eEechhhHhh
Confidence 3555555443
No 277
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=27.99 E-value=56 Score=23.51 Aligned_cols=35 Identities=14% Similarity=0.146 Sum_probs=19.0
Q ss_pred eeCCCCCcccCChhHHHHHHHhh-----cCCcceeCCCcchhccC
Q psy10073 87 FICVACDYFTIISQNMRNHTLIH-----LGDKQFKCCLCSYGAYQ 126 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h-----~~~~~~~C~~C~~~f~~ 126 (144)
..|+.||.. ..|.. .... .+.+...|..|+...+.
T Consensus 225 ~~C~~Cg~~----~~l~y-~~~e~~~~~~~~r~e~C~~C~~YlK~ 264 (305)
T TIGR01562 225 VKCSHCEES----KHLAY-LSLEHDAEKAVLKAETCDSCQGYLKI 264 (305)
T ss_pred ccCCCCCCC----Cceee-EeecCCCCCcceEEeeccccccchhh
Confidence 689999863 11211 1111 12355689999855443
No 278
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=27.67 E-value=40 Score=15.79 Aligned_cols=16 Identities=19% Similarity=0.260 Sum_probs=9.2
Q ss_pred eecCccCCccCCcccc
Q psy10073 16 KTCLYCNKYVPSDIDV 31 (144)
Q Consensus 16 ~~C~~C~~~f~~~~~l 31 (144)
-.|+.|++.|-..++-
T Consensus 3 ~~CprC~kg~Hwa~~C 18 (36)
T PF14787_consen 3 GLCPRCGKGFHWASEC 18 (36)
T ss_dssp -C-TTTSSSCS-TTT-
T ss_pred ccCcccCCCcchhhhh
Confidence 3588888888776553
No 279
>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=27.53 E-value=44 Score=23.93 Aligned_cols=8 Identities=38% Similarity=0.750 Sum_probs=4.6
Q ss_pred eecCccCC
Q psy10073 16 KTCLYCNK 23 (144)
Q Consensus 16 ~~C~~C~~ 23 (144)
|.|+.|+.
T Consensus 259 ~~C~~C~~ 266 (299)
T TIGR01385 259 FTCGKCKQ 266 (299)
T ss_pred ccCCCCCC
Confidence 55666653
No 280
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=27.50 E-value=15 Score=29.57 Aligned_cols=31 Identities=19% Similarity=0.306 Sum_probs=17.1
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchh
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYG 123 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 123 (144)
-.|+.|.+.+.++.+-+-| -.+-.|..||-.
T Consensus 119 ~~C~~C~~ey~~p~~rr~h------~~~~~C~~Cgp~ 149 (711)
T TIGR00143 119 PLCPDCAKEYKDPLDRRFH------AQPIACPRCGPQ 149 (711)
T ss_pred cCCHHHHHHhcCCccccCC------CCCccCCCCCcE
Confidence 3677777766665443222 134567777643
No 281
>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=27.49 E-value=35 Score=17.13 Aligned_cols=8 Identities=25% Similarity=0.708 Sum_probs=4.1
Q ss_pred CeeCCCCC
Q psy10073 50 PQSCKHCK 57 (144)
Q Consensus 50 ~~~C~~C~ 57 (144)
=|.|..|+
T Consensus 26 Cf~C~~C~ 33 (58)
T PF00412_consen 26 CFKCSKCG 33 (58)
T ss_dssp TSBETTTT
T ss_pred ccccCCCC
Confidence 34555555
No 282
>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=27.01 E-value=36 Score=16.28 Aligned_cols=8 Identities=25% Similarity=0.808 Sum_probs=4.0
Q ss_pred CeeCCCCC
Q psy10073 50 PQSCKHCK 57 (144)
Q Consensus 50 ~~~C~~C~ 57 (144)
.+.|+.||
T Consensus 19 ~~vC~~CG 26 (43)
T PF08271_consen 19 ELVCPNCG 26 (43)
T ss_dssp EEEETTT-
T ss_pred eEECCCCC
Confidence 35566666
No 283
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=26.89 E-value=29 Score=18.11 Aligned_cols=38 Identities=16% Similarity=0.258 Sum_probs=18.5
Q ss_pred eeCCCCCcccCChhHH--HHHHHhhcCCcceeCCCcchhcc
Q psy10073 87 FICVACDYFTIISQNM--RNHTLIHLGDKQFKCCLCSYGAY 125 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l--~~H~~~h~~~~~~~C~~C~~~f~ 125 (144)
..|..|++.+.-...- ..-++. .....|.|+.|.-...
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLrn-rPi~tYmC~eC~~RI~ 42 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLRN-RPIHTYMCDECKERIR 42 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhhc-CCCcceeChhHHHHHh
Confidence 4677777655432221 111221 1233488888865433
No 284
>PF04641 Rtf2: Rtf2 RING-finger
Probab=26.69 E-value=34 Score=23.81 Aligned_cols=48 Identities=15% Similarity=0.216 Sum_probs=25.0
Q ss_pred CCceecCccCCccCCccccccccCCCCCCccccC----CCCCeeCCCCC-CCcch
Q psy10073 13 STKKTCLYCNKYVPSDIDVFIGHCQTCPNMSFLN----SVIPQSCKHCK-NFTSS 62 (144)
Q Consensus 13 ~~~~~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~----~~~~~~C~~C~-~f~~~ 62 (144)
...|.|++.++.|.....+.. -..|||.-.-. ......|+.|| .|...
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~--l~~cG~V~s~~alke~k~~~~Cp~c~~~f~~~ 163 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVY--LRPCGCVFSEKALKELKKSKKCPVCGKPFTEE 163 (260)
T ss_pred CceeECCCCCcccCCceeEEE--EcCCCCEeeHHHHHhhcccccccccCCccccC
Confidence 446899998888865433322 12455522110 01123477777 66544
No 285
>KOG4118|consensus
Probab=26.49 E-value=39 Score=18.17 Aligned_cols=25 Identities=28% Similarity=0.578 Sum_probs=14.2
Q ss_pred eeCCCcchhccChHHHHHHHHhhcC
Q psy10073 115 FKCCLCSYGAYQKEKLQFHVKNKHS 139 (144)
Q Consensus 115 ~~C~~C~~~f~~~~~l~~H~~~h~~ 139 (144)
|+|.+|-........+..|....+.
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHp 63 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHP 63 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCC
Confidence 5566666555555556666554443
No 286
>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=26.32 E-value=25 Score=16.79 Aligned_cols=16 Identities=25% Similarity=0.669 Sum_probs=5.7
Q ss_pred cCccCCccCCcccccc
Q psy10073 18 CLYCNKYVPSDIDVFI 33 (144)
Q Consensus 18 C~~C~~~f~~~~~l~~ 33 (144)
|..|++.+.....+..
T Consensus 1 C~~C~~~~~~~~~~~v 16 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHV 16 (47)
T ss_dssp -TTT--B--GG-GEEE
T ss_pred CCCCCCcCccCcceEe
Confidence 5667776666544444
No 287
>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=26.17 E-value=93 Score=20.81 Aligned_cols=40 Identities=10% Similarity=0.157 Sum_probs=22.3
Q ss_pred cCCCCCceeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcch
Q psy10073 80 PDPVKYKFICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSY 122 (144)
Q Consensus 80 ~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 122 (144)
.|..-....|..|+..+.....+. ..........|+.|+.
T Consensus 89 lHG~~~~~~C~~C~~~~~~~~~~~---~~~~~~~~p~C~~Cgg 128 (206)
T cd01410 89 LHGNMFIEVCKSCGPEYVRDDVVE---TRGDKETGRRCHACGG 128 (206)
T ss_pred ecCCcCcccCCCCCCccchHHHHH---HhhcCCCCCcCCCCcC
Confidence 444445578999997765543322 1111223456888874
No 288
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=26.10 E-value=50 Score=17.15 Aligned_cols=14 Identities=21% Similarity=0.508 Sum_probs=7.9
Q ss_pred CCCCeeCCCCC-CCc
Q psy10073 47 SVIPQSCKHCK-NFT 60 (144)
Q Consensus 47 ~~~~~~C~~C~-~f~ 60 (144)
+++---|+.|+ .|.
T Consensus 36 ~~rYngCPfC~~~~~ 50 (55)
T PF14447_consen 36 GERYNGCPFCGTPFE 50 (55)
T ss_pred hhhccCCCCCCCccc
Confidence 34444577777 554
No 289
>KOG2817|consensus
Probab=26.06 E-value=32 Score=25.52 Aligned_cols=8 Identities=38% Similarity=0.920 Sum_probs=4.5
Q ss_pred eeCCCCCc
Q psy10073 87 FICVACDY 94 (144)
Q Consensus 87 ~~C~~C~~ 94 (144)
|+||+|+.
T Consensus 375 fKCPYCP~ 382 (394)
T KOG2817|consen 375 FKCPYCPV 382 (394)
T ss_pred eeCCCCCc
Confidence 55666554
No 290
>KOG2071|consensus
Probab=26.02 E-value=52 Score=25.84 Aligned_cols=25 Identities=24% Similarity=0.202 Sum_probs=21.5
Q ss_pred ceeCCCCCcccCChhHHHHHHHhhc
Q psy10073 86 KFICVACDYFTIISQNMRNHTLIHL 110 (144)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~H~~~h~ 110 (144)
+-.|..||.+|.+......|+..|.
T Consensus 418 pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 418 PNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cchhcccccccccchhhhhHhhhhh
Confidence 3899999999999998888887764
No 291
>PRK12860 transcriptional activator FlhC; Provisional
Probab=25.94 E-value=54 Score=21.79 Aligned_cols=6 Identities=50% Similarity=1.586 Sum_probs=2.7
Q ss_pred eeCCCC
Q psy10073 87 FICVAC 92 (144)
Q Consensus 87 ~~C~~C 92 (144)
|.|+.|
T Consensus 155 f~CplC 160 (189)
T PRK12860 155 FVCGLC 160 (189)
T ss_pred CcCCCC
Confidence 444444
No 292
>PLN03239 histone acetyltransferase; Provisional
Probab=25.90 E-value=57 Score=23.94 Aligned_cols=25 Identities=16% Similarity=0.042 Sum_probs=21.6
Q ss_pred CcceeCCCcchhccChHHHHHHHHh
Q psy10073 112 DKQFKCCLCSYGAYQKEKLQFHVKN 136 (144)
Q Consensus 112 ~~~~~C~~C~~~f~~~~~l~~H~~~ 136 (144)
+.-|.|+.|-+-|.+...|.+|+..
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~~ 128 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQAK 128 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHHh
Confidence 4579999999999999999999753
No 293
>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=25.80 E-value=23 Score=29.11 Aligned_cols=9 Identities=22% Similarity=0.910 Sum_probs=0.0
Q ss_pred eeCCCCCcc
Q psy10073 87 FICVACDYF 95 (144)
Q Consensus 87 ~~C~~C~~~ 95 (144)
|.|+.|+..
T Consensus 681 ~~Cp~C~~~ 689 (900)
T PF03833_consen 681 YVCPDCGIE 689 (900)
T ss_dssp ---------
T ss_pred eeccccccc
Confidence 566666553
No 294
>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=25.65 E-value=30 Score=17.35 Aligned_cols=9 Identities=33% Similarity=1.102 Sum_probs=3.5
Q ss_pred ceeCCCcch
Q psy10073 114 QFKCCLCSY 122 (144)
Q Consensus 114 ~~~C~~C~~ 122 (144)
.|.|++|++
T Consensus 41 ~W~CPiC~~ 49 (50)
T PF02891_consen 41 KWKCPICNK 49 (50)
T ss_dssp --B-TTT--
T ss_pred CeECcCCcC
Confidence 388888875
No 295
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=25.58 E-value=30 Score=17.66 Aligned_cols=11 Identities=27% Similarity=0.842 Sum_probs=6.6
Q ss_pred ecCccCCccCC
Q psy10073 17 TCLYCNKYVPS 27 (144)
Q Consensus 17 ~C~~C~~~f~~ 27 (144)
.|++||..+..
T Consensus 2 ~CPyCge~~~~ 12 (52)
T PF14255_consen 2 QCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCeeEE
Confidence 46666665544
No 296
>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=25.34 E-value=31 Score=15.29 Aligned_cols=14 Identities=29% Similarity=0.396 Sum_probs=6.8
Q ss_pred CceecCccCCccCC
Q psy10073 14 TKKTCLYCNKYVPS 27 (144)
Q Consensus 14 ~~~~C~~C~~~f~~ 27 (144)
..|.|+.|+..+-+
T Consensus 12 ~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 12 AKYRCPRCGARYCS 25 (30)
T ss_dssp ESEE-TTT--EESS
T ss_pred CEEECCCcCCceeC
Confidence 35778887766543
No 297
>KOG1994|consensus
Probab=25.04 E-value=40 Score=23.12 Aligned_cols=19 Identities=16% Similarity=0.448 Sum_probs=17.9
Q ss_pred eeCCCCCcccCChhHHHHH
Q psy10073 87 FICVACDYFTIISQNMRNH 105 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H 105 (144)
|-|-.||..|.+...|..|
T Consensus 240 ~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 240 YYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred eEEEEeccccCCHHHHHHh
Confidence 9999999999999999877
No 298
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=25.01 E-value=65 Score=25.26 Aligned_cols=40 Identities=13% Similarity=0.247 Sum_probs=22.6
Q ss_pred eecCccCCccCCc-cccccccCCCCCCccccCCCCCeeCCCCC-CCcch
Q psy10073 16 KTCLYCNKYVPSD-IDVFIGHCQTCPNMSFLNSVIPQSCKHCK-NFTSS 62 (144)
Q Consensus 16 ~~C~~C~~~f~~~-~~l~~H~c~~c~h~~~h~~~~~~~C~~C~-~f~~~ 62 (144)
..|+.||..+.-. .+|+- ....-....-|.|+.|| .....
T Consensus 201 vpCPhCg~~~~l~~~~l~w-------~~~~~~~~a~y~C~~Cg~~i~e~ 242 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKW-------DKGEAPETARYVCPHCGCEIEEH 242 (557)
T ss_pred ccCCCCCCCccccccceee-------cCCCCccceEEECCCCcCCCCHH
Confidence 4789998877654 22222 00001122348999999 77665
No 299
>PRK04023 DNA polymerase II large subunit; Validated
Probab=24.70 E-value=79 Score=26.88 Aligned_cols=9 Identities=33% Similarity=0.833 Sum_probs=5.8
Q ss_pred eecCccCCc
Q psy10073 16 KTCLYCNKY 24 (144)
Q Consensus 16 ~~C~~C~~~ 24 (144)
..|+.||..
T Consensus 627 RfCpsCG~~ 635 (1121)
T PRK04023 627 RKCPSCGKE 635 (1121)
T ss_pred ccCCCCCCc
Confidence 467777765
No 300
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=24.61 E-value=95 Score=23.30 Aligned_cols=38 Identities=18% Similarity=0.269 Sum_probs=22.9
Q ss_pred CCCCceecCccCCccCCccccccc---cCCCCCCccccCCCC
Q psy10073 11 PLSTKKTCLYCNKYVPSDIDVFIG---HCQTCPNMSFLNSVI 49 (144)
Q Consensus 11 ~~~~~~~C~~C~~~f~~~~~l~~H---~c~~c~h~~~h~~~~ 49 (144)
+..+.-.|++||..+.-. .|..+ .|..|||.-+-.++.
T Consensus 14 ~~~~~~~C~eCd~~~~~P-~l~~~q~A~CPRC~~~l~~~~~~ 54 (418)
T COG2995 14 PPGHLILCPECDMLVSLP-RLDSGQSAYCPRCGHTLTRGGDW 54 (418)
T ss_pred CccceecCCCCCceeccc-cCCCCCcccCCCCCCccccCCCC
Confidence 344457899999888765 44443 555666654444433
No 301
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=24.46 E-value=1.1e+02 Score=21.90 Aligned_cols=25 Identities=24% Similarity=0.365 Sum_probs=21.7
Q ss_pred CcceeCCCcchhccChHHHHHHHHh
Q psy10073 112 DKQFKCCLCSYGAYQKEKLQFHVKN 136 (144)
Q Consensus 112 ~~~~~C~~C~~~f~~~~~l~~H~~~ 136 (144)
..-|.|+.|-+-|.+...|.+|+..
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHh
Confidence 5679999999999999999999874
No 302
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=24.39 E-value=46 Score=23.82 Aligned_cols=12 Identities=25% Similarity=0.758 Sum_probs=5.7
Q ss_pred eeCCCCC-CCcch
Q psy10073 51 QSCKHCK-NFTSS 62 (144)
Q Consensus 51 ~~C~~C~-~f~~~ 62 (144)
+.|+.|+ -|.-.
T Consensus 58 ~vcp~c~~h~rlt 70 (296)
T CHL00174 58 NICEQCGYHLKMS 70 (296)
T ss_pred CCCCCCCCCcCCC
Confidence 4455555 44433
No 303
>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=24.19 E-value=47 Score=23.60 Aligned_cols=12 Identities=17% Similarity=0.720 Sum_probs=6.5
Q ss_pred eeCCCCC-CCcch
Q psy10073 51 QSCKHCK-NFTSS 62 (144)
Q Consensus 51 ~~C~~C~-~f~~~ 62 (144)
+.|+.|| -|.-.
T Consensus 46 ~vc~~c~~h~rl~ 58 (285)
T TIGR00515 46 EVCPKCDHHMRMD 58 (285)
T ss_pred CCCCCCCCcCcCC
Confidence 5566666 55443
No 304
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=23.79 E-value=43 Score=19.08 Aligned_cols=37 Identities=19% Similarity=0.462 Sum_probs=24.0
Q ss_pred ecCccCCccCCccccccccCCCCCCccccCCCCCeeCCCCC-CCcch
Q psy10073 17 TCLYCNKYVPSDIDVFIGHCQTCPNMSFLNSVIPQSCKHCK-NFTSS 62 (144)
Q Consensus 17 ~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~~~~~~~C~~C~-~f~~~ 62 (144)
.|-.||..+.....+.. .+...+++|-|..|. .+...
T Consensus 2 ~C~HCg~~~p~~~~~~~---------~~~g~~~~FCC~GC~~V~~~i 39 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITV---------EIDGEERPFCCPGCQAVYQLI 39 (88)
T ss_pred CCCCCCCCCCCCCCeee---------eeCCCccccccHHHHHHHHHH
Confidence 58889888864443332 333456789999998 65444
No 305
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=23.66 E-value=58 Score=19.47 Aligned_cols=11 Identities=27% Similarity=0.754 Sum_probs=7.2
Q ss_pred eCCCCC-CCcch
Q psy10073 52 SCKHCK-NFTSS 62 (144)
Q Consensus 52 ~C~~C~-~f~~~ 62 (144)
-|+.|+ .....
T Consensus 62 ~CP~C~~~~~~~ 73 (111)
T PF14319_consen 62 HCPSCQAKATEQ 73 (111)
T ss_pred CCCCCCChHHHH
Confidence 588888 54443
No 306
>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=23.17 E-value=1.5e+02 Score=17.48 Aligned_cols=36 Identities=6% Similarity=0.052 Sum_probs=22.7
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcchh
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSYG 123 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 123 (144)
|.|+.=|..|.+...+...+..-. .+.|.|...|++
T Consensus 4 f~i~~T~EiF~dYe~Y~~R~~~y~-~~vwtC~~TGk~ 39 (102)
T PF10537_consen 4 FYIPFTGEIFRDYEEYLKRMILYN-QRVWTCEITGKS 39 (102)
T ss_pred EEeCCCCcccCCHHHHHHHHHHHh-CCeeEEecCCCC
Confidence 667777777777766665554433 456777766653
No 307
>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=23.07 E-value=36 Score=18.18 Aligned_cols=11 Identities=27% Similarity=0.519 Sum_probs=8.1
Q ss_pred eeCCCCCcccC
Q psy10073 87 FICVACDYFTI 97 (144)
Q Consensus 87 ~~C~~C~~~f~ 97 (144)
..|+.|++.|.
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 77777777764
No 308
>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=23.06 E-value=35 Score=20.56 Aligned_cols=14 Identities=21% Similarity=0.377 Sum_probs=8.4
Q ss_pred ceecCccCCccCCc
Q psy10073 15 KKTCLYCNKYVPSD 28 (144)
Q Consensus 15 ~~~C~~C~~~f~~~ 28 (144)
...|..|+..|...
T Consensus 54 ~~~C~~C~~~fg~l 67 (118)
T PF02318_consen 54 ERHCARCGKPFGFL 67 (118)
T ss_dssp CSB-TTTS-BCSCT
T ss_pred CcchhhhCCccccc
Confidence 35789998887644
No 309
>PF14369 zf-RING_3: zinc-finger
Probab=22.98 E-value=60 Score=14.95 Aligned_cols=10 Identities=20% Similarity=0.464 Sum_probs=5.5
Q ss_pred ecCccCCccC
Q psy10073 17 TCLYCNKYVP 26 (144)
Q Consensus 17 ~C~~C~~~f~ 26 (144)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 3666665553
No 310
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=22.87 E-value=54 Score=21.45 Aligned_cols=20 Identities=10% Similarity=0.310 Sum_probs=14.7
Q ss_pred cceeCCCcchhccChHHHHH
Q psy10073 113 KQFKCCLCSYGAYQKEKLQF 132 (144)
Q Consensus 113 ~~~~C~~C~~~f~~~~~l~~ 132 (144)
..+.|..||+.|.....+..
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~~ 132 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVAL 132 (181)
T ss_pred ccCcCcccCCccCcHhHHHH
Confidence 46789999999986655543
No 311
>KOG2807|consensus
Probab=22.87 E-value=39 Score=24.51 Aligned_cols=29 Identities=21% Similarity=0.559 Sum_probs=21.6
Q ss_pred eeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcc
Q psy10073 87 FICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCS 121 (144)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~ 121 (144)
|.|+.|...|-..-+...|...| .|+.|.
T Consensus 346 y~C~~Ck~~FCldCDv~iHesLh------~CpgCe 374 (378)
T KOG2807|consen 346 YRCESCKNVFCLDCDVFIHESLH------NCPGCE 374 (378)
T ss_pred EEchhccceeeccchHHHHhhhh------cCCCcC
Confidence 99999999888777777775554 466664
No 312
>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=22.86 E-value=44 Score=19.53 Aligned_cols=12 Identities=25% Similarity=0.343 Sum_probs=4.1
Q ss_pred eeCCCCCcccCC
Q psy10073 87 FICVACDYFTII 98 (144)
Q Consensus 87 ~~C~~C~~~f~~ 98 (144)
|-|..|-+.|.+
T Consensus 38 FCCd~ca~EF~n 49 (105)
T PF11494_consen 38 FCCDDCAKEFKN 49 (105)
T ss_dssp SS--SSSS-TTS
T ss_pred EEcHHHHHHHHH
Confidence 444445444443
No 313
>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=22.85 E-value=69 Score=14.13 Aligned_cols=9 Identities=22% Similarity=0.774 Sum_probs=3.9
Q ss_pred CCeeCCCCC
Q psy10073 49 IPQSCKHCK 57 (144)
Q Consensus 49 ~~~~C~~C~ 57 (144)
..-.|+.|+
T Consensus 20 ~~r~C~~Cg 28 (32)
T PF09297_consen 20 WARRCPSCG 28 (32)
T ss_dssp S-EEESSSS
T ss_pred CEeECCCCc
Confidence 334455554
No 314
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=22.80 E-value=88 Score=20.44 Aligned_cols=12 Identities=25% Similarity=0.509 Sum_probs=6.3
Q ss_pred CceeCCCCCccc
Q psy10073 85 YKFICVACDYFT 96 (144)
Q Consensus 85 ~~~~C~~C~~~f 96 (144)
..|.|..|.++|
T Consensus 123 VLFRC~~C~Raw 134 (175)
T PF15446_consen 123 VLFRCTSCHRAW 134 (175)
T ss_pred eEEecCCcccee
Confidence 345565555544
No 315
>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=22.80 E-value=1.9e+02 Score=18.76 Aligned_cols=57 Identities=18% Similarity=0.243 Sum_probs=33.7
Q ss_pred CceeCCCCCcccCChhHHHHHHHhhcCCcceeCC--CcchhccChHHHHHHHHh-hcCCCCC
Q psy10073 85 YKFICVACDYFTIISQNMRNHTLIHLGDKQFKCC--LCSYGAYQKEKLQFHVKN-KHSTKVK 143 (144)
Q Consensus 85 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~--~C~~~f~~~~~l~~H~~~-h~~~kp~ 143 (144)
....|+.|.-........ .-.+.+...|+-.|. .|.+. -+...|.+|.+. |-..+|-
T Consensus 79 ~~L~CPLCRG~V~GWtvv-e~AR~~LN~K~RsC~~e~C~F~-GtY~eLrKHar~~HP~~rP~ 138 (162)
T PF07800_consen 79 PELACPLCRGEVKGWTVV-EPARRFLNAKKRSCSQESCSFS-GTYSELRKHARSEHPSARPS 138 (162)
T ss_pred ccccCccccCceeceEEc-hHHHHHhccCCccCcccccccc-cCHHHHHHHHHhhCCCCCCc
Confidence 357899996433332222 224455566776674 46533 356799999875 5566663
No 316
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=22.74 E-value=1.3e+02 Score=19.82 Aligned_cols=8 Identities=13% Similarity=0.102 Sum_probs=3.9
Q ss_pred HHHHHHHh
Q psy10073 101 NMRNHTLI 108 (144)
Q Consensus 101 ~l~~H~~~ 108 (144)
.|..|...
T Consensus 62 ~l~~Hl~~ 69 (198)
T PF03145_consen 62 ELLDHLRD 69 (198)
T ss_dssp CHHHHHHH
T ss_pred HHHHHHHH
Confidence 45555444
No 317
>PF15616 TerY-C: TerY-C metal binding domain
Probab=22.73 E-value=91 Score=19.41 Aligned_cols=9 Identities=22% Similarity=0.442 Sum_probs=7.0
Q ss_pred eeCCCCCcc
Q psy10073 87 FICVACDYF 95 (144)
Q Consensus 87 ~~C~~C~~~ 95 (144)
..|+.|+..
T Consensus 106 ~~CPwCg~~ 114 (131)
T PF15616_consen 106 VTCPWCGNE 114 (131)
T ss_pred EECCCCCCe
Confidence 788888864
No 318
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=22.35 E-value=15 Score=19.84 Aligned_cols=8 Identities=38% Similarity=0.845 Sum_probs=2.6
Q ss_pred CeeCCCCC
Q psy10073 50 PQSCKHCK 57 (144)
Q Consensus 50 ~~~C~~C~ 57 (144)
--+|+.|.
T Consensus 29 iv~C~gC~ 36 (66)
T PF05180_consen 29 IVQCPGCK 36 (66)
T ss_dssp EEE-TTS-
T ss_pred EEECCCCc
Confidence 34444444
No 319
>KOG1088|consensus
Probab=22.24 E-value=47 Score=20.18 Aligned_cols=20 Identities=15% Similarity=0.253 Sum_probs=14.7
Q ss_pred CCCCceeCCCCCcccCChhH
Q psy10073 82 PVKYKFICVACDYFTIISQN 101 (144)
Q Consensus 82 ~~~~~~~C~~C~~~f~~~~~ 101 (144)
-.++...|++||+.|.-...
T Consensus 94 v~EG~l~CpetG~vfpI~~G 113 (124)
T KOG1088|consen 94 VIEGELVCPETGRVFPISDG 113 (124)
T ss_pred hccceEecCCCCcEeecccC
Confidence 34445999999999976544
No 320
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.18 E-value=37 Score=17.05 Aligned_cols=12 Identities=17% Similarity=0.340 Sum_probs=6.9
Q ss_pred eCCCcchhccCh
Q psy10073 116 KCCLCSYGAYQK 127 (144)
Q Consensus 116 ~C~~C~~~f~~~ 127 (144)
.|++|++.|+..
T Consensus 14 ICpvCqRPFsWR 25 (54)
T COG4338 14 ICPVCQRPFSWR 25 (54)
T ss_pred hhhhhcCchHHH
Confidence 466666666543
No 321
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=22.15 E-value=87 Score=23.93 Aligned_cols=24 Identities=38% Similarity=0.526 Sum_probs=18.8
Q ss_pred CcceeCCCcchhccChHHHHHHHH
Q psy10073 112 DKQFKCCLCSYGAYQKEKLQFHVK 135 (144)
Q Consensus 112 ~~~~~C~~C~~~f~~~~~l~~H~~ 135 (144)
..-|.|+.|-+-|.+...|.+|+.
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~ 219 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMK 219 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHh
Confidence 445888888888888888888876
No 322
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=21.99 E-value=60 Score=21.63 Aligned_cols=13 Identities=23% Similarity=0.647 Sum_probs=9.4
Q ss_pred CeeCCCCC-CCcch
Q psy10073 50 PQSCKHCK-NFTSS 62 (144)
Q Consensus 50 ~~~C~~C~-~f~~~ 62 (144)
.|.|+.|| +....
T Consensus 30 sf~C~~CGyr~~ev 43 (192)
T TIGR00310 30 STICEHCGYRSNDV 43 (192)
T ss_pred EEECCCCCCcccee
Confidence 48899999 65443
No 323
>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=21.68 E-value=71 Score=15.55 Aligned_cols=15 Identities=13% Similarity=0.324 Sum_probs=8.5
Q ss_pred CCCeeCCCCC-CCcch
Q psy10073 48 VIPQSCKHCK-NFTSS 62 (144)
Q Consensus 48 ~~~~~C~~C~-~f~~~ 62 (144)
.....|+.|+ .|-..
T Consensus 12 ~~~i~C~~C~~~~H~~ 27 (51)
T PF00628_consen 12 GDMIQCDSCNRWYHQE 27 (51)
T ss_dssp SSEEEBSTTSCEEETT
T ss_pred CCeEEcCCCChhhCcc
Confidence 3445677776 55444
No 324
>PTZ00064 histone acetyltransferase; Provisional
Probab=21.56 E-value=1e+02 Score=24.02 Aligned_cols=25 Identities=20% Similarity=0.222 Sum_probs=20.1
Q ss_pred CcceeCCCcchhccChHHHHHHHHh
Q psy10073 112 DKQFKCCLCSYGAYQKEKLQFHVKN 136 (144)
Q Consensus 112 ~~~~~C~~C~~~f~~~~~l~~H~~~ 136 (144)
+.-|.|+.|-+-|.+...|.+|+..
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHhc
Confidence 4568888888888888888888763
No 325
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=21.52 E-value=62 Score=22.41 Aligned_cols=8 Identities=25% Similarity=0.766 Sum_probs=4.4
Q ss_pred eeCCCCCc
Q psy10073 87 FICVACDY 94 (144)
Q Consensus 87 ~~C~~C~~ 94 (144)
..||.||+
T Consensus 222 v~CP~CgR 229 (239)
T COG1579 222 VFCPYCGR 229 (239)
T ss_pred ccCCccch
Confidence 45555554
No 326
>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=21.22 E-value=1.1e+02 Score=20.73 Aligned_cols=39 Identities=13% Similarity=0.172 Sum_probs=23.0
Q ss_pred ccCCCCCceeCCCCCcccCChhHHHHHHHhhcCCcceeCCCcch
Q psy10073 79 RPDPVKYKFICVACDYFTIISQNMRNHTLIHLGDKQFKCCLCSY 122 (144)
Q Consensus 79 ~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 122 (144)
..|..-....|..|+..+..... . .. .....-.|+.|+.
T Consensus 106 elHG~l~~~~C~~C~~~~~~~~~-~---~~-~~~~~p~C~~Cgg 144 (222)
T cd01413 106 ELHGTLQTAYCVNCGSKYDLEEV-K---YA-KKHEVPRCPKCGG 144 (222)
T ss_pred EccCCcCcceECCCCCCcchhHH-H---Hh-ccCCCCcCCCCCC
Confidence 34555556889999988765432 1 11 1122346888873
No 327
>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=21.14 E-value=81 Score=19.78 Aligned_cols=19 Identities=16% Similarity=0.317 Sum_probs=14.6
Q ss_pred ceeCCCCCcccCChhHHHH
Q psy10073 86 KFICVACDYFTIISQNMRN 104 (144)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~ 104 (144)
-+.|+.|++.|-.-+.+.+
T Consensus 124 f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred EEECCCCCCEecccccHHH
Confidence 3899999999977665543
No 328
>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=20.62 E-value=60 Score=14.15 Aligned_cols=8 Identities=25% Similarity=0.625 Sum_probs=4.0
Q ss_pred CeeCCCCC
Q psy10073 50 PQSCKHCK 57 (144)
Q Consensus 50 ~~~C~~C~ 57 (144)
-|.|..|+
T Consensus 15 ~Y~C~~c~ 22 (30)
T PF03107_consen 15 FYHCSECC 22 (30)
T ss_pred eEEeCCCC
Confidence 35555554
No 329
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=20.58 E-value=1.4e+02 Score=17.36 Aligned_cols=29 Identities=24% Similarity=0.528 Sum_probs=16.9
Q ss_pred CCceecCccCCccCCcc--ccccccCCCCCC
Q psy10073 13 STKKTCLYCNKYVPSDI--DVFIGHCQTCPN 41 (144)
Q Consensus 13 ~~~~~C~~C~~~f~~~~--~l~~H~c~~c~h 41 (144)
...|.|..||....-.. +-.+.+|..|.+
T Consensus 2 ~~~F~C~~CG~~V~p~~~g~~~RNHCP~CL~ 32 (92)
T PF12647_consen 2 NESFTCVHCGLTVSPLAAGSAHRNHCPSCLS 32 (92)
T ss_pred CcccCccccCCCcccCCCCCCccCcCccccc
Confidence 35689999998765422 222335555554
No 330
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=20.56 E-value=40 Score=17.51 Aligned_cols=11 Identities=27% Similarity=0.483 Sum_probs=3.1
Q ss_pred ceecCccCCcc
Q psy10073 15 KKTCLYCNKYV 25 (144)
Q Consensus 15 ~~~C~~C~~~f 25 (144)
.|.|++||.+-
T Consensus 33 ~y~Cp~CgAtG 43 (55)
T PF05741_consen 33 KYVCPICGATG 43 (55)
T ss_dssp G---TTT---G
T ss_pred cCcCCCCcCcC
Confidence 47777777653
No 331
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=20.55 E-value=55 Score=23.38 Aligned_cols=12 Identities=25% Similarity=0.684 Sum_probs=6.3
Q ss_pred eeCCCCC-CCcch
Q psy10073 51 QSCKHCK-NFTSS 62 (144)
Q Consensus 51 ~~C~~C~-~f~~~ 62 (144)
+.|+.|+ -|.-.
T Consensus 47 ~vc~~c~~h~rl~ 59 (292)
T PRK05654 47 NVCPKCGHHMRIS 59 (292)
T ss_pred CCCCCCCCCeeCC
Confidence 4566666 54433
No 332
>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=20.46 E-value=43 Score=17.51 Aligned_cols=12 Identities=33% Similarity=0.514 Sum_probs=5.2
Q ss_pred eecCccCCccCC
Q psy10073 16 KTCLYCNKYVPS 27 (144)
Q Consensus 16 ~~C~~C~~~f~~ 27 (144)
..|++|++.+..
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 467777776554
No 333
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.39 E-value=75 Score=25.84 Aligned_cols=7 Identities=29% Similarity=0.990 Sum_probs=4.6
Q ss_pred eeCCCCC
Q psy10073 51 QSCKHCK 57 (144)
Q Consensus 51 ~~C~~C~ 57 (144)
+.||.||
T Consensus 660 ~~CP~CG 666 (711)
T PRK09263 660 FTCPKCG 666 (711)
T ss_pred CcCcCCC
Confidence 5666666
No 334
>PLN02748 tRNA dimethylallyltransferase
Probab=20.36 E-value=78 Score=24.33 Aligned_cols=24 Identities=17% Similarity=0.351 Sum_probs=19.5
Q ss_pred CceeCCCCCc-ccCChhHHHHHHHh
Q psy10073 85 YKFICVACDY-FTIISQNMRNHTLI 108 (144)
Q Consensus 85 ~~~~C~~C~~-~f~~~~~l~~H~~~ 108 (144)
+.|.|+.|++ .+........|++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 4588999997 78888888888754
No 335
>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=20.34 E-value=84 Score=15.47 Aligned_cols=12 Identities=25% Similarity=0.761 Sum_probs=5.8
Q ss_pred CceecCccCCcc
Q psy10073 14 TKKTCLYCNKYV 25 (144)
Q Consensus 14 ~~~~C~~C~~~f 25 (144)
.+-.|..|++..
T Consensus 10 ~~~~C~~C~~~i 21 (53)
T PF00130_consen 10 KPTYCDVCGKFI 21 (53)
T ss_dssp STEB-TTSSSBE
T ss_pred CCCCCcccCccc
Confidence 344566666544
No 336
>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=20.30 E-value=41 Score=19.90 Aligned_cols=11 Identities=36% Similarity=0.948 Sum_probs=5.6
Q ss_pred CeeCCCCC-CCc
Q psy10073 50 PQSCKHCK-NFT 60 (144)
Q Consensus 50 ~~~C~~C~-~f~ 60 (144)
...|..|+ .|.
T Consensus 52 ~lvC~~C~~~~~ 63 (102)
T PF10080_consen 52 QLVCKNCGVRFN 63 (102)
T ss_pred EEEEecCCCEEe
Confidence 34555555 443
No 337
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=20.29 E-value=1.1e+02 Score=24.72 Aligned_cols=37 Identities=19% Similarity=0.439 Sum_probs=22.7
Q ss_pred ecCccCCccCCccccccccCCCCCCccccCCCCCeeCCCCC-CCcch
Q psy10073 17 TCLYCNKYVPSDIDVFIGHCQTCPNMSFLNSVIPQSCKHCK-NFTSS 62 (144)
Q Consensus 17 ~C~~C~~~f~~~~~l~~H~c~~c~h~~~h~~~~~~~C~~C~-~f~~~ 62 (144)
-|+.||..+.. -.|..||.... ...--|+.|| ...+.
T Consensus 17 FC~~CG~~l~~------~~Cp~CG~~~~---~~~~fC~~CG~~~~~~ 54 (645)
T PRK14559 17 FCQKCGTSLTH------KPCPQCGTEVP---VDEAHCPNCGAETGTI 54 (645)
T ss_pred cccccCCCCCC------CcCCCCCCCCC---cccccccccCCcccch
Confidence 47778776642 25778887532 2223488888 65555
Done!